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Experiential Learning and Evidence-Based Teaching Powerful Tools in Assessing STEM
CompetenciesXavier University of Louisiana
New Orleans LA 70125
Mary Carmichael Course Coordinator for Freshman Biology and Assessment Coordinator for the Biology DepartmentAndrea Edwards Conrad N Hilton Endowed Chair in Computer ScienceShubha Ireland Professor of Biology PD for HHMI supported project lsquoScicomprsquo and Special Assistant to the Provost for Life Sciences Education
bull Founded in 1925 only historically Black Roman Catholic institution in the US
bull Primarily undergraduate HBCU (~ 2200 in the CAS ~ 2900 total)
bull Strong liberal arts base
bull Nationally recognized for its success in STEM education
bull ~ 72 STEM majors (33-35 in Biology alone)
bull Top producer of African American graduates in biological and biomedical sciences and physics
bull Tops the nation in number of graduates who complete medical school and in graduates who go on to obtain PhDs in life sciences
httpwwwnsfgovstatisticsinfbriefnsf13323
httpwwwnsfgovstatistics2015nsf15311tablespdftab7-10pdf
bull Students applying for and receiving financial aid ndash 87bull Students receiving Pell Grants ndash over 65bull Underprepared students exhibiting the will to succeed accepted bull Based on high school GPAs and ACTSAT scores students and other factors
classified in three academic risk categories (low medium and high)bull First time freshmen graduation rate is ~ 65 (internal data)bull Transfer students (mostly pre-Pharms join at the 2nd year level)
Project Scicomp2012-2017
Competency-based curricular reforms and their positive influence on URM
learning and retention
Goals of Project Scicomp
bull Implement curricular reforms to reflect the scientific competency recommendations through newer teaching testing and assessment approaches (that would be sustainable after the end of funding)
bull Increase student retention in the sciences
bull Increase number of students going to medical or graduate schools or in the workforce
Guiding Documents
Years 1 - 3 Biology 1210L and 1220L were developed received academic assembly approval and were piloted in Fall 2012
The main goal of these courses was to introduce the fundamentals of scientific competencies and research-related active learning exercises in a stress-free environment
Based on the formative and summative assessments of these courses we have made several adjustments as we offer these courses each semester
Pre- and post-course diagnostic tests
Biology 1230 lecture and lab underwent changes in content and in the style of teaching testing and assessing
Weekly meetings for more sharing of ideas on best practices
Student self-assessment of performance
Student pre- and post- surveys on perspectives about Biology
Online homework assignments and clicker questions for formative assessment OpScan scanner and LXR Test softwarefor increased assessment capabilities
Curricular changes across STEM disciplines and dissemination
XU Center For the Advancement of Teaching and SERG
AAAS VampC HHMI NAS GCSI Grinnell NYU Faculty Resource Network
On and off campus collaborations
Focus on Science majorsduring their freshman year
bull Math in biology (Foundations I and II)
bull BioSQuaRE Test and its significance
bull Computer Applications (exercise on BLAST)
bull Biophysics (exercise on electricity)
bull Biol 1230 (leader lecture course for newer assessments
Foundations I and II (Biol 1210L and Biol 1220L)
bull Biol 1210L Introduces basic principles and applications of math physics and chemistry in biology and research Emphasis on group projects active learning discussions readingcomprehension of scientific articlespassages experimentation data collection data analysis and use of computers
bull Biol 1220L Focuses on statistics using data collected by students using systems like the Bean beetle and plant seeds Also reinforcement of measurement conversions dilutions stock solutions and back calculations using living systems typically bacteria Continuation of primary literature discussionsanalysis
1210L Active Learning110$in$50m
L$110$in$100
mL$
110$in$30m
L$
Infect=99 recovery=99
STUDIES ON PIGMENTATION OF SERRATIA MARCESCENS
I SPECTRAL AND PAPER CHROMATOGRAPHIC PROPERTIES OF PRODIGIOSIN
ROBERT P WILLIAMS JAMES A GREEN2 AND DONALD A RAPPOPORT
Departments of Microbiology Biochemistry and Radiology Baylor University College of Medicine Houston Texas
Received for publication June 23 1955
APPLIED MICROBIOLOGY Mar 1973 p 396-402 Vol 25 No 3 Copyright 0 1973 American Society for Microbiology Printed in USA
Biosynthesis of Prodigiosin a Secondary Metabolite of Serratia marcescensROBERT P WILLIAMS
Department of Microbiology Baylor College of Medicine Houston Texas 77025 Received for publication 30 October 1972
Prodigiosenes (prodigiosin and prodigiosin-like pigments) are known to be synthesized by only one genus of Eubacteriales and by two genera of Actinomycetales Biosynthesis by Serratia marcqscens occurs over a relatively narrow range of temperatures although the bacteria grow over a broad range When cultures of S marcescenswere incubated at 27 C in 10 casein hydrolysate viable count and protein attained maximal values within 24 to 48 h whereas prodigiosin did not reach a maximum until 96 h The greatest amount of pigment was synthesized when cultures were in the senescent phase of growth Suspensions of nonproliferating bacteria incubated at 27 C in only i-alanine also synthesized prodigiosin although at a slower rate than growing cultures Kinetics of growth for the wild-type red S marcescens and a white mutant were identical when incubated at 27 C but the wild type produced abundant pigment These results plus other data obtained from the literature suggest that prodigiosin is a secondary metabolite The importance of this proposal to understanding the function of prodigiosin in S marcescens is discussed
Zooming ahead to recent yearshelliphellip From 1955 to 2017
MybioSorcecomhttpswwwmybiosourcecom
Product DescriptionProdigiosin is an intensely red pyrrole pigment produced by several bacteria most notably Serratia marcescens Prodigiosin has a broad biological profile with activity against fungi tumor cell lines and malaria It was shown to be an immunosuppressant in 2007 The mode of action of prodigiosin has recently received considerable attention as an inducer of apoptosis in human primary cancer cells via caspase activation Prodigiosin also acts as an inducer of p21WAF1CIP1 expression via transforming growth factor-B receptor pathway and of NAG-1activation by acting on glycogen synthase kinase-3B
Evidence of ldquomath-gaprdquo
bull ACT College Readiness Benchmark
ndash 50 chance of obtaining a B or
better or ~75 chance of obtaining
a C or higher in a corresponding
first-year course
ACT Site
ndash Math = Algebra I
ndash Science = Biology IBased on sample of 214 institutions and gt230000
students from US Benchmarks = median course
placement values and represent a ldquotypicalrdquo set of
expectations
Percent of ACT-Tested High School Graduates Meeting ACT Benchmarks
Pe
rce
nt
Few 12th Grade Students Interested
in STEM and Proficient in Math
Business-Higher Ed Forum Research Brief (2011)Included in 2012 PCAST Appendix E
STEM interested
AND Math Proficient
NOT STEM
interestedMath
ProficientNOT STEM
interested
NOT Math
Proficient
STEM
interested
NOT Math
Proficient
Biological Quantitative Reasoning
Exam (BioSQuaRE) ndash Q6 consortium
BioSQuaRE TeamBiology
Paul Overvoorde (Macalester)
Peter Brodfuehrer Greg Davis (Bryn Mawr)
Charles Umbanhowar (St Olaf)
Marion Preest (Keck Science Center Claremont Colleges)
Steve Adolph Cathy McFadden (Harvey Mudd)
Educational PsychologyStatistics
Andy Zieffler Laure Le (U Minnesota)
Laura Zeigler (Iowa State)
Erik Larson (Macalester)- Sociology
ldquoOtherrdquo
Liz Stanhope (Lewis and Clark) ndash Math
Jason Belitsky (Oberlin) ndash Chemistry
Marcelo Vinces (Oberlin) ndash Quantitative Skills Center
Tabassum Haque (Oberlin) ndash Institutional Research
Alignment of Learning Outcomes
bull 14 + 38 faculty
bull Mapping of learning outcomes with
previous national reports
ndash BIO2010
ndash Vision and Changes
ndash Next Gen Science Standards for Science
and Engineering
ndash Revised AP Biology requirements
ndash Preparing Future Physicians
bull Comparison to previously created
Quantitative Literacy Efforts (eg
QRLA TOSLS)
Mapping Learning Outcomes to National Reports
ContentStudents should
be able to
BIO20
10
Vision
amp
Chang
e
SFFPAP
Bio
NGSS
SampE
Algebra
functions
and
modeling
Carry out basic mathematical
computations (eg proportional reasoning
unit conversion center and variation)
X X X X X
Recognize and use logarithmic or
exponential relationshipsX X
Fit a model such as population growth X X
Use a representation or a model to make
predictionsX X X X X
Describeinfer relationships between
variables (scatterplots regression
network diagrams maps)
X X
Perform logicalalgorithmic reasoning X X X X
Statistics
and
probability
Calculate or use the concept of the
likelihood of an eventX X X
Calculate or use conditional probability X X X
Recognize and interpret what summary
statistics representX X X
Identify different types of error X
Recognize that biological systems are
inherently variable (eg stochastic vs
deterministic)
X X
Formulate hypothesis statements X X X X
Understand what a p-value is X X X X
Understand when causal claims can be
made (eg correlation vs causation)X X X X
Visualizati
on
Choose the appropriate type of graph X X X X X
Interpret a graph (eg functional
relationships logarithmic relationships)X X X X X
Be able to use a table X X X
Use spatial reasoning to interpret
multidimensional numerical and visual
data (geographic information)
X
Stanhope et al (2017) Development of a Biological
Science Quantitative Reasoning Exam (BioSQuaRE)
CBE- Life Science Education Winter edition
December 1 2017
bull identification and validation of learning domains
bull iterative development of BioSQuaRE Instrument
bull evidence of validity
bull discussion of instruments utility for students individual
faculty and departments or programs
Visit wwwmacalestereduhhmibiosquare for more information
BLASTing Human and Other Organisms
bull Our goal is to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus(snake) The objective is to find and precisely map the coding regions using NCBIrsquos BLASTp search tool
bull Answer the following questions for each of the 4 organisms1 Describe the summary distributions2 Interpret the score the percent identity and the E-value If
obtain hit(s) are they likely due to chance If no hits why3 Analyze the alignments
Describe these Summary Distributions
Chimp
Cow
Snake
Chicken
Interpret the Scores E-values and Identities
Chimp
Cow
Snake
Chicken
Analyze the Alignments
Chimp
Cow
Snake
Chicken
Additional Questions of Interest
bull Our goal was to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus (snake) The objective is to find and precisely map the coding regions
bull Answer the following questions1 This presentation is showing only highly significant pairs How
do you think the alignments (scores e-values identities) differ if we analyze low significant pairs
2 Can you infer that this protein does not exist in this organism3 Give alternative explanations for the differences in scores e-
values and identities4 Is there an evolutionary relationship between sequences
Am J Hum Genet 2008 Dec 12 83(6) 769ndash780 Published online 2008 Dec 5 doi 101016jajhg200811004
Ribosomal Protein L5 and L11 Mutations Are Associated with Cleft Palate and Abnormal Thumbs in Diamond-Blackfan Anemia Patients
Hanna T Gazda12lowast
Mee Rie Sheen1
Adrianna Vlachos34
Valerie Choesmel56
Marie-Franccediloise ODonohue
56Hal Schneider
1Natasha Darras
1Catherine Hasman
1Colin A
Sieff27
Peter E Newburger8
Sarah E Ball9
Edyta Niewiadomska10
Michal Matysiak10
Jan M Zaucha
11Bertil Glader
12Charlotte Niemeyer
13Joerg J Meerpohl
13Eva Atsidaftos
34Jeffrey
M Lipton34
Pierre-Emmanuel Gleizes56
and Alan H Beggs12
Author information Article notes Copyright and License information AbstractDiamond-Blackfan anemia (DBA) a congenital bone-marrow-failure syndrome is characterized by red blood cell aplasia macrocytic anemia clinical heterogeneity and increased risk of malignancy Although anemia is the most prominent feature of DBA the disease is also characterized by growth retardation and congenital anomalies that are present in sim30ndash50 of patients The disease has been associated with mutations in four ribosomal protein (RP) genes RPS19 RPS24 RPS17 and RPL35A in about 30 of patients However the genetic basis of the remaining 70 of cases is still unknown Here we report the second known mutation in RPS17 and probable pathogenic mutations in three more RP genes RPL5 RPL11 and RPS7 In addition we identified rare variants of unknown significance in three other genes RPL36 RPS15 and RPS27A Remarkably careful review of the clinical data showed that mutations in RPL5 are associated with multiple physical abnormalities including craniofacial thumb and heart anomalies whereas isolated thumb malformations are predominantly present in patients carrying mutations in RPL11 We also demonstrate that mutations of RPL5 RPL11 or RPS7 in DBA cells is associated with diverse defects in the maturation of ribosomal RNAs in the large or the small ribosomal subunit production pathway expanding the repertoire of ribosomal RNA processing defects associated with DBA
Develop more inquiry-based lab exercises1 C elegans crosses (Peter Barrett in Genetics lab)
2 Modifications on DNA transformation and lac operon exercises (PB)
3 The lsquotermitersquo experiment in Biol 1230L (Kristal Huggins and SKI)
4 In Cell Biology lab C elegans (endocytosis experiments) experiments with Planaria regeneration (adapted from MITHHMI) and recently with Daphnia (the water flea a small crustacean) adapted from the Nuffield Foundation where students expose the Daphnia to various cardioactive compounds measure changes in heart rate caused by effects on cellular receptors and design follow-up experiments (PB)
Assessment Strategies for Project Scicomp
Formative and summative
General scheme
bull Assessment tasks based on objectives
bull Develop assessment tools and pilot for validation
bull Apply to larger audience
bull Collect and score
bull Share and analyze data
Coordinated course sequences and our curricular design serve as a good platform
for intra and interdepartmental discussions
(weekly meetings lsquoSERGrsquo etc)
Labs
bull General observation on student participationinitiative
bull Data sheets (say 10 collecthellipsay any 4)
bull Midterm skills practical stations and multiple choice (excellent determinant)
bull Quizzes (5-10 depending on the lab)
bull Final exams
Course based research experiencee(CRE)
bull How they design their experiment
bull Notebooks lab techniques
bull Participation in class discussions
bull Ability to troubleshoot
bull Midterm Skills and oral exam along with traditional exam
bull Short answer (non multiple choice) questions
bull Research paper presentations
CREs at Xavier
bull Phage and Genomics
bull lsquoUndergraduate Researchrsquo for credits
bull Introduction to Mammalian Tissue Culture
The SEA-PHAGES ProgramhttpsseaphagesorgThe official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program
SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is a two-semester discovery-based undergraduate research course that begins with simple digging in the soil to find new viruses but progresses through a variety of microbiology techniques and eventually to complex genome annotation and bioinformatic analyses
CBE Life Sci Educ 2016 fall15(3) pii ar38 doi 101187cbe16-01-0078Increasing URM Undergraduate Student Success through Assessment-Driven Interventions A Multiyear Study Using Freshman-Level General Biology as a Model SystemCarmichael MC1 St Clair C1 Edwards AM2 Barrett P1 McFerrin H1 Davenport I1 Awad M1 Kundu A1 Ireland SK3
AbstractXavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students In this multiyear study with sim5500 participants data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course The three hour-long exams were common and administered concurrently to all students New exam questions were developed using Blooms taxonomy and exam results were analyzed statistically with validated assessment tools All but the comprehensive final exam were returned to students for self-evaluation and remediation Among other approaches course rigor was monitored by using an identical set of 60 questions on the final exam across 10 semesters Analysis of the identical sets of 60 final exam questions revealed that overall averages increased from 729 (2010) to 835 (2015) Regression analysis demonstrated a statistically significant correlation between high-risk students and their averages on the 60 questions Additional analysis demonstrated statistically significant improvements for at least one letter grade from midterm to final and a 20 increase in the course pass rates over time also for the high-risk population These results support the hypothesis that our data-driven interventions and assessment techniques are successful in improving student retention particularly for our academically at-risk students
Lecture Biol 1230
bull Competency E4 (chemistry in biology atomic bonds metabolic pathways thermodynamics)
bull Quizzes (formative assessment with Clickers)
bull The coordinator prepares the three lsquoOne hour examsrsquo (questions not from the textbook) instructors again reviewcomment
bull Question types range (content versus applications) and also lsquoBack pagersquo ( 20 of the exam grade) Formative assessment using the LXRtest software (Opscan6 scanner)
Final exam not returned cumulative and has had 60 questions (good discriminators based on the rpbvalues) commonly used on ALL final exams for the past five years Powerful tool for measuring studentsrsquo learning and applications over time and based on academic risk categories
Last Name First Name
Biology 1230 Exam 1 ldquoBack Pagerdquo Score _ 20 pts
I 5 pts Complete the following table for the 3 major components (subatomic particles) of the atom
hint electrical charge = positive negative or neutral and mass = 1 dalton or 11800 dalton 1 pt each
Particle Electrical Charge Mass
1 Proton 1 dalton
2 Electron
3 Neutron
II 5 pts In your own words compare and contrast the following two atoms A and B use the back of the previous page to
make as many observations as you can about similarities (and what they mean) and differences (and what they mean)
between the atoms
A B
III 5 pts Match the following by placing the corresponding in the space provided 1 pt each
_____ tertiary structure 1 produce H2O
_____ two ester linkages 2 is responsible for the 3-dimensional shape of a protein
_____ phosphodiester bonds 3 exist within diglycerides (diacylglyerols) and phospholipids
_____ dehydration synthesis reactions 4 are a type of lipid
_____ steroids 5 are formed when nucleic acids are synthesized
IV 5 pts Circle each of the variable (R) groups in the molecules shown below (3 pts)
a Which lsquoRrsquo group is polar ______ (write the corresponding in the space provided) (1 pt)
b Which lsquoRrsquo group is ionic ______ (write the corresponding in the space provided) (1 pt)
NH3+ OH CH3
1 2 3
12 neutrons
11 protons
10 electrons
13 neutrons
11 protons
11 electrons
Bio1230 Exam 1
Clickers and immediate feedback
Name _____________________________________________________________________________________________
This is a worksheet for your self-evaluation of study habits and exam preparedness Your answers on the corresponding
online exam surveys are confidential
~The average number of hours I spent per week reading the chapters andor reviewingprocessing class notes was (circle the
appropriate response)
zero to one one to two two to four greater than four
~I read the assignment before coming to class (circle the appropriate response)
never sometimes regularly
~I asked my instructor questions when I was confused about textbook material andor lecture material (circle the appropriate
response)
never sometimes regularly
~Overall I spent _____ hours specifically studying for this exam (Please fill in the blank)
~Prior to taking the exam I expected to get an approximate grade of (fill in the blank) _____
~My actual grade was a(n) (fill in the blank) _____
~Check all of the statements that apply to your performance on the exam
____ studied the right information ____ did not study the right information
____ studied the right information but did not ____ studied the right information and
understand it thought I understood it
____ used the class outlines to study ____ thought college would be easier
____ did not know what to study ____ other _____________________
____ did not think I would need to know the information in such detail
Analysis of Missed Questions I answered the question incorrectly because I Insert question number below in the correct category
did not study the information
studied the information but forgot it
did not understand the information in the
summary notes
confused similar concepts or terms (ie
isotopes and isomers)
misread or misunderstood the question
did not consider all of the answer choices
knew the correct answer - but chose an
incorrect answer by mistake
List other reason(s)
List other reason(s)
Please answer additional self-evaluation questions on the back of this page
Self-Evaluation of Study Habits amp Exam Preparedness for Biology 1230 Exam I or II or III (circle one)
Going forwardhellip
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
bull Founded in 1925 only historically Black Roman Catholic institution in the US
bull Primarily undergraduate HBCU (~ 2200 in the CAS ~ 2900 total)
bull Strong liberal arts base
bull Nationally recognized for its success in STEM education
bull ~ 72 STEM majors (33-35 in Biology alone)
bull Top producer of African American graduates in biological and biomedical sciences and physics
bull Tops the nation in number of graduates who complete medical school and in graduates who go on to obtain PhDs in life sciences
httpwwwnsfgovstatisticsinfbriefnsf13323
httpwwwnsfgovstatistics2015nsf15311tablespdftab7-10pdf
bull Students applying for and receiving financial aid ndash 87bull Students receiving Pell Grants ndash over 65bull Underprepared students exhibiting the will to succeed accepted bull Based on high school GPAs and ACTSAT scores students and other factors
classified in three academic risk categories (low medium and high)bull First time freshmen graduation rate is ~ 65 (internal data)bull Transfer students (mostly pre-Pharms join at the 2nd year level)
Project Scicomp2012-2017
Competency-based curricular reforms and their positive influence on URM
learning and retention
Goals of Project Scicomp
bull Implement curricular reforms to reflect the scientific competency recommendations through newer teaching testing and assessment approaches (that would be sustainable after the end of funding)
bull Increase student retention in the sciences
bull Increase number of students going to medical or graduate schools or in the workforce
Guiding Documents
Years 1 - 3 Biology 1210L and 1220L were developed received academic assembly approval and were piloted in Fall 2012
The main goal of these courses was to introduce the fundamentals of scientific competencies and research-related active learning exercises in a stress-free environment
Based on the formative and summative assessments of these courses we have made several adjustments as we offer these courses each semester
Pre- and post-course diagnostic tests
Biology 1230 lecture and lab underwent changes in content and in the style of teaching testing and assessing
Weekly meetings for more sharing of ideas on best practices
Student self-assessment of performance
Student pre- and post- surveys on perspectives about Biology
Online homework assignments and clicker questions for formative assessment OpScan scanner and LXR Test softwarefor increased assessment capabilities
Curricular changes across STEM disciplines and dissemination
XU Center For the Advancement of Teaching and SERG
AAAS VampC HHMI NAS GCSI Grinnell NYU Faculty Resource Network
On and off campus collaborations
Focus on Science majorsduring their freshman year
bull Math in biology (Foundations I and II)
bull BioSQuaRE Test and its significance
bull Computer Applications (exercise on BLAST)
bull Biophysics (exercise on electricity)
bull Biol 1230 (leader lecture course for newer assessments
Foundations I and II (Biol 1210L and Biol 1220L)
bull Biol 1210L Introduces basic principles and applications of math physics and chemistry in biology and research Emphasis on group projects active learning discussions readingcomprehension of scientific articlespassages experimentation data collection data analysis and use of computers
bull Biol 1220L Focuses on statistics using data collected by students using systems like the Bean beetle and plant seeds Also reinforcement of measurement conversions dilutions stock solutions and back calculations using living systems typically bacteria Continuation of primary literature discussionsanalysis
1210L Active Learning110$in$50m
L$110$in$100
mL$
110$in$30m
L$
Infect=99 recovery=99
STUDIES ON PIGMENTATION OF SERRATIA MARCESCENS
I SPECTRAL AND PAPER CHROMATOGRAPHIC PROPERTIES OF PRODIGIOSIN
ROBERT P WILLIAMS JAMES A GREEN2 AND DONALD A RAPPOPORT
Departments of Microbiology Biochemistry and Radiology Baylor University College of Medicine Houston Texas
Received for publication June 23 1955
APPLIED MICROBIOLOGY Mar 1973 p 396-402 Vol 25 No 3 Copyright 0 1973 American Society for Microbiology Printed in USA
Biosynthesis of Prodigiosin a Secondary Metabolite of Serratia marcescensROBERT P WILLIAMS
Department of Microbiology Baylor College of Medicine Houston Texas 77025 Received for publication 30 October 1972
Prodigiosenes (prodigiosin and prodigiosin-like pigments) are known to be synthesized by only one genus of Eubacteriales and by two genera of Actinomycetales Biosynthesis by Serratia marcqscens occurs over a relatively narrow range of temperatures although the bacteria grow over a broad range When cultures of S marcescenswere incubated at 27 C in 10 casein hydrolysate viable count and protein attained maximal values within 24 to 48 h whereas prodigiosin did not reach a maximum until 96 h The greatest amount of pigment was synthesized when cultures were in the senescent phase of growth Suspensions of nonproliferating bacteria incubated at 27 C in only i-alanine also synthesized prodigiosin although at a slower rate than growing cultures Kinetics of growth for the wild-type red S marcescens and a white mutant were identical when incubated at 27 C but the wild type produced abundant pigment These results plus other data obtained from the literature suggest that prodigiosin is a secondary metabolite The importance of this proposal to understanding the function of prodigiosin in S marcescens is discussed
Zooming ahead to recent yearshelliphellip From 1955 to 2017
MybioSorcecomhttpswwwmybiosourcecom
Product DescriptionProdigiosin is an intensely red pyrrole pigment produced by several bacteria most notably Serratia marcescens Prodigiosin has a broad biological profile with activity against fungi tumor cell lines and malaria It was shown to be an immunosuppressant in 2007 The mode of action of prodigiosin has recently received considerable attention as an inducer of apoptosis in human primary cancer cells via caspase activation Prodigiosin also acts as an inducer of p21WAF1CIP1 expression via transforming growth factor-B receptor pathway and of NAG-1activation by acting on glycogen synthase kinase-3B
Evidence of ldquomath-gaprdquo
bull ACT College Readiness Benchmark
ndash 50 chance of obtaining a B or
better or ~75 chance of obtaining
a C or higher in a corresponding
first-year course
ACT Site
ndash Math = Algebra I
ndash Science = Biology IBased on sample of 214 institutions and gt230000
students from US Benchmarks = median course
placement values and represent a ldquotypicalrdquo set of
expectations
Percent of ACT-Tested High School Graduates Meeting ACT Benchmarks
Pe
rce
nt
Few 12th Grade Students Interested
in STEM and Proficient in Math
Business-Higher Ed Forum Research Brief (2011)Included in 2012 PCAST Appendix E
STEM interested
AND Math Proficient
NOT STEM
interestedMath
ProficientNOT STEM
interested
NOT Math
Proficient
STEM
interested
NOT Math
Proficient
Biological Quantitative Reasoning
Exam (BioSQuaRE) ndash Q6 consortium
BioSQuaRE TeamBiology
Paul Overvoorde (Macalester)
Peter Brodfuehrer Greg Davis (Bryn Mawr)
Charles Umbanhowar (St Olaf)
Marion Preest (Keck Science Center Claremont Colleges)
Steve Adolph Cathy McFadden (Harvey Mudd)
Educational PsychologyStatistics
Andy Zieffler Laure Le (U Minnesota)
Laura Zeigler (Iowa State)
Erik Larson (Macalester)- Sociology
ldquoOtherrdquo
Liz Stanhope (Lewis and Clark) ndash Math
Jason Belitsky (Oberlin) ndash Chemistry
Marcelo Vinces (Oberlin) ndash Quantitative Skills Center
Tabassum Haque (Oberlin) ndash Institutional Research
Alignment of Learning Outcomes
bull 14 + 38 faculty
bull Mapping of learning outcomes with
previous national reports
ndash BIO2010
ndash Vision and Changes
ndash Next Gen Science Standards for Science
and Engineering
ndash Revised AP Biology requirements
ndash Preparing Future Physicians
bull Comparison to previously created
Quantitative Literacy Efforts (eg
QRLA TOSLS)
Mapping Learning Outcomes to National Reports
ContentStudents should
be able to
BIO20
10
Vision
amp
Chang
e
SFFPAP
Bio
NGSS
SampE
Algebra
functions
and
modeling
Carry out basic mathematical
computations (eg proportional reasoning
unit conversion center and variation)
X X X X X
Recognize and use logarithmic or
exponential relationshipsX X
Fit a model such as population growth X X
Use a representation or a model to make
predictionsX X X X X
Describeinfer relationships between
variables (scatterplots regression
network diagrams maps)
X X
Perform logicalalgorithmic reasoning X X X X
Statistics
and
probability
Calculate or use the concept of the
likelihood of an eventX X X
Calculate or use conditional probability X X X
Recognize and interpret what summary
statistics representX X X
Identify different types of error X
Recognize that biological systems are
inherently variable (eg stochastic vs
deterministic)
X X
Formulate hypothesis statements X X X X
Understand what a p-value is X X X X
Understand when causal claims can be
made (eg correlation vs causation)X X X X
Visualizati
on
Choose the appropriate type of graph X X X X X
Interpret a graph (eg functional
relationships logarithmic relationships)X X X X X
Be able to use a table X X X
Use spatial reasoning to interpret
multidimensional numerical and visual
data (geographic information)
X
Stanhope et al (2017) Development of a Biological
Science Quantitative Reasoning Exam (BioSQuaRE)
CBE- Life Science Education Winter edition
December 1 2017
bull identification and validation of learning domains
bull iterative development of BioSQuaRE Instrument
bull evidence of validity
bull discussion of instruments utility for students individual
faculty and departments or programs
Visit wwwmacalestereduhhmibiosquare for more information
BLASTing Human and Other Organisms
bull Our goal is to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus(snake) The objective is to find and precisely map the coding regions using NCBIrsquos BLASTp search tool
bull Answer the following questions for each of the 4 organisms1 Describe the summary distributions2 Interpret the score the percent identity and the E-value If
obtain hit(s) are they likely due to chance If no hits why3 Analyze the alignments
Describe these Summary Distributions
Chimp
Cow
Snake
Chicken
Interpret the Scores E-values and Identities
Chimp
Cow
Snake
Chicken
Analyze the Alignments
Chimp
Cow
Snake
Chicken
Additional Questions of Interest
bull Our goal was to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus (snake) The objective is to find and precisely map the coding regions
bull Answer the following questions1 This presentation is showing only highly significant pairs How
do you think the alignments (scores e-values identities) differ if we analyze low significant pairs
2 Can you infer that this protein does not exist in this organism3 Give alternative explanations for the differences in scores e-
values and identities4 Is there an evolutionary relationship between sequences
Am J Hum Genet 2008 Dec 12 83(6) 769ndash780 Published online 2008 Dec 5 doi 101016jajhg200811004
Ribosomal Protein L5 and L11 Mutations Are Associated with Cleft Palate and Abnormal Thumbs in Diamond-Blackfan Anemia Patients
Hanna T Gazda12lowast
Mee Rie Sheen1
Adrianna Vlachos34
Valerie Choesmel56
Marie-Franccediloise ODonohue
56Hal Schneider
1Natasha Darras
1Catherine Hasman
1Colin A
Sieff27
Peter E Newburger8
Sarah E Ball9
Edyta Niewiadomska10
Michal Matysiak10
Jan M Zaucha
11Bertil Glader
12Charlotte Niemeyer
13Joerg J Meerpohl
13Eva Atsidaftos
34Jeffrey
M Lipton34
Pierre-Emmanuel Gleizes56
and Alan H Beggs12
Author information Article notes Copyright and License information AbstractDiamond-Blackfan anemia (DBA) a congenital bone-marrow-failure syndrome is characterized by red blood cell aplasia macrocytic anemia clinical heterogeneity and increased risk of malignancy Although anemia is the most prominent feature of DBA the disease is also characterized by growth retardation and congenital anomalies that are present in sim30ndash50 of patients The disease has been associated with mutations in four ribosomal protein (RP) genes RPS19 RPS24 RPS17 and RPL35A in about 30 of patients However the genetic basis of the remaining 70 of cases is still unknown Here we report the second known mutation in RPS17 and probable pathogenic mutations in three more RP genes RPL5 RPL11 and RPS7 In addition we identified rare variants of unknown significance in three other genes RPL36 RPS15 and RPS27A Remarkably careful review of the clinical data showed that mutations in RPL5 are associated with multiple physical abnormalities including craniofacial thumb and heart anomalies whereas isolated thumb malformations are predominantly present in patients carrying mutations in RPL11 We also demonstrate that mutations of RPL5 RPL11 or RPS7 in DBA cells is associated with diverse defects in the maturation of ribosomal RNAs in the large or the small ribosomal subunit production pathway expanding the repertoire of ribosomal RNA processing defects associated with DBA
Develop more inquiry-based lab exercises1 C elegans crosses (Peter Barrett in Genetics lab)
2 Modifications on DNA transformation and lac operon exercises (PB)
3 The lsquotermitersquo experiment in Biol 1230L (Kristal Huggins and SKI)
4 In Cell Biology lab C elegans (endocytosis experiments) experiments with Planaria regeneration (adapted from MITHHMI) and recently with Daphnia (the water flea a small crustacean) adapted from the Nuffield Foundation where students expose the Daphnia to various cardioactive compounds measure changes in heart rate caused by effects on cellular receptors and design follow-up experiments (PB)
Assessment Strategies for Project Scicomp
Formative and summative
General scheme
bull Assessment tasks based on objectives
bull Develop assessment tools and pilot for validation
bull Apply to larger audience
bull Collect and score
bull Share and analyze data
Coordinated course sequences and our curricular design serve as a good platform
for intra and interdepartmental discussions
(weekly meetings lsquoSERGrsquo etc)
Labs
bull General observation on student participationinitiative
bull Data sheets (say 10 collecthellipsay any 4)
bull Midterm skills practical stations and multiple choice (excellent determinant)
bull Quizzes (5-10 depending on the lab)
bull Final exams
Course based research experiencee(CRE)
bull How they design their experiment
bull Notebooks lab techniques
bull Participation in class discussions
bull Ability to troubleshoot
bull Midterm Skills and oral exam along with traditional exam
bull Short answer (non multiple choice) questions
bull Research paper presentations
CREs at Xavier
bull Phage and Genomics
bull lsquoUndergraduate Researchrsquo for credits
bull Introduction to Mammalian Tissue Culture
The SEA-PHAGES ProgramhttpsseaphagesorgThe official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program
SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is a two-semester discovery-based undergraduate research course that begins with simple digging in the soil to find new viruses but progresses through a variety of microbiology techniques and eventually to complex genome annotation and bioinformatic analyses
CBE Life Sci Educ 2016 fall15(3) pii ar38 doi 101187cbe16-01-0078Increasing URM Undergraduate Student Success through Assessment-Driven Interventions A Multiyear Study Using Freshman-Level General Biology as a Model SystemCarmichael MC1 St Clair C1 Edwards AM2 Barrett P1 McFerrin H1 Davenport I1 Awad M1 Kundu A1 Ireland SK3
AbstractXavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students In this multiyear study with sim5500 participants data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course The three hour-long exams were common and administered concurrently to all students New exam questions were developed using Blooms taxonomy and exam results were analyzed statistically with validated assessment tools All but the comprehensive final exam were returned to students for self-evaluation and remediation Among other approaches course rigor was monitored by using an identical set of 60 questions on the final exam across 10 semesters Analysis of the identical sets of 60 final exam questions revealed that overall averages increased from 729 (2010) to 835 (2015) Regression analysis demonstrated a statistically significant correlation between high-risk students and their averages on the 60 questions Additional analysis demonstrated statistically significant improvements for at least one letter grade from midterm to final and a 20 increase in the course pass rates over time also for the high-risk population These results support the hypothesis that our data-driven interventions and assessment techniques are successful in improving student retention particularly for our academically at-risk students
Lecture Biol 1230
bull Competency E4 (chemistry in biology atomic bonds metabolic pathways thermodynamics)
bull Quizzes (formative assessment with Clickers)
bull The coordinator prepares the three lsquoOne hour examsrsquo (questions not from the textbook) instructors again reviewcomment
bull Question types range (content versus applications) and also lsquoBack pagersquo ( 20 of the exam grade) Formative assessment using the LXRtest software (Opscan6 scanner)
Final exam not returned cumulative and has had 60 questions (good discriminators based on the rpbvalues) commonly used on ALL final exams for the past five years Powerful tool for measuring studentsrsquo learning and applications over time and based on academic risk categories
Last Name First Name
Biology 1230 Exam 1 ldquoBack Pagerdquo Score _ 20 pts
I 5 pts Complete the following table for the 3 major components (subatomic particles) of the atom
hint electrical charge = positive negative or neutral and mass = 1 dalton or 11800 dalton 1 pt each
Particle Electrical Charge Mass
1 Proton 1 dalton
2 Electron
3 Neutron
II 5 pts In your own words compare and contrast the following two atoms A and B use the back of the previous page to
make as many observations as you can about similarities (and what they mean) and differences (and what they mean)
between the atoms
A B
III 5 pts Match the following by placing the corresponding in the space provided 1 pt each
_____ tertiary structure 1 produce H2O
_____ two ester linkages 2 is responsible for the 3-dimensional shape of a protein
_____ phosphodiester bonds 3 exist within diglycerides (diacylglyerols) and phospholipids
_____ dehydration synthesis reactions 4 are a type of lipid
_____ steroids 5 are formed when nucleic acids are synthesized
IV 5 pts Circle each of the variable (R) groups in the molecules shown below (3 pts)
a Which lsquoRrsquo group is polar ______ (write the corresponding in the space provided) (1 pt)
b Which lsquoRrsquo group is ionic ______ (write the corresponding in the space provided) (1 pt)
NH3+ OH CH3
1 2 3
12 neutrons
11 protons
10 electrons
13 neutrons
11 protons
11 electrons
Bio1230 Exam 1
Clickers and immediate feedback
Name _____________________________________________________________________________________________
This is a worksheet for your self-evaluation of study habits and exam preparedness Your answers on the corresponding
online exam surveys are confidential
~The average number of hours I spent per week reading the chapters andor reviewingprocessing class notes was (circle the
appropriate response)
zero to one one to two two to four greater than four
~I read the assignment before coming to class (circle the appropriate response)
never sometimes regularly
~I asked my instructor questions when I was confused about textbook material andor lecture material (circle the appropriate
response)
never sometimes regularly
~Overall I spent _____ hours specifically studying for this exam (Please fill in the blank)
~Prior to taking the exam I expected to get an approximate grade of (fill in the blank) _____
~My actual grade was a(n) (fill in the blank) _____
~Check all of the statements that apply to your performance on the exam
____ studied the right information ____ did not study the right information
____ studied the right information but did not ____ studied the right information and
understand it thought I understood it
____ used the class outlines to study ____ thought college would be easier
____ did not know what to study ____ other _____________________
____ did not think I would need to know the information in such detail
Analysis of Missed Questions I answered the question incorrectly because I Insert question number below in the correct category
did not study the information
studied the information but forgot it
did not understand the information in the
summary notes
confused similar concepts or terms (ie
isotopes and isomers)
misread or misunderstood the question
did not consider all of the answer choices
knew the correct answer - but chose an
incorrect answer by mistake
List other reason(s)
List other reason(s)
Please answer additional self-evaluation questions on the back of this page
Self-Evaluation of Study Habits amp Exam Preparedness for Biology 1230 Exam I or II or III (circle one)
Going forwardhellip
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
bull Students applying for and receiving financial aid ndash 87bull Students receiving Pell Grants ndash over 65bull Underprepared students exhibiting the will to succeed accepted bull Based on high school GPAs and ACTSAT scores students and other factors
classified in three academic risk categories (low medium and high)bull First time freshmen graduation rate is ~ 65 (internal data)bull Transfer students (mostly pre-Pharms join at the 2nd year level)
Project Scicomp2012-2017
Competency-based curricular reforms and their positive influence on URM
learning and retention
Goals of Project Scicomp
bull Implement curricular reforms to reflect the scientific competency recommendations through newer teaching testing and assessment approaches (that would be sustainable after the end of funding)
bull Increase student retention in the sciences
bull Increase number of students going to medical or graduate schools or in the workforce
Guiding Documents
Years 1 - 3 Biology 1210L and 1220L were developed received academic assembly approval and were piloted in Fall 2012
The main goal of these courses was to introduce the fundamentals of scientific competencies and research-related active learning exercises in a stress-free environment
Based on the formative and summative assessments of these courses we have made several adjustments as we offer these courses each semester
Pre- and post-course diagnostic tests
Biology 1230 lecture and lab underwent changes in content and in the style of teaching testing and assessing
Weekly meetings for more sharing of ideas on best practices
Student self-assessment of performance
Student pre- and post- surveys on perspectives about Biology
Online homework assignments and clicker questions for formative assessment OpScan scanner and LXR Test softwarefor increased assessment capabilities
Curricular changes across STEM disciplines and dissemination
XU Center For the Advancement of Teaching and SERG
AAAS VampC HHMI NAS GCSI Grinnell NYU Faculty Resource Network
On and off campus collaborations
Focus on Science majorsduring their freshman year
bull Math in biology (Foundations I and II)
bull BioSQuaRE Test and its significance
bull Computer Applications (exercise on BLAST)
bull Biophysics (exercise on electricity)
bull Biol 1230 (leader lecture course for newer assessments
Foundations I and II (Biol 1210L and Biol 1220L)
bull Biol 1210L Introduces basic principles and applications of math physics and chemistry in biology and research Emphasis on group projects active learning discussions readingcomprehension of scientific articlespassages experimentation data collection data analysis and use of computers
bull Biol 1220L Focuses on statistics using data collected by students using systems like the Bean beetle and plant seeds Also reinforcement of measurement conversions dilutions stock solutions and back calculations using living systems typically bacteria Continuation of primary literature discussionsanalysis
1210L Active Learning110$in$50m
L$110$in$100
mL$
110$in$30m
L$
Infect=99 recovery=99
STUDIES ON PIGMENTATION OF SERRATIA MARCESCENS
I SPECTRAL AND PAPER CHROMATOGRAPHIC PROPERTIES OF PRODIGIOSIN
ROBERT P WILLIAMS JAMES A GREEN2 AND DONALD A RAPPOPORT
Departments of Microbiology Biochemistry and Radiology Baylor University College of Medicine Houston Texas
Received for publication June 23 1955
APPLIED MICROBIOLOGY Mar 1973 p 396-402 Vol 25 No 3 Copyright 0 1973 American Society for Microbiology Printed in USA
Biosynthesis of Prodigiosin a Secondary Metabolite of Serratia marcescensROBERT P WILLIAMS
Department of Microbiology Baylor College of Medicine Houston Texas 77025 Received for publication 30 October 1972
Prodigiosenes (prodigiosin and prodigiosin-like pigments) are known to be synthesized by only one genus of Eubacteriales and by two genera of Actinomycetales Biosynthesis by Serratia marcqscens occurs over a relatively narrow range of temperatures although the bacteria grow over a broad range When cultures of S marcescenswere incubated at 27 C in 10 casein hydrolysate viable count and protein attained maximal values within 24 to 48 h whereas prodigiosin did not reach a maximum until 96 h The greatest amount of pigment was synthesized when cultures were in the senescent phase of growth Suspensions of nonproliferating bacteria incubated at 27 C in only i-alanine also synthesized prodigiosin although at a slower rate than growing cultures Kinetics of growth for the wild-type red S marcescens and a white mutant were identical when incubated at 27 C but the wild type produced abundant pigment These results plus other data obtained from the literature suggest that prodigiosin is a secondary metabolite The importance of this proposal to understanding the function of prodigiosin in S marcescens is discussed
Zooming ahead to recent yearshelliphellip From 1955 to 2017
MybioSorcecomhttpswwwmybiosourcecom
Product DescriptionProdigiosin is an intensely red pyrrole pigment produced by several bacteria most notably Serratia marcescens Prodigiosin has a broad biological profile with activity against fungi tumor cell lines and malaria It was shown to be an immunosuppressant in 2007 The mode of action of prodigiosin has recently received considerable attention as an inducer of apoptosis in human primary cancer cells via caspase activation Prodigiosin also acts as an inducer of p21WAF1CIP1 expression via transforming growth factor-B receptor pathway and of NAG-1activation by acting on glycogen synthase kinase-3B
Evidence of ldquomath-gaprdquo
bull ACT College Readiness Benchmark
ndash 50 chance of obtaining a B or
better or ~75 chance of obtaining
a C or higher in a corresponding
first-year course
ACT Site
ndash Math = Algebra I
ndash Science = Biology IBased on sample of 214 institutions and gt230000
students from US Benchmarks = median course
placement values and represent a ldquotypicalrdquo set of
expectations
Percent of ACT-Tested High School Graduates Meeting ACT Benchmarks
Pe
rce
nt
Few 12th Grade Students Interested
in STEM and Proficient in Math
Business-Higher Ed Forum Research Brief (2011)Included in 2012 PCAST Appendix E
STEM interested
AND Math Proficient
NOT STEM
interestedMath
ProficientNOT STEM
interested
NOT Math
Proficient
STEM
interested
NOT Math
Proficient
Biological Quantitative Reasoning
Exam (BioSQuaRE) ndash Q6 consortium
BioSQuaRE TeamBiology
Paul Overvoorde (Macalester)
Peter Brodfuehrer Greg Davis (Bryn Mawr)
Charles Umbanhowar (St Olaf)
Marion Preest (Keck Science Center Claremont Colleges)
Steve Adolph Cathy McFadden (Harvey Mudd)
Educational PsychologyStatistics
Andy Zieffler Laure Le (U Minnesota)
Laura Zeigler (Iowa State)
Erik Larson (Macalester)- Sociology
ldquoOtherrdquo
Liz Stanhope (Lewis and Clark) ndash Math
Jason Belitsky (Oberlin) ndash Chemistry
Marcelo Vinces (Oberlin) ndash Quantitative Skills Center
Tabassum Haque (Oberlin) ndash Institutional Research
Alignment of Learning Outcomes
bull 14 + 38 faculty
bull Mapping of learning outcomes with
previous national reports
ndash BIO2010
ndash Vision and Changes
ndash Next Gen Science Standards for Science
and Engineering
ndash Revised AP Biology requirements
ndash Preparing Future Physicians
bull Comparison to previously created
Quantitative Literacy Efforts (eg
QRLA TOSLS)
Mapping Learning Outcomes to National Reports
ContentStudents should
be able to
BIO20
10
Vision
amp
Chang
e
SFFPAP
Bio
NGSS
SampE
Algebra
functions
and
modeling
Carry out basic mathematical
computations (eg proportional reasoning
unit conversion center and variation)
X X X X X
Recognize and use logarithmic or
exponential relationshipsX X
Fit a model such as population growth X X
Use a representation or a model to make
predictionsX X X X X
Describeinfer relationships between
variables (scatterplots regression
network diagrams maps)
X X
Perform logicalalgorithmic reasoning X X X X
Statistics
and
probability
Calculate or use the concept of the
likelihood of an eventX X X
Calculate or use conditional probability X X X
Recognize and interpret what summary
statistics representX X X
Identify different types of error X
Recognize that biological systems are
inherently variable (eg stochastic vs
deterministic)
X X
Formulate hypothesis statements X X X X
Understand what a p-value is X X X X
Understand when causal claims can be
made (eg correlation vs causation)X X X X
Visualizati
on
Choose the appropriate type of graph X X X X X
Interpret a graph (eg functional
relationships logarithmic relationships)X X X X X
Be able to use a table X X X
Use spatial reasoning to interpret
multidimensional numerical and visual
data (geographic information)
X
Stanhope et al (2017) Development of a Biological
Science Quantitative Reasoning Exam (BioSQuaRE)
CBE- Life Science Education Winter edition
December 1 2017
bull identification and validation of learning domains
bull iterative development of BioSQuaRE Instrument
bull evidence of validity
bull discussion of instruments utility for students individual
faculty and departments or programs
Visit wwwmacalestereduhhmibiosquare for more information
BLASTing Human and Other Organisms
bull Our goal is to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus(snake) The objective is to find and precisely map the coding regions using NCBIrsquos BLASTp search tool
bull Answer the following questions for each of the 4 organisms1 Describe the summary distributions2 Interpret the score the percent identity and the E-value If
obtain hit(s) are they likely due to chance If no hits why3 Analyze the alignments
Describe these Summary Distributions
Chimp
Cow
Snake
Chicken
Interpret the Scores E-values and Identities
Chimp
Cow
Snake
Chicken
Analyze the Alignments
Chimp
Cow
Snake
Chicken
Additional Questions of Interest
bull Our goal was to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus (snake) The objective is to find and precisely map the coding regions
bull Answer the following questions1 This presentation is showing only highly significant pairs How
do you think the alignments (scores e-values identities) differ if we analyze low significant pairs
2 Can you infer that this protein does not exist in this organism3 Give alternative explanations for the differences in scores e-
values and identities4 Is there an evolutionary relationship between sequences
Am J Hum Genet 2008 Dec 12 83(6) 769ndash780 Published online 2008 Dec 5 doi 101016jajhg200811004
Ribosomal Protein L5 and L11 Mutations Are Associated with Cleft Palate and Abnormal Thumbs in Diamond-Blackfan Anemia Patients
Hanna T Gazda12lowast
Mee Rie Sheen1
Adrianna Vlachos34
Valerie Choesmel56
Marie-Franccediloise ODonohue
56Hal Schneider
1Natasha Darras
1Catherine Hasman
1Colin A
Sieff27
Peter E Newburger8
Sarah E Ball9
Edyta Niewiadomska10
Michal Matysiak10
Jan M Zaucha
11Bertil Glader
12Charlotte Niemeyer
13Joerg J Meerpohl
13Eva Atsidaftos
34Jeffrey
M Lipton34
Pierre-Emmanuel Gleizes56
and Alan H Beggs12
Author information Article notes Copyright and License information AbstractDiamond-Blackfan anemia (DBA) a congenital bone-marrow-failure syndrome is characterized by red blood cell aplasia macrocytic anemia clinical heterogeneity and increased risk of malignancy Although anemia is the most prominent feature of DBA the disease is also characterized by growth retardation and congenital anomalies that are present in sim30ndash50 of patients The disease has been associated with mutations in four ribosomal protein (RP) genes RPS19 RPS24 RPS17 and RPL35A in about 30 of patients However the genetic basis of the remaining 70 of cases is still unknown Here we report the second known mutation in RPS17 and probable pathogenic mutations in three more RP genes RPL5 RPL11 and RPS7 In addition we identified rare variants of unknown significance in three other genes RPL36 RPS15 and RPS27A Remarkably careful review of the clinical data showed that mutations in RPL5 are associated with multiple physical abnormalities including craniofacial thumb and heart anomalies whereas isolated thumb malformations are predominantly present in patients carrying mutations in RPL11 We also demonstrate that mutations of RPL5 RPL11 or RPS7 in DBA cells is associated with diverse defects in the maturation of ribosomal RNAs in the large or the small ribosomal subunit production pathway expanding the repertoire of ribosomal RNA processing defects associated with DBA
Develop more inquiry-based lab exercises1 C elegans crosses (Peter Barrett in Genetics lab)
2 Modifications on DNA transformation and lac operon exercises (PB)
3 The lsquotermitersquo experiment in Biol 1230L (Kristal Huggins and SKI)
4 In Cell Biology lab C elegans (endocytosis experiments) experiments with Planaria regeneration (adapted from MITHHMI) and recently with Daphnia (the water flea a small crustacean) adapted from the Nuffield Foundation where students expose the Daphnia to various cardioactive compounds measure changes in heart rate caused by effects on cellular receptors and design follow-up experiments (PB)
Assessment Strategies for Project Scicomp
Formative and summative
General scheme
bull Assessment tasks based on objectives
bull Develop assessment tools and pilot for validation
bull Apply to larger audience
bull Collect and score
bull Share and analyze data
Coordinated course sequences and our curricular design serve as a good platform
for intra and interdepartmental discussions
(weekly meetings lsquoSERGrsquo etc)
Labs
bull General observation on student participationinitiative
bull Data sheets (say 10 collecthellipsay any 4)
bull Midterm skills practical stations and multiple choice (excellent determinant)
bull Quizzes (5-10 depending on the lab)
bull Final exams
Course based research experiencee(CRE)
bull How they design their experiment
bull Notebooks lab techniques
bull Participation in class discussions
bull Ability to troubleshoot
bull Midterm Skills and oral exam along with traditional exam
bull Short answer (non multiple choice) questions
bull Research paper presentations
CREs at Xavier
bull Phage and Genomics
bull lsquoUndergraduate Researchrsquo for credits
bull Introduction to Mammalian Tissue Culture
The SEA-PHAGES ProgramhttpsseaphagesorgThe official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program
SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is a two-semester discovery-based undergraduate research course that begins with simple digging in the soil to find new viruses but progresses through a variety of microbiology techniques and eventually to complex genome annotation and bioinformatic analyses
CBE Life Sci Educ 2016 fall15(3) pii ar38 doi 101187cbe16-01-0078Increasing URM Undergraduate Student Success through Assessment-Driven Interventions A Multiyear Study Using Freshman-Level General Biology as a Model SystemCarmichael MC1 St Clair C1 Edwards AM2 Barrett P1 McFerrin H1 Davenport I1 Awad M1 Kundu A1 Ireland SK3
AbstractXavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students In this multiyear study with sim5500 participants data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course The three hour-long exams were common and administered concurrently to all students New exam questions were developed using Blooms taxonomy and exam results were analyzed statistically with validated assessment tools All but the comprehensive final exam were returned to students for self-evaluation and remediation Among other approaches course rigor was monitored by using an identical set of 60 questions on the final exam across 10 semesters Analysis of the identical sets of 60 final exam questions revealed that overall averages increased from 729 (2010) to 835 (2015) Regression analysis demonstrated a statistically significant correlation between high-risk students and their averages on the 60 questions Additional analysis demonstrated statistically significant improvements for at least one letter grade from midterm to final and a 20 increase in the course pass rates over time also for the high-risk population These results support the hypothesis that our data-driven interventions and assessment techniques are successful in improving student retention particularly for our academically at-risk students
Lecture Biol 1230
bull Competency E4 (chemistry in biology atomic bonds metabolic pathways thermodynamics)
bull Quizzes (formative assessment with Clickers)
bull The coordinator prepares the three lsquoOne hour examsrsquo (questions not from the textbook) instructors again reviewcomment
bull Question types range (content versus applications) and also lsquoBack pagersquo ( 20 of the exam grade) Formative assessment using the LXRtest software (Opscan6 scanner)
Final exam not returned cumulative and has had 60 questions (good discriminators based on the rpbvalues) commonly used on ALL final exams for the past five years Powerful tool for measuring studentsrsquo learning and applications over time and based on academic risk categories
Last Name First Name
Biology 1230 Exam 1 ldquoBack Pagerdquo Score _ 20 pts
I 5 pts Complete the following table for the 3 major components (subatomic particles) of the atom
hint electrical charge = positive negative or neutral and mass = 1 dalton or 11800 dalton 1 pt each
Particle Electrical Charge Mass
1 Proton 1 dalton
2 Electron
3 Neutron
II 5 pts In your own words compare and contrast the following two atoms A and B use the back of the previous page to
make as many observations as you can about similarities (and what they mean) and differences (and what they mean)
between the atoms
A B
III 5 pts Match the following by placing the corresponding in the space provided 1 pt each
_____ tertiary structure 1 produce H2O
_____ two ester linkages 2 is responsible for the 3-dimensional shape of a protein
_____ phosphodiester bonds 3 exist within diglycerides (diacylglyerols) and phospholipids
_____ dehydration synthesis reactions 4 are a type of lipid
_____ steroids 5 are formed when nucleic acids are synthesized
IV 5 pts Circle each of the variable (R) groups in the molecules shown below (3 pts)
a Which lsquoRrsquo group is polar ______ (write the corresponding in the space provided) (1 pt)
b Which lsquoRrsquo group is ionic ______ (write the corresponding in the space provided) (1 pt)
NH3+ OH CH3
1 2 3
12 neutrons
11 protons
10 electrons
13 neutrons
11 protons
11 electrons
Bio1230 Exam 1
Clickers and immediate feedback
Name _____________________________________________________________________________________________
This is a worksheet for your self-evaluation of study habits and exam preparedness Your answers on the corresponding
online exam surveys are confidential
~The average number of hours I spent per week reading the chapters andor reviewingprocessing class notes was (circle the
appropriate response)
zero to one one to two two to four greater than four
~I read the assignment before coming to class (circle the appropriate response)
never sometimes regularly
~I asked my instructor questions when I was confused about textbook material andor lecture material (circle the appropriate
response)
never sometimes regularly
~Overall I spent _____ hours specifically studying for this exam (Please fill in the blank)
~Prior to taking the exam I expected to get an approximate grade of (fill in the blank) _____
~My actual grade was a(n) (fill in the blank) _____
~Check all of the statements that apply to your performance on the exam
____ studied the right information ____ did not study the right information
____ studied the right information but did not ____ studied the right information and
understand it thought I understood it
____ used the class outlines to study ____ thought college would be easier
____ did not know what to study ____ other _____________________
____ did not think I would need to know the information in such detail
Analysis of Missed Questions I answered the question incorrectly because I Insert question number below in the correct category
did not study the information
studied the information but forgot it
did not understand the information in the
summary notes
confused similar concepts or terms (ie
isotopes and isomers)
misread or misunderstood the question
did not consider all of the answer choices
knew the correct answer - but chose an
incorrect answer by mistake
List other reason(s)
List other reason(s)
Please answer additional self-evaluation questions on the back of this page
Self-Evaluation of Study Habits amp Exam Preparedness for Biology 1230 Exam I or II or III (circle one)
Going forwardhellip
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
Project Scicomp2012-2017
Competency-based curricular reforms and their positive influence on URM
learning and retention
Goals of Project Scicomp
bull Implement curricular reforms to reflect the scientific competency recommendations through newer teaching testing and assessment approaches (that would be sustainable after the end of funding)
bull Increase student retention in the sciences
bull Increase number of students going to medical or graduate schools or in the workforce
Guiding Documents
Years 1 - 3 Biology 1210L and 1220L were developed received academic assembly approval and were piloted in Fall 2012
The main goal of these courses was to introduce the fundamentals of scientific competencies and research-related active learning exercises in a stress-free environment
Based on the formative and summative assessments of these courses we have made several adjustments as we offer these courses each semester
Pre- and post-course diagnostic tests
Biology 1230 lecture and lab underwent changes in content and in the style of teaching testing and assessing
Weekly meetings for more sharing of ideas on best practices
Student self-assessment of performance
Student pre- and post- surveys on perspectives about Biology
Online homework assignments and clicker questions for formative assessment OpScan scanner and LXR Test softwarefor increased assessment capabilities
Curricular changes across STEM disciplines and dissemination
XU Center For the Advancement of Teaching and SERG
AAAS VampC HHMI NAS GCSI Grinnell NYU Faculty Resource Network
On and off campus collaborations
Focus on Science majorsduring their freshman year
bull Math in biology (Foundations I and II)
bull BioSQuaRE Test and its significance
bull Computer Applications (exercise on BLAST)
bull Biophysics (exercise on electricity)
bull Biol 1230 (leader lecture course for newer assessments
Foundations I and II (Biol 1210L and Biol 1220L)
bull Biol 1210L Introduces basic principles and applications of math physics and chemistry in biology and research Emphasis on group projects active learning discussions readingcomprehension of scientific articlespassages experimentation data collection data analysis and use of computers
bull Biol 1220L Focuses on statistics using data collected by students using systems like the Bean beetle and plant seeds Also reinforcement of measurement conversions dilutions stock solutions and back calculations using living systems typically bacteria Continuation of primary literature discussionsanalysis
1210L Active Learning110$in$50m
L$110$in$100
mL$
110$in$30m
L$
Infect=99 recovery=99
STUDIES ON PIGMENTATION OF SERRATIA MARCESCENS
I SPECTRAL AND PAPER CHROMATOGRAPHIC PROPERTIES OF PRODIGIOSIN
ROBERT P WILLIAMS JAMES A GREEN2 AND DONALD A RAPPOPORT
Departments of Microbiology Biochemistry and Radiology Baylor University College of Medicine Houston Texas
Received for publication June 23 1955
APPLIED MICROBIOLOGY Mar 1973 p 396-402 Vol 25 No 3 Copyright 0 1973 American Society for Microbiology Printed in USA
Biosynthesis of Prodigiosin a Secondary Metabolite of Serratia marcescensROBERT P WILLIAMS
Department of Microbiology Baylor College of Medicine Houston Texas 77025 Received for publication 30 October 1972
Prodigiosenes (prodigiosin and prodigiosin-like pigments) are known to be synthesized by only one genus of Eubacteriales and by two genera of Actinomycetales Biosynthesis by Serratia marcqscens occurs over a relatively narrow range of temperatures although the bacteria grow over a broad range When cultures of S marcescenswere incubated at 27 C in 10 casein hydrolysate viable count and protein attained maximal values within 24 to 48 h whereas prodigiosin did not reach a maximum until 96 h The greatest amount of pigment was synthesized when cultures were in the senescent phase of growth Suspensions of nonproliferating bacteria incubated at 27 C in only i-alanine also synthesized prodigiosin although at a slower rate than growing cultures Kinetics of growth for the wild-type red S marcescens and a white mutant were identical when incubated at 27 C but the wild type produced abundant pigment These results plus other data obtained from the literature suggest that prodigiosin is a secondary metabolite The importance of this proposal to understanding the function of prodigiosin in S marcescens is discussed
Zooming ahead to recent yearshelliphellip From 1955 to 2017
MybioSorcecomhttpswwwmybiosourcecom
Product DescriptionProdigiosin is an intensely red pyrrole pigment produced by several bacteria most notably Serratia marcescens Prodigiosin has a broad biological profile with activity against fungi tumor cell lines and malaria It was shown to be an immunosuppressant in 2007 The mode of action of prodigiosin has recently received considerable attention as an inducer of apoptosis in human primary cancer cells via caspase activation Prodigiosin also acts as an inducer of p21WAF1CIP1 expression via transforming growth factor-B receptor pathway and of NAG-1activation by acting on glycogen synthase kinase-3B
Evidence of ldquomath-gaprdquo
bull ACT College Readiness Benchmark
ndash 50 chance of obtaining a B or
better or ~75 chance of obtaining
a C or higher in a corresponding
first-year course
ACT Site
ndash Math = Algebra I
ndash Science = Biology IBased on sample of 214 institutions and gt230000
students from US Benchmarks = median course
placement values and represent a ldquotypicalrdquo set of
expectations
Percent of ACT-Tested High School Graduates Meeting ACT Benchmarks
Pe
rce
nt
Few 12th Grade Students Interested
in STEM and Proficient in Math
Business-Higher Ed Forum Research Brief (2011)Included in 2012 PCAST Appendix E
STEM interested
AND Math Proficient
NOT STEM
interestedMath
ProficientNOT STEM
interested
NOT Math
Proficient
STEM
interested
NOT Math
Proficient
Biological Quantitative Reasoning
Exam (BioSQuaRE) ndash Q6 consortium
BioSQuaRE TeamBiology
Paul Overvoorde (Macalester)
Peter Brodfuehrer Greg Davis (Bryn Mawr)
Charles Umbanhowar (St Olaf)
Marion Preest (Keck Science Center Claremont Colleges)
Steve Adolph Cathy McFadden (Harvey Mudd)
Educational PsychologyStatistics
Andy Zieffler Laure Le (U Minnesota)
Laura Zeigler (Iowa State)
Erik Larson (Macalester)- Sociology
ldquoOtherrdquo
Liz Stanhope (Lewis and Clark) ndash Math
Jason Belitsky (Oberlin) ndash Chemistry
Marcelo Vinces (Oberlin) ndash Quantitative Skills Center
Tabassum Haque (Oberlin) ndash Institutional Research
Alignment of Learning Outcomes
bull 14 + 38 faculty
bull Mapping of learning outcomes with
previous national reports
ndash BIO2010
ndash Vision and Changes
ndash Next Gen Science Standards for Science
and Engineering
ndash Revised AP Biology requirements
ndash Preparing Future Physicians
bull Comparison to previously created
Quantitative Literacy Efforts (eg
QRLA TOSLS)
Mapping Learning Outcomes to National Reports
ContentStudents should
be able to
BIO20
10
Vision
amp
Chang
e
SFFPAP
Bio
NGSS
SampE
Algebra
functions
and
modeling
Carry out basic mathematical
computations (eg proportional reasoning
unit conversion center and variation)
X X X X X
Recognize and use logarithmic or
exponential relationshipsX X
Fit a model such as population growth X X
Use a representation or a model to make
predictionsX X X X X
Describeinfer relationships between
variables (scatterplots regression
network diagrams maps)
X X
Perform logicalalgorithmic reasoning X X X X
Statistics
and
probability
Calculate or use the concept of the
likelihood of an eventX X X
Calculate or use conditional probability X X X
Recognize and interpret what summary
statistics representX X X
Identify different types of error X
Recognize that biological systems are
inherently variable (eg stochastic vs
deterministic)
X X
Formulate hypothesis statements X X X X
Understand what a p-value is X X X X
Understand when causal claims can be
made (eg correlation vs causation)X X X X
Visualizati
on
Choose the appropriate type of graph X X X X X
Interpret a graph (eg functional
relationships logarithmic relationships)X X X X X
Be able to use a table X X X
Use spatial reasoning to interpret
multidimensional numerical and visual
data (geographic information)
X
Stanhope et al (2017) Development of a Biological
Science Quantitative Reasoning Exam (BioSQuaRE)
CBE- Life Science Education Winter edition
December 1 2017
bull identification and validation of learning domains
bull iterative development of BioSQuaRE Instrument
bull evidence of validity
bull discussion of instruments utility for students individual
faculty and departments or programs
Visit wwwmacalestereduhhmibiosquare for more information
BLASTing Human and Other Organisms
bull Our goal is to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus(snake) The objective is to find and precisely map the coding regions using NCBIrsquos BLASTp search tool
bull Answer the following questions for each of the 4 organisms1 Describe the summary distributions2 Interpret the score the percent identity and the E-value If
obtain hit(s) are they likely due to chance If no hits why3 Analyze the alignments
Describe these Summary Distributions
Chimp
Cow
Snake
Chicken
Interpret the Scores E-values and Identities
Chimp
Cow
Snake
Chicken
Analyze the Alignments
Chimp
Cow
Snake
Chicken
Additional Questions of Interest
bull Our goal was to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus (snake) The objective is to find and precisely map the coding regions
bull Answer the following questions1 This presentation is showing only highly significant pairs How
do you think the alignments (scores e-values identities) differ if we analyze low significant pairs
2 Can you infer that this protein does not exist in this organism3 Give alternative explanations for the differences in scores e-
values and identities4 Is there an evolutionary relationship between sequences
Am J Hum Genet 2008 Dec 12 83(6) 769ndash780 Published online 2008 Dec 5 doi 101016jajhg200811004
Ribosomal Protein L5 and L11 Mutations Are Associated with Cleft Palate and Abnormal Thumbs in Diamond-Blackfan Anemia Patients
Hanna T Gazda12lowast
Mee Rie Sheen1
Adrianna Vlachos34
Valerie Choesmel56
Marie-Franccediloise ODonohue
56Hal Schneider
1Natasha Darras
1Catherine Hasman
1Colin A
Sieff27
Peter E Newburger8
Sarah E Ball9
Edyta Niewiadomska10
Michal Matysiak10
Jan M Zaucha
11Bertil Glader
12Charlotte Niemeyer
13Joerg J Meerpohl
13Eva Atsidaftos
34Jeffrey
M Lipton34
Pierre-Emmanuel Gleizes56
and Alan H Beggs12
Author information Article notes Copyright and License information AbstractDiamond-Blackfan anemia (DBA) a congenital bone-marrow-failure syndrome is characterized by red blood cell aplasia macrocytic anemia clinical heterogeneity and increased risk of malignancy Although anemia is the most prominent feature of DBA the disease is also characterized by growth retardation and congenital anomalies that are present in sim30ndash50 of patients The disease has been associated with mutations in four ribosomal protein (RP) genes RPS19 RPS24 RPS17 and RPL35A in about 30 of patients However the genetic basis of the remaining 70 of cases is still unknown Here we report the second known mutation in RPS17 and probable pathogenic mutations in three more RP genes RPL5 RPL11 and RPS7 In addition we identified rare variants of unknown significance in three other genes RPL36 RPS15 and RPS27A Remarkably careful review of the clinical data showed that mutations in RPL5 are associated with multiple physical abnormalities including craniofacial thumb and heart anomalies whereas isolated thumb malformations are predominantly present in patients carrying mutations in RPL11 We also demonstrate that mutations of RPL5 RPL11 or RPS7 in DBA cells is associated with diverse defects in the maturation of ribosomal RNAs in the large or the small ribosomal subunit production pathway expanding the repertoire of ribosomal RNA processing defects associated with DBA
Develop more inquiry-based lab exercises1 C elegans crosses (Peter Barrett in Genetics lab)
2 Modifications on DNA transformation and lac operon exercises (PB)
3 The lsquotermitersquo experiment in Biol 1230L (Kristal Huggins and SKI)
4 In Cell Biology lab C elegans (endocytosis experiments) experiments with Planaria regeneration (adapted from MITHHMI) and recently with Daphnia (the water flea a small crustacean) adapted from the Nuffield Foundation where students expose the Daphnia to various cardioactive compounds measure changes in heart rate caused by effects on cellular receptors and design follow-up experiments (PB)
Assessment Strategies for Project Scicomp
Formative and summative
General scheme
bull Assessment tasks based on objectives
bull Develop assessment tools and pilot for validation
bull Apply to larger audience
bull Collect and score
bull Share and analyze data
Coordinated course sequences and our curricular design serve as a good platform
for intra and interdepartmental discussions
(weekly meetings lsquoSERGrsquo etc)
Labs
bull General observation on student participationinitiative
bull Data sheets (say 10 collecthellipsay any 4)
bull Midterm skills practical stations and multiple choice (excellent determinant)
bull Quizzes (5-10 depending on the lab)
bull Final exams
Course based research experiencee(CRE)
bull How they design their experiment
bull Notebooks lab techniques
bull Participation in class discussions
bull Ability to troubleshoot
bull Midterm Skills and oral exam along with traditional exam
bull Short answer (non multiple choice) questions
bull Research paper presentations
CREs at Xavier
bull Phage and Genomics
bull lsquoUndergraduate Researchrsquo for credits
bull Introduction to Mammalian Tissue Culture
The SEA-PHAGES ProgramhttpsseaphagesorgThe official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program
SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is a two-semester discovery-based undergraduate research course that begins with simple digging in the soil to find new viruses but progresses through a variety of microbiology techniques and eventually to complex genome annotation and bioinformatic analyses
CBE Life Sci Educ 2016 fall15(3) pii ar38 doi 101187cbe16-01-0078Increasing URM Undergraduate Student Success through Assessment-Driven Interventions A Multiyear Study Using Freshman-Level General Biology as a Model SystemCarmichael MC1 St Clair C1 Edwards AM2 Barrett P1 McFerrin H1 Davenport I1 Awad M1 Kundu A1 Ireland SK3
AbstractXavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students In this multiyear study with sim5500 participants data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course The three hour-long exams were common and administered concurrently to all students New exam questions were developed using Blooms taxonomy and exam results were analyzed statistically with validated assessment tools All but the comprehensive final exam were returned to students for self-evaluation and remediation Among other approaches course rigor was monitored by using an identical set of 60 questions on the final exam across 10 semesters Analysis of the identical sets of 60 final exam questions revealed that overall averages increased from 729 (2010) to 835 (2015) Regression analysis demonstrated a statistically significant correlation between high-risk students and their averages on the 60 questions Additional analysis demonstrated statistically significant improvements for at least one letter grade from midterm to final and a 20 increase in the course pass rates over time also for the high-risk population These results support the hypothesis that our data-driven interventions and assessment techniques are successful in improving student retention particularly for our academically at-risk students
Lecture Biol 1230
bull Competency E4 (chemistry in biology atomic bonds metabolic pathways thermodynamics)
bull Quizzes (formative assessment with Clickers)
bull The coordinator prepares the three lsquoOne hour examsrsquo (questions not from the textbook) instructors again reviewcomment
bull Question types range (content versus applications) and also lsquoBack pagersquo ( 20 of the exam grade) Formative assessment using the LXRtest software (Opscan6 scanner)
Final exam not returned cumulative and has had 60 questions (good discriminators based on the rpbvalues) commonly used on ALL final exams for the past five years Powerful tool for measuring studentsrsquo learning and applications over time and based on academic risk categories
Last Name First Name
Biology 1230 Exam 1 ldquoBack Pagerdquo Score _ 20 pts
I 5 pts Complete the following table for the 3 major components (subatomic particles) of the atom
hint electrical charge = positive negative or neutral and mass = 1 dalton or 11800 dalton 1 pt each
Particle Electrical Charge Mass
1 Proton 1 dalton
2 Electron
3 Neutron
II 5 pts In your own words compare and contrast the following two atoms A and B use the back of the previous page to
make as many observations as you can about similarities (and what they mean) and differences (and what they mean)
between the atoms
A B
III 5 pts Match the following by placing the corresponding in the space provided 1 pt each
_____ tertiary structure 1 produce H2O
_____ two ester linkages 2 is responsible for the 3-dimensional shape of a protein
_____ phosphodiester bonds 3 exist within diglycerides (diacylglyerols) and phospholipids
_____ dehydration synthesis reactions 4 are a type of lipid
_____ steroids 5 are formed when nucleic acids are synthesized
IV 5 pts Circle each of the variable (R) groups in the molecules shown below (3 pts)
a Which lsquoRrsquo group is polar ______ (write the corresponding in the space provided) (1 pt)
b Which lsquoRrsquo group is ionic ______ (write the corresponding in the space provided) (1 pt)
NH3+ OH CH3
1 2 3
12 neutrons
11 protons
10 electrons
13 neutrons
11 protons
11 electrons
Bio1230 Exam 1
Clickers and immediate feedback
Name _____________________________________________________________________________________________
This is a worksheet for your self-evaluation of study habits and exam preparedness Your answers on the corresponding
online exam surveys are confidential
~The average number of hours I spent per week reading the chapters andor reviewingprocessing class notes was (circle the
appropriate response)
zero to one one to two two to four greater than four
~I read the assignment before coming to class (circle the appropriate response)
never sometimes regularly
~I asked my instructor questions when I was confused about textbook material andor lecture material (circle the appropriate
response)
never sometimes regularly
~Overall I spent _____ hours specifically studying for this exam (Please fill in the blank)
~Prior to taking the exam I expected to get an approximate grade of (fill in the blank) _____
~My actual grade was a(n) (fill in the blank) _____
~Check all of the statements that apply to your performance on the exam
____ studied the right information ____ did not study the right information
____ studied the right information but did not ____ studied the right information and
understand it thought I understood it
____ used the class outlines to study ____ thought college would be easier
____ did not know what to study ____ other _____________________
____ did not think I would need to know the information in such detail
Analysis of Missed Questions I answered the question incorrectly because I Insert question number below in the correct category
did not study the information
studied the information but forgot it
did not understand the information in the
summary notes
confused similar concepts or terms (ie
isotopes and isomers)
misread or misunderstood the question
did not consider all of the answer choices
knew the correct answer - but chose an
incorrect answer by mistake
List other reason(s)
List other reason(s)
Please answer additional self-evaluation questions on the back of this page
Self-Evaluation of Study Habits amp Exam Preparedness for Biology 1230 Exam I or II or III (circle one)
Going forwardhellip
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
Goals of Project Scicomp
bull Implement curricular reforms to reflect the scientific competency recommendations through newer teaching testing and assessment approaches (that would be sustainable after the end of funding)
bull Increase student retention in the sciences
bull Increase number of students going to medical or graduate schools or in the workforce
Guiding Documents
Years 1 - 3 Biology 1210L and 1220L were developed received academic assembly approval and were piloted in Fall 2012
The main goal of these courses was to introduce the fundamentals of scientific competencies and research-related active learning exercises in a stress-free environment
Based on the formative and summative assessments of these courses we have made several adjustments as we offer these courses each semester
Pre- and post-course diagnostic tests
Biology 1230 lecture and lab underwent changes in content and in the style of teaching testing and assessing
Weekly meetings for more sharing of ideas on best practices
Student self-assessment of performance
Student pre- and post- surveys on perspectives about Biology
Online homework assignments and clicker questions for formative assessment OpScan scanner and LXR Test softwarefor increased assessment capabilities
Curricular changes across STEM disciplines and dissemination
XU Center For the Advancement of Teaching and SERG
AAAS VampC HHMI NAS GCSI Grinnell NYU Faculty Resource Network
On and off campus collaborations
Focus on Science majorsduring their freshman year
bull Math in biology (Foundations I and II)
bull BioSQuaRE Test and its significance
bull Computer Applications (exercise on BLAST)
bull Biophysics (exercise on electricity)
bull Biol 1230 (leader lecture course for newer assessments
Foundations I and II (Biol 1210L and Biol 1220L)
bull Biol 1210L Introduces basic principles and applications of math physics and chemistry in biology and research Emphasis on group projects active learning discussions readingcomprehension of scientific articlespassages experimentation data collection data analysis and use of computers
bull Biol 1220L Focuses on statistics using data collected by students using systems like the Bean beetle and plant seeds Also reinforcement of measurement conversions dilutions stock solutions and back calculations using living systems typically bacteria Continuation of primary literature discussionsanalysis
1210L Active Learning110$in$50m
L$110$in$100
mL$
110$in$30m
L$
Infect=99 recovery=99
STUDIES ON PIGMENTATION OF SERRATIA MARCESCENS
I SPECTRAL AND PAPER CHROMATOGRAPHIC PROPERTIES OF PRODIGIOSIN
ROBERT P WILLIAMS JAMES A GREEN2 AND DONALD A RAPPOPORT
Departments of Microbiology Biochemistry and Radiology Baylor University College of Medicine Houston Texas
Received for publication June 23 1955
APPLIED MICROBIOLOGY Mar 1973 p 396-402 Vol 25 No 3 Copyright 0 1973 American Society for Microbiology Printed in USA
Biosynthesis of Prodigiosin a Secondary Metabolite of Serratia marcescensROBERT P WILLIAMS
Department of Microbiology Baylor College of Medicine Houston Texas 77025 Received for publication 30 October 1972
Prodigiosenes (prodigiosin and prodigiosin-like pigments) are known to be synthesized by only one genus of Eubacteriales and by two genera of Actinomycetales Biosynthesis by Serratia marcqscens occurs over a relatively narrow range of temperatures although the bacteria grow over a broad range When cultures of S marcescenswere incubated at 27 C in 10 casein hydrolysate viable count and protein attained maximal values within 24 to 48 h whereas prodigiosin did not reach a maximum until 96 h The greatest amount of pigment was synthesized when cultures were in the senescent phase of growth Suspensions of nonproliferating bacteria incubated at 27 C in only i-alanine also synthesized prodigiosin although at a slower rate than growing cultures Kinetics of growth for the wild-type red S marcescens and a white mutant were identical when incubated at 27 C but the wild type produced abundant pigment These results plus other data obtained from the literature suggest that prodigiosin is a secondary metabolite The importance of this proposal to understanding the function of prodigiosin in S marcescens is discussed
Zooming ahead to recent yearshelliphellip From 1955 to 2017
MybioSorcecomhttpswwwmybiosourcecom
Product DescriptionProdigiosin is an intensely red pyrrole pigment produced by several bacteria most notably Serratia marcescens Prodigiosin has a broad biological profile with activity against fungi tumor cell lines and malaria It was shown to be an immunosuppressant in 2007 The mode of action of prodigiosin has recently received considerable attention as an inducer of apoptosis in human primary cancer cells via caspase activation Prodigiosin also acts as an inducer of p21WAF1CIP1 expression via transforming growth factor-B receptor pathway and of NAG-1activation by acting on glycogen synthase kinase-3B
Evidence of ldquomath-gaprdquo
bull ACT College Readiness Benchmark
ndash 50 chance of obtaining a B or
better or ~75 chance of obtaining
a C or higher in a corresponding
first-year course
ACT Site
ndash Math = Algebra I
ndash Science = Biology IBased on sample of 214 institutions and gt230000
students from US Benchmarks = median course
placement values and represent a ldquotypicalrdquo set of
expectations
Percent of ACT-Tested High School Graduates Meeting ACT Benchmarks
Pe
rce
nt
Few 12th Grade Students Interested
in STEM and Proficient in Math
Business-Higher Ed Forum Research Brief (2011)Included in 2012 PCAST Appendix E
STEM interested
AND Math Proficient
NOT STEM
interestedMath
ProficientNOT STEM
interested
NOT Math
Proficient
STEM
interested
NOT Math
Proficient
Biological Quantitative Reasoning
Exam (BioSQuaRE) ndash Q6 consortium
BioSQuaRE TeamBiology
Paul Overvoorde (Macalester)
Peter Brodfuehrer Greg Davis (Bryn Mawr)
Charles Umbanhowar (St Olaf)
Marion Preest (Keck Science Center Claremont Colleges)
Steve Adolph Cathy McFadden (Harvey Mudd)
Educational PsychologyStatistics
Andy Zieffler Laure Le (U Minnesota)
Laura Zeigler (Iowa State)
Erik Larson (Macalester)- Sociology
ldquoOtherrdquo
Liz Stanhope (Lewis and Clark) ndash Math
Jason Belitsky (Oberlin) ndash Chemistry
Marcelo Vinces (Oberlin) ndash Quantitative Skills Center
Tabassum Haque (Oberlin) ndash Institutional Research
Alignment of Learning Outcomes
bull 14 + 38 faculty
bull Mapping of learning outcomes with
previous national reports
ndash BIO2010
ndash Vision and Changes
ndash Next Gen Science Standards for Science
and Engineering
ndash Revised AP Biology requirements
ndash Preparing Future Physicians
bull Comparison to previously created
Quantitative Literacy Efforts (eg
QRLA TOSLS)
Mapping Learning Outcomes to National Reports
ContentStudents should
be able to
BIO20
10
Vision
amp
Chang
e
SFFPAP
Bio
NGSS
SampE
Algebra
functions
and
modeling
Carry out basic mathematical
computations (eg proportional reasoning
unit conversion center and variation)
X X X X X
Recognize and use logarithmic or
exponential relationshipsX X
Fit a model such as population growth X X
Use a representation or a model to make
predictionsX X X X X
Describeinfer relationships between
variables (scatterplots regression
network diagrams maps)
X X
Perform logicalalgorithmic reasoning X X X X
Statistics
and
probability
Calculate or use the concept of the
likelihood of an eventX X X
Calculate or use conditional probability X X X
Recognize and interpret what summary
statistics representX X X
Identify different types of error X
Recognize that biological systems are
inherently variable (eg stochastic vs
deterministic)
X X
Formulate hypothesis statements X X X X
Understand what a p-value is X X X X
Understand when causal claims can be
made (eg correlation vs causation)X X X X
Visualizati
on
Choose the appropriate type of graph X X X X X
Interpret a graph (eg functional
relationships logarithmic relationships)X X X X X
Be able to use a table X X X
Use spatial reasoning to interpret
multidimensional numerical and visual
data (geographic information)
X
Stanhope et al (2017) Development of a Biological
Science Quantitative Reasoning Exam (BioSQuaRE)
CBE- Life Science Education Winter edition
December 1 2017
bull identification and validation of learning domains
bull iterative development of BioSQuaRE Instrument
bull evidence of validity
bull discussion of instruments utility for students individual
faculty and departments or programs
Visit wwwmacalestereduhhmibiosquare for more information
BLASTing Human and Other Organisms
bull Our goal is to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus(snake) The objective is to find and precisely map the coding regions using NCBIrsquos BLASTp search tool
bull Answer the following questions for each of the 4 organisms1 Describe the summary distributions2 Interpret the score the percent identity and the E-value If
obtain hit(s) are they likely due to chance If no hits why3 Analyze the alignments
Describe these Summary Distributions
Chimp
Cow
Snake
Chicken
Interpret the Scores E-values and Identities
Chimp
Cow
Snake
Chicken
Analyze the Alignments
Chimp
Cow
Snake
Chicken
Additional Questions of Interest
bull Our goal was to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus (snake) The objective is to find and precisely map the coding regions
bull Answer the following questions1 This presentation is showing only highly significant pairs How
do you think the alignments (scores e-values identities) differ if we analyze low significant pairs
2 Can you infer that this protein does not exist in this organism3 Give alternative explanations for the differences in scores e-
values and identities4 Is there an evolutionary relationship between sequences
Am J Hum Genet 2008 Dec 12 83(6) 769ndash780 Published online 2008 Dec 5 doi 101016jajhg200811004
Ribosomal Protein L5 and L11 Mutations Are Associated with Cleft Palate and Abnormal Thumbs in Diamond-Blackfan Anemia Patients
Hanna T Gazda12lowast
Mee Rie Sheen1
Adrianna Vlachos34
Valerie Choesmel56
Marie-Franccediloise ODonohue
56Hal Schneider
1Natasha Darras
1Catherine Hasman
1Colin A
Sieff27
Peter E Newburger8
Sarah E Ball9
Edyta Niewiadomska10
Michal Matysiak10
Jan M Zaucha
11Bertil Glader
12Charlotte Niemeyer
13Joerg J Meerpohl
13Eva Atsidaftos
34Jeffrey
M Lipton34
Pierre-Emmanuel Gleizes56
and Alan H Beggs12
Author information Article notes Copyright and License information AbstractDiamond-Blackfan anemia (DBA) a congenital bone-marrow-failure syndrome is characterized by red blood cell aplasia macrocytic anemia clinical heterogeneity and increased risk of malignancy Although anemia is the most prominent feature of DBA the disease is also characterized by growth retardation and congenital anomalies that are present in sim30ndash50 of patients The disease has been associated with mutations in four ribosomal protein (RP) genes RPS19 RPS24 RPS17 and RPL35A in about 30 of patients However the genetic basis of the remaining 70 of cases is still unknown Here we report the second known mutation in RPS17 and probable pathogenic mutations in three more RP genes RPL5 RPL11 and RPS7 In addition we identified rare variants of unknown significance in three other genes RPL36 RPS15 and RPS27A Remarkably careful review of the clinical data showed that mutations in RPL5 are associated with multiple physical abnormalities including craniofacial thumb and heart anomalies whereas isolated thumb malformations are predominantly present in patients carrying mutations in RPL11 We also demonstrate that mutations of RPL5 RPL11 or RPS7 in DBA cells is associated with diverse defects in the maturation of ribosomal RNAs in the large or the small ribosomal subunit production pathway expanding the repertoire of ribosomal RNA processing defects associated with DBA
Develop more inquiry-based lab exercises1 C elegans crosses (Peter Barrett in Genetics lab)
2 Modifications on DNA transformation and lac operon exercises (PB)
3 The lsquotermitersquo experiment in Biol 1230L (Kristal Huggins and SKI)
4 In Cell Biology lab C elegans (endocytosis experiments) experiments with Planaria regeneration (adapted from MITHHMI) and recently with Daphnia (the water flea a small crustacean) adapted from the Nuffield Foundation where students expose the Daphnia to various cardioactive compounds measure changes in heart rate caused by effects on cellular receptors and design follow-up experiments (PB)
Assessment Strategies for Project Scicomp
Formative and summative
General scheme
bull Assessment tasks based on objectives
bull Develop assessment tools and pilot for validation
bull Apply to larger audience
bull Collect and score
bull Share and analyze data
Coordinated course sequences and our curricular design serve as a good platform
for intra and interdepartmental discussions
(weekly meetings lsquoSERGrsquo etc)
Labs
bull General observation on student participationinitiative
bull Data sheets (say 10 collecthellipsay any 4)
bull Midterm skills practical stations and multiple choice (excellent determinant)
bull Quizzes (5-10 depending on the lab)
bull Final exams
Course based research experiencee(CRE)
bull How they design their experiment
bull Notebooks lab techniques
bull Participation in class discussions
bull Ability to troubleshoot
bull Midterm Skills and oral exam along with traditional exam
bull Short answer (non multiple choice) questions
bull Research paper presentations
CREs at Xavier
bull Phage and Genomics
bull lsquoUndergraduate Researchrsquo for credits
bull Introduction to Mammalian Tissue Culture
The SEA-PHAGES ProgramhttpsseaphagesorgThe official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program
SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is a two-semester discovery-based undergraduate research course that begins with simple digging in the soil to find new viruses but progresses through a variety of microbiology techniques and eventually to complex genome annotation and bioinformatic analyses
CBE Life Sci Educ 2016 fall15(3) pii ar38 doi 101187cbe16-01-0078Increasing URM Undergraduate Student Success through Assessment-Driven Interventions A Multiyear Study Using Freshman-Level General Biology as a Model SystemCarmichael MC1 St Clair C1 Edwards AM2 Barrett P1 McFerrin H1 Davenport I1 Awad M1 Kundu A1 Ireland SK3
AbstractXavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students In this multiyear study with sim5500 participants data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course The three hour-long exams were common and administered concurrently to all students New exam questions were developed using Blooms taxonomy and exam results were analyzed statistically with validated assessment tools All but the comprehensive final exam were returned to students for self-evaluation and remediation Among other approaches course rigor was monitored by using an identical set of 60 questions on the final exam across 10 semesters Analysis of the identical sets of 60 final exam questions revealed that overall averages increased from 729 (2010) to 835 (2015) Regression analysis demonstrated a statistically significant correlation between high-risk students and their averages on the 60 questions Additional analysis demonstrated statistically significant improvements for at least one letter grade from midterm to final and a 20 increase in the course pass rates over time also for the high-risk population These results support the hypothesis that our data-driven interventions and assessment techniques are successful in improving student retention particularly for our academically at-risk students
Lecture Biol 1230
bull Competency E4 (chemistry in biology atomic bonds metabolic pathways thermodynamics)
bull Quizzes (formative assessment with Clickers)
bull The coordinator prepares the three lsquoOne hour examsrsquo (questions not from the textbook) instructors again reviewcomment
bull Question types range (content versus applications) and also lsquoBack pagersquo ( 20 of the exam grade) Formative assessment using the LXRtest software (Opscan6 scanner)
Final exam not returned cumulative and has had 60 questions (good discriminators based on the rpbvalues) commonly used on ALL final exams for the past five years Powerful tool for measuring studentsrsquo learning and applications over time and based on academic risk categories
Last Name First Name
Biology 1230 Exam 1 ldquoBack Pagerdquo Score _ 20 pts
I 5 pts Complete the following table for the 3 major components (subatomic particles) of the atom
hint electrical charge = positive negative or neutral and mass = 1 dalton or 11800 dalton 1 pt each
Particle Electrical Charge Mass
1 Proton 1 dalton
2 Electron
3 Neutron
II 5 pts In your own words compare and contrast the following two atoms A and B use the back of the previous page to
make as many observations as you can about similarities (and what they mean) and differences (and what they mean)
between the atoms
A B
III 5 pts Match the following by placing the corresponding in the space provided 1 pt each
_____ tertiary structure 1 produce H2O
_____ two ester linkages 2 is responsible for the 3-dimensional shape of a protein
_____ phosphodiester bonds 3 exist within diglycerides (diacylglyerols) and phospholipids
_____ dehydration synthesis reactions 4 are a type of lipid
_____ steroids 5 are formed when nucleic acids are synthesized
IV 5 pts Circle each of the variable (R) groups in the molecules shown below (3 pts)
a Which lsquoRrsquo group is polar ______ (write the corresponding in the space provided) (1 pt)
b Which lsquoRrsquo group is ionic ______ (write the corresponding in the space provided) (1 pt)
NH3+ OH CH3
1 2 3
12 neutrons
11 protons
10 electrons
13 neutrons
11 protons
11 electrons
Bio1230 Exam 1
Clickers and immediate feedback
Name _____________________________________________________________________________________________
This is a worksheet for your self-evaluation of study habits and exam preparedness Your answers on the corresponding
online exam surveys are confidential
~The average number of hours I spent per week reading the chapters andor reviewingprocessing class notes was (circle the
appropriate response)
zero to one one to two two to four greater than four
~I read the assignment before coming to class (circle the appropriate response)
never sometimes regularly
~I asked my instructor questions when I was confused about textbook material andor lecture material (circle the appropriate
response)
never sometimes regularly
~Overall I spent _____ hours specifically studying for this exam (Please fill in the blank)
~Prior to taking the exam I expected to get an approximate grade of (fill in the blank) _____
~My actual grade was a(n) (fill in the blank) _____
~Check all of the statements that apply to your performance on the exam
____ studied the right information ____ did not study the right information
____ studied the right information but did not ____ studied the right information and
understand it thought I understood it
____ used the class outlines to study ____ thought college would be easier
____ did not know what to study ____ other _____________________
____ did not think I would need to know the information in such detail
Analysis of Missed Questions I answered the question incorrectly because I Insert question number below in the correct category
did not study the information
studied the information but forgot it
did not understand the information in the
summary notes
confused similar concepts or terms (ie
isotopes and isomers)
misread or misunderstood the question
did not consider all of the answer choices
knew the correct answer - but chose an
incorrect answer by mistake
List other reason(s)
List other reason(s)
Please answer additional self-evaluation questions on the back of this page
Self-Evaluation of Study Habits amp Exam Preparedness for Biology 1230 Exam I or II or III (circle one)
Going forwardhellip
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
Guiding Documents
Years 1 - 3 Biology 1210L and 1220L were developed received academic assembly approval and were piloted in Fall 2012
The main goal of these courses was to introduce the fundamentals of scientific competencies and research-related active learning exercises in a stress-free environment
Based on the formative and summative assessments of these courses we have made several adjustments as we offer these courses each semester
Pre- and post-course diagnostic tests
Biology 1230 lecture and lab underwent changes in content and in the style of teaching testing and assessing
Weekly meetings for more sharing of ideas on best practices
Student self-assessment of performance
Student pre- and post- surveys on perspectives about Biology
Online homework assignments and clicker questions for formative assessment OpScan scanner and LXR Test softwarefor increased assessment capabilities
Curricular changes across STEM disciplines and dissemination
XU Center For the Advancement of Teaching and SERG
AAAS VampC HHMI NAS GCSI Grinnell NYU Faculty Resource Network
On and off campus collaborations
Focus on Science majorsduring their freshman year
bull Math in biology (Foundations I and II)
bull BioSQuaRE Test and its significance
bull Computer Applications (exercise on BLAST)
bull Biophysics (exercise on electricity)
bull Biol 1230 (leader lecture course for newer assessments
Foundations I and II (Biol 1210L and Biol 1220L)
bull Biol 1210L Introduces basic principles and applications of math physics and chemistry in biology and research Emphasis on group projects active learning discussions readingcomprehension of scientific articlespassages experimentation data collection data analysis and use of computers
bull Biol 1220L Focuses on statistics using data collected by students using systems like the Bean beetle and plant seeds Also reinforcement of measurement conversions dilutions stock solutions and back calculations using living systems typically bacteria Continuation of primary literature discussionsanalysis
1210L Active Learning110$in$50m
L$110$in$100
mL$
110$in$30m
L$
Infect=99 recovery=99
STUDIES ON PIGMENTATION OF SERRATIA MARCESCENS
I SPECTRAL AND PAPER CHROMATOGRAPHIC PROPERTIES OF PRODIGIOSIN
ROBERT P WILLIAMS JAMES A GREEN2 AND DONALD A RAPPOPORT
Departments of Microbiology Biochemistry and Radiology Baylor University College of Medicine Houston Texas
Received for publication June 23 1955
APPLIED MICROBIOLOGY Mar 1973 p 396-402 Vol 25 No 3 Copyright 0 1973 American Society for Microbiology Printed in USA
Biosynthesis of Prodigiosin a Secondary Metabolite of Serratia marcescensROBERT P WILLIAMS
Department of Microbiology Baylor College of Medicine Houston Texas 77025 Received for publication 30 October 1972
Prodigiosenes (prodigiosin and prodigiosin-like pigments) are known to be synthesized by only one genus of Eubacteriales and by two genera of Actinomycetales Biosynthesis by Serratia marcqscens occurs over a relatively narrow range of temperatures although the bacteria grow over a broad range When cultures of S marcescenswere incubated at 27 C in 10 casein hydrolysate viable count and protein attained maximal values within 24 to 48 h whereas prodigiosin did not reach a maximum until 96 h The greatest amount of pigment was synthesized when cultures were in the senescent phase of growth Suspensions of nonproliferating bacteria incubated at 27 C in only i-alanine also synthesized prodigiosin although at a slower rate than growing cultures Kinetics of growth for the wild-type red S marcescens and a white mutant were identical when incubated at 27 C but the wild type produced abundant pigment These results plus other data obtained from the literature suggest that prodigiosin is a secondary metabolite The importance of this proposal to understanding the function of prodigiosin in S marcescens is discussed
Zooming ahead to recent yearshelliphellip From 1955 to 2017
MybioSorcecomhttpswwwmybiosourcecom
Product DescriptionProdigiosin is an intensely red pyrrole pigment produced by several bacteria most notably Serratia marcescens Prodigiosin has a broad biological profile with activity against fungi tumor cell lines and malaria It was shown to be an immunosuppressant in 2007 The mode of action of prodigiosin has recently received considerable attention as an inducer of apoptosis in human primary cancer cells via caspase activation Prodigiosin also acts as an inducer of p21WAF1CIP1 expression via transforming growth factor-B receptor pathway and of NAG-1activation by acting on glycogen synthase kinase-3B
Evidence of ldquomath-gaprdquo
bull ACT College Readiness Benchmark
ndash 50 chance of obtaining a B or
better or ~75 chance of obtaining
a C or higher in a corresponding
first-year course
ACT Site
ndash Math = Algebra I
ndash Science = Biology IBased on sample of 214 institutions and gt230000
students from US Benchmarks = median course
placement values and represent a ldquotypicalrdquo set of
expectations
Percent of ACT-Tested High School Graduates Meeting ACT Benchmarks
Pe
rce
nt
Few 12th Grade Students Interested
in STEM and Proficient in Math
Business-Higher Ed Forum Research Brief (2011)Included in 2012 PCAST Appendix E
STEM interested
AND Math Proficient
NOT STEM
interestedMath
ProficientNOT STEM
interested
NOT Math
Proficient
STEM
interested
NOT Math
Proficient
Biological Quantitative Reasoning
Exam (BioSQuaRE) ndash Q6 consortium
BioSQuaRE TeamBiology
Paul Overvoorde (Macalester)
Peter Brodfuehrer Greg Davis (Bryn Mawr)
Charles Umbanhowar (St Olaf)
Marion Preest (Keck Science Center Claremont Colleges)
Steve Adolph Cathy McFadden (Harvey Mudd)
Educational PsychologyStatistics
Andy Zieffler Laure Le (U Minnesota)
Laura Zeigler (Iowa State)
Erik Larson (Macalester)- Sociology
ldquoOtherrdquo
Liz Stanhope (Lewis and Clark) ndash Math
Jason Belitsky (Oberlin) ndash Chemistry
Marcelo Vinces (Oberlin) ndash Quantitative Skills Center
Tabassum Haque (Oberlin) ndash Institutional Research
Alignment of Learning Outcomes
bull 14 + 38 faculty
bull Mapping of learning outcomes with
previous national reports
ndash BIO2010
ndash Vision and Changes
ndash Next Gen Science Standards for Science
and Engineering
ndash Revised AP Biology requirements
ndash Preparing Future Physicians
bull Comparison to previously created
Quantitative Literacy Efforts (eg
QRLA TOSLS)
Mapping Learning Outcomes to National Reports
ContentStudents should
be able to
BIO20
10
Vision
amp
Chang
e
SFFPAP
Bio
NGSS
SampE
Algebra
functions
and
modeling
Carry out basic mathematical
computations (eg proportional reasoning
unit conversion center and variation)
X X X X X
Recognize and use logarithmic or
exponential relationshipsX X
Fit a model such as population growth X X
Use a representation or a model to make
predictionsX X X X X
Describeinfer relationships between
variables (scatterplots regression
network diagrams maps)
X X
Perform logicalalgorithmic reasoning X X X X
Statistics
and
probability
Calculate or use the concept of the
likelihood of an eventX X X
Calculate or use conditional probability X X X
Recognize and interpret what summary
statistics representX X X
Identify different types of error X
Recognize that biological systems are
inherently variable (eg stochastic vs
deterministic)
X X
Formulate hypothesis statements X X X X
Understand what a p-value is X X X X
Understand when causal claims can be
made (eg correlation vs causation)X X X X
Visualizati
on
Choose the appropriate type of graph X X X X X
Interpret a graph (eg functional
relationships logarithmic relationships)X X X X X
Be able to use a table X X X
Use spatial reasoning to interpret
multidimensional numerical and visual
data (geographic information)
X
Stanhope et al (2017) Development of a Biological
Science Quantitative Reasoning Exam (BioSQuaRE)
CBE- Life Science Education Winter edition
December 1 2017
bull identification and validation of learning domains
bull iterative development of BioSQuaRE Instrument
bull evidence of validity
bull discussion of instruments utility for students individual
faculty and departments or programs
Visit wwwmacalestereduhhmibiosquare for more information
BLASTing Human and Other Organisms
bull Our goal is to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus(snake) The objective is to find and precisely map the coding regions using NCBIrsquos BLASTp search tool
bull Answer the following questions for each of the 4 organisms1 Describe the summary distributions2 Interpret the score the percent identity and the E-value If
obtain hit(s) are they likely due to chance If no hits why3 Analyze the alignments
Describe these Summary Distributions
Chimp
Cow
Snake
Chicken
Interpret the Scores E-values and Identities
Chimp
Cow
Snake
Chicken
Analyze the Alignments
Chimp
Cow
Snake
Chicken
Additional Questions of Interest
bull Our goal was to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus (snake) The objective is to find and precisely map the coding regions
bull Answer the following questions1 This presentation is showing only highly significant pairs How
do you think the alignments (scores e-values identities) differ if we analyze low significant pairs
2 Can you infer that this protein does not exist in this organism3 Give alternative explanations for the differences in scores e-
values and identities4 Is there an evolutionary relationship between sequences
Am J Hum Genet 2008 Dec 12 83(6) 769ndash780 Published online 2008 Dec 5 doi 101016jajhg200811004
Ribosomal Protein L5 and L11 Mutations Are Associated with Cleft Palate and Abnormal Thumbs in Diamond-Blackfan Anemia Patients
Hanna T Gazda12lowast
Mee Rie Sheen1
Adrianna Vlachos34
Valerie Choesmel56
Marie-Franccediloise ODonohue
56Hal Schneider
1Natasha Darras
1Catherine Hasman
1Colin A
Sieff27
Peter E Newburger8
Sarah E Ball9
Edyta Niewiadomska10
Michal Matysiak10
Jan M Zaucha
11Bertil Glader
12Charlotte Niemeyer
13Joerg J Meerpohl
13Eva Atsidaftos
34Jeffrey
M Lipton34
Pierre-Emmanuel Gleizes56
and Alan H Beggs12
Author information Article notes Copyright and License information AbstractDiamond-Blackfan anemia (DBA) a congenital bone-marrow-failure syndrome is characterized by red blood cell aplasia macrocytic anemia clinical heterogeneity and increased risk of malignancy Although anemia is the most prominent feature of DBA the disease is also characterized by growth retardation and congenital anomalies that are present in sim30ndash50 of patients The disease has been associated with mutations in four ribosomal protein (RP) genes RPS19 RPS24 RPS17 and RPL35A in about 30 of patients However the genetic basis of the remaining 70 of cases is still unknown Here we report the second known mutation in RPS17 and probable pathogenic mutations in three more RP genes RPL5 RPL11 and RPS7 In addition we identified rare variants of unknown significance in three other genes RPL36 RPS15 and RPS27A Remarkably careful review of the clinical data showed that mutations in RPL5 are associated with multiple physical abnormalities including craniofacial thumb and heart anomalies whereas isolated thumb malformations are predominantly present in patients carrying mutations in RPL11 We also demonstrate that mutations of RPL5 RPL11 or RPS7 in DBA cells is associated with diverse defects in the maturation of ribosomal RNAs in the large or the small ribosomal subunit production pathway expanding the repertoire of ribosomal RNA processing defects associated with DBA
Develop more inquiry-based lab exercises1 C elegans crosses (Peter Barrett in Genetics lab)
2 Modifications on DNA transformation and lac operon exercises (PB)
3 The lsquotermitersquo experiment in Biol 1230L (Kristal Huggins and SKI)
4 In Cell Biology lab C elegans (endocytosis experiments) experiments with Planaria regeneration (adapted from MITHHMI) and recently with Daphnia (the water flea a small crustacean) adapted from the Nuffield Foundation where students expose the Daphnia to various cardioactive compounds measure changes in heart rate caused by effects on cellular receptors and design follow-up experiments (PB)
Assessment Strategies for Project Scicomp
Formative and summative
General scheme
bull Assessment tasks based on objectives
bull Develop assessment tools and pilot for validation
bull Apply to larger audience
bull Collect and score
bull Share and analyze data
Coordinated course sequences and our curricular design serve as a good platform
for intra and interdepartmental discussions
(weekly meetings lsquoSERGrsquo etc)
Labs
bull General observation on student participationinitiative
bull Data sheets (say 10 collecthellipsay any 4)
bull Midterm skills practical stations and multiple choice (excellent determinant)
bull Quizzes (5-10 depending on the lab)
bull Final exams
Course based research experiencee(CRE)
bull How they design their experiment
bull Notebooks lab techniques
bull Participation in class discussions
bull Ability to troubleshoot
bull Midterm Skills and oral exam along with traditional exam
bull Short answer (non multiple choice) questions
bull Research paper presentations
CREs at Xavier
bull Phage and Genomics
bull lsquoUndergraduate Researchrsquo for credits
bull Introduction to Mammalian Tissue Culture
The SEA-PHAGES ProgramhttpsseaphagesorgThe official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program
SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is a two-semester discovery-based undergraduate research course that begins with simple digging in the soil to find new viruses but progresses through a variety of microbiology techniques and eventually to complex genome annotation and bioinformatic analyses
CBE Life Sci Educ 2016 fall15(3) pii ar38 doi 101187cbe16-01-0078Increasing URM Undergraduate Student Success through Assessment-Driven Interventions A Multiyear Study Using Freshman-Level General Biology as a Model SystemCarmichael MC1 St Clair C1 Edwards AM2 Barrett P1 McFerrin H1 Davenport I1 Awad M1 Kundu A1 Ireland SK3
AbstractXavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students In this multiyear study with sim5500 participants data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course The three hour-long exams were common and administered concurrently to all students New exam questions were developed using Blooms taxonomy and exam results were analyzed statistically with validated assessment tools All but the comprehensive final exam were returned to students for self-evaluation and remediation Among other approaches course rigor was monitored by using an identical set of 60 questions on the final exam across 10 semesters Analysis of the identical sets of 60 final exam questions revealed that overall averages increased from 729 (2010) to 835 (2015) Regression analysis demonstrated a statistically significant correlation between high-risk students and their averages on the 60 questions Additional analysis demonstrated statistically significant improvements for at least one letter grade from midterm to final and a 20 increase in the course pass rates over time also for the high-risk population These results support the hypothesis that our data-driven interventions and assessment techniques are successful in improving student retention particularly for our academically at-risk students
Lecture Biol 1230
bull Competency E4 (chemistry in biology atomic bonds metabolic pathways thermodynamics)
bull Quizzes (formative assessment with Clickers)
bull The coordinator prepares the three lsquoOne hour examsrsquo (questions not from the textbook) instructors again reviewcomment
bull Question types range (content versus applications) and also lsquoBack pagersquo ( 20 of the exam grade) Formative assessment using the LXRtest software (Opscan6 scanner)
Final exam not returned cumulative and has had 60 questions (good discriminators based on the rpbvalues) commonly used on ALL final exams for the past five years Powerful tool for measuring studentsrsquo learning and applications over time and based on academic risk categories
Last Name First Name
Biology 1230 Exam 1 ldquoBack Pagerdquo Score _ 20 pts
I 5 pts Complete the following table for the 3 major components (subatomic particles) of the atom
hint electrical charge = positive negative or neutral and mass = 1 dalton or 11800 dalton 1 pt each
Particle Electrical Charge Mass
1 Proton 1 dalton
2 Electron
3 Neutron
II 5 pts In your own words compare and contrast the following two atoms A and B use the back of the previous page to
make as many observations as you can about similarities (and what they mean) and differences (and what they mean)
between the atoms
A B
III 5 pts Match the following by placing the corresponding in the space provided 1 pt each
_____ tertiary structure 1 produce H2O
_____ two ester linkages 2 is responsible for the 3-dimensional shape of a protein
_____ phosphodiester bonds 3 exist within diglycerides (diacylglyerols) and phospholipids
_____ dehydration synthesis reactions 4 are a type of lipid
_____ steroids 5 are formed when nucleic acids are synthesized
IV 5 pts Circle each of the variable (R) groups in the molecules shown below (3 pts)
a Which lsquoRrsquo group is polar ______ (write the corresponding in the space provided) (1 pt)
b Which lsquoRrsquo group is ionic ______ (write the corresponding in the space provided) (1 pt)
NH3+ OH CH3
1 2 3
12 neutrons
11 protons
10 electrons
13 neutrons
11 protons
11 electrons
Bio1230 Exam 1
Clickers and immediate feedback
Name _____________________________________________________________________________________________
This is a worksheet for your self-evaluation of study habits and exam preparedness Your answers on the corresponding
online exam surveys are confidential
~The average number of hours I spent per week reading the chapters andor reviewingprocessing class notes was (circle the
appropriate response)
zero to one one to two two to four greater than four
~I read the assignment before coming to class (circle the appropriate response)
never sometimes regularly
~I asked my instructor questions when I was confused about textbook material andor lecture material (circle the appropriate
response)
never sometimes regularly
~Overall I spent _____ hours specifically studying for this exam (Please fill in the blank)
~Prior to taking the exam I expected to get an approximate grade of (fill in the blank) _____
~My actual grade was a(n) (fill in the blank) _____
~Check all of the statements that apply to your performance on the exam
____ studied the right information ____ did not study the right information
____ studied the right information but did not ____ studied the right information and
understand it thought I understood it
____ used the class outlines to study ____ thought college would be easier
____ did not know what to study ____ other _____________________
____ did not think I would need to know the information in such detail
Analysis of Missed Questions I answered the question incorrectly because I Insert question number below in the correct category
did not study the information
studied the information but forgot it
did not understand the information in the
summary notes
confused similar concepts or terms (ie
isotopes and isomers)
misread or misunderstood the question
did not consider all of the answer choices
knew the correct answer - but chose an
incorrect answer by mistake
List other reason(s)
List other reason(s)
Please answer additional self-evaluation questions on the back of this page
Self-Evaluation of Study Habits amp Exam Preparedness for Biology 1230 Exam I or II or III (circle one)
Going forwardhellip
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
Years 1 - 3 Biology 1210L and 1220L were developed received academic assembly approval and were piloted in Fall 2012
The main goal of these courses was to introduce the fundamentals of scientific competencies and research-related active learning exercises in a stress-free environment
Based on the formative and summative assessments of these courses we have made several adjustments as we offer these courses each semester
Pre- and post-course diagnostic tests
Biology 1230 lecture and lab underwent changes in content and in the style of teaching testing and assessing
Weekly meetings for more sharing of ideas on best practices
Student self-assessment of performance
Student pre- and post- surveys on perspectives about Biology
Online homework assignments and clicker questions for formative assessment OpScan scanner and LXR Test softwarefor increased assessment capabilities
Curricular changes across STEM disciplines and dissemination
XU Center For the Advancement of Teaching and SERG
AAAS VampC HHMI NAS GCSI Grinnell NYU Faculty Resource Network
On and off campus collaborations
Focus on Science majorsduring their freshman year
bull Math in biology (Foundations I and II)
bull BioSQuaRE Test and its significance
bull Computer Applications (exercise on BLAST)
bull Biophysics (exercise on electricity)
bull Biol 1230 (leader lecture course for newer assessments
Foundations I and II (Biol 1210L and Biol 1220L)
bull Biol 1210L Introduces basic principles and applications of math physics and chemistry in biology and research Emphasis on group projects active learning discussions readingcomprehension of scientific articlespassages experimentation data collection data analysis and use of computers
bull Biol 1220L Focuses on statistics using data collected by students using systems like the Bean beetle and plant seeds Also reinforcement of measurement conversions dilutions stock solutions and back calculations using living systems typically bacteria Continuation of primary literature discussionsanalysis
1210L Active Learning110$in$50m
L$110$in$100
mL$
110$in$30m
L$
Infect=99 recovery=99
STUDIES ON PIGMENTATION OF SERRATIA MARCESCENS
I SPECTRAL AND PAPER CHROMATOGRAPHIC PROPERTIES OF PRODIGIOSIN
ROBERT P WILLIAMS JAMES A GREEN2 AND DONALD A RAPPOPORT
Departments of Microbiology Biochemistry and Radiology Baylor University College of Medicine Houston Texas
Received for publication June 23 1955
APPLIED MICROBIOLOGY Mar 1973 p 396-402 Vol 25 No 3 Copyright 0 1973 American Society for Microbiology Printed in USA
Biosynthesis of Prodigiosin a Secondary Metabolite of Serratia marcescensROBERT P WILLIAMS
Department of Microbiology Baylor College of Medicine Houston Texas 77025 Received for publication 30 October 1972
Prodigiosenes (prodigiosin and prodigiosin-like pigments) are known to be synthesized by only one genus of Eubacteriales and by two genera of Actinomycetales Biosynthesis by Serratia marcqscens occurs over a relatively narrow range of temperatures although the bacteria grow over a broad range When cultures of S marcescenswere incubated at 27 C in 10 casein hydrolysate viable count and protein attained maximal values within 24 to 48 h whereas prodigiosin did not reach a maximum until 96 h The greatest amount of pigment was synthesized when cultures were in the senescent phase of growth Suspensions of nonproliferating bacteria incubated at 27 C in only i-alanine also synthesized prodigiosin although at a slower rate than growing cultures Kinetics of growth for the wild-type red S marcescens and a white mutant were identical when incubated at 27 C but the wild type produced abundant pigment These results plus other data obtained from the literature suggest that prodigiosin is a secondary metabolite The importance of this proposal to understanding the function of prodigiosin in S marcescens is discussed
Zooming ahead to recent yearshelliphellip From 1955 to 2017
MybioSorcecomhttpswwwmybiosourcecom
Product DescriptionProdigiosin is an intensely red pyrrole pigment produced by several bacteria most notably Serratia marcescens Prodigiosin has a broad biological profile with activity against fungi tumor cell lines and malaria It was shown to be an immunosuppressant in 2007 The mode of action of prodigiosin has recently received considerable attention as an inducer of apoptosis in human primary cancer cells via caspase activation Prodigiosin also acts as an inducer of p21WAF1CIP1 expression via transforming growth factor-B receptor pathway and of NAG-1activation by acting on glycogen synthase kinase-3B
Evidence of ldquomath-gaprdquo
bull ACT College Readiness Benchmark
ndash 50 chance of obtaining a B or
better or ~75 chance of obtaining
a C or higher in a corresponding
first-year course
ACT Site
ndash Math = Algebra I
ndash Science = Biology IBased on sample of 214 institutions and gt230000
students from US Benchmarks = median course
placement values and represent a ldquotypicalrdquo set of
expectations
Percent of ACT-Tested High School Graduates Meeting ACT Benchmarks
Pe
rce
nt
Few 12th Grade Students Interested
in STEM and Proficient in Math
Business-Higher Ed Forum Research Brief (2011)Included in 2012 PCAST Appendix E
STEM interested
AND Math Proficient
NOT STEM
interestedMath
ProficientNOT STEM
interested
NOT Math
Proficient
STEM
interested
NOT Math
Proficient
Biological Quantitative Reasoning
Exam (BioSQuaRE) ndash Q6 consortium
BioSQuaRE TeamBiology
Paul Overvoorde (Macalester)
Peter Brodfuehrer Greg Davis (Bryn Mawr)
Charles Umbanhowar (St Olaf)
Marion Preest (Keck Science Center Claremont Colleges)
Steve Adolph Cathy McFadden (Harvey Mudd)
Educational PsychologyStatistics
Andy Zieffler Laure Le (U Minnesota)
Laura Zeigler (Iowa State)
Erik Larson (Macalester)- Sociology
ldquoOtherrdquo
Liz Stanhope (Lewis and Clark) ndash Math
Jason Belitsky (Oberlin) ndash Chemistry
Marcelo Vinces (Oberlin) ndash Quantitative Skills Center
Tabassum Haque (Oberlin) ndash Institutional Research
Alignment of Learning Outcomes
bull 14 + 38 faculty
bull Mapping of learning outcomes with
previous national reports
ndash BIO2010
ndash Vision and Changes
ndash Next Gen Science Standards for Science
and Engineering
ndash Revised AP Biology requirements
ndash Preparing Future Physicians
bull Comparison to previously created
Quantitative Literacy Efforts (eg
QRLA TOSLS)
Mapping Learning Outcomes to National Reports
ContentStudents should
be able to
BIO20
10
Vision
amp
Chang
e
SFFPAP
Bio
NGSS
SampE
Algebra
functions
and
modeling
Carry out basic mathematical
computations (eg proportional reasoning
unit conversion center and variation)
X X X X X
Recognize and use logarithmic or
exponential relationshipsX X
Fit a model such as population growth X X
Use a representation or a model to make
predictionsX X X X X
Describeinfer relationships between
variables (scatterplots regression
network diagrams maps)
X X
Perform logicalalgorithmic reasoning X X X X
Statistics
and
probability
Calculate or use the concept of the
likelihood of an eventX X X
Calculate or use conditional probability X X X
Recognize and interpret what summary
statistics representX X X
Identify different types of error X
Recognize that biological systems are
inherently variable (eg stochastic vs
deterministic)
X X
Formulate hypothesis statements X X X X
Understand what a p-value is X X X X
Understand when causal claims can be
made (eg correlation vs causation)X X X X
Visualizati
on
Choose the appropriate type of graph X X X X X
Interpret a graph (eg functional
relationships logarithmic relationships)X X X X X
Be able to use a table X X X
Use spatial reasoning to interpret
multidimensional numerical and visual
data (geographic information)
X
Stanhope et al (2017) Development of a Biological
Science Quantitative Reasoning Exam (BioSQuaRE)
CBE- Life Science Education Winter edition
December 1 2017
bull identification and validation of learning domains
bull iterative development of BioSQuaRE Instrument
bull evidence of validity
bull discussion of instruments utility for students individual
faculty and departments or programs
Visit wwwmacalestereduhhmibiosquare for more information
BLASTing Human and Other Organisms
bull Our goal is to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus(snake) The objective is to find and precisely map the coding regions using NCBIrsquos BLASTp search tool
bull Answer the following questions for each of the 4 organisms1 Describe the summary distributions2 Interpret the score the percent identity and the E-value If
obtain hit(s) are they likely due to chance If no hits why3 Analyze the alignments
Describe these Summary Distributions
Chimp
Cow
Snake
Chicken
Interpret the Scores E-values and Identities
Chimp
Cow
Snake
Chicken
Analyze the Alignments
Chimp
Cow
Snake
Chicken
Additional Questions of Interest
bull Our goal was to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus (snake) The objective is to find and precisely map the coding regions
bull Answer the following questions1 This presentation is showing only highly significant pairs How
do you think the alignments (scores e-values identities) differ if we analyze low significant pairs
2 Can you infer that this protein does not exist in this organism3 Give alternative explanations for the differences in scores e-
values and identities4 Is there an evolutionary relationship between sequences
Am J Hum Genet 2008 Dec 12 83(6) 769ndash780 Published online 2008 Dec 5 doi 101016jajhg200811004
Ribosomal Protein L5 and L11 Mutations Are Associated with Cleft Palate and Abnormal Thumbs in Diamond-Blackfan Anemia Patients
Hanna T Gazda12lowast
Mee Rie Sheen1
Adrianna Vlachos34
Valerie Choesmel56
Marie-Franccediloise ODonohue
56Hal Schneider
1Natasha Darras
1Catherine Hasman
1Colin A
Sieff27
Peter E Newburger8
Sarah E Ball9
Edyta Niewiadomska10
Michal Matysiak10
Jan M Zaucha
11Bertil Glader
12Charlotte Niemeyer
13Joerg J Meerpohl
13Eva Atsidaftos
34Jeffrey
M Lipton34
Pierre-Emmanuel Gleizes56
and Alan H Beggs12
Author information Article notes Copyright and License information AbstractDiamond-Blackfan anemia (DBA) a congenital bone-marrow-failure syndrome is characterized by red blood cell aplasia macrocytic anemia clinical heterogeneity and increased risk of malignancy Although anemia is the most prominent feature of DBA the disease is also characterized by growth retardation and congenital anomalies that are present in sim30ndash50 of patients The disease has been associated with mutations in four ribosomal protein (RP) genes RPS19 RPS24 RPS17 and RPL35A in about 30 of patients However the genetic basis of the remaining 70 of cases is still unknown Here we report the second known mutation in RPS17 and probable pathogenic mutations in three more RP genes RPL5 RPL11 and RPS7 In addition we identified rare variants of unknown significance in three other genes RPL36 RPS15 and RPS27A Remarkably careful review of the clinical data showed that mutations in RPL5 are associated with multiple physical abnormalities including craniofacial thumb and heart anomalies whereas isolated thumb malformations are predominantly present in patients carrying mutations in RPL11 We also demonstrate that mutations of RPL5 RPL11 or RPS7 in DBA cells is associated with diverse defects in the maturation of ribosomal RNAs in the large or the small ribosomal subunit production pathway expanding the repertoire of ribosomal RNA processing defects associated with DBA
Develop more inquiry-based lab exercises1 C elegans crosses (Peter Barrett in Genetics lab)
2 Modifications on DNA transformation and lac operon exercises (PB)
3 The lsquotermitersquo experiment in Biol 1230L (Kristal Huggins and SKI)
4 In Cell Biology lab C elegans (endocytosis experiments) experiments with Planaria regeneration (adapted from MITHHMI) and recently with Daphnia (the water flea a small crustacean) adapted from the Nuffield Foundation where students expose the Daphnia to various cardioactive compounds measure changes in heart rate caused by effects on cellular receptors and design follow-up experiments (PB)
Assessment Strategies for Project Scicomp
Formative and summative
General scheme
bull Assessment tasks based on objectives
bull Develop assessment tools and pilot for validation
bull Apply to larger audience
bull Collect and score
bull Share and analyze data
Coordinated course sequences and our curricular design serve as a good platform
for intra and interdepartmental discussions
(weekly meetings lsquoSERGrsquo etc)
Labs
bull General observation on student participationinitiative
bull Data sheets (say 10 collecthellipsay any 4)
bull Midterm skills practical stations and multiple choice (excellent determinant)
bull Quizzes (5-10 depending on the lab)
bull Final exams
Course based research experiencee(CRE)
bull How they design their experiment
bull Notebooks lab techniques
bull Participation in class discussions
bull Ability to troubleshoot
bull Midterm Skills and oral exam along with traditional exam
bull Short answer (non multiple choice) questions
bull Research paper presentations
CREs at Xavier
bull Phage and Genomics
bull lsquoUndergraduate Researchrsquo for credits
bull Introduction to Mammalian Tissue Culture
The SEA-PHAGES ProgramhttpsseaphagesorgThe official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program
SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is a two-semester discovery-based undergraduate research course that begins with simple digging in the soil to find new viruses but progresses through a variety of microbiology techniques and eventually to complex genome annotation and bioinformatic analyses
CBE Life Sci Educ 2016 fall15(3) pii ar38 doi 101187cbe16-01-0078Increasing URM Undergraduate Student Success through Assessment-Driven Interventions A Multiyear Study Using Freshman-Level General Biology as a Model SystemCarmichael MC1 St Clair C1 Edwards AM2 Barrett P1 McFerrin H1 Davenport I1 Awad M1 Kundu A1 Ireland SK3
AbstractXavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students In this multiyear study with sim5500 participants data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course The three hour-long exams were common and administered concurrently to all students New exam questions were developed using Blooms taxonomy and exam results were analyzed statistically with validated assessment tools All but the comprehensive final exam were returned to students for self-evaluation and remediation Among other approaches course rigor was monitored by using an identical set of 60 questions on the final exam across 10 semesters Analysis of the identical sets of 60 final exam questions revealed that overall averages increased from 729 (2010) to 835 (2015) Regression analysis demonstrated a statistically significant correlation between high-risk students and their averages on the 60 questions Additional analysis demonstrated statistically significant improvements for at least one letter grade from midterm to final and a 20 increase in the course pass rates over time also for the high-risk population These results support the hypothesis that our data-driven interventions and assessment techniques are successful in improving student retention particularly for our academically at-risk students
Lecture Biol 1230
bull Competency E4 (chemistry in biology atomic bonds metabolic pathways thermodynamics)
bull Quizzes (formative assessment with Clickers)
bull The coordinator prepares the three lsquoOne hour examsrsquo (questions not from the textbook) instructors again reviewcomment
bull Question types range (content versus applications) and also lsquoBack pagersquo ( 20 of the exam grade) Formative assessment using the LXRtest software (Opscan6 scanner)
Final exam not returned cumulative and has had 60 questions (good discriminators based on the rpbvalues) commonly used on ALL final exams for the past five years Powerful tool for measuring studentsrsquo learning and applications over time and based on academic risk categories
Last Name First Name
Biology 1230 Exam 1 ldquoBack Pagerdquo Score _ 20 pts
I 5 pts Complete the following table for the 3 major components (subatomic particles) of the atom
hint electrical charge = positive negative or neutral and mass = 1 dalton or 11800 dalton 1 pt each
Particle Electrical Charge Mass
1 Proton 1 dalton
2 Electron
3 Neutron
II 5 pts In your own words compare and contrast the following two atoms A and B use the back of the previous page to
make as many observations as you can about similarities (and what they mean) and differences (and what they mean)
between the atoms
A B
III 5 pts Match the following by placing the corresponding in the space provided 1 pt each
_____ tertiary structure 1 produce H2O
_____ two ester linkages 2 is responsible for the 3-dimensional shape of a protein
_____ phosphodiester bonds 3 exist within diglycerides (diacylglyerols) and phospholipids
_____ dehydration synthesis reactions 4 are a type of lipid
_____ steroids 5 are formed when nucleic acids are synthesized
IV 5 pts Circle each of the variable (R) groups in the molecules shown below (3 pts)
a Which lsquoRrsquo group is polar ______ (write the corresponding in the space provided) (1 pt)
b Which lsquoRrsquo group is ionic ______ (write the corresponding in the space provided) (1 pt)
NH3+ OH CH3
1 2 3
12 neutrons
11 protons
10 electrons
13 neutrons
11 protons
11 electrons
Bio1230 Exam 1
Clickers and immediate feedback
Name _____________________________________________________________________________________________
This is a worksheet for your self-evaluation of study habits and exam preparedness Your answers on the corresponding
online exam surveys are confidential
~The average number of hours I spent per week reading the chapters andor reviewingprocessing class notes was (circle the
appropriate response)
zero to one one to two two to four greater than four
~I read the assignment before coming to class (circle the appropriate response)
never sometimes regularly
~I asked my instructor questions when I was confused about textbook material andor lecture material (circle the appropriate
response)
never sometimes regularly
~Overall I spent _____ hours specifically studying for this exam (Please fill in the blank)
~Prior to taking the exam I expected to get an approximate grade of (fill in the blank) _____
~My actual grade was a(n) (fill in the blank) _____
~Check all of the statements that apply to your performance on the exam
____ studied the right information ____ did not study the right information
____ studied the right information but did not ____ studied the right information and
understand it thought I understood it
____ used the class outlines to study ____ thought college would be easier
____ did not know what to study ____ other _____________________
____ did not think I would need to know the information in such detail
Analysis of Missed Questions I answered the question incorrectly because I Insert question number below in the correct category
did not study the information
studied the information but forgot it
did not understand the information in the
summary notes
confused similar concepts or terms (ie
isotopes and isomers)
misread or misunderstood the question
did not consider all of the answer choices
knew the correct answer - but chose an
incorrect answer by mistake
List other reason(s)
List other reason(s)
Please answer additional self-evaluation questions on the back of this page
Self-Evaluation of Study Habits amp Exam Preparedness for Biology 1230 Exam I or II or III (circle one)
Going forwardhellip
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
Focus on Science majorsduring their freshman year
bull Math in biology (Foundations I and II)
bull BioSQuaRE Test and its significance
bull Computer Applications (exercise on BLAST)
bull Biophysics (exercise on electricity)
bull Biol 1230 (leader lecture course for newer assessments
Foundations I and II (Biol 1210L and Biol 1220L)
bull Biol 1210L Introduces basic principles and applications of math physics and chemistry in biology and research Emphasis on group projects active learning discussions readingcomprehension of scientific articlespassages experimentation data collection data analysis and use of computers
bull Biol 1220L Focuses on statistics using data collected by students using systems like the Bean beetle and plant seeds Also reinforcement of measurement conversions dilutions stock solutions and back calculations using living systems typically bacteria Continuation of primary literature discussionsanalysis
1210L Active Learning110$in$50m
L$110$in$100
mL$
110$in$30m
L$
Infect=99 recovery=99
STUDIES ON PIGMENTATION OF SERRATIA MARCESCENS
I SPECTRAL AND PAPER CHROMATOGRAPHIC PROPERTIES OF PRODIGIOSIN
ROBERT P WILLIAMS JAMES A GREEN2 AND DONALD A RAPPOPORT
Departments of Microbiology Biochemistry and Radiology Baylor University College of Medicine Houston Texas
Received for publication June 23 1955
APPLIED MICROBIOLOGY Mar 1973 p 396-402 Vol 25 No 3 Copyright 0 1973 American Society for Microbiology Printed in USA
Biosynthesis of Prodigiosin a Secondary Metabolite of Serratia marcescensROBERT P WILLIAMS
Department of Microbiology Baylor College of Medicine Houston Texas 77025 Received for publication 30 October 1972
Prodigiosenes (prodigiosin and prodigiosin-like pigments) are known to be synthesized by only one genus of Eubacteriales and by two genera of Actinomycetales Biosynthesis by Serratia marcqscens occurs over a relatively narrow range of temperatures although the bacteria grow over a broad range When cultures of S marcescenswere incubated at 27 C in 10 casein hydrolysate viable count and protein attained maximal values within 24 to 48 h whereas prodigiosin did not reach a maximum until 96 h The greatest amount of pigment was synthesized when cultures were in the senescent phase of growth Suspensions of nonproliferating bacteria incubated at 27 C in only i-alanine also synthesized prodigiosin although at a slower rate than growing cultures Kinetics of growth for the wild-type red S marcescens and a white mutant were identical when incubated at 27 C but the wild type produced abundant pigment These results plus other data obtained from the literature suggest that prodigiosin is a secondary metabolite The importance of this proposal to understanding the function of prodigiosin in S marcescens is discussed
Zooming ahead to recent yearshelliphellip From 1955 to 2017
MybioSorcecomhttpswwwmybiosourcecom
Product DescriptionProdigiosin is an intensely red pyrrole pigment produced by several bacteria most notably Serratia marcescens Prodigiosin has a broad biological profile with activity against fungi tumor cell lines and malaria It was shown to be an immunosuppressant in 2007 The mode of action of prodigiosin has recently received considerable attention as an inducer of apoptosis in human primary cancer cells via caspase activation Prodigiosin also acts as an inducer of p21WAF1CIP1 expression via transforming growth factor-B receptor pathway and of NAG-1activation by acting on glycogen synthase kinase-3B
Evidence of ldquomath-gaprdquo
bull ACT College Readiness Benchmark
ndash 50 chance of obtaining a B or
better or ~75 chance of obtaining
a C or higher in a corresponding
first-year course
ACT Site
ndash Math = Algebra I
ndash Science = Biology IBased on sample of 214 institutions and gt230000
students from US Benchmarks = median course
placement values and represent a ldquotypicalrdquo set of
expectations
Percent of ACT-Tested High School Graduates Meeting ACT Benchmarks
Pe
rce
nt
Few 12th Grade Students Interested
in STEM and Proficient in Math
Business-Higher Ed Forum Research Brief (2011)Included in 2012 PCAST Appendix E
STEM interested
AND Math Proficient
NOT STEM
interestedMath
ProficientNOT STEM
interested
NOT Math
Proficient
STEM
interested
NOT Math
Proficient
Biological Quantitative Reasoning
Exam (BioSQuaRE) ndash Q6 consortium
BioSQuaRE TeamBiology
Paul Overvoorde (Macalester)
Peter Brodfuehrer Greg Davis (Bryn Mawr)
Charles Umbanhowar (St Olaf)
Marion Preest (Keck Science Center Claremont Colleges)
Steve Adolph Cathy McFadden (Harvey Mudd)
Educational PsychologyStatistics
Andy Zieffler Laure Le (U Minnesota)
Laura Zeigler (Iowa State)
Erik Larson (Macalester)- Sociology
ldquoOtherrdquo
Liz Stanhope (Lewis and Clark) ndash Math
Jason Belitsky (Oberlin) ndash Chemistry
Marcelo Vinces (Oberlin) ndash Quantitative Skills Center
Tabassum Haque (Oberlin) ndash Institutional Research
Alignment of Learning Outcomes
bull 14 + 38 faculty
bull Mapping of learning outcomes with
previous national reports
ndash BIO2010
ndash Vision and Changes
ndash Next Gen Science Standards for Science
and Engineering
ndash Revised AP Biology requirements
ndash Preparing Future Physicians
bull Comparison to previously created
Quantitative Literacy Efforts (eg
QRLA TOSLS)
Mapping Learning Outcomes to National Reports
ContentStudents should
be able to
BIO20
10
Vision
amp
Chang
e
SFFPAP
Bio
NGSS
SampE
Algebra
functions
and
modeling
Carry out basic mathematical
computations (eg proportional reasoning
unit conversion center and variation)
X X X X X
Recognize and use logarithmic or
exponential relationshipsX X
Fit a model such as population growth X X
Use a representation or a model to make
predictionsX X X X X
Describeinfer relationships between
variables (scatterplots regression
network diagrams maps)
X X
Perform logicalalgorithmic reasoning X X X X
Statistics
and
probability
Calculate or use the concept of the
likelihood of an eventX X X
Calculate or use conditional probability X X X
Recognize and interpret what summary
statistics representX X X
Identify different types of error X
Recognize that biological systems are
inherently variable (eg stochastic vs
deterministic)
X X
Formulate hypothesis statements X X X X
Understand what a p-value is X X X X
Understand when causal claims can be
made (eg correlation vs causation)X X X X
Visualizati
on
Choose the appropriate type of graph X X X X X
Interpret a graph (eg functional
relationships logarithmic relationships)X X X X X
Be able to use a table X X X
Use spatial reasoning to interpret
multidimensional numerical and visual
data (geographic information)
X
Stanhope et al (2017) Development of a Biological
Science Quantitative Reasoning Exam (BioSQuaRE)
CBE- Life Science Education Winter edition
December 1 2017
bull identification and validation of learning domains
bull iterative development of BioSQuaRE Instrument
bull evidence of validity
bull discussion of instruments utility for students individual
faculty and departments or programs
Visit wwwmacalestereduhhmibiosquare for more information
BLASTing Human and Other Organisms
bull Our goal is to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus(snake) The objective is to find and precisely map the coding regions using NCBIrsquos BLASTp search tool
bull Answer the following questions for each of the 4 organisms1 Describe the summary distributions2 Interpret the score the percent identity and the E-value If
obtain hit(s) are they likely due to chance If no hits why3 Analyze the alignments
Describe these Summary Distributions
Chimp
Cow
Snake
Chicken
Interpret the Scores E-values and Identities
Chimp
Cow
Snake
Chicken
Analyze the Alignments
Chimp
Cow
Snake
Chicken
Additional Questions of Interest
bull Our goal was to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus (snake) The objective is to find and precisely map the coding regions
bull Answer the following questions1 This presentation is showing only highly significant pairs How
do you think the alignments (scores e-values identities) differ if we analyze low significant pairs
2 Can you infer that this protein does not exist in this organism3 Give alternative explanations for the differences in scores e-
values and identities4 Is there an evolutionary relationship between sequences
Am J Hum Genet 2008 Dec 12 83(6) 769ndash780 Published online 2008 Dec 5 doi 101016jajhg200811004
Ribosomal Protein L5 and L11 Mutations Are Associated with Cleft Palate and Abnormal Thumbs in Diamond-Blackfan Anemia Patients
Hanna T Gazda12lowast
Mee Rie Sheen1
Adrianna Vlachos34
Valerie Choesmel56
Marie-Franccediloise ODonohue
56Hal Schneider
1Natasha Darras
1Catherine Hasman
1Colin A
Sieff27
Peter E Newburger8
Sarah E Ball9
Edyta Niewiadomska10
Michal Matysiak10
Jan M Zaucha
11Bertil Glader
12Charlotte Niemeyer
13Joerg J Meerpohl
13Eva Atsidaftos
34Jeffrey
M Lipton34
Pierre-Emmanuel Gleizes56
and Alan H Beggs12
Author information Article notes Copyright and License information AbstractDiamond-Blackfan anemia (DBA) a congenital bone-marrow-failure syndrome is characterized by red blood cell aplasia macrocytic anemia clinical heterogeneity and increased risk of malignancy Although anemia is the most prominent feature of DBA the disease is also characterized by growth retardation and congenital anomalies that are present in sim30ndash50 of patients The disease has been associated with mutations in four ribosomal protein (RP) genes RPS19 RPS24 RPS17 and RPL35A in about 30 of patients However the genetic basis of the remaining 70 of cases is still unknown Here we report the second known mutation in RPS17 and probable pathogenic mutations in three more RP genes RPL5 RPL11 and RPS7 In addition we identified rare variants of unknown significance in three other genes RPL36 RPS15 and RPS27A Remarkably careful review of the clinical data showed that mutations in RPL5 are associated with multiple physical abnormalities including craniofacial thumb and heart anomalies whereas isolated thumb malformations are predominantly present in patients carrying mutations in RPL11 We also demonstrate that mutations of RPL5 RPL11 or RPS7 in DBA cells is associated with diverse defects in the maturation of ribosomal RNAs in the large or the small ribosomal subunit production pathway expanding the repertoire of ribosomal RNA processing defects associated with DBA
Develop more inquiry-based lab exercises1 C elegans crosses (Peter Barrett in Genetics lab)
2 Modifications on DNA transformation and lac operon exercises (PB)
3 The lsquotermitersquo experiment in Biol 1230L (Kristal Huggins and SKI)
4 In Cell Biology lab C elegans (endocytosis experiments) experiments with Planaria regeneration (adapted from MITHHMI) and recently with Daphnia (the water flea a small crustacean) adapted from the Nuffield Foundation where students expose the Daphnia to various cardioactive compounds measure changes in heart rate caused by effects on cellular receptors and design follow-up experiments (PB)
Assessment Strategies for Project Scicomp
Formative and summative
General scheme
bull Assessment tasks based on objectives
bull Develop assessment tools and pilot for validation
bull Apply to larger audience
bull Collect and score
bull Share and analyze data
Coordinated course sequences and our curricular design serve as a good platform
for intra and interdepartmental discussions
(weekly meetings lsquoSERGrsquo etc)
Labs
bull General observation on student participationinitiative
bull Data sheets (say 10 collecthellipsay any 4)
bull Midterm skills practical stations and multiple choice (excellent determinant)
bull Quizzes (5-10 depending on the lab)
bull Final exams
Course based research experiencee(CRE)
bull How they design their experiment
bull Notebooks lab techniques
bull Participation in class discussions
bull Ability to troubleshoot
bull Midterm Skills and oral exam along with traditional exam
bull Short answer (non multiple choice) questions
bull Research paper presentations
CREs at Xavier
bull Phage and Genomics
bull lsquoUndergraduate Researchrsquo for credits
bull Introduction to Mammalian Tissue Culture
The SEA-PHAGES ProgramhttpsseaphagesorgThe official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program
SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is a two-semester discovery-based undergraduate research course that begins with simple digging in the soil to find new viruses but progresses through a variety of microbiology techniques and eventually to complex genome annotation and bioinformatic analyses
CBE Life Sci Educ 2016 fall15(3) pii ar38 doi 101187cbe16-01-0078Increasing URM Undergraduate Student Success through Assessment-Driven Interventions A Multiyear Study Using Freshman-Level General Biology as a Model SystemCarmichael MC1 St Clair C1 Edwards AM2 Barrett P1 McFerrin H1 Davenport I1 Awad M1 Kundu A1 Ireland SK3
AbstractXavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students In this multiyear study with sim5500 participants data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course The three hour-long exams were common and administered concurrently to all students New exam questions were developed using Blooms taxonomy and exam results were analyzed statistically with validated assessment tools All but the comprehensive final exam were returned to students for self-evaluation and remediation Among other approaches course rigor was monitored by using an identical set of 60 questions on the final exam across 10 semesters Analysis of the identical sets of 60 final exam questions revealed that overall averages increased from 729 (2010) to 835 (2015) Regression analysis demonstrated a statistically significant correlation between high-risk students and their averages on the 60 questions Additional analysis demonstrated statistically significant improvements for at least one letter grade from midterm to final and a 20 increase in the course pass rates over time also for the high-risk population These results support the hypothesis that our data-driven interventions and assessment techniques are successful in improving student retention particularly for our academically at-risk students
Lecture Biol 1230
bull Competency E4 (chemistry in biology atomic bonds metabolic pathways thermodynamics)
bull Quizzes (formative assessment with Clickers)
bull The coordinator prepares the three lsquoOne hour examsrsquo (questions not from the textbook) instructors again reviewcomment
bull Question types range (content versus applications) and also lsquoBack pagersquo ( 20 of the exam grade) Formative assessment using the LXRtest software (Opscan6 scanner)
Final exam not returned cumulative and has had 60 questions (good discriminators based on the rpbvalues) commonly used on ALL final exams for the past five years Powerful tool for measuring studentsrsquo learning and applications over time and based on academic risk categories
Last Name First Name
Biology 1230 Exam 1 ldquoBack Pagerdquo Score _ 20 pts
I 5 pts Complete the following table for the 3 major components (subatomic particles) of the atom
hint electrical charge = positive negative or neutral and mass = 1 dalton or 11800 dalton 1 pt each
Particle Electrical Charge Mass
1 Proton 1 dalton
2 Electron
3 Neutron
II 5 pts In your own words compare and contrast the following two atoms A and B use the back of the previous page to
make as many observations as you can about similarities (and what they mean) and differences (and what they mean)
between the atoms
A B
III 5 pts Match the following by placing the corresponding in the space provided 1 pt each
_____ tertiary structure 1 produce H2O
_____ two ester linkages 2 is responsible for the 3-dimensional shape of a protein
_____ phosphodiester bonds 3 exist within diglycerides (diacylglyerols) and phospholipids
_____ dehydration synthesis reactions 4 are a type of lipid
_____ steroids 5 are formed when nucleic acids are synthesized
IV 5 pts Circle each of the variable (R) groups in the molecules shown below (3 pts)
a Which lsquoRrsquo group is polar ______ (write the corresponding in the space provided) (1 pt)
b Which lsquoRrsquo group is ionic ______ (write the corresponding in the space provided) (1 pt)
NH3+ OH CH3
1 2 3
12 neutrons
11 protons
10 electrons
13 neutrons
11 protons
11 electrons
Bio1230 Exam 1
Clickers and immediate feedback
Name _____________________________________________________________________________________________
This is a worksheet for your self-evaluation of study habits and exam preparedness Your answers on the corresponding
online exam surveys are confidential
~The average number of hours I spent per week reading the chapters andor reviewingprocessing class notes was (circle the
appropriate response)
zero to one one to two two to four greater than four
~I read the assignment before coming to class (circle the appropriate response)
never sometimes regularly
~I asked my instructor questions when I was confused about textbook material andor lecture material (circle the appropriate
response)
never sometimes regularly
~Overall I spent _____ hours specifically studying for this exam (Please fill in the blank)
~Prior to taking the exam I expected to get an approximate grade of (fill in the blank) _____
~My actual grade was a(n) (fill in the blank) _____
~Check all of the statements that apply to your performance on the exam
____ studied the right information ____ did not study the right information
____ studied the right information but did not ____ studied the right information and
understand it thought I understood it
____ used the class outlines to study ____ thought college would be easier
____ did not know what to study ____ other _____________________
____ did not think I would need to know the information in such detail
Analysis of Missed Questions I answered the question incorrectly because I Insert question number below in the correct category
did not study the information
studied the information but forgot it
did not understand the information in the
summary notes
confused similar concepts or terms (ie
isotopes and isomers)
misread or misunderstood the question
did not consider all of the answer choices
knew the correct answer - but chose an
incorrect answer by mistake
List other reason(s)
List other reason(s)
Please answer additional self-evaluation questions on the back of this page
Self-Evaluation of Study Habits amp Exam Preparedness for Biology 1230 Exam I or II or III (circle one)
Going forwardhellip
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
Foundations I and II (Biol 1210L and Biol 1220L)
bull Biol 1210L Introduces basic principles and applications of math physics and chemistry in biology and research Emphasis on group projects active learning discussions readingcomprehension of scientific articlespassages experimentation data collection data analysis and use of computers
bull Biol 1220L Focuses on statistics using data collected by students using systems like the Bean beetle and plant seeds Also reinforcement of measurement conversions dilutions stock solutions and back calculations using living systems typically bacteria Continuation of primary literature discussionsanalysis
1210L Active Learning110$in$50m
L$110$in$100
mL$
110$in$30m
L$
Infect=99 recovery=99
STUDIES ON PIGMENTATION OF SERRATIA MARCESCENS
I SPECTRAL AND PAPER CHROMATOGRAPHIC PROPERTIES OF PRODIGIOSIN
ROBERT P WILLIAMS JAMES A GREEN2 AND DONALD A RAPPOPORT
Departments of Microbiology Biochemistry and Radiology Baylor University College of Medicine Houston Texas
Received for publication June 23 1955
APPLIED MICROBIOLOGY Mar 1973 p 396-402 Vol 25 No 3 Copyright 0 1973 American Society for Microbiology Printed in USA
Biosynthesis of Prodigiosin a Secondary Metabolite of Serratia marcescensROBERT P WILLIAMS
Department of Microbiology Baylor College of Medicine Houston Texas 77025 Received for publication 30 October 1972
Prodigiosenes (prodigiosin and prodigiosin-like pigments) are known to be synthesized by only one genus of Eubacteriales and by two genera of Actinomycetales Biosynthesis by Serratia marcqscens occurs over a relatively narrow range of temperatures although the bacteria grow over a broad range When cultures of S marcescenswere incubated at 27 C in 10 casein hydrolysate viable count and protein attained maximal values within 24 to 48 h whereas prodigiosin did not reach a maximum until 96 h The greatest amount of pigment was synthesized when cultures were in the senescent phase of growth Suspensions of nonproliferating bacteria incubated at 27 C in only i-alanine also synthesized prodigiosin although at a slower rate than growing cultures Kinetics of growth for the wild-type red S marcescens and a white mutant were identical when incubated at 27 C but the wild type produced abundant pigment These results plus other data obtained from the literature suggest that prodigiosin is a secondary metabolite The importance of this proposal to understanding the function of prodigiosin in S marcescens is discussed
Zooming ahead to recent yearshelliphellip From 1955 to 2017
MybioSorcecomhttpswwwmybiosourcecom
Product DescriptionProdigiosin is an intensely red pyrrole pigment produced by several bacteria most notably Serratia marcescens Prodigiosin has a broad biological profile with activity against fungi tumor cell lines and malaria It was shown to be an immunosuppressant in 2007 The mode of action of prodigiosin has recently received considerable attention as an inducer of apoptosis in human primary cancer cells via caspase activation Prodigiosin also acts as an inducer of p21WAF1CIP1 expression via transforming growth factor-B receptor pathway and of NAG-1activation by acting on glycogen synthase kinase-3B
Evidence of ldquomath-gaprdquo
bull ACT College Readiness Benchmark
ndash 50 chance of obtaining a B or
better or ~75 chance of obtaining
a C or higher in a corresponding
first-year course
ACT Site
ndash Math = Algebra I
ndash Science = Biology IBased on sample of 214 institutions and gt230000
students from US Benchmarks = median course
placement values and represent a ldquotypicalrdquo set of
expectations
Percent of ACT-Tested High School Graduates Meeting ACT Benchmarks
Pe
rce
nt
Few 12th Grade Students Interested
in STEM and Proficient in Math
Business-Higher Ed Forum Research Brief (2011)Included in 2012 PCAST Appendix E
STEM interested
AND Math Proficient
NOT STEM
interestedMath
ProficientNOT STEM
interested
NOT Math
Proficient
STEM
interested
NOT Math
Proficient
Biological Quantitative Reasoning
Exam (BioSQuaRE) ndash Q6 consortium
BioSQuaRE TeamBiology
Paul Overvoorde (Macalester)
Peter Brodfuehrer Greg Davis (Bryn Mawr)
Charles Umbanhowar (St Olaf)
Marion Preest (Keck Science Center Claremont Colleges)
Steve Adolph Cathy McFadden (Harvey Mudd)
Educational PsychologyStatistics
Andy Zieffler Laure Le (U Minnesota)
Laura Zeigler (Iowa State)
Erik Larson (Macalester)- Sociology
ldquoOtherrdquo
Liz Stanhope (Lewis and Clark) ndash Math
Jason Belitsky (Oberlin) ndash Chemistry
Marcelo Vinces (Oberlin) ndash Quantitative Skills Center
Tabassum Haque (Oberlin) ndash Institutional Research
Alignment of Learning Outcomes
bull 14 + 38 faculty
bull Mapping of learning outcomes with
previous national reports
ndash BIO2010
ndash Vision and Changes
ndash Next Gen Science Standards for Science
and Engineering
ndash Revised AP Biology requirements
ndash Preparing Future Physicians
bull Comparison to previously created
Quantitative Literacy Efforts (eg
QRLA TOSLS)
Mapping Learning Outcomes to National Reports
ContentStudents should
be able to
BIO20
10
Vision
amp
Chang
e
SFFPAP
Bio
NGSS
SampE
Algebra
functions
and
modeling
Carry out basic mathematical
computations (eg proportional reasoning
unit conversion center and variation)
X X X X X
Recognize and use logarithmic or
exponential relationshipsX X
Fit a model such as population growth X X
Use a representation or a model to make
predictionsX X X X X
Describeinfer relationships between
variables (scatterplots regression
network diagrams maps)
X X
Perform logicalalgorithmic reasoning X X X X
Statistics
and
probability
Calculate or use the concept of the
likelihood of an eventX X X
Calculate or use conditional probability X X X
Recognize and interpret what summary
statistics representX X X
Identify different types of error X
Recognize that biological systems are
inherently variable (eg stochastic vs
deterministic)
X X
Formulate hypothesis statements X X X X
Understand what a p-value is X X X X
Understand when causal claims can be
made (eg correlation vs causation)X X X X
Visualizati
on
Choose the appropriate type of graph X X X X X
Interpret a graph (eg functional
relationships logarithmic relationships)X X X X X
Be able to use a table X X X
Use spatial reasoning to interpret
multidimensional numerical and visual
data (geographic information)
X
Stanhope et al (2017) Development of a Biological
Science Quantitative Reasoning Exam (BioSQuaRE)
CBE- Life Science Education Winter edition
December 1 2017
bull identification and validation of learning domains
bull iterative development of BioSQuaRE Instrument
bull evidence of validity
bull discussion of instruments utility for students individual
faculty and departments or programs
Visit wwwmacalestereduhhmibiosquare for more information
BLASTing Human and Other Organisms
bull Our goal is to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus(snake) The objective is to find and precisely map the coding regions using NCBIrsquos BLASTp search tool
bull Answer the following questions for each of the 4 organisms1 Describe the summary distributions2 Interpret the score the percent identity and the E-value If
obtain hit(s) are they likely due to chance If no hits why3 Analyze the alignments
Describe these Summary Distributions
Chimp
Cow
Snake
Chicken
Interpret the Scores E-values and Identities
Chimp
Cow
Snake
Chicken
Analyze the Alignments
Chimp
Cow
Snake
Chicken
Additional Questions of Interest
bull Our goal was to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus (snake) The objective is to find and precisely map the coding regions
bull Answer the following questions1 This presentation is showing only highly significant pairs How
do you think the alignments (scores e-values identities) differ if we analyze low significant pairs
2 Can you infer that this protein does not exist in this organism3 Give alternative explanations for the differences in scores e-
values and identities4 Is there an evolutionary relationship between sequences
Am J Hum Genet 2008 Dec 12 83(6) 769ndash780 Published online 2008 Dec 5 doi 101016jajhg200811004
Ribosomal Protein L5 and L11 Mutations Are Associated with Cleft Palate and Abnormal Thumbs in Diamond-Blackfan Anemia Patients
Hanna T Gazda12lowast
Mee Rie Sheen1
Adrianna Vlachos34
Valerie Choesmel56
Marie-Franccediloise ODonohue
56Hal Schneider
1Natasha Darras
1Catherine Hasman
1Colin A
Sieff27
Peter E Newburger8
Sarah E Ball9
Edyta Niewiadomska10
Michal Matysiak10
Jan M Zaucha
11Bertil Glader
12Charlotte Niemeyer
13Joerg J Meerpohl
13Eva Atsidaftos
34Jeffrey
M Lipton34
Pierre-Emmanuel Gleizes56
and Alan H Beggs12
Author information Article notes Copyright and License information AbstractDiamond-Blackfan anemia (DBA) a congenital bone-marrow-failure syndrome is characterized by red blood cell aplasia macrocytic anemia clinical heterogeneity and increased risk of malignancy Although anemia is the most prominent feature of DBA the disease is also characterized by growth retardation and congenital anomalies that are present in sim30ndash50 of patients The disease has been associated with mutations in four ribosomal protein (RP) genes RPS19 RPS24 RPS17 and RPL35A in about 30 of patients However the genetic basis of the remaining 70 of cases is still unknown Here we report the second known mutation in RPS17 and probable pathogenic mutations in three more RP genes RPL5 RPL11 and RPS7 In addition we identified rare variants of unknown significance in three other genes RPL36 RPS15 and RPS27A Remarkably careful review of the clinical data showed that mutations in RPL5 are associated with multiple physical abnormalities including craniofacial thumb and heart anomalies whereas isolated thumb malformations are predominantly present in patients carrying mutations in RPL11 We also demonstrate that mutations of RPL5 RPL11 or RPS7 in DBA cells is associated with diverse defects in the maturation of ribosomal RNAs in the large or the small ribosomal subunit production pathway expanding the repertoire of ribosomal RNA processing defects associated with DBA
Develop more inquiry-based lab exercises1 C elegans crosses (Peter Barrett in Genetics lab)
2 Modifications on DNA transformation and lac operon exercises (PB)
3 The lsquotermitersquo experiment in Biol 1230L (Kristal Huggins and SKI)
4 In Cell Biology lab C elegans (endocytosis experiments) experiments with Planaria regeneration (adapted from MITHHMI) and recently with Daphnia (the water flea a small crustacean) adapted from the Nuffield Foundation where students expose the Daphnia to various cardioactive compounds measure changes in heart rate caused by effects on cellular receptors and design follow-up experiments (PB)
Assessment Strategies for Project Scicomp
Formative and summative
General scheme
bull Assessment tasks based on objectives
bull Develop assessment tools and pilot for validation
bull Apply to larger audience
bull Collect and score
bull Share and analyze data
Coordinated course sequences and our curricular design serve as a good platform
for intra and interdepartmental discussions
(weekly meetings lsquoSERGrsquo etc)
Labs
bull General observation on student participationinitiative
bull Data sheets (say 10 collecthellipsay any 4)
bull Midterm skills practical stations and multiple choice (excellent determinant)
bull Quizzes (5-10 depending on the lab)
bull Final exams
Course based research experiencee(CRE)
bull How they design their experiment
bull Notebooks lab techniques
bull Participation in class discussions
bull Ability to troubleshoot
bull Midterm Skills and oral exam along with traditional exam
bull Short answer (non multiple choice) questions
bull Research paper presentations
CREs at Xavier
bull Phage and Genomics
bull lsquoUndergraduate Researchrsquo for credits
bull Introduction to Mammalian Tissue Culture
The SEA-PHAGES ProgramhttpsseaphagesorgThe official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program
SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is a two-semester discovery-based undergraduate research course that begins with simple digging in the soil to find new viruses but progresses through a variety of microbiology techniques and eventually to complex genome annotation and bioinformatic analyses
CBE Life Sci Educ 2016 fall15(3) pii ar38 doi 101187cbe16-01-0078Increasing URM Undergraduate Student Success through Assessment-Driven Interventions A Multiyear Study Using Freshman-Level General Biology as a Model SystemCarmichael MC1 St Clair C1 Edwards AM2 Barrett P1 McFerrin H1 Davenport I1 Awad M1 Kundu A1 Ireland SK3
AbstractXavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students In this multiyear study with sim5500 participants data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course The three hour-long exams were common and administered concurrently to all students New exam questions were developed using Blooms taxonomy and exam results were analyzed statistically with validated assessment tools All but the comprehensive final exam were returned to students for self-evaluation and remediation Among other approaches course rigor was monitored by using an identical set of 60 questions on the final exam across 10 semesters Analysis of the identical sets of 60 final exam questions revealed that overall averages increased from 729 (2010) to 835 (2015) Regression analysis demonstrated a statistically significant correlation between high-risk students and their averages on the 60 questions Additional analysis demonstrated statistically significant improvements for at least one letter grade from midterm to final and a 20 increase in the course pass rates over time also for the high-risk population These results support the hypothesis that our data-driven interventions and assessment techniques are successful in improving student retention particularly for our academically at-risk students
Lecture Biol 1230
bull Competency E4 (chemistry in biology atomic bonds metabolic pathways thermodynamics)
bull Quizzes (formative assessment with Clickers)
bull The coordinator prepares the three lsquoOne hour examsrsquo (questions not from the textbook) instructors again reviewcomment
bull Question types range (content versus applications) and also lsquoBack pagersquo ( 20 of the exam grade) Formative assessment using the LXRtest software (Opscan6 scanner)
Final exam not returned cumulative and has had 60 questions (good discriminators based on the rpbvalues) commonly used on ALL final exams for the past five years Powerful tool for measuring studentsrsquo learning and applications over time and based on academic risk categories
Last Name First Name
Biology 1230 Exam 1 ldquoBack Pagerdquo Score _ 20 pts
I 5 pts Complete the following table for the 3 major components (subatomic particles) of the atom
hint electrical charge = positive negative or neutral and mass = 1 dalton or 11800 dalton 1 pt each
Particle Electrical Charge Mass
1 Proton 1 dalton
2 Electron
3 Neutron
II 5 pts In your own words compare and contrast the following two atoms A and B use the back of the previous page to
make as many observations as you can about similarities (and what they mean) and differences (and what they mean)
between the atoms
A B
III 5 pts Match the following by placing the corresponding in the space provided 1 pt each
_____ tertiary structure 1 produce H2O
_____ two ester linkages 2 is responsible for the 3-dimensional shape of a protein
_____ phosphodiester bonds 3 exist within diglycerides (diacylglyerols) and phospholipids
_____ dehydration synthesis reactions 4 are a type of lipid
_____ steroids 5 are formed when nucleic acids are synthesized
IV 5 pts Circle each of the variable (R) groups in the molecules shown below (3 pts)
a Which lsquoRrsquo group is polar ______ (write the corresponding in the space provided) (1 pt)
b Which lsquoRrsquo group is ionic ______ (write the corresponding in the space provided) (1 pt)
NH3+ OH CH3
1 2 3
12 neutrons
11 protons
10 electrons
13 neutrons
11 protons
11 electrons
Bio1230 Exam 1
Clickers and immediate feedback
Name _____________________________________________________________________________________________
This is a worksheet for your self-evaluation of study habits and exam preparedness Your answers on the corresponding
online exam surveys are confidential
~The average number of hours I spent per week reading the chapters andor reviewingprocessing class notes was (circle the
appropriate response)
zero to one one to two two to four greater than four
~I read the assignment before coming to class (circle the appropriate response)
never sometimes regularly
~I asked my instructor questions when I was confused about textbook material andor lecture material (circle the appropriate
response)
never sometimes regularly
~Overall I spent _____ hours specifically studying for this exam (Please fill in the blank)
~Prior to taking the exam I expected to get an approximate grade of (fill in the blank) _____
~My actual grade was a(n) (fill in the blank) _____
~Check all of the statements that apply to your performance on the exam
____ studied the right information ____ did not study the right information
____ studied the right information but did not ____ studied the right information and
understand it thought I understood it
____ used the class outlines to study ____ thought college would be easier
____ did not know what to study ____ other _____________________
____ did not think I would need to know the information in such detail
Analysis of Missed Questions I answered the question incorrectly because I Insert question number below in the correct category
did not study the information
studied the information but forgot it
did not understand the information in the
summary notes
confused similar concepts or terms (ie
isotopes and isomers)
misread or misunderstood the question
did not consider all of the answer choices
knew the correct answer - but chose an
incorrect answer by mistake
List other reason(s)
List other reason(s)
Please answer additional self-evaluation questions on the back of this page
Self-Evaluation of Study Habits amp Exam Preparedness for Biology 1230 Exam I or II or III (circle one)
Going forwardhellip
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
1210L Active Learning110$in$50m
L$110$in$100
mL$
110$in$30m
L$
Infect=99 recovery=99
STUDIES ON PIGMENTATION OF SERRATIA MARCESCENS
I SPECTRAL AND PAPER CHROMATOGRAPHIC PROPERTIES OF PRODIGIOSIN
ROBERT P WILLIAMS JAMES A GREEN2 AND DONALD A RAPPOPORT
Departments of Microbiology Biochemistry and Radiology Baylor University College of Medicine Houston Texas
Received for publication June 23 1955
APPLIED MICROBIOLOGY Mar 1973 p 396-402 Vol 25 No 3 Copyright 0 1973 American Society for Microbiology Printed in USA
Biosynthesis of Prodigiosin a Secondary Metabolite of Serratia marcescensROBERT P WILLIAMS
Department of Microbiology Baylor College of Medicine Houston Texas 77025 Received for publication 30 October 1972
Prodigiosenes (prodigiosin and prodigiosin-like pigments) are known to be synthesized by only one genus of Eubacteriales and by two genera of Actinomycetales Biosynthesis by Serratia marcqscens occurs over a relatively narrow range of temperatures although the bacteria grow over a broad range When cultures of S marcescenswere incubated at 27 C in 10 casein hydrolysate viable count and protein attained maximal values within 24 to 48 h whereas prodigiosin did not reach a maximum until 96 h The greatest amount of pigment was synthesized when cultures were in the senescent phase of growth Suspensions of nonproliferating bacteria incubated at 27 C in only i-alanine also synthesized prodigiosin although at a slower rate than growing cultures Kinetics of growth for the wild-type red S marcescens and a white mutant were identical when incubated at 27 C but the wild type produced abundant pigment These results plus other data obtained from the literature suggest that prodigiosin is a secondary metabolite The importance of this proposal to understanding the function of prodigiosin in S marcescens is discussed
Zooming ahead to recent yearshelliphellip From 1955 to 2017
MybioSorcecomhttpswwwmybiosourcecom
Product DescriptionProdigiosin is an intensely red pyrrole pigment produced by several bacteria most notably Serratia marcescens Prodigiosin has a broad biological profile with activity against fungi tumor cell lines and malaria It was shown to be an immunosuppressant in 2007 The mode of action of prodigiosin has recently received considerable attention as an inducer of apoptosis in human primary cancer cells via caspase activation Prodigiosin also acts as an inducer of p21WAF1CIP1 expression via transforming growth factor-B receptor pathway and of NAG-1activation by acting on glycogen synthase kinase-3B
Evidence of ldquomath-gaprdquo
bull ACT College Readiness Benchmark
ndash 50 chance of obtaining a B or
better or ~75 chance of obtaining
a C or higher in a corresponding
first-year course
ACT Site
ndash Math = Algebra I
ndash Science = Biology IBased on sample of 214 institutions and gt230000
students from US Benchmarks = median course
placement values and represent a ldquotypicalrdquo set of
expectations
Percent of ACT-Tested High School Graduates Meeting ACT Benchmarks
Pe
rce
nt
Few 12th Grade Students Interested
in STEM and Proficient in Math
Business-Higher Ed Forum Research Brief (2011)Included in 2012 PCAST Appendix E
STEM interested
AND Math Proficient
NOT STEM
interestedMath
ProficientNOT STEM
interested
NOT Math
Proficient
STEM
interested
NOT Math
Proficient
Biological Quantitative Reasoning
Exam (BioSQuaRE) ndash Q6 consortium
BioSQuaRE TeamBiology
Paul Overvoorde (Macalester)
Peter Brodfuehrer Greg Davis (Bryn Mawr)
Charles Umbanhowar (St Olaf)
Marion Preest (Keck Science Center Claremont Colleges)
Steve Adolph Cathy McFadden (Harvey Mudd)
Educational PsychologyStatistics
Andy Zieffler Laure Le (U Minnesota)
Laura Zeigler (Iowa State)
Erik Larson (Macalester)- Sociology
ldquoOtherrdquo
Liz Stanhope (Lewis and Clark) ndash Math
Jason Belitsky (Oberlin) ndash Chemistry
Marcelo Vinces (Oberlin) ndash Quantitative Skills Center
Tabassum Haque (Oberlin) ndash Institutional Research
Alignment of Learning Outcomes
bull 14 + 38 faculty
bull Mapping of learning outcomes with
previous national reports
ndash BIO2010
ndash Vision and Changes
ndash Next Gen Science Standards for Science
and Engineering
ndash Revised AP Biology requirements
ndash Preparing Future Physicians
bull Comparison to previously created
Quantitative Literacy Efforts (eg
QRLA TOSLS)
Mapping Learning Outcomes to National Reports
ContentStudents should
be able to
BIO20
10
Vision
amp
Chang
e
SFFPAP
Bio
NGSS
SampE
Algebra
functions
and
modeling
Carry out basic mathematical
computations (eg proportional reasoning
unit conversion center and variation)
X X X X X
Recognize and use logarithmic or
exponential relationshipsX X
Fit a model such as population growth X X
Use a representation or a model to make
predictionsX X X X X
Describeinfer relationships between
variables (scatterplots regression
network diagrams maps)
X X
Perform logicalalgorithmic reasoning X X X X
Statistics
and
probability
Calculate or use the concept of the
likelihood of an eventX X X
Calculate or use conditional probability X X X
Recognize and interpret what summary
statistics representX X X
Identify different types of error X
Recognize that biological systems are
inherently variable (eg stochastic vs
deterministic)
X X
Formulate hypothesis statements X X X X
Understand what a p-value is X X X X
Understand when causal claims can be
made (eg correlation vs causation)X X X X
Visualizati
on
Choose the appropriate type of graph X X X X X
Interpret a graph (eg functional
relationships logarithmic relationships)X X X X X
Be able to use a table X X X
Use spatial reasoning to interpret
multidimensional numerical and visual
data (geographic information)
X
Stanhope et al (2017) Development of a Biological
Science Quantitative Reasoning Exam (BioSQuaRE)
CBE- Life Science Education Winter edition
December 1 2017
bull identification and validation of learning domains
bull iterative development of BioSQuaRE Instrument
bull evidence of validity
bull discussion of instruments utility for students individual
faculty and departments or programs
Visit wwwmacalestereduhhmibiosquare for more information
BLASTing Human and Other Organisms
bull Our goal is to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus(snake) The objective is to find and precisely map the coding regions using NCBIrsquos BLASTp search tool
bull Answer the following questions for each of the 4 organisms1 Describe the summary distributions2 Interpret the score the percent identity and the E-value If
obtain hit(s) are they likely due to chance If no hits why3 Analyze the alignments
Describe these Summary Distributions
Chimp
Cow
Snake
Chicken
Interpret the Scores E-values and Identities
Chimp
Cow
Snake
Chicken
Analyze the Alignments
Chimp
Cow
Snake
Chicken
Additional Questions of Interest
bull Our goal was to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus (snake) The objective is to find and precisely map the coding regions
bull Answer the following questions1 This presentation is showing only highly significant pairs How
do you think the alignments (scores e-values identities) differ if we analyze low significant pairs
2 Can you infer that this protein does not exist in this organism3 Give alternative explanations for the differences in scores e-
values and identities4 Is there an evolutionary relationship between sequences
Am J Hum Genet 2008 Dec 12 83(6) 769ndash780 Published online 2008 Dec 5 doi 101016jajhg200811004
Ribosomal Protein L5 and L11 Mutations Are Associated with Cleft Palate and Abnormal Thumbs in Diamond-Blackfan Anemia Patients
Hanna T Gazda12lowast
Mee Rie Sheen1
Adrianna Vlachos34
Valerie Choesmel56
Marie-Franccediloise ODonohue
56Hal Schneider
1Natasha Darras
1Catherine Hasman
1Colin A
Sieff27
Peter E Newburger8
Sarah E Ball9
Edyta Niewiadomska10
Michal Matysiak10
Jan M Zaucha
11Bertil Glader
12Charlotte Niemeyer
13Joerg J Meerpohl
13Eva Atsidaftos
34Jeffrey
M Lipton34
Pierre-Emmanuel Gleizes56
and Alan H Beggs12
Author information Article notes Copyright and License information AbstractDiamond-Blackfan anemia (DBA) a congenital bone-marrow-failure syndrome is characterized by red blood cell aplasia macrocytic anemia clinical heterogeneity and increased risk of malignancy Although anemia is the most prominent feature of DBA the disease is also characterized by growth retardation and congenital anomalies that are present in sim30ndash50 of patients The disease has been associated with mutations in four ribosomal protein (RP) genes RPS19 RPS24 RPS17 and RPL35A in about 30 of patients However the genetic basis of the remaining 70 of cases is still unknown Here we report the second known mutation in RPS17 and probable pathogenic mutations in three more RP genes RPL5 RPL11 and RPS7 In addition we identified rare variants of unknown significance in three other genes RPL36 RPS15 and RPS27A Remarkably careful review of the clinical data showed that mutations in RPL5 are associated with multiple physical abnormalities including craniofacial thumb and heart anomalies whereas isolated thumb malformations are predominantly present in patients carrying mutations in RPL11 We also demonstrate that mutations of RPL5 RPL11 or RPS7 in DBA cells is associated with diverse defects in the maturation of ribosomal RNAs in the large or the small ribosomal subunit production pathway expanding the repertoire of ribosomal RNA processing defects associated with DBA
Develop more inquiry-based lab exercises1 C elegans crosses (Peter Barrett in Genetics lab)
2 Modifications on DNA transformation and lac operon exercises (PB)
3 The lsquotermitersquo experiment in Biol 1230L (Kristal Huggins and SKI)
4 In Cell Biology lab C elegans (endocytosis experiments) experiments with Planaria regeneration (adapted from MITHHMI) and recently with Daphnia (the water flea a small crustacean) adapted from the Nuffield Foundation where students expose the Daphnia to various cardioactive compounds measure changes in heart rate caused by effects on cellular receptors and design follow-up experiments (PB)
Assessment Strategies for Project Scicomp
Formative and summative
General scheme
bull Assessment tasks based on objectives
bull Develop assessment tools and pilot for validation
bull Apply to larger audience
bull Collect and score
bull Share and analyze data
Coordinated course sequences and our curricular design serve as a good platform
for intra and interdepartmental discussions
(weekly meetings lsquoSERGrsquo etc)
Labs
bull General observation on student participationinitiative
bull Data sheets (say 10 collecthellipsay any 4)
bull Midterm skills practical stations and multiple choice (excellent determinant)
bull Quizzes (5-10 depending on the lab)
bull Final exams
Course based research experiencee(CRE)
bull How they design their experiment
bull Notebooks lab techniques
bull Participation in class discussions
bull Ability to troubleshoot
bull Midterm Skills and oral exam along with traditional exam
bull Short answer (non multiple choice) questions
bull Research paper presentations
CREs at Xavier
bull Phage and Genomics
bull lsquoUndergraduate Researchrsquo for credits
bull Introduction to Mammalian Tissue Culture
The SEA-PHAGES ProgramhttpsseaphagesorgThe official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program
SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is a two-semester discovery-based undergraduate research course that begins with simple digging in the soil to find new viruses but progresses through a variety of microbiology techniques and eventually to complex genome annotation and bioinformatic analyses
CBE Life Sci Educ 2016 fall15(3) pii ar38 doi 101187cbe16-01-0078Increasing URM Undergraduate Student Success through Assessment-Driven Interventions A Multiyear Study Using Freshman-Level General Biology as a Model SystemCarmichael MC1 St Clair C1 Edwards AM2 Barrett P1 McFerrin H1 Davenport I1 Awad M1 Kundu A1 Ireland SK3
AbstractXavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students In this multiyear study with sim5500 participants data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course The three hour-long exams were common and administered concurrently to all students New exam questions were developed using Blooms taxonomy and exam results were analyzed statistically with validated assessment tools All but the comprehensive final exam were returned to students for self-evaluation and remediation Among other approaches course rigor was monitored by using an identical set of 60 questions on the final exam across 10 semesters Analysis of the identical sets of 60 final exam questions revealed that overall averages increased from 729 (2010) to 835 (2015) Regression analysis demonstrated a statistically significant correlation between high-risk students and their averages on the 60 questions Additional analysis demonstrated statistically significant improvements for at least one letter grade from midterm to final and a 20 increase in the course pass rates over time also for the high-risk population These results support the hypothesis that our data-driven interventions and assessment techniques are successful in improving student retention particularly for our academically at-risk students
Lecture Biol 1230
bull Competency E4 (chemistry in biology atomic bonds metabolic pathways thermodynamics)
bull Quizzes (formative assessment with Clickers)
bull The coordinator prepares the three lsquoOne hour examsrsquo (questions not from the textbook) instructors again reviewcomment
bull Question types range (content versus applications) and also lsquoBack pagersquo ( 20 of the exam grade) Formative assessment using the LXRtest software (Opscan6 scanner)
Final exam not returned cumulative and has had 60 questions (good discriminators based on the rpbvalues) commonly used on ALL final exams for the past five years Powerful tool for measuring studentsrsquo learning and applications over time and based on academic risk categories
Last Name First Name
Biology 1230 Exam 1 ldquoBack Pagerdquo Score _ 20 pts
I 5 pts Complete the following table for the 3 major components (subatomic particles) of the atom
hint electrical charge = positive negative or neutral and mass = 1 dalton or 11800 dalton 1 pt each
Particle Electrical Charge Mass
1 Proton 1 dalton
2 Electron
3 Neutron
II 5 pts In your own words compare and contrast the following two atoms A and B use the back of the previous page to
make as many observations as you can about similarities (and what they mean) and differences (and what they mean)
between the atoms
A B
III 5 pts Match the following by placing the corresponding in the space provided 1 pt each
_____ tertiary structure 1 produce H2O
_____ two ester linkages 2 is responsible for the 3-dimensional shape of a protein
_____ phosphodiester bonds 3 exist within diglycerides (diacylglyerols) and phospholipids
_____ dehydration synthesis reactions 4 are a type of lipid
_____ steroids 5 are formed when nucleic acids are synthesized
IV 5 pts Circle each of the variable (R) groups in the molecules shown below (3 pts)
a Which lsquoRrsquo group is polar ______ (write the corresponding in the space provided) (1 pt)
b Which lsquoRrsquo group is ionic ______ (write the corresponding in the space provided) (1 pt)
NH3+ OH CH3
1 2 3
12 neutrons
11 protons
10 electrons
13 neutrons
11 protons
11 electrons
Bio1230 Exam 1
Clickers and immediate feedback
Name _____________________________________________________________________________________________
This is a worksheet for your self-evaluation of study habits and exam preparedness Your answers on the corresponding
online exam surveys are confidential
~The average number of hours I spent per week reading the chapters andor reviewingprocessing class notes was (circle the
appropriate response)
zero to one one to two two to four greater than four
~I read the assignment before coming to class (circle the appropriate response)
never sometimes regularly
~I asked my instructor questions when I was confused about textbook material andor lecture material (circle the appropriate
response)
never sometimes regularly
~Overall I spent _____ hours specifically studying for this exam (Please fill in the blank)
~Prior to taking the exam I expected to get an approximate grade of (fill in the blank) _____
~My actual grade was a(n) (fill in the blank) _____
~Check all of the statements that apply to your performance on the exam
____ studied the right information ____ did not study the right information
____ studied the right information but did not ____ studied the right information and
understand it thought I understood it
____ used the class outlines to study ____ thought college would be easier
____ did not know what to study ____ other _____________________
____ did not think I would need to know the information in such detail
Analysis of Missed Questions I answered the question incorrectly because I Insert question number below in the correct category
did not study the information
studied the information but forgot it
did not understand the information in the
summary notes
confused similar concepts or terms (ie
isotopes and isomers)
misread or misunderstood the question
did not consider all of the answer choices
knew the correct answer - but chose an
incorrect answer by mistake
List other reason(s)
List other reason(s)
Please answer additional self-evaluation questions on the back of this page
Self-Evaluation of Study Habits amp Exam Preparedness for Biology 1230 Exam I or II or III (circle one)
Going forwardhellip
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
STUDIES ON PIGMENTATION OF SERRATIA MARCESCENS
I SPECTRAL AND PAPER CHROMATOGRAPHIC PROPERTIES OF PRODIGIOSIN
ROBERT P WILLIAMS JAMES A GREEN2 AND DONALD A RAPPOPORT
Departments of Microbiology Biochemistry and Radiology Baylor University College of Medicine Houston Texas
Received for publication June 23 1955
APPLIED MICROBIOLOGY Mar 1973 p 396-402 Vol 25 No 3 Copyright 0 1973 American Society for Microbiology Printed in USA
Biosynthesis of Prodigiosin a Secondary Metabolite of Serratia marcescensROBERT P WILLIAMS
Department of Microbiology Baylor College of Medicine Houston Texas 77025 Received for publication 30 October 1972
Prodigiosenes (prodigiosin and prodigiosin-like pigments) are known to be synthesized by only one genus of Eubacteriales and by two genera of Actinomycetales Biosynthesis by Serratia marcqscens occurs over a relatively narrow range of temperatures although the bacteria grow over a broad range When cultures of S marcescenswere incubated at 27 C in 10 casein hydrolysate viable count and protein attained maximal values within 24 to 48 h whereas prodigiosin did not reach a maximum until 96 h The greatest amount of pigment was synthesized when cultures were in the senescent phase of growth Suspensions of nonproliferating bacteria incubated at 27 C in only i-alanine also synthesized prodigiosin although at a slower rate than growing cultures Kinetics of growth for the wild-type red S marcescens and a white mutant were identical when incubated at 27 C but the wild type produced abundant pigment These results plus other data obtained from the literature suggest that prodigiosin is a secondary metabolite The importance of this proposal to understanding the function of prodigiosin in S marcescens is discussed
Zooming ahead to recent yearshelliphellip From 1955 to 2017
MybioSorcecomhttpswwwmybiosourcecom
Product DescriptionProdigiosin is an intensely red pyrrole pigment produced by several bacteria most notably Serratia marcescens Prodigiosin has a broad biological profile with activity against fungi tumor cell lines and malaria It was shown to be an immunosuppressant in 2007 The mode of action of prodigiosin has recently received considerable attention as an inducer of apoptosis in human primary cancer cells via caspase activation Prodigiosin also acts as an inducer of p21WAF1CIP1 expression via transforming growth factor-B receptor pathway and of NAG-1activation by acting on glycogen synthase kinase-3B
Evidence of ldquomath-gaprdquo
bull ACT College Readiness Benchmark
ndash 50 chance of obtaining a B or
better or ~75 chance of obtaining
a C or higher in a corresponding
first-year course
ACT Site
ndash Math = Algebra I
ndash Science = Biology IBased on sample of 214 institutions and gt230000
students from US Benchmarks = median course
placement values and represent a ldquotypicalrdquo set of
expectations
Percent of ACT-Tested High School Graduates Meeting ACT Benchmarks
Pe
rce
nt
Few 12th Grade Students Interested
in STEM and Proficient in Math
Business-Higher Ed Forum Research Brief (2011)Included in 2012 PCAST Appendix E
STEM interested
AND Math Proficient
NOT STEM
interestedMath
ProficientNOT STEM
interested
NOT Math
Proficient
STEM
interested
NOT Math
Proficient
Biological Quantitative Reasoning
Exam (BioSQuaRE) ndash Q6 consortium
BioSQuaRE TeamBiology
Paul Overvoorde (Macalester)
Peter Brodfuehrer Greg Davis (Bryn Mawr)
Charles Umbanhowar (St Olaf)
Marion Preest (Keck Science Center Claremont Colleges)
Steve Adolph Cathy McFadden (Harvey Mudd)
Educational PsychologyStatistics
Andy Zieffler Laure Le (U Minnesota)
Laura Zeigler (Iowa State)
Erik Larson (Macalester)- Sociology
ldquoOtherrdquo
Liz Stanhope (Lewis and Clark) ndash Math
Jason Belitsky (Oberlin) ndash Chemistry
Marcelo Vinces (Oberlin) ndash Quantitative Skills Center
Tabassum Haque (Oberlin) ndash Institutional Research
Alignment of Learning Outcomes
bull 14 + 38 faculty
bull Mapping of learning outcomes with
previous national reports
ndash BIO2010
ndash Vision and Changes
ndash Next Gen Science Standards for Science
and Engineering
ndash Revised AP Biology requirements
ndash Preparing Future Physicians
bull Comparison to previously created
Quantitative Literacy Efforts (eg
QRLA TOSLS)
Mapping Learning Outcomes to National Reports
ContentStudents should
be able to
BIO20
10
Vision
amp
Chang
e
SFFPAP
Bio
NGSS
SampE
Algebra
functions
and
modeling
Carry out basic mathematical
computations (eg proportional reasoning
unit conversion center and variation)
X X X X X
Recognize and use logarithmic or
exponential relationshipsX X
Fit a model such as population growth X X
Use a representation or a model to make
predictionsX X X X X
Describeinfer relationships between
variables (scatterplots regression
network diagrams maps)
X X
Perform logicalalgorithmic reasoning X X X X
Statistics
and
probability
Calculate or use the concept of the
likelihood of an eventX X X
Calculate or use conditional probability X X X
Recognize and interpret what summary
statistics representX X X
Identify different types of error X
Recognize that biological systems are
inherently variable (eg stochastic vs
deterministic)
X X
Formulate hypothesis statements X X X X
Understand what a p-value is X X X X
Understand when causal claims can be
made (eg correlation vs causation)X X X X
Visualizati
on
Choose the appropriate type of graph X X X X X
Interpret a graph (eg functional
relationships logarithmic relationships)X X X X X
Be able to use a table X X X
Use spatial reasoning to interpret
multidimensional numerical and visual
data (geographic information)
X
Stanhope et al (2017) Development of a Biological
Science Quantitative Reasoning Exam (BioSQuaRE)
CBE- Life Science Education Winter edition
December 1 2017
bull identification and validation of learning domains
bull iterative development of BioSQuaRE Instrument
bull evidence of validity
bull discussion of instruments utility for students individual
faculty and departments or programs
Visit wwwmacalestereduhhmibiosquare for more information
BLASTing Human and Other Organisms
bull Our goal is to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus(snake) The objective is to find and precisely map the coding regions using NCBIrsquos BLASTp search tool
bull Answer the following questions for each of the 4 organisms1 Describe the summary distributions2 Interpret the score the percent identity and the E-value If
obtain hit(s) are they likely due to chance If no hits why3 Analyze the alignments
Describe these Summary Distributions
Chimp
Cow
Snake
Chicken
Interpret the Scores E-values and Identities
Chimp
Cow
Snake
Chicken
Analyze the Alignments
Chimp
Cow
Snake
Chicken
Additional Questions of Interest
bull Our goal was to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus (snake) The objective is to find and precisely map the coding regions
bull Answer the following questions1 This presentation is showing only highly significant pairs How
do you think the alignments (scores e-values identities) differ if we analyze low significant pairs
2 Can you infer that this protein does not exist in this organism3 Give alternative explanations for the differences in scores e-
values and identities4 Is there an evolutionary relationship between sequences
Am J Hum Genet 2008 Dec 12 83(6) 769ndash780 Published online 2008 Dec 5 doi 101016jajhg200811004
Ribosomal Protein L5 and L11 Mutations Are Associated with Cleft Palate and Abnormal Thumbs in Diamond-Blackfan Anemia Patients
Hanna T Gazda12lowast
Mee Rie Sheen1
Adrianna Vlachos34
Valerie Choesmel56
Marie-Franccediloise ODonohue
56Hal Schneider
1Natasha Darras
1Catherine Hasman
1Colin A
Sieff27
Peter E Newburger8
Sarah E Ball9
Edyta Niewiadomska10
Michal Matysiak10
Jan M Zaucha
11Bertil Glader
12Charlotte Niemeyer
13Joerg J Meerpohl
13Eva Atsidaftos
34Jeffrey
M Lipton34
Pierre-Emmanuel Gleizes56
and Alan H Beggs12
Author information Article notes Copyright and License information AbstractDiamond-Blackfan anemia (DBA) a congenital bone-marrow-failure syndrome is characterized by red blood cell aplasia macrocytic anemia clinical heterogeneity and increased risk of malignancy Although anemia is the most prominent feature of DBA the disease is also characterized by growth retardation and congenital anomalies that are present in sim30ndash50 of patients The disease has been associated with mutations in four ribosomal protein (RP) genes RPS19 RPS24 RPS17 and RPL35A in about 30 of patients However the genetic basis of the remaining 70 of cases is still unknown Here we report the second known mutation in RPS17 and probable pathogenic mutations in three more RP genes RPL5 RPL11 and RPS7 In addition we identified rare variants of unknown significance in three other genes RPL36 RPS15 and RPS27A Remarkably careful review of the clinical data showed that mutations in RPL5 are associated with multiple physical abnormalities including craniofacial thumb and heart anomalies whereas isolated thumb malformations are predominantly present in patients carrying mutations in RPL11 We also demonstrate that mutations of RPL5 RPL11 or RPS7 in DBA cells is associated with diverse defects in the maturation of ribosomal RNAs in the large or the small ribosomal subunit production pathway expanding the repertoire of ribosomal RNA processing defects associated with DBA
Develop more inquiry-based lab exercises1 C elegans crosses (Peter Barrett in Genetics lab)
2 Modifications on DNA transformation and lac operon exercises (PB)
3 The lsquotermitersquo experiment in Biol 1230L (Kristal Huggins and SKI)
4 In Cell Biology lab C elegans (endocytosis experiments) experiments with Planaria regeneration (adapted from MITHHMI) and recently with Daphnia (the water flea a small crustacean) adapted from the Nuffield Foundation where students expose the Daphnia to various cardioactive compounds measure changes in heart rate caused by effects on cellular receptors and design follow-up experiments (PB)
Assessment Strategies for Project Scicomp
Formative and summative
General scheme
bull Assessment tasks based on objectives
bull Develop assessment tools and pilot for validation
bull Apply to larger audience
bull Collect and score
bull Share and analyze data
Coordinated course sequences and our curricular design serve as a good platform
for intra and interdepartmental discussions
(weekly meetings lsquoSERGrsquo etc)
Labs
bull General observation on student participationinitiative
bull Data sheets (say 10 collecthellipsay any 4)
bull Midterm skills practical stations and multiple choice (excellent determinant)
bull Quizzes (5-10 depending on the lab)
bull Final exams
Course based research experiencee(CRE)
bull How they design their experiment
bull Notebooks lab techniques
bull Participation in class discussions
bull Ability to troubleshoot
bull Midterm Skills and oral exam along with traditional exam
bull Short answer (non multiple choice) questions
bull Research paper presentations
CREs at Xavier
bull Phage and Genomics
bull lsquoUndergraduate Researchrsquo for credits
bull Introduction to Mammalian Tissue Culture
The SEA-PHAGES ProgramhttpsseaphagesorgThe official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program
SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is a two-semester discovery-based undergraduate research course that begins with simple digging in the soil to find new viruses but progresses through a variety of microbiology techniques and eventually to complex genome annotation and bioinformatic analyses
CBE Life Sci Educ 2016 fall15(3) pii ar38 doi 101187cbe16-01-0078Increasing URM Undergraduate Student Success through Assessment-Driven Interventions A Multiyear Study Using Freshman-Level General Biology as a Model SystemCarmichael MC1 St Clair C1 Edwards AM2 Barrett P1 McFerrin H1 Davenport I1 Awad M1 Kundu A1 Ireland SK3
AbstractXavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students In this multiyear study with sim5500 participants data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course The three hour-long exams were common and administered concurrently to all students New exam questions were developed using Blooms taxonomy and exam results were analyzed statistically with validated assessment tools All but the comprehensive final exam were returned to students for self-evaluation and remediation Among other approaches course rigor was monitored by using an identical set of 60 questions on the final exam across 10 semesters Analysis of the identical sets of 60 final exam questions revealed that overall averages increased from 729 (2010) to 835 (2015) Regression analysis demonstrated a statistically significant correlation between high-risk students and their averages on the 60 questions Additional analysis demonstrated statistically significant improvements for at least one letter grade from midterm to final and a 20 increase in the course pass rates over time also for the high-risk population These results support the hypothesis that our data-driven interventions and assessment techniques are successful in improving student retention particularly for our academically at-risk students
Lecture Biol 1230
bull Competency E4 (chemistry in biology atomic bonds metabolic pathways thermodynamics)
bull Quizzes (formative assessment with Clickers)
bull The coordinator prepares the three lsquoOne hour examsrsquo (questions not from the textbook) instructors again reviewcomment
bull Question types range (content versus applications) and also lsquoBack pagersquo ( 20 of the exam grade) Formative assessment using the LXRtest software (Opscan6 scanner)
Final exam not returned cumulative and has had 60 questions (good discriminators based on the rpbvalues) commonly used on ALL final exams for the past five years Powerful tool for measuring studentsrsquo learning and applications over time and based on academic risk categories
Last Name First Name
Biology 1230 Exam 1 ldquoBack Pagerdquo Score _ 20 pts
I 5 pts Complete the following table for the 3 major components (subatomic particles) of the atom
hint electrical charge = positive negative or neutral and mass = 1 dalton or 11800 dalton 1 pt each
Particle Electrical Charge Mass
1 Proton 1 dalton
2 Electron
3 Neutron
II 5 pts In your own words compare and contrast the following two atoms A and B use the back of the previous page to
make as many observations as you can about similarities (and what they mean) and differences (and what they mean)
between the atoms
A B
III 5 pts Match the following by placing the corresponding in the space provided 1 pt each
_____ tertiary structure 1 produce H2O
_____ two ester linkages 2 is responsible for the 3-dimensional shape of a protein
_____ phosphodiester bonds 3 exist within diglycerides (diacylglyerols) and phospholipids
_____ dehydration synthesis reactions 4 are a type of lipid
_____ steroids 5 are formed when nucleic acids are synthesized
IV 5 pts Circle each of the variable (R) groups in the molecules shown below (3 pts)
a Which lsquoRrsquo group is polar ______ (write the corresponding in the space provided) (1 pt)
b Which lsquoRrsquo group is ionic ______ (write the corresponding in the space provided) (1 pt)
NH3+ OH CH3
1 2 3
12 neutrons
11 protons
10 electrons
13 neutrons
11 protons
11 electrons
Bio1230 Exam 1
Clickers and immediate feedback
Name _____________________________________________________________________________________________
This is a worksheet for your self-evaluation of study habits and exam preparedness Your answers on the corresponding
online exam surveys are confidential
~The average number of hours I spent per week reading the chapters andor reviewingprocessing class notes was (circle the
appropriate response)
zero to one one to two two to four greater than four
~I read the assignment before coming to class (circle the appropriate response)
never sometimes regularly
~I asked my instructor questions when I was confused about textbook material andor lecture material (circle the appropriate
response)
never sometimes regularly
~Overall I spent _____ hours specifically studying for this exam (Please fill in the blank)
~Prior to taking the exam I expected to get an approximate grade of (fill in the blank) _____
~My actual grade was a(n) (fill in the blank) _____
~Check all of the statements that apply to your performance on the exam
____ studied the right information ____ did not study the right information
____ studied the right information but did not ____ studied the right information and
understand it thought I understood it
____ used the class outlines to study ____ thought college would be easier
____ did not know what to study ____ other _____________________
____ did not think I would need to know the information in such detail
Analysis of Missed Questions I answered the question incorrectly because I Insert question number below in the correct category
did not study the information
studied the information but forgot it
did not understand the information in the
summary notes
confused similar concepts or terms (ie
isotopes and isomers)
misread or misunderstood the question
did not consider all of the answer choices
knew the correct answer - but chose an
incorrect answer by mistake
List other reason(s)
List other reason(s)
Please answer additional self-evaluation questions on the back of this page
Self-Evaluation of Study Habits amp Exam Preparedness for Biology 1230 Exam I or II or III (circle one)
Going forwardhellip
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
APPLIED MICROBIOLOGY Mar 1973 p 396-402 Vol 25 No 3 Copyright 0 1973 American Society for Microbiology Printed in USA
Biosynthesis of Prodigiosin a Secondary Metabolite of Serratia marcescensROBERT P WILLIAMS
Department of Microbiology Baylor College of Medicine Houston Texas 77025 Received for publication 30 October 1972
Prodigiosenes (prodigiosin and prodigiosin-like pigments) are known to be synthesized by only one genus of Eubacteriales and by two genera of Actinomycetales Biosynthesis by Serratia marcqscens occurs over a relatively narrow range of temperatures although the bacteria grow over a broad range When cultures of S marcescenswere incubated at 27 C in 10 casein hydrolysate viable count and protein attained maximal values within 24 to 48 h whereas prodigiosin did not reach a maximum until 96 h The greatest amount of pigment was synthesized when cultures were in the senescent phase of growth Suspensions of nonproliferating bacteria incubated at 27 C in only i-alanine also synthesized prodigiosin although at a slower rate than growing cultures Kinetics of growth for the wild-type red S marcescens and a white mutant were identical when incubated at 27 C but the wild type produced abundant pigment These results plus other data obtained from the literature suggest that prodigiosin is a secondary metabolite The importance of this proposal to understanding the function of prodigiosin in S marcescens is discussed
Zooming ahead to recent yearshelliphellip From 1955 to 2017
MybioSorcecomhttpswwwmybiosourcecom
Product DescriptionProdigiosin is an intensely red pyrrole pigment produced by several bacteria most notably Serratia marcescens Prodigiosin has a broad biological profile with activity against fungi tumor cell lines and malaria It was shown to be an immunosuppressant in 2007 The mode of action of prodigiosin has recently received considerable attention as an inducer of apoptosis in human primary cancer cells via caspase activation Prodigiosin also acts as an inducer of p21WAF1CIP1 expression via transforming growth factor-B receptor pathway and of NAG-1activation by acting on glycogen synthase kinase-3B
Evidence of ldquomath-gaprdquo
bull ACT College Readiness Benchmark
ndash 50 chance of obtaining a B or
better or ~75 chance of obtaining
a C or higher in a corresponding
first-year course
ACT Site
ndash Math = Algebra I
ndash Science = Biology IBased on sample of 214 institutions and gt230000
students from US Benchmarks = median course
placement values and represent a ldquotypicalrdquo set of
expectations
Percent of ACT-Tested High School Graduates Meeting ACT Benchmarks
Pe
rce
nt
Few 12th Grade Students Interested
in STEM and Proficient in Math
Business-Higher Ed Forum Research Brief (2011)Included in 2012 PCAST Appendix E
STEM interested
AND Math Proficient
NOT STEM
interestedMath
ProficientNOT STEM
interested
NOT Math
Proficient
STEM
interested
NOT Math
Proficient
Biological Quantitative Reasoning
Exam (BioSQuaRE) ndash Q6 consortium
BioSQuaRE TeamBiology
Paul Overvoorde (Macalester)
Peter Brodfuehrer Greg Davis (Bryn Mawr)
Charles Umbanhowar (St Olaf)
Marion Preest (Keck Science Center Claremont Colleges)
Steve Adolph Cathy McFadden (Harvey Mudd)
Educational PsychologyStatistics
Andy Zieffler Laure Le (U Minnesota)
Laura Zeigler (Iowa State)
Erik Larson (Macalester)- Sociology
ldquoOtherrdquo
Liz Stanhope (Lewis and Clark) ndash Math
Jason Belitsky (Oberlin) ndash Chemistry
Marcelo Vinces (Oberlin) ndash Quantitative Skills Center
Tabassum Haque (Oberlin) ndash Institutional Research
Alignment of Learning Outcomes
bull 14 + 38 faculty
bull Mapping of learning outcomes with
previous national reports
ndash BIO2010
ndash Vision and Changes
ndash Next Gen Science Standards for Science
and Engineering
ndash Revised AP Biology requirements
ndash Preparing Future Physicians
bull Comparison to previously created
Quantitative Literacy Efforts (eg
QRLA TOSLS)
Mapping Learning Outcomes to National Reports
ContentStudents should
be able to
BIO20
10
Vision
amp
Chang
e
SFFPAP
Bio
NGSS
SampE
Algebra
functions
and
modeling
Carry out basic mathematical
computations (eg proportional reasoning
unit conversion center and variation)
X X X X X
Recognize and use logarithmic or
exponential relationshipsX X
Fit a model such as population growth X X
Use a representation or a model to make
predictionsX X X X X
Describeinfer relationships between
variables (scatterplots regression
network diagrams maps)
X X
Perform logicalalgorithmic reasoning X X X X
Statistics
and
probability
Calculate or use the concept of the
likelihood of an eventX X X
Calculate or use conditional probability X X X
Recognize and interpret what summary
statistics representX X X
Identify different types of error X
Recognize that biological systems are
inherently variable (eg stochastic vs
deterministic)
X X
Formulate hypothesis statements X X X X
Understand what a p-value is X X X X
Understand when causal claims can be
made (eg correlation vs causation)X X X X
Visualizati
on
Choose the appropriate type of graph X X X X X
Interpret a graph (eg functional
relationships logarithmic relationships)X X X X X
Be able to use a table X X X
Use spatial reasoning to interpret
multidimensional numerical and visual
data (geographic information)
X
Stanhope et al (2017) Development of a Biological
Science Quantitative Reasoning Exam (BioSQuaRE)
CBE- Life Science Education Winter edition
December 1 2017
bull identification and validation of learning domains
bull iterative development of BioSQuaRE Instrument
bull evidence of validity
bull discussion of instruments utility for students individual
faculty and departments or programs
Visit wwwmacalestereduhhmibiosquare for more information
BLASTing Human and Other Organisms
bull Our goal is to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus(snake) The objective is to find and precisely map the coding regions using NCBIrsquos BLASTp search tool
bull Answer the following questions for each of the 4 organisms1 Describe the summary distributions2 Interpret the score the percent identity and the E-value If
obtain hit(s) are they likely due to chance If no hits why3 Analyze the alignments
Describe these Summary Distributions
Chimp
Cow
Snake
Chicken
Interpret the Scores E-values and Identities
Chimp
Cow
Snake
Chicken
Analyze the Alignments
Chimp
Cow
Snake
Chicken
Additional Questions of Interest
bull Our goal was to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus (snake) The objective is to find and precisely map the coding regions
bull Answer the following questions1 This presentation is showing only highly significant pairs How
do you think the alignments (scores e-values identities) differ if we analyze low significant pairs
2 Can you infer that this protein does not exist in this organism3 Give alternative explanations for the differences in scores e-
values and identities4 Is there an evolutionary relationship between sequences
Am J Hum Genet 2008 Dec 12 83(6) 769ndash780 Published online 2008 Dec 5 doi 101016jajhg200811004
Ribosomal Protein L5 and L11 Mutations Are Associated with Cleft Palate and Abnormal Thumbs in Diamond-Blackfan Anemia Patients
Hanna T Gazda12lowast
Mee Rie Sheen1
Adrianna Vlachos34
Valerie Choesmel56
Marie-Franccediloise ODonohue
56Hal Schneider
1Natasha Darras
1Catherine Hasman
1Colin A
Sieff27
Peter E Newburger8
Sarah E Ball9
Edyta Niewiadomska10
Michal Matysiak10
Jan M Zaucha
11Bertil Glader
12Charlotte Niemeyer
13Joerg J Meerpohl
13Eva Atsidaftos
34Jeffrey
M Lipton34
Pierre-Emmanuel Gleizes56
and Alan H Beggs12
Author information Article notes Copyright and License information AbstractDiamond-Blackfan anemia (DBA) a congenital bone-marrow-failure syndrome is characterized by red blood cell aplasia macrocytic anemia clinical heterogeneity and increased risk of malignancy Although anemia is the most prominent feature of DBA the disease is also characterized by growth retardation and congenital anomalies that are present in sim30ndash50 of patients The disease has been associated with mutations in four ribosomal protein (RP) genes RPS19 RPS24 RPS17 and RPL35A in about 30 of patients However the genetic basis of the remaining 70 of cases is still unknown Here we report the second known mutation in RPS17 and probable pathogenic mutations in three more RP genes RPL5 RPL11 and RPS7 In addition we identified rare variants of unknown significance in three other genes RPL36 RPS15 and RPS27A Remarkably careful review of the clinical data showed that mutations in RPL5 are associated with multiple physical abnormalities including craniofacial thumb and heart anomalies whereas isolated thumb malformations are predominantly present in patients carrying mutations in RPL11 We also demonstrate that mutations of RPL5 RPL11 or RPS7 in DBA cells is associated with diverse defects in the maturation of ribosomal RNAs in the large or the small ribosomal subunit production pathway expanding the repertoire of ribosomal RNA processing defects associated with DBA
Develop more inquiry-based lab exercises1 C elegans crosses (Peter Barrett in Genetics lab)
2 Modifications on DNA transformation and lac operon exercises (PB)
3 The lsquotermitersquo experiment in Biol 1230L (Kristal Huggins and SKI)
4 In Cell Biology lab C elegans (endocytosis experiments) experiments with Planaria regeneration (adapted from MITHHMI) and recently with Daphnia (the water flea a small crustacean) adapted from the Nuffield Foundation where students expose the Daphnia to various cardioactive compounds measure changes in heart rate caused by effects on cellular receptors and design follow-up experiments (PB)
Assessment Strategies for Project Scicomp
Formative and summative
General scheme
bull Assessment tasks based on objectives
bull Develop assessment tools and pilot for validation
bull Apply to larger audience
bull Collect and score
bull Share and analyze data
Coordinated course sequences and our curricular design serve as a good platform
for intra and interdepartmental discussions
(weekly meetings lsquoSERGrsquo etc)
Labs
bull General observation on student participationinitiative
bull Data sheets (say 10 collecthellipsay any 4)
bull Midterm skills practical stations and multiple choice (excellent determinant)
bull Quizzes (5-10 depending on the lab)
bull Final exams
Course based research experiencee(CRE)
bull How they design their experiment
bull Notebooks lab techniques
bull Participation in class discussions
bull Ability to troubleshoot
bull Midterm Skills and oral exam along with traditional exam
bull Short answer (non multiple choice) questions
bull Research paper presentations
CREs at Xavier
bull Phage and Genomics
bull lsquoUndergraduate Researchrsquo for credits
bull Introduction to Mammalian Tissue Culture
The SEA-PHAGES ProgramhttpsseaphagesorgThe official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program
SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is a two-semester discovery-based undergraduate research course that begins with simple digging in the soil to find new viruses but progresses through a variety of microbiology techniques and eventually to complex genome annotation and bioinformatic analyses
CBE Life Sci Educ 2016 fall15(3) pii ar38 doi 101187cbe16-01-0078Increasing URM Undergraduate Student Success through Assessment-Driven Interventions A Multiyear Study Using Freshman-Level General Biology as a Model SystemCarmichael MC1 St Clair C1 Edwards AM2 Barrett P1 McFerrin H1 Davenport I1 Awad M1 Kundu A1 Ireland SK3
AbstractXavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students In this multiyear study with sim5500 participants data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course The three hour-long exams were common and administered concurrently to all students New exam questions were developed using Blooms taxonomy and exam results were analyzed statistically with validated assessment tools All but the comprehensive final exam were returned to students for self-evaluation and remediation Among other approaches course rigor was monitored by using an identical set of 60 questions on the final exam across 10 semesters Analysis of the identical sets of 60 final exam questions revealed that overall averages increased from 729 (2010) to 835 (2015) Regression analysis demonstrated a statistically significant correlation between high-risk students and their averages on the 60 questions Additional analysis demonstrated statistically significant improvements for at least one letter grade from midterm to final and a 20 increase in the course pass rates over time also for the high-risk population These results support the hypothesis that our data-driven interventions and assessment techniques are successful in improving student retention particularly for our academically at-risk students
Lecture Biol 1230
bull Competency E4 (chemistry in biology atomic bonds metabolic pathways thermodynamics)
bull Quizzes (formative assessment with Clickers)
bull The coordinator prepares the three lsquoOne hour examsrsquo (questions not from the textbook) instructors again reviewcomment
bull Question types range (content versus applications) and also lsquoBack pagersquo ( 20 of the exam grade) Formative assessment using the LXRtest software (Opscan6 scanner)
Final exam not returned cumulative and has had 60 questions (good discriminators based on the rpbvalues) commonly used on ALL final exams for the past five years Powerful tool for measuring studentsrsquo learning and applications over time and based on academic risk categories
Last Name First Name
Biology 1230 Exam 1 ldquoBack Pagerdquo Score _ 20 pts
I 5 pts Complete the following table for the 3 major components (subatomic particles) of the atom
hint electrical charge = positive negative or neutral and mass = 1 dalton or 11800 dalton 1 pt each
Particle Electrical Charge Mass
1 Proton 1 dalton
2 Electron
3 Neutron
II 5 pts In your own words compare and contrast the following two atoms A and B use the back of the previous page to
make as many observations as you can about similarities (and what they mean) and differences (and what they mean)
between the atoms
A B
III 5 pts Match the following by placing the corresponding in the space provided 1 pt each
_____ tertiary structure 1 produce H2O
_____ two ester linkages 2 is responsible for the 3-dimensional shape of a protein
_____ phosphodiester bonds 3 exist within diglycerides (diacylglyerols) and phospholipids
_____ dehydration synthesis reactions 4 are a type of lipid
_____ steroids 5 are formed when nucleic acids are synthesized
IV 5 pts Circle each of the variable (R) groups in the molecules shown below (3 pts)
a Which lsquoRrsquo group is polar ______ (write the corresponding in the space provided) (1 pt)
b Which lsquoRrsquo group is ionic ______ (write the corresponding in the space provided) (1 pt)
NH3+ OH CH3
1 2 3
12 neutrons
11 protons
10 electrons
13 neutrons
11 protons
11 electrons
Bio1230 Exam 1
Clickers and immediate feedback
Name _____________________________________________________________________________________________
This is a worksheet for your self-evaluation of study habits and exam preparedness Your answers on the corresponding
online exam surveys are confidential
~The average number of hours I spent per week reading the chapters andor reviewingprocessing class notes was (circle the
appropriate response)
zero to one one to two two to four greater than four
~I read the assignment before coming to class (circle the appropriate response)
never sometimes regularly
~I asked my instructor questions when I was confused about textbook material andor lecture material (circle the appropriate
response)
never sometimes regularly
~Overall I spent _____ hours specifically studying for this exam (Please fill in the blank)
~Prior to taking the exam I expected to get an approximate grade of (fill in the blank) _____
~My actual grade was a(n) (fill in the blank) _____
~Check all of the statements that apply to your performance on the exam
____ studied the right information ____ did not study the right information
____ studied the right information but did not ____ studied the right information and
understand it thought I understood it
____ used the class outlines to study ____ thought college would be easier
____ did not know what to study ____ other _____________________
____ did not think I would need to know the information in such detail
Analysis of Missed Questions I answered the question incorrectly because I Insert question number below in the correct category
did not study the information
studied the information but forgot it
did not understand the information in the
summary notes
confused similar concepts or terms (ie
isotopes and isomers)
misread or misunderstood the question
did not consider all of the answer choices
knew the correct answer - but chose an
incorrect answer by mistake
List other reason(s)
List other reason(s)
Please answer additional self-evaluation questions on the back of this page
Self-Evaluation of Study Habits amp Exam Preparedness for Biology 1230 Exam I or II or III (circle one)
Going forwardhellip
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
Zooming ahead to recent yearshelliphellip From 1955 to 2017
MybioSorcecomhttpswwwmybiosourcecom
Product DescriptionProdigiosin is an intensely red pyrrole pigment produced by several bacteria most notably Serratia marcescens Prodigiosin has a broad biological profile with activity against fungi tumor cell lines and malaria It was shown to be an immunosuppressant in 2007 The mode of action of prodigiosin has recently received considerable attention as an inducer of apoptosis in human primary cancer cells via caspase activation Prodigiosin also acts as an inducer of p21WAF1CIP1 expression via transforming growth factor-B receptor pathway and of NAG-1activation by acting on glycogen synthase kinase-3B
Evidence of ldquomath-gaprdquo
bull ACT College Readiness Benchmark
ndash 50 chance of obtaining a B or
better or ~75 chance of obtaining
a C or higher in a corresponding
first-year course
ACT Site
ndash Math = Algebra I
ndash Science = Biology IBased on sample of 214 institutions and gt230000
students from US Benchmarks = median course
placement values and represent a ldquotypicalrdquo set of
expectations
Percent of ACT-Tested High School Graduates Meeting ACT Benchmarks
Pe
rce
nt
Few 12th Grade Students Interested
in STEM and Proficient in Math
Business-Higher Ed Forum Research Brief (2011)Included in 2012 PCAST Appendix E
STEM interested
AND Math Proficient
NOT STEM
interestedMath
ProficientNOT STEM
interested
NOT Math
Proficient
STEM
interested
NOT Math
Proficient
Biological Quantitative Reasoning
Exam (BioSQuaRE) ndash Q6 consortium
BioSQuaRE TeamBiology
Paul Overvoorde (Macalester)
Peter Brodfuehrer Greg Davis (Bryn Mawr)
Charles Umbanhowar (St Olaf)
Marion Preest (Keck Science Center Claremont Colleges)
Steve Adolph Cathy McFadden (Harvey Mudd)
Educational PsychologyStatistics
Andy Zieffler Laure Le (U Minnesota)
Laura Zeigler (Iowa State)
Erik Larson (Macalester)- Sociology
ldquoOtherrdquo
Liz Stanhope (Lewis and Clark) ndash Math
Jason Belitsky (Oberlin) ndash Chemistry
Marcelo Vinces (Oberlin) ndash Quantitative Skills Center
Tabassum Haque (Oberlin) ndash Institutional Research
Alignment of Learning Outcomes
bull 14 + 38 faculty
bull Mapping of learning outcomes with
previous national reports
ndash BIO2010
ndash Vision and Changes
ndash Next Gen Science Standards for Science
and Engineering
ndash Revised AP Biology requirements
ndash Preparing Future Physicians
bull Comparison to previously created
Quantitative Literacy Efforts (eg
QRLA TOSLS)
Mapping Learning Outcomes to National Reports
ContentStudents should
be able to
BIO20
10
Vision
amp
Chang
e
SFFPAP
Bio
NGSS
SampE
Algebra
functions
and
modeling
Carry out basic mathematical
computations (eg proportional reasoning
unit conversion center and variation)
X X X X X
Recognize and use logarithmic or
exponential relationshipsX X
Fit a model such as population growth X X
Use a representation or a model to make
predictionsX X X X X
Describeinfer relationships between
variables (scatterplots regression
network diagrams maps)
X X
Perform logicalalgorithmic reasoning X X X X
Statistics
and
probability
Calculate or use the concept of the
likelihood of an eventX X X
Calculate or use conditional probability X X X
Recognize and interpret what summary
statistics representX X X
Identify different types of error X
Recognize that biological systems are
inherently variable (eg stochastic vs
deterministic)
X X
Formulate hypothesis statements X X X X
Understand what a p-value is X X X X
Understand when causal claims can be
made (eg correlation vs causation)X X X X
Visualizati
on
Choose the appropriate type of graph X X X X X
Interpret a graph (eg functional
relationships logarithmic relationships)X X X X X
Be able to use a table X X X
Use spatial reasoning to interpret
multidimensional numerical and visual
data (geographic information)
X
Stanhope et al (2017) Development of a Biological
Science Quantitative Reasoning Exam (BioSQuaRE)
CBE- Life Science Education Winter edition
December 1 2017
bull identification and validation of learning domains
bull iterative development of BioSQuaRE Instrument
bull evidence of validity
bull discussion of instruments utility for students individual
faculty and departments or programs
Visit wwwmacalestereduhhmibiosquare for more information
BLASTing Human and Other Organisms
bull Our goal is to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus(snake) The objective is to find and precisely map the coding regions using NCBIrsquos BLASTp search tool
bull Answer the following questions for each of the 4 organisms1 Describe the summary distributions2 Interpret the score the percent identity and the E-value If
obtain hit(s) are they likely due to chance If no hits why3 Analyze the alignments
Describe these Summary Distributions
Chimp
Cow
Snake
Chicken
Interpret the Scores E-values and Identities
Chimp
Cow
Snake
Chicken
Analyze the Alignments
Chimp
Cow
Snake
Chicken
Additional Questions of Interest
bull Our goal was to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus (snake) The objective is to find and precisely map the coding regions
bull Answer the following questions1 This presentation is showing only highly significant pairs How
do you think the alignments (scores e-values identities) differ if we analyze low significant pairs
2 Can you infer that this protein does not exist in this organism3 Give alternative explanations for the differences in scores e-
values and identities4 Is there an evolutionary relationship between sequences
Am J Hum Genet 2008 Dec 12 83(6) 769ndash780 Published online 2008 Dec 5 doi 101016jajhg200811004
Ribosomal Protein L5 and L11 Mutations Are Associated with Cleft Palate and Abnormal Thumbs in Diamond-Blackfan Anemia Patients
Hanna T Gazda12lowast
Mee Rie Sheen1
Adrianna Vlachos34
Valerie Choesmel56
Marie-Franccediloise ODonohue
56Hal Schneider
1Natasha Darras
1Catherine Hasman
1Colin A
Sieff27
Peter E Newburger8
Sarah E Ball9
Edyta Niewiadomska10
Michal Matysiak10
Jan M Zaucha
11Bertil Glader
12Charlotte Niemeyer
13Joerg J Meerpohl
13Eva Atsidaftos
34Jeffrey
M Lipton34
Pierre-Emmanuel Gleizes56
and Alan H Beggs12
Author information Article notes Copyright and License information AbstractDiamond-Blackfan anemia (DBA) a congenital bone-marrow-failure syndrome is characterized by red blood cell aplasia macrocytic anemia clinical heterogeneity and increased risk of malignancy Although anemia is the most prominent feature of DBA the disease is also characterized by growth retardation and congenital anomalies that are present in sim30ndash50 of patients The disease has been associated with mutations in four ribosomal protein (RP) genes RPS19 RPS24 RPS17 and RPL35A in about 30 of patients However the genetic basis of the remaining 70 of cases is still unknown Here we report the second known mutation in RPS17 and probable pathogenic mutations in three more RP genes RPL5 RPL11 and RPS7 In addition we identified rare variants of unknown significance in three other genes RPL36 RPS15 and RPS27A Remarkably careful review of the clinical data showed that mutations in RPL5 are associated with multiple physical abnormalities including craniofacial thumb and heart anomalies whereas isolated thumb malformations are predominantly present in patients carrying mutations in RPL11 We also demonstrate that mutations of RPL5 RPL11 or RPS7 in DBA cells is associated with diverse defects in the maturation of ribosomal RNAs in the large or the small ribosomal subunit production pathway expanding the repertoire of ribosomal RNA processing defects associated with DBA
Develop more inquiry-based lab exercises1 C elegans crosses (Peter Barrett in Genetics lab)
2 Modifications on DNA transformation and lac operon exercises (PB)
3 The lsquotermitersquo experiment in Biol 1230L (Kristal Huggins and SKI)
4 In Cell Biology lab C elegans (endocytosis experiments) experiments with Planaria regeneration (adapted from MITHHMI) and recently with Daphnia (the water flea a small crustacean) adapted from the Nuffield Foundation where students expose the Daphnia to various cardioactive compounds measure changes in heart rate caused by effects on cellular receptors and design follow-up experiments (PB)
Assessment Strategies for Project Scicomp
Formative and summative
General scheme
bull Assessment tasks based on objectives
bull Develop assessment tools and pilot for validation
bull Apply to larger audience
bull Collect and score
bull Share and analyze data
Coordinated course sequences and our curricular design serve as a good platform
for intra and interdepartmental discussions
(weekly meetings lsquoSERGrsquo etc)
Labs
bull General observation on student participationinitiative
bull Data sheets (say 10 collecthellipsay any 4)
bull Midterm skills practical stations and multiple choice (excellent determinant)
bull Quizzes (5-10 depending on the lab)
bull Final exams
Course based research experiencee(CRE)
bull How they design their experiment
bull Notebooks lab techniques
bull Participation in class discussions
bull Ability to troubleshoot
bull Midterm Skills and oral exam along with traditional exam
bull Short answer (non multiple choice) questions
bull Research paper presentations
CREs at Xavier
bull Phage and Genomics
bull lsquoUndergraduate Researchrsquo for credits
bull Introduction to Mammalian Tissue Culture
The SEA-PHAGES ProgramhttpsseaphagesorgThe official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program
SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is a two-semester discovery-based undergraduate research course that begins with simple digging in the soil to find new viruses but progresses through a variety of microbiology techniques and eventually to complex genome annotation and bioinformatic analyses
CBE Life Sci Educ 2016 fall15(3) pii ar38 doi 101187cbe16-01-0078Increasing URM Undergraduate Student Success through Assessment-Driven Interventions A Multiyear Study Using Freshman-Level General Biology as a Model SystemCarmichael MC1 St Clair C1 Edwards AM2 Barrett P1 McFerrin H1 Davenport I1 Awad M1 Kundu A1 Ireland SK3
AbstractXavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students In this multiyear study with sim5500 participants data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course The three hour-long exams were common and administered concurrently to all students New exam questions were developed using Blooms taxonomy and exam results were analyzed statistically with validated assessment tools All but the comprehensive final exam were returned to students for self-evaluation and remediation Among other approaches course rigor was monitored by using an identical set of 60 questions on the final exam across 10 semesters Analysis of the identical sets of 60 final exam questions revealed that overall averages increased from 729 (2010) to 835 (2015) Regression analysis demonstrated a statistically significant correlation between high-risk students and their averages on the 60 questions Additional analysis demonstrated statistically significant improvements for at least one letter grade from midterm to final and a 20 increase in the course pass rates over time also for the high-risk population These results support the hypothesis that our data-driven interventions and assessment techniques are successful in improving student retention particularly for our academically at-risk students
Lecture Biol 1230
bull Competency E4 (chemistry in biology atomic bonds metabolic pathways thermodynamics)
bull Quizzes (formative assessment with Clickers)
bull The coordinator prepares the three lsquoOne hour examsrsquo (questions not from the textbook) instructors again reviewcomment
bull Question types range (content versus applications) and also lsquoBack pagersquo ( 20 of the exam grade) Formative assessment using the LXRtest software (Opscan6 scanner)
Final exam not returned cumulative and has had 60 questions (good discriminators based on the rpbvalues) commonly used on ALL final exams for the past five years Powerful tool for measuring studentsrsquo learning and applications over time and based on academic risk categories
Last Name First Name
Biology 1230 Exam 1 ldquoBack Pagerdquo Score _ 20 pts
I 5 pts Complete the following table for the 3 major components (subatomic particles) of the atom
hint electrical charge = positive negative or neutral and mass = 1 dalton or 11800 dalton 1 pt each
Particle Electrical Charge Mass
1 Proton 1 dalton
2 Electron
3 Neutron
II 5 pts In your own words compare and contrast the following two atoms A and B use the back of the previous page to
make as many observations as you can about similarities (and what they mean) and differences (and what they mean)
between the atoms
A B
III 5 pts Match the following by placing the corresponding in the space provided 1 pt each
_____ tertiary structure 1 produce H2O
_____ two ester linkages 2 is responsible for the 3-dimensional shape of a protein
_____ phosphodiester bonds 3 exist within diglycerides (diacylglyerols) and phospholipids
_____ dehydration synthesis reactions 4 are a type of lipid
_____ steroids 5 are formed when nucleic acids are synthesized
IV 5 pts Circle each of the variable (R) groups in the molecules shown below (3 pts)
a Which lsquoRrsquo group is polar ______ (write the corresponding in the space provided) (1 pt)
b Which lsquoRrsquo group is ionic ______ (write the corresponding in the space provided) (1 pt)
NH3+ OH CH3
1 2 3
12 neutrons
11 protons
10 electrons
13 neutrons
11 protons
11 electrons
Bio1230 Exam 1
Clickers and immediate feedback
Name _____________________________________________________________________________________________
This is a worksheet for your self-evaluation of study habits and exam preparedness Your answers on the corresponding
online exam surveys are confidential
~The average number of hours I spent per week reading the chapters andor reviewingprocessing class notes was (circle the
appropriate response)
zero to one one to two two to four greater than four
~I read the assignment before coming to class (circle the appropriate response)
never sometimes regularly
~I asked my instructor questions when I was confused about textbook material andor lecture material (circle the appropriate
response)
never sometimes regularly
~Overall I spent _____ hours specifically studying for this exam (Please fill in the blank)
~Prior to taking the exam I expected to get an approximate grade of (fill in the blank) _____
~My actual grade was a(n) (fill in the blank) _____
~Check all of the statements that apply to your performance on the exam
____ studied the right information ____ did not study the right information
____ studied the right information but did not ____ studied the right information and
understand it thought I understood it
____ used the class outlines to study ____ thought college would be easier
____ did not know what to study ____ other _____________________
____ did not think I would need to know the information in such detail
Analysis of Missed Questions I answered the question incorrectly because I Insert question number below in the correct category
did not study the information
studied the information but forgot it
did not understand the information in the
summary notes
confused similar concepts or terms (ie
isotopes and isomers)
misread or misunderstood the question
did not consider all of the answer choices
knew the correct answer - but chose an
incorrect answer by mistake
List other reason(s)
List other reason(s)
Please answer additional self-evaluation questions on the back of this page
Self-Evaluation of Study Habits amp Exam Preparedness for Biology 1230 Exam I or II or III (circle one)
Going forwardhellip
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
Evidence of ldquomath-gaprdquo
bull ACT College Readiness Benchmark
ndash 50 chance of obtaining a B or
better or ~75 chance of obtaining
a C or higher in a corresponding
first-year course
ACT Site
ndash Math = Algebra I
ndash Science = Biology IBased on sample of 214 institutions and gt230000
students from US Benchmarks = median course
placement values and represent a ldquotypicalrdquo set of
expectations
Percent of ACT-Tested High School Graduates Meeting ACT Benchmarks
Pe
rce
nt
Few 12th Grade Students Interested
in STEM and Proficient in Math
Business-Higher Ed Forum Research Brief (2011)Included in 2012 PCAST Appendix E
STEM interested
AND Math Proficient
NOT STEM
interestedMath
ProficientNOT STEM
interested
NOT Math
Proficient
STEM
interested
NOT Math
Proficient
Biological Quantitative Reasoning
Exam (BioSQuaRE) ndash Q6 consortium
BioSQuaRE TeamBiology
Paul Overvoorde (Macalester)
Peter Brodfuehrer Greg Davis (Bryn Mawr)
Charles Umbanhowar (St Olaf)
Marion Preest (Keck Science Center Claremont Colleges)
Steve Adolph Cathy McFadden (Harvey Mudd)
Educational PsychologyStatistics
Andy Zieffler Laure Le (U Minnesota)
Laura Zeigler (Iowa State)
Erik Larson (Macalester)- Sociology
ldquoOtherrdquo
Liz Stanhope (Lewis and Clark) ndash Math
Jason Belitsky (Oberlin) ndash Chemistry
Marcelo Vinces (Oberlin) ndash Quantitative Skills Center
Tabassum Haque (Oberlin) ndash Institutional Research
Alignment of Learning Outcomes
bull 14 + 38 faculty
bull Mapping of learning outcomes with
previous national reports
ndash BIO2010
ndash Vision and Changes
ndash Next Gen Science Standards for Science
and Engineering
ndash Revised AP Biology requirements
ndash Preparing Future Physicians
bull Comparison to previously created
Quantitative Literacy Efforts (eg
QRLA TOSLS)
Mapping Learning Outcomes to National Reports
ContentStudents should
be able to
BIO20
10
Vision
amp
Chang
e
SFFPAP
Bio
NGSS
SampE
Algebra
functions
and
modeling
Carry out basic mathematical
computations (eg proportional reasoning
unit conversion center and variation)
X X X X X
Recognize and use logarithmic or
exponential relationshipsX X
Fit a model such as population growth X X
Use a representation or a model to make
predictionsX X X X X
Describeinfer relationships between
variables (scatterplots regression
network diagrams maps)
X X
Perform logicalalgorithmic reasoning X X X X
Statistics
and
probability
Calculate or use the concept of the
likelihood of an eventX X X
Calculate or use conditional probability X X X
Recognize and interpret what summary
statistics representX X X
Identify different types of error X
Recognize that biological systems are
inherently variable (eg stochastic vs
deterministic)
X X
Formulate hypothesis statements X X X X
Understand what a p-value is X X X X
Understand when causal claims can be
made (eg correlation vs causation)X X X X
Visualizati
on
Choose the appropriate type of graph X X X X X
Interpret a graph (eg functional
relationships logarithmic relationships)X X X X X
Be able to use a table X X X
Use spatial reasoning to interpret
multidimensional numerical and visual
data (geographic information)
X
Stanhope et al (2017) Development of a Biological
Science Quantitative Reasoning Exam (BioSQuaRE)
CBE- Life Science Education Winter edition
December 1 2017
bull identification and validation of learning domains
bull iterative development of BioSQuaRE Instrument
bull evidence of validity
bull discussion of instruments utility for students individual
faculty and departments or programs
Visit wwwmacalestereduhhmibiosquare for more information
BLASTing Human and Other Organisms
bull Our goal is to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus(snake) The objective is to find and precisely map the coding regions using NCBIrsquos BLASTp search tool
bull Answer the following questions for each of the 4 organisms1 Describe the summary distributions2 Interpret the score the percent identity and the E-value If
obtain hit(s) are they likely due to chance If no hits why3 Analyze the alignments
Describe these Summary Distributions
Chimp
Cow
Snake
Chicken
Interpret the Scores E-values and Identities
Chimp
Cow
Snake
Chicken
Analyze the Alignments
Chimp
Cow
Snake
Chicken
Additional Questions of Interest
bull Our goal was to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus (snake) The objective is to find and precisely map the coding regions
bull Answer the following questions1 This presentation is showing only highly significant pairs How
do you think the alignments (scores e-values identities) differ if we analyze low significant pairs
2 Can you infer that this protein does not exist in this organism3 Give alternative explanations for the differences in scores e-
values and identities4 Is there an evolutionary relationship between sequences
Am J Hum Genet 2008 Dec 12 83(6) 769ndash780 Published online 2008 Dec 5 doi 101016jajhg200811004
Ribosomal Protein L5 and L11 Mutations Are Associated with Cleft Palate and Abnormal Thumbs in Diamond-Blackfan Anemia Patients
Hanna T Gazda12lowast
Mee Rie Sheen1
Adrianna Vlachos34
Valerie Choesmel56
Marie-Franccediloise ODonohue
56Hal Schneider
1Natasha Darras
1Catherine Hasman
1Colin A
Sieff27
Peter E Newburger8
Sarah E Ball9
Edyta Niewiadomska10
Michal Matysiak10
Jan M Zaucha
11Bertil Glader
12Charlotte Niemeyer
13Joerg J Meerpohl
13Eva Atsidaftos
34Jeffrey
M Lipton34
Pierre-Emmanuel Gleizes56
and Alan H Beggs12
Author information Article notes Copyright and License information AbstractDiamond-Blackfan anemia (DBA) a congenital bone-marrow-failure syndrome is characterized by red blood cell aplasia macrocytic anemia clinical heterogeneity and increased risk of malignancy Although anemia is the most prominent feature of DBA the disease is also characterized by growth retardation and congenital anomalies that are present in sim30ndash50 of patients The disease has been associated with mutations in four ribosomal protein (RP) genes RPS19 RPS24 RPS17 and RPL35A in about 30 of patients However the genetic basis of the remaining 70 of cases is still unknown Here we report the second known mutation in RPS17 and probable pathogenic mutations in three more RP genes RPL5 RPL11 and RPS7 In addition we identified rare variants of unknown significance in three other genes RPL36 RPS15 and RPS27A Remarkably careful review of the clinical data showed that mutations in RPL5 are associated with multiple physical abnormalities including craniofacial thumb and heart anomalies whereas isolated thumb malformations are predominantly present in patients carrying mutations in RPL11 We also demonstrate that mutations of RPL5 RPL11 or RPS7 in DBA cells is associated with diverse defects in the maturation of ribosomal RNAs in the large or the small ribosomal subunit production pathway expanding the repertoire of ribosomal RNA processing defects associated with DBA
Develop more inquiry-based lab exercises1 C elegans crosses (Peter Barrett in Genetics lab)
2 Modifications on DNA transformation and lac operon exercises (PB)
3 The lsquotermitersquo experiment in Biol 1230L (Kristal Huggins and SKI)
4 In Cell Biology lab C elegans (endocytosis experiments) experiments with Planaria regeneration (adapted from MITHHMI) and recently with Daphnia (the water flea a small crustacean) adapted from the Nuffield Foundation where students expose the Daphnia to various cardioactive compounds measure changes in heart rate caused by effects on cellular receptors and design follow-up experiments (PB)
Assessment Strategies for Project Scicomp
Formative and summative
General scheme
bull Assessment tasks based on objectives
bull Develop assessment tools and pilot for validation
bull Apply to larger audience
bull Collect and score
bull Share and analyze data
Coordinated course sequences and our curricular design serve as a good platform
for intra and interdepartmental discussions
(weekly meetings lsquoSERGrsquo etc)
Labs
bull General observation on student participationinitiative
bull Data sheets (say 10 collecthellipsay any 4)
bull Midterm skills practical stations and multiple choice (excellent determinant)
bull Quizzes (5-10 depending on the lab)
bull Final exams
Course based research experiencee(CRE)
bull How they design their experiment
bull Notebooks lab techniques
bull Participation in class discussions
bull Ability to troubleshoot
bull Midterm Skills and oral exam along with traditional exam
bull Short answer (non multiple choice) questions
bull Research paper presentations
CREs at Xavier
bull Phage and Genomics
bull lsquoUndergraduate Researchrsquo for credits
bull Introduction to Mammalian Tissue Culture
The SEA-PHAGES ProgramhttpsseaphagesorgThe official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program
SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is a two-semester discovery-based undergraduate research course that begins with simple digging in the soil to find new viruses but progresses through a variety of microbiology techniques and eventually to complex genome annotation and bioinformatic analyses
CBE Life Sci Educ 2016 fall15(3) pii ar38 doi 101187cbe16-01-0078Increasing URM Undergraduate Student Success through Assessment-Driven Interventions A Multiyear Study Using Freshman-Level General Biology as a Model SystemCarmichael MC1 St Clair C1 Edwards AM2 Barrett P1 McFerrin H1 Davenport I1 Awad M1 Kundu A1 Ireland SK3
AbstractXavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students In this multiyear study with sim5500 participants data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course The three hour-long exams were common and administered concurrently to all students New exam questions were developed using Blooms taxonomy and exam results were analyzed statistically with validated assessment tools All but the comprehensive final exam were returned to students for self-evaluation and remediation Among other approaches course rigor was monitored by using an identical set of 60 questions on the final exam across 10 semesters Analysis of the identical sets of 60 final exam questions revealed that overall averages increased from 729 (2010) to 835 (2015) Regression analysis demonstrated a statistically significant correlation between high-risk students and their averages on the 60 questions Additional analysis demonstrated statistically significant improvements for at least one letter grade from midterm to final and a 20 increase in the course pass rates over time also for the high-risk population These results support the hypothesis that our data-driven interventions and assessment techniques are successful in improving student retention particularly for our academically at-risk students
Lecture Biol 1230
bull Competency E4 (chemistry in biology atomic bonds metabolic pathways thermodynamics)
bull Quizzes (formative assessment with Clickers)
bull The coordinator prepares the three lsquoOne hour examsrsquo (questions not from the textbook) instructors again reviewcomment
bull Question types range (content versus applications) and also lsquoBack pagersquo ( 20 of the exam grade) Formative assessment using the LXRtest software (Opscan6 scanner)
Final exam not returned cumulative and has had 60 questions (good discriminators based on the rpbvalues) commonly used on ALL final exams for the past five years Powerful tool for measuring studentsrsquo learning and applications over time and based on academic risk categories
Last Name First Name
Biology 1230 Exam 1 ldquoBack Pagerdquo Score _ 20 pts
I 5 pts Complete the following table for the 3 major components (subatomic particles) of the atom
hint electrical charge = positive negative or neutral and mass = 1 dalton or 11800 dalton 1 pt each
Particle Electrical Charge Mass
1 Proton 1 dalton
2 Electron
3 Neutron
II 5 pts In your own words compare and contrast the following two atoms A and B use the back of the previous page to
make as many observations as you can about similarities (and what they mean) and differences (and what they mean)
between the atoms
A B
III 5 pts Match the following by placing the corresponding in the space provided 1 pt each
_____ tertiary structure 1 produce H2O
_____ two ester linkages 2 is responsible for the 3-dimensional shape of a protein
_____ phosphodiester bonds 3 exist within diglycerides (diacylglyerols) and phospholipids
_____ dehydration synthesis reactions 4 are a type of lipid
_____ steroids 5 are formed when nucleic acids are synthesized
IV 5 pts Circle each of the variable (R) groups in the molecules shown below (3 pts)
a Which lsquoRrsquo group is polar ______ (write the corresponding in the space provided) (1 pt)
b Which lsquoRrsquo group is ionic ______ (write the corresponding in the space provided) (1 pt)
NH3+ OH CH3
1 2 3
12 neutrons
11 protons
10 electrons
13 neutrons
11 protons
11 electrons
Bio1230 Exam 1
Clickers and immediate feedback
Name _____________________________________________________________________________________________
This is a worksheet for your self-evaluation of study habits and exam preparedness Your answers on the corresponding
online exam surveys are confidential
~The average number of hours I spent per week reading the chapters andor reviewingprocessing class notes was (circle the
appropriate response)
zero to one one to two two to four greater than four
~I read the assignment before coming to class (circle the appropriate response)
never sometimes regularly
~I asked my instructor questions when I was confused about textbook material andor lecture material (circle the appropriate
response)
never sometimes regularly
~Overall I spent _____ hours specifically studying for this exam (Please fill in the blank)
~Prior to taking the exam I expected to get an approximate grade of (fill in the blank) _____
~My actual grade was a(n) (fill in the blank) _____
~Check all of the statements that apply to your performance on the exam
____ studied the right information ____ did not study the right information
____ studied the right information but did not ____ studied the right information and
understand it thought I understood it
____ used the class outlines to study ____ thought college would be easier
____ did not know what to study ____ other _____________________
____ did not think I would need to know the information in such detail
Analysis of Missed Questions I answered the question incorrectly because I Insert question number below in the correct category
did not study the information
studied the information but forgot it
did not understand the information in the
summary notes
confused similar concepts or terms (ie
isotopes and isomers)
misread or misunderstood the question
did not consider all of the answer choices
knew the correct answer - but chose an
incorrect answer by mistake
List other reason(s)
List other reason(s)
Please answer additional self-evaluation questions on the back of this page
Self-Evaluation of Study Habits amp Exam Preparedness for Biology 1230 Exam I or II or III (circle one)
Going forwardhellip
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
Percent of ACT-Tested High School Graduates Meeting ACT Benchmarks
Pe
rce
nt
Few 12th Grade Students Interested
in STEM and Proficient in Math
Business-Higher Ed Forum Research Brief (2011)Included in 2012 PCAST Appendix E
STEM interested
AND Math Proficient
NOT STEM
interestedMath
ProficientNOT STEM
interested
NOT Math
Proficient
STEM
interested
NOT Math
Proficient
Biological Quantitative Reasoning
Exam (BioSQuaRE) ndash Q6 consortium
BioSQuaRE TeamBiology
Paul Overvoorde (Macalester)
Peter Brodfuehrer Greg Davis (Bryn Mawr)
Charles Umbanhowar (St Olaf)
Marion Preest (Keck Science Center Claremont Colleges)
Steve Adolph Cathy McFadden (Harvey Mudd)
Educational PsychologyStatistics
Andy Zieffler Laure Le (U Minnesota)
Laura Zeigler (Iowa State)
Erik Larson (Macalester)- Sociology
ldquoOtherrdquo
Liz Stanhope (Lewis and Clark) ndash Math
Jason Belitsky (Oberlin) ndash Chemistry
Marcelo Vinces (Oberlin) ndash Quantitative Skills Center
Tabassum Haque (Oberlin) ndash Institutional Research
Alignment of Learning Outcomes
bull 14 + 38 faculty
bull Mapping of learning outcomes with
previous national reports
ndash BIO2010
ndash Vision and Changes
ndash Next Gen Science Standards for Science
and Engineering
ndash Revised AP Biology requirements
ndash Preparing Future Physicians
bull Comparison to previously created
Quantitative Literacy Efforts (eg
QRLA TOSLS)
Mapping Learning Outcomes to National Reports
ContentStudents should
be able to
BIO20
10
Vision
amp
Chang
e
SFFPAP
Bio
NGSS
SampE
Algebra
functions
and
modeling
Carry out basic mathematical
computations (eg proportional reasoning
unit conversion center and variation)
X X X X X
Recognize and use logarithmic or
exponential relationshipsX X
Fit a model such as population growth X X
Use a representation or a model to make
predictionsX X X X X
Describeinfer relationships between
variables (scatterplots regression
network diagrams maps)
X X
Perform logicalalgorithmic reasoning X X X X
Statistics
and
probability
Calculate or use the concept of the
likelihood of an eventX X X
Calculate or use conditional probability X X X
Recognize and interpret what summary
statistics representX X X
Identify different types of error X
Recognize that biological systems are
inherently variable (eg stochastic vs
deterministic)
X X
Formulate hypothesis statements X X X X
Understand what a p-value is X X X X
Understand when causal claims can be
made (eg correlation vs causation)X X X X
Visualizati
on
Choose the appropriate type of graph X X X X X
Interpret a graph (eg functional
relationships logarithmic relationships)X X X X X
Be able to use a table X X X
Use spatial reasoning to interpret
multidimensional numerical and visual
data (geographic information)
X
Stanhope et al (2017) Development of a Biological
Science Quantitative Reasoning Exam (BioSQuaRE)
CBE- Life Science Education Winter edition
December 1 2017
bull identification and validation of learning domains
bull iterative development of BioSQuaRE Instrument
bull evidence of validity
bull discussion of instruments utility for students individual
faculty and departments or programs
Visit wwwmacalestereduhhmibiosquare for more information
BLASTing Human and Other Organisms
bull Our goal is to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus(snake) The objective is to find and precisely map the coding regions using NCBIrsquos BLASTp search tool
bull Answer the following questions for each of the 4 organisms1 Describe the summary distributions2 Interpret the score the percent identity and the E-value If
obtain hit(s) are they likely due to chance If no hits why3 Analyze the alignments
Describe these Summary Distributions
Chimp
Cow
Snake
Chicken
Interpret the Scores E-values and Identities
Chimp
Cow
Snake
Chicken
Analyze the Alignments
Chimp
Cow
Snake
Chicken
Additional Questions of Interest
bull Our goal was to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus (snake) The objective is to find and precisely map the coding regions
bull Answer the following questions1 This presentation is showing only highly significant pairs How
do you think the alignments (scores e-values identities) differ if we analyze low significant pairs
2 Can you infer that this protein does not exist in this organism3 Give alternative explanations for the differences in scores e-
values and identities4 Is there an evolutionary relationship between sequences
Am J Hum Genet 2008 Dec 12 83(6) 769ndash780 Published online 2008 Dec 5 doi 101016jajhg200811004
Ribosomal Protein L5 and L11 Mutations Are Associated with Cleft Palate and Abnormal Thumbs in Diamond-Blackfan Anemia Patients
Hanna T Gazda12lowast
Mee Rie Sheen1
Adrianna Vlachos34
Valerie Choesmel56
Marie-Franccediloise ODonohue
56Hal Schneider
1Natasha Darras
1Catherine Hasman
1Colin A
Sieff27
Peter E Newburger8
Sarah E Ball9
Edyta Niewiadomska10
Michal Matysiak10
Jan M Zaucha
11Bertil Glader
12Charlotte Niemeyer
13Joerg J Meerpohl
13Eva Atsidaftos
34Jeffrey
M Lipton34
Pierre-Emmanuel Gleizes56
and Alan H Beggs12
Author information Article notes Copyright and License information AbstractDiamond-Blackfan anemia (DBA) a congenital bone-marrow-failure syndrome is characterized by red blood cell aplasia macrocytic anemia clinical heterogeneity and increased risk of malignancy Although anemia is the most prominent feature of DBA the disease is also characterized by growth retardation and congenital anomalies that are present in sim30ndash50 of patients The disease has been associated with mutations in four ribosomal protein (RP) genes RPS19 RPS24 RPS17 and RPL35A in about 30 of patients However the genetic basis of the remaining 70 of cases is still unknown Here we report the second known mutation in RPS17 and probable pathogenic mutations in three more RP genes RPL5 RPL11 and RPS7 In addition we identified rare variants of unknown significance in three other genes RPL36 RPS15 and RPS27A Remarkably careful review of the clinical data showed that mutations in RPL5 are associated with multiple physical abnormalities including craniofacial thumb and heart anomalies whereas isolated thumb malformations are predominantly present in patients carrying mutations in RPL11 We also demonstrate that mutations of RPL5 RPL11 or RPS7 in DBA cells is associated with diverse defects in the maturation of ribosomal RNAs in the large or the small ribosomal subunit production pathway expanding the repertoire of ribosomal RNA processing defects associated with DBA
Develop more inquiry-based lab exercises1 C elegans crosses (Peter Barrett in Genetics lab)
2 Modifications on DNA transformation and lac operon exercises (PB)
3 The lsquotermitersquo experiment in Biol 1230L (Kristal Huggins and SKI)
4 In Cell Biology lab C elegans (endocytosis experiments) experiments with Planaria regeneration (adapted from MITHHMI) and recently with Daphnia (the water flea a small crustacean) adapted from the Nuffield Foundation where students expose the Daphnia to various cardioactive compounds measure changes in heart rate caused by effects on cellular receptors and design follow-up experiments (PB)
Assessment Strategies for Project Scicomp
Formative and summative
General scheme
bull Assessment tasks based on objectives
bull Develop assessment tools and pilot for validation
bull Apply to larger audience
bull Collect and score
bull Share and analyze data
Coordinated course sequences and our curricular design serve as a good platform
for intra and interdepartmental discussions
(weekly meetings lsquoSERGrsquo etc)
Labs
bull General observation on student participationinitiative
bull Data sheets (say 10 collecthellipsay any 4)
bull Midterm skills practical stations and multiple choice (excellent determinant)
bull Quizzes (5-10 depending on the lab)
bull Final exams
Course based research experiencee(CRE)
bull How they design their experiment
bull Notebooks lab techniques
bull Participation in class discussions
bull Ability to troubleshoot
bull Midterm Skills and oral exam along with traditional exam
bull Short answer (non multiple choice) questions
bull Research paper presentations
CREs at Xavier
bull Phage and Genomics
bull lsquoUndergraduate Researchrsquo for credits
bull Introduction to Mammalian Tissue Culture
The SEA-PHAGES ProgramhttpsseaphagesorgThe official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program
SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is a two-semester discovery-based undergraduate research course that begins with simple digging in the soil to find new viruses but progresses through a variety of microbiology techniques and eventually to complex genome annotation and bioinformatic analyses
CBE Life Sci Educ 2016 fall15(3) pii ar38 doi 101187cbe16-01-0078Increasing URM Undergraduate Student Success through Assessment-Driven Interventions A Multiyear Study Using Freshman-Level General Biology as a Model SystemCarmichael MC1 St Clair C1 Edwards AM2 Barrett P1 McFerrin H1 Davenport I1 Awad M1 Kundu A1 Ireland SK3
AbstractXavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students In this multiyear study with sim5500 participants data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course The three hour-long exams were common and administered concurrently to all students New exam questions were developed using Blooms taxonomy and exam results were analyzed statistically with validated assessment tools All but the comprehensive final exam were returned to students for self-evaluation and remediation Among other approaches course rigor was monitored by using an identical set of 60 questions on the final exam across 10 semesters Analysis of the identical sets of 60 final exam questions revealed that overall averages increased from 729 (2010) to 835 (2015) Regression analysis demonstrated a statistically significant correlation between high-risk students and their averages on the 60 questions Additional analysis demonstrated statistically significant improvements for at least one letter grade from midterm to final and a 20 increase in the course pass rates over time also for the high-risk population These results support the hypothesis that our data-driven interventions and assessment techniques are successful in improving student retention particularly for our academically at-risk students
Lecture Biol 1230
bull Competency E4 (chemistry in biology atomic bonds metabolic pathways thermodynamics)
bull Quizzes (formative assessment with Clickers)
bull The coordinator prepares the three lsquoOne hour examsrsquo (questions not from the textbook) instructors again reviewcomment
bull Question types range (content versus applications) and also lsquoBack pagersquo ( 20 of the exam grade) Formative assessment using the LXRtest software (Opscan6 scanner)
Final exam not returned cumulative and has had 60 questions (good discriminators based on the rpbvalues) commonly used on ALL final exams for the past five years Powerful tool for measuring studentsrsquo learning and applications over time and based on academic risk categories
Last Name First Name
Biology 1230 Exam 1 ldquoBack Pagerdquo Score _ 20 pts
I 5 pts Complete the following table for the 3 major components (subatomic particles) of the atom
hint electrical charge = positive negative or neutral and mass = 1 dalton or 11800 dalton 1 pt each
Particle Electrical Charge Mass
1 Proton 1 dalton
2 Electron
3 Neutron
II 5 pts In your own words compare and contrast the following two atoms A and B use the back of the previous page to
make as many observations as you can about similarities (and what they mean) and differences (and what they mean)
between the atoms
A B
III 5 pts Match the following by placing the corresponding in the space provided 1 pt each
_____ tertiary structure 1 produce H2O
_____ two ester linkages 2 is responsible for the 3-dimensional shape of a protein
_____ phosphodiester bonds 3 exist within diglycerides (diacylglyerols) and phospholipids
_____ dehydration synthesis reactions 4 are a type of lipid
_____ steroids 5 are formed when nucleic acids are synthesized
IV 5 pts Circle each of the variable (R) groups in the molecules shown below (3 pts)
a Which lsquoRrsquo group is polar ______ (write the corresponding in the space provided) (1 pt)
b Which lsquoRrsquo group is ionic ______ (write the corresponding in the space provided) (1 pt)
NH3+ OH CH3
1 2 3
12 neutrons
11 protons
10 electrons
13 neutrons
11 protons
11 electrons
Bio1230 Exam 1
Clickers and immediate feedback
Name _____________________________________________________________________________________________
This is a worksheet for your self-evaluation of study habits and exam preparedness Your answers on the corresponding
online exam surveys are confidential
~The average number of hours I spent per week reading the chapters andor reviewingprocessing class notes was (circle the
appropriate response)
zero to one one to two two to four greater than four
~I read the assignment before coming to class (circle the appropriate response)
never sometimes regularly
~I asked my instructor questions when I was confused about textbook material andor lecture material (circle the appropriate
response)
never sometimes regularly
~Overall I spent _____ hours specifically studying for this exam (Please fill in the blank)
~Prior to taking the exam I expected to get an approximate grade of (fill in the blank) _____
~My actual grade was a(n) (fill in the blank) _____
~Check all of the statements that apply to your performance on the exam
____ studied the right information ____ did not study the right information
____ studied the right information but did not ____ studied the right information and
understand it thought I understood it
____ used the class outlines to study ____ thought college would be easier
____ did not know what to study ____ other _____________________
____ did not think I would need to know the information in such detail
Analysis of Missed Questions I answered the question incorrectly because I Insert question number below in the correct category
did not study the information
studied the information but forgot it
did not understand the information in the
summary notes
confused similar concepts or terms (ie
isotopes and isomers)
misread or misunderstood the question
did not consider all of the answer choices
knew the correct answer - but chose an
incorrect answer by mistake
List other reason(s)
List other reason(s)
Please answer additional self-evaluation questions on the back of this page
Self-Evaluation of Study Habits amp Exam Preparedness for Biology 1230 Exam I or II or III (circle one)
Going forwardhellip
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
Few 12th Grade Students Interested
in STEM and Proficient in Math
Business-Higher Ed Forum Research Brief (2011)Included in 2012 PCAST Appendix E
STEM interested
AND Math Proficient
NOT STEM
interestedMath
ProficientNOT STEM
interested
NOT Math
Proficient
STEM
interested
NOT Math
Proficient
Biological Quantitative Reasoning
Exam (BioSQuaRE) ndash Q6 consortium
BioSQuaRE TeamBiology
Paul Overvoorde (Macalester)
Peter Brodfuehrer Greg Davis (Bryn Mawr)
Charles Umbanhowar (St Olaf)
Marion Preest (Keck Science Center Claremont Colleges)
Steve Adolph Cathy McFadden (Harvey Mudd)
Educational PsychologyStatistics
Andy Zieffler Laure Le (U Minnesota)
Laura Zeigler (Iowa State)
Erik Larson (Macalester)- Sociology
ldquoOtherrdquo
Liz Stanhope (Lewis and Clark) ndash Math
Jason Belitsky (Oberlin) ndash Chemistry
Marcelo Vinces (Oberlin) ndash Quantitative Skills Center
Tabassum Haque (Oberlin) ndash Institutional Research
Alignment of Learning Outcomes
bull 14 + 38 faculty
bull Mapping of learning outcomes with
previous national reports
ndash BIO2010
ndash Vision and Changes
ndash Next Gen Science Standards for Science
and Engineering
ndash Revised AP Biology requirements
ndash Preparing Future Physicians
bull Comparison to previously created
Quantitative Literacy Efforts (eg
QRLA TOSLS)
Mapping Learning Outcomes to National Reports
ContentStudents should
be able to
BIO20
10
Vision
amp
Chang
e
SFFPAP
Bio
NGSS
SampE
Algebra
functions
and
modeling
Carry out basic mathematical
computations (eg proportional reasoning
unit conversion center and variation)
X X X X X
Recognize and use logarithmic or
exponential relationshipsX X
Fit a model such as population growth X X
Use a representation or a model to make
predictionsX X X X X
Describeinfer relationships between
variables (scatterplots regression
network diagrams maps)
X X
Perform logicalalgorithmic reasoning X X X X
Statistics
and
probability
Calculate or use the concept of the
likelihood of an eventX X X
Calculate or use conditional probability X X X
Recognize and interpret what summary
statistics representX X X
Identify different types of error X
Recognize that biological systems are
inherently variable (eg stochastic vs
deterministic)
X X
Formulate hypothesis statements X X X X
Understand what a p-value is X X X X
Understand when causal claims can be
made (eg correlation vs causation)X X X X
Visualizati
on
Choose the appropriate type of graph X X X X X
Interpret a graph (eg functional
relationships logarithmic relationships)X X X X X
Be able to use a table X X X
Use spatial reasoning to interpret
multidimensional numerical and visual
data (geographic information)
X
Stanhope et al (2017) Development of a Biological
Science Quantitative Reasoning Exam (BioSQuaRE)
CBE- Life Science Education Winter edition
December 1 2017
bull identification and validation of learning domains
bull iterative development of BioSQuaRE Instrument
bull evidence of validity
bull discussion of instruments utility for students individual
faculty and departments or programs
Visit wwwmacalestereduhhmibiosquare for more information
BLASTing Human and Other Organisms
bull Our goal is to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus(snake) The objective is to find and precisely map the coding regions using NCBIrsquos BLASTp search tool
bull Answer the following questions for each of the 4 organisms1 Describe the summary distributions2 Interpret the score the percent identity and the E-value If
obtain hit(s) are they likely due to chance If no hits why3 Analyze the alignments
Describe these Summary Distributions
Chimp
Cow
Snake
Chicken
Interpret the Scores E-values and Identities
Chimp
Cow
Snake
Chicken
Analyze the Alignments
Chimp
Cow
Snake
Chicken
Additional Questions of Interest
bull Our goal was to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus (snake) The objective is to find and precisely map the coding regions
bull Answer the following questions1 This presentation is showing only highly significant pairs How
do you think the alignments (scores e-values identities) differ if we analyze low significant pairs
2 Can you infer that this protein does not exist in this organism3 Give alternative explanations for the differences in scores e-
values and identities4 Is there an evolutionary relationship between sequences
Am J Hum Genet 2008 Dec 12 83(6) 769ndash780 Published online 2008 Dec 5 doi 101016jajhg200811004
Ribosomal Protein L5 and L11 Mutations Are Associated with Cleft Palate and Abnormal Thumbs in Diamond-Blackfan Anemia Patients
Hanna T Gazda12lowast
Mee Rie Sheen1
Adrianna Vlachos34
Valerie Choesmel56
Marie-Franccediloise ODonohue
56Hal Schneider
1Natasha Darras
1Catherine Hasman
1Colin A
Sieff27
Peter E Newburger8
Sarah E Ball9
Edyta Niewiadomska10
Michal Matysiak10
Jan M Zaucha
11Bertil Glader
12Charlotte Niemeyer
13Joerg J Meerpohl
13Eva Atsidaftos
34Jeffrey
M Lipton34
Pierre-Emmanuel Gleizes56
and Alan H Beggs12
Author information Article notes Copyright and License information AbstractDiamond-Blackfan anemia (DBA) a congenital bone-marrow-failure syndrome is characterized by red blood cell aplasia macrocytic anemia clinical heterogeneity and increased risk of malignancy Although anemia is the most prominent feature of DBA the disease is also characterized by growth retardation and congenital anomalies that are present in sim30ndash50 of patients The disease has been associated with mutations in four ribosomal protein (RP) genes RPS19 RPS24 RPS17 and RPL35A in about 30 of patients However the genetic basis of the remaining 70 of cases is still unknown Here we report the second known mutation in RPS17 and probable pathogenic mutations in three more RP genes RPL5 RPL11 and RPS7 In addition we identified rare variants of unknown significance in three other genes RPL36 RPS15 and RPS27A Remarkably careful review of the clinical data showed that mutations in RPL5 are associated with multiple physical abnormalities including craniofacial thumb and heart anomalies whereas isolated thumb malformations are predominantly present in patients carrying mutations in RPL11 We also demonstrate that mutations of RPL5 RPL11 or RPS7 in DBA cells is associated with diverse defects in the maturation of ribosomal RNAs in the large or the small ribosomal subunit production pathway expanding the repertoire of ribosomal RNA processing defects associated with DBA
Develop more inquiry-based lab exercises1 C elegans crosses (Peter Barrett in Genetics lab)
2 Modifications on DNA transformation and lac operon exercises (PB)
3 The lsquotermitersquo experiment in Biol 1230L (Kristal Huggins and SKI)
4 In Cell Biology lab C elegans (endocytosis experiments) experiments with Planaria regeneration (adapted from MITHHMI) and recently with Daphnia (the water flea a small crustacean) adapted from the Nuffield Foundation where students expose the Daphnia to various cardioactive compounds measure changes in heart rate caused by effects on cellular receptors and design follow-up experiments (PB)
Assessment Strategies for Project Scicomp
Formative and summative
General scheme
bull Assessment tasks based on objectives
bull Develop assessment tools and pilot for validation
bull Apply to larger audience
bull Collect and score
bull Share and analyze data
Coordinated course sequences and our curricular design serve as a good platform
for intra and interdepartmental discussions
(weekly meetings lsquoSERGrsquo etc)
Labs
bull General observation on student participationinitiative
bull Data sheets (say 10 collecthellipsay any 4)
bull Midterm skills practical stations and multiple choice (excellent determinant)
bull Quizzes (5-10 depending on the lab)
bull Final exams
Course based research experiencee(CRE)
bull How they design their experiment
bull Notebooks lab techniques
bull Participation in class discussions
bull Ability to troubleshoot
bull Midterm Skills and oral exam along with traditional exam
bull Short answer (non multiple choice) questions
bull Research paper presentations
CREs at Xavier
bull Phage and Genomics
bull lsquoUndergraduate Researchrsquo for credits
bull Introduction to Mammalian Tissue Culture
The SEA-PHAGES ProgramhttpsseaphagesorgThe official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program
SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is a two-semester discovery-based undergraduate research course that begins with simple digging in the soil to find new viruses but progresses through a variety of microbiology techniques and eventually to complex genome annotation and bioinformatic analyses
CBE Life Sci Educ 2016 fall15(3) pii ar38 doi 101187cbe16-01-0078Increasing URM Undergraduate Student Success through Assessment-Driven Interventions A Multiyear Study Using Freshman-Level General Biology as a Model SystemCarmichael MC1 St Clair C1 Edwards AM2 Barrett P1 McFerrin H1 Davenport I1 Awad M1 Kundu A1 Ireland SK3
AbstractXavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students In this multiyear study with sim5500 participants data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course The three hour-long exams were common and administered concurrently to all students New exam questions were developed using Blooms taxonomy and exam results were analyzed statistically with validated assessment tools All but the comprehensive final exam were returned to students for self-evaluation and remediation Among other approaches course rigor was monitored by using an identical set of 60 questions on the final exam across 10 semesters Analysis of the identical sets of 60 final exam questions revealed that overall averages increased from 729 (2010) to 835 (2015) Regression analysis demonstrated a statistically significant correlation between high-risk students and their averages on the 60 questions Additional analysis demonstrated statistically significant improvements for at least one letter grade from midterm to final and a 20 increase in the course pass rates over time also for the high-risk population These results support the hypothesis that our data-driven interventions and assessment techniques are successful in improving student retention particularly for our academically at-risk students
Lecture Biol 1230
bull Competency E4 (chemistry in biology atomic bonds metabolic pathways thermodynamics)
bull Quizzes (formative assessment with Clickers)
bull The coordinator prepares the three lsquoOne hour examsrsquo (questions not from the textbook) instructors again reviewcomment
bull Question types range (content versus applications) and also lsquoBack pagersquo ( 20 of the exam grade) Formative assessment using the LXRtest software (Opscan6 scanner)
Final exam not returned cumulative and has had 60 questions (good discriminators based on the rpbvalues) commonly used on ALL final exams for the past five years Powerful tool for measuring studentsrsquo learning and applications over time and based on academic risk categories
Last Name First Name
Biology 1230 Exam 1 ldquoBack Pagerdquo Score _ 20 pts
I 5 pts Complete the following table for the 3 major components (subatomic particles) of the atom
hint electrical charge = positive negative or neutral and mass = 1 dalton or 11800 dalton 1 pt each
Particle Electrical Charge Mass
1 Proton 1 dalton
2 Electron
3 Neutron
II 5 pts In your own words compare and contrast the following two atoms A and B use the back of the previous page to
make as many observations as you can about similarities (and what they mean) and differences (and what they mean)
between the atoms
A B
III 5 pts Match the following by placing the corresponding in the space provided 1 pt each
_____ tertiary structure 1 produce H2O
_____ two ester linkages 2 is responsible for the 3-dimensional shape of a protein
_____ phosphodiester bonds 3 exist within diglycerides (diacylglyerols) and phospholipids
_____ dehydration synthesis reactions 4 are a type of lipid
_____ steroids 5 are formed when nucleic acids are synthesized
IV 5 pts Circle each of the variable (R) groups in the molecules shown below (3 pts)
a Which lsquoRrsquo group is polar ______ (write the corresponding in the space provided) (1 pt)
b Which lsquoRrsquo group is ionic ______ (write the corresponding in the space provided) (1 pt)
NH3+ OH CH3
1 2 3
12 neutrons
11 protons
10 electrons
13 neutrons
11 protons
11 electrons
Bio1230 Exam 1
Clickers and immediate feedback
Name _____________________________________________________________________________________________
This is a worksheet for your self-evaluation of study habits and exam preparedness Your answers on the corresponding
online exam surveys are confidential
~The average number of hours I spent per week reading the chapters andor reviewingprocessing class notes was (circle the
appropriate response)
zero to one one to two two to four greater than four
~I read the assignment before coming to class (circle the appropriate response)
never sometimes regularly
~I asked my instructor questions when I was confused about textbook material andor lecture material (circle the appropriate
response)
never sometimes regularly
~Overall I spent _____ hours specifically studying for this exam (Please fill in the blank)
~Prior to taking the exam I expected to get an approximate grade of (fill in the blank) _____
~My actual grade was a(n) (fill in the blank) _____
~Check all of the statements that apply to your performance on the exam
____ studied the right information ____ did not study the right information
____ studied the right information but did not ____ studied the right information and
understand it thought I understood it
____ used the class outlines to study ____ thought college would be easier
____ did not know what to study ____ other _____________________
____ did not think I would need to know the information in such detail
Analysis of Missed Questions I answered the question incorrectly because I Insert question number below in the correct category
did not study the information
studied the information but forgot it
did not understand the information in the
summary notes
confused similar concepts or terms (ie
isotopes and isomers)
misread or misunderstood the question
did not consider all of the answer choices
knew the correct answer - but chose an
incorrect answer by mistake
List other reason(s)
List other reason(s)
Please answer additional self-evaluation questions on the back of this page
Self-Evaluation of Study Habits amp Exam Preparedness for Biology 1230 Exam I or II or III (circle one)
Going forwardhellip
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
Biological Quantitative Reasoning
Exam (BioSQuaRE) ndash Q6 consortium
BioSQuaRE TeamBiology
Paul Overvoorde (Macalester)
Peter Brodfuehrer Greg Davis (Bryn Mawr)
Charles Umbanhowar (St Olaf)
Marion Preest (Keck Science Center Claremont Colleges)
Steve Adolph Cathy McFadden (Harvey Mudd)
Educational PsychologyStatistics
Andy Zieffler Laure Le (U Minnesota)
Laura Zeigler (Iowa State)
Erik Larson (Macalester)- Sociology
ldquoOtherrdquo
Liz Stanhope (Lewis and Clark) ndash Math
Jason Belitsky (Oberlin) ndash Chemistry
Marcelo Vinces (Oberlin) ndash Quantitative Skills Center
Tabassum Haque (Oberlin) ndash Institutional Research
Alignment of Learning Outcomes
bull 14 + 38 faculty
bull Mapping of learning outcomes with
previous national reports
ndash BIO2010
ndash Vision and Changes
ndash Next Gen Science Standards for Science
and Engineering
ndash Revised AP Biology requirements
ndash Preparing Future Physicians
bull Comparison to previously created
Quantitative Literacy Efforts (eg
QRLA TOSLS)
Mapping Learning Outcomes to National Reports
ContentStudents should
be able to
BIO20
10
Vision
amp
Chang
e
SFFPAP
Bio
NGSS
SampE
Algebra
functions
and
modeling
Carry out basic mathematical
computations (eg proportional reasoning
unit conversion center and variation)
X X X X X
Recognize and use logarithmic or
exponential relationshipsX X
Fit a model such as population growth X X
Use a representation or a model to make
predictionsX X X X X
Describeinfer relationships between
variables (scatterplots regression
network diagrams maps)
X X
Perform logicalalgorithmic reasoning X X X X
Statistics
and
probability
Calculate or use the concept of the
likelihood of an eventX X X
Calculate or use conditional probability X X X
Recognize and interpret what summary
statistics representX X X
Identify different types of error X
Recognize that biological systems are
inherently variable (eg stochastic vs
deterministic)
X X
Formulate hypothesis statements X X X X
Understand what a p-value is X X X X
Understand when causal claims can be
made (eg correlation vs causation)X X X X
Visualizati
on
Choose the appropriate type of graph X X X X X
Interpret a graph (eg functional
relationships logarithmic relationships)X X X X X
Be able to use a table X X X
Use spatial reasoning to interpret
multidimensional numerical and visual
data (geographic information)
X
Stanhope et al (2017) Development of a Biological
Science Quantitative Reasoning Exam (BioSQuaRE)
CBE- Life Science Education Winter edition
December 1 2017
bull identification and validation of learning domains
bull iterative development of BioSQuaRE Instrument
bull evidence of validity
bull discussion of instruments utility for students individual
faculty and departments or programs
Visit wwwmacalestereduhhmibiosquare for more information
BLASTing Human and Other Organisms
bull Our goal is to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus(snake) The objective is to find and precisely map the coding regions using NCBIrsquos BLASTp search tool
bull Answer the following questions for each of the 4 organisms1 Describe the summary distributions2 Interpret the score the percent identity and the E-value If
obtain hit(s) are they likely due to chance If no hits why3 Analyze the alignments
Describe these Summary Distributions
Chimp
Cow
Snake
Chicken
Interpret the Scores E-values and Identities
Chimp
Cow
Snake
Chicken
Analyze the Alignments
Chimp
Cow
Snake
Chicken
Additional Questions of Interest
bull Our goal was to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus (snake) The objective is to find and precisely map the coding regions
bull Answer the following questions1 This presentation is showing only highly significant pairs How
do you think the alignments (scores e-values identities) differ if we analyze low significant pairs
2 Can you infer that this protein does not exist in this organism3 Give alternative explanations for the differences in scores e-
values and identities4 Is there an evolutionary relationship between sequences
Am J Hum Genet 2008 Dec 12 83(6) 769ndash780 Published online 2008 Dec 5 doi 101016jajhg200811004
Ribosomal Protein L5 and L11 Mutations Are Associated with Cleft Palate and Abnormal Thumbs in Diamond-Blackfan Anemia Patients
Hanna T Gazda12lowast
Mee Rie Sheen1
Adrianna Vlachos34
Valerie Choesmel56
Marie-Franccediloise ODonohue
56Hal Schneider
1Natasha Darras
1Catherine Hasman
1Colin A
Sieff27
Peter E Newburger8
Sarah E Ball9
Edyta Niewiadomska10
Michal Matysiak10
Jan M Zaucha
11Bertil Glader
12Charlotte Niemeyer
13Joerg J Meerpohl
13Eva Atsidaftos
34Jeffrey
M Lipton34
Pierre-Emmanuel Gleizes56
and Alan H Beggs12
Author information Article notes Copyright and License information AbstractDiamond-Blackfan anemia (DBA) a congenital bone-marrow-failure syndrome is characterized by red blood cell aplasia macrocytic anemia clinical heterogeneity and increased risk of malignancy Although anemia is the most prominent feature of DBA the disease is also characterized by growth retardation and congenital anomalies that are present in sim30ndash50 of patients The disease has been associated with mutations in four ribosomal protein (RP) genes RPS19 RPS24 RPS17 and RPL35A in about 30 of patients However the genetic basis of the remaining 70 of cases is still unknown Here we report the second known mutation in RPS17 and probable pathogenic mutations in three more RP genes RPL5 RPL11 and RPS7 In addition we identified rare variants of unknown significance in three other genes RPL36 RPS15 and RPS27A Remarkably careful review of the clinical data showed that mutations in RPL5 are associated with multiple physical abnormalities including craniofacial thumb and heart anomalies whereas isolated thumb malformations are predominantly present in patients carrying mutations in RPL11 We also demonstrate that mutations of RPL5 RPL11 or RPS7 in DBA cells is associated with diverse defects in the maturation of ribosomal RNAs in the large or the small ribosomal subunit production pathway expanding the repertoire of ribosomal RNA processing defects associated with DBA
Develop more inquiry-based lab exercises1 C elegans crosses (Peter Barrett in Genetics lab)
2 Modifications on DNA transformation and lac operon exercises (PB)
3 The lsquotermitersquo experiment in Biol 1230L (Kristal Huggins and SKI)
4 In Cell Biology lab C elegans (endocytosis experiments) experiments with Planaria regeneration (adapted from MITHHMI) and recently with Daphnia (the water flea a small crustacean) adapted from the Nuffield Foundation where students expose the Daphnia to various cardioactive compounds measure changes in heart rate caused by effects on cellular receptors and design follow-up experiments (PB)
Assessment Strategies for Project Scicomp
Formative and summative
General scheme
bull Assessment tasks based on objectives
bull Develop assessment tools and pilot for validation
bull Apply to larger audience
bull Collect and score
bull Share and analyze data
Coordinated course sequences and our curricular design serve as a good platform
for intra and interdepartmental discussions
(weekly meetings lsquoSERGrsquo etc)
Labs
bull General observation on student participationinitiative
bull Data sheets (say 10 collecthellipsay any 4)
bull Midterm skills practical stations and multiple choice (excellent determinant)
bull Quizzes (5-10 depending on the lab)
bull Final exams
Course based research experiencee(CRE)
bull How they design their experiment
bull Notebooks lab techniques
bull Participation in class discussions
bull Ability to troubleshoot
bull Midterm Skills and oral exam along with traditional exam
bull Short answer (non multiple choice) questions
bull Research paper presentations
CREs at Xavier
bull Phage and Genomics
bull lsquoUndergraduate Researchrsquo for credits
bull Introduction to Mammalian Tissue Culture
The SEA-PHAGES ProgramhttpsseaphagesorgThe official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program
SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is a two-semester discovery-based undergraduate research course that begins with simple digging in the soil to find new viruses but progresses through a variety of microbiology techniques and eventually to complex genome annotation and bioinformatic analyses
CBE Life Sci Educ 2016 fall15(3) pii ar38 doi 101187cbe16-01-0078Increasing URM Undergraduate Student Success through Assessment-Driven Interventions A Multiyear Study Using Freshman-Level General Biology as a Model SystemCarmichael MC1 St Clair C1 Edwards AM2 Barrett P1 McFerrin H1 Davenport I1 Awad M1 Kundu A1 Ireland SK3
AbstractXavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students In this multiyear study with sim5500 participants data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course The three hour-long exams were common and administered concurrently to all students New exam questions were developed using Blooms taxonomy and exam results were analyzed statistically with validated assessment tools All but the comprehensive final exam were returned to students for self-evaluation and remediation Among other approaches course rigor was monitored by using an identical set of 60 questions on the final exam across 10 semesters Analysis of the identical sets of 60 final exam questions revealed that overall averages increased from 729 (2010) to 835 (2015) Regression analysis demonstrated a statistically significant correlation between high-risk students and their averages on the 60 questions Additional analysis demonstrated statistically significant improvements for at least one letter grade from midterm to final and a 20 increase in the course pass rates over time also for the high-risk population These results support the hypothesis that our data-driven interventions and assessment techniques are successful in improving student retention particularly for our academically at-risk students
Lecture Biol 1230
bull Competency E4 (chemistry in biology atomic bonds metabolic pathways thermodynamics)
bull Quizzes (formative assessment with Clickers)
bull The coordinator prepares the three lsquoOne hour examsrsquo (questions not from the textbook) instructors again reviewcomment
bull Question types range (content versus applications) and also lsquoBack pagersquo ( 20 of the exam grade) Formative assessment using the LXRtest software (Opscan6 scanner)
Final exam not returned cumulative and has had 60 questions (good discriminators based on the rpbvalues) commonly used on ALL final exams for the past five years Powerful tool for measuring studentsrsquo learning and applications over time and based on academic risk categories
Last Name First Name
Biology 1230 Exam 1 ldquoBack Pagerdquo Score _ 20 pts
I 5 pts Complete the following table for the 3 major components (subatomic particles) of the atom
hint electrical charge = positive negative or neutral and mass = 1 dalton or 11800 dalton 1 pt each
Particle Electrical Charge Mass
1 Proton 1 dalton
2 Electron
3 Neutron
II 5 pts In your own words compare and contrast the following two atoms A and B use the back of the previous page to
make as many observations as you can about similarities (and what they mean) and differences (and what they mean)
between the atoms
A B
III 5 pts Match the following by placing the corresponding in the space provided 1 pt each
_____ tertiary structure 1 produce H2O
_____ two ester linkages 2 is responsible for the 3-dimensional shape of a protein
_____ phosphodiester bonds 3 exist within diglycerides (diacylglyerols) and phospholipids
_____ dehydration synthesis reactions 4 are a type of lipid
_____ steroids 5 are formed when nucleic acids are synthesized
IV 5 pts Circle each of the variable (R) groups in the molecules shown below (3 pts)
a Which lsquoRrsquo group is polar ______ (write the corresponding in the space provided) (1 pt)
b Which lsquoRrsquo group is ionic ______ (write the corresponding in the space provided) (1 pt)
NH3+ OH CH3
1 2 3
12 neutrons
11 protons
10 electrons
13 neutrons
11 protons
11 electrons
Bio1230 Exam 1
Clickers and immediate feedback
Name _____________________________________________________________________________________________
This is a worksheet for your self-evaluation of study habits and exam preparedness Your answers on the corresponding
online exam surveys are confidential
~The average number of hours I spent per week reading the chapters andor reviewingprocessing class notes was (circle the
appropriate response)
zero to one one to two two to four greater than four
~I read the assignment before coming to class (circle the appropriate response)
never sometimes regularly
~I asked my instructor questions when I was confused about textbook material andor lecture material (circle the appropriate
response)
never sometimes regularly
~Overall I spent _____ hours specifically studying for this exam (Please fill in the blank)
~Prior to taking the exam I expected to get an approximate grade of (fill in the blank) _____
~My actual grade was a(n) (fill in the blank) _____
~Check all of the statements that apply to your performance on the exam
____ studied the right information ____ did not study the right information
____ studied the right information but did not ____ studied the right information and
understand it thought I understood it
____ used the class outlines to study ____ thought college would be easier
____ did not know what to study ____ other _____________________
____ did not think I would need to know the information in such detail
Analysis of Missed Questions I answered the question incorrectly because I Insert question number below in the correct category
did not study the information
studied the information but forgot it
did not understand the information in the
summary notes
confused similar concepts or terms (ie
isotopes and isomers)
misread or misunderstood the question
did not consider all of the answer choices
knew the correct answer - but chose an
incorrect answer by mistake
List other reason(s)
List other reason(s)
Please answer additional self-evaluation questions on the back of this page
Self-Evaluation of Study Habits amp Exam Preparedness for Biology 1230 Exam I or II or III (circle one)
Going forwardhellip
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
BioSQuaRE TeamBiology
Paul Overvoorde (Macalester)
Peter Brodfuehrer Greg Davis (Bryn Mawr)
Charles Umbanhowar (St Olaf)
Marion Preest (Keck Science Center Claremont Colleges)
Steve Adolph Cathy McFadden (Harvey Mudd)
Educational PsychologyStatistics
Andy Zieffler Laure Le (U Minnesota)
Laura Zeigler (Iowa State)
Erik Larson (Macalester)- Sociology
ldquoOtherrdquo
Liz Stanhope (Lewis and Clark) ndash Math
Jason Belitsky (Oberlin) ndash Chemistry
Marcelo Vinces (Oberlin) ndash Quantitative Skills Center
Tabassum Haque (Oberlin) ndash Institutional Research
Alignment of Learning Outcomes
bull 14 + 38 faculty
bull Mapping of learning outcomes with
previous national reports
ndash BIO2010
ndash Vision and Changes
ndash Next Gen Science Standards for Science
and Engineering
ndash Revised AP Biology requirements
ndash Preparing Future Physicians
bull Comparison to previously created
Quantitative Literacy Efforts (eg
QRLA TOSLS)
Mapping Learning Outcomes to National Reports
ContentStudents should
be able to
BIO20
10
Vision
amp
Chang
e
SFFPAP
Bio
NGSS
SampE
Algebra
functions
and
modeling
Carry out basic mathematical
computations (eg proportional reasoning
unit conversion center and variation)
X X X X X
Recognize and use logarithmic or
exponential relationshipsX X
Fit a model such as population growth X X
Use a representation or a model to make
predictionsX X X X X
Describeinfer relationships between
variables (scatterplots regression
network diagrams maps)
X X
Perform logicalalgorithmic reasoning X X X X
Statistics
and
probability
Calculate or use the concept of the
likelihood of an eventX X X
Calculate or use conditional probability X X X
Recognize and interpret what summary
statistics representX X X
Identify different types of error X
Recognize that biological systems are
inherently variable (eg stochastic vs
deterministic)
X X
Formulate hypothesis statements X X X X
Understand what a p-value is X X X X
Understand when causal claims can be
made (eg correlation vs causation)X X X X
Visualizati
on
Choose the appropriate type of graph X X X X X
Interpret a graph (eg functional
relationships logarithmic relationships)X X X X X
Be able to use a table X X X
Use spatial reasoning to interpret
multidimensional numerical and visual
data (geographic information)
X
Stanhope et al (2017) Development of a Biological
Science Quantitative Reasoning Exam (BioSQuaRE)
CBE- Life Science Education Winter edition
December 1 2017
bull identification and validation of learning domains
bull iterative development of BioSQuaRE Instrument
bull evidence of validity
bull discussion of instruments utility for students individual
faculty and departments or programs
Visit wwwmacalestereduhhmibiosquare for more information
BLASTing Human and Other Organisms
bull Our goal is to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus(snake) The objective is to find and precisely map the coding regions using NCBIrsquos BLASTp search tool
bull Answer the following questions for each of the 4 organisms1 Describe the summary distributions2 Interpret the score the percent identity and the E-value If
obtain hit(s) are they likely due to chance If no hits why3 Analyze the alignments
Describe these Summary Distributions
Chimp
Cow
Snake
Chicken
Interpret the Scores E-values and Identities
Chimp
Cow
Snake
Chicken
Analyze the Alignments
Chimp
Cow
Snake
Chicken
Additional Questions of Interest
bull Our goal was to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus (snake) The objective is to find and precisely map the coding regions
bull Answer the following questions1 This presentation is showing only highly significant pairs How
do you think the alignments (scores e-values identities) differ if we analyze low significant pairs
2 Can you infer that this protein does not exist in this organism3 Give alternative explanations for the differences in scores e-
values and identities4 Is there an evolutionary relationship between sequences
Am J Hum Genet 2008 Dec 12 83(6) 769ndash780 Published online 2008 Dec 5 doi 101016jajhg200811004
Ribosomal Protein L5 and L11 Mutations Are Associated with Cleft Palate and Abnormal Thumbs in Diamond-Blackfan Anemia Patients
Hanna T Gazda12lowast
Mee Rie Sheen1
Adrianna Vlachos34
Valerie Choesmel56
Marie-Franccediloise ODonohue
56Hal Schneider
1Natasha Darras
1Catherine Hasman
1Colin A
Sieff27
Peter E Newburger8
Sarah E Ball9
Edyta Niewiadomska10
Michal Matysiak10
Jan M Zaucha
11Bertil Glader
12Charlotte Niemeyer
13Joerg J Meerpohl
13Eva Atsidaftos
34Jeffrey
M Lipton34
Pierre-Emmanuel Gleizes56
and Alan H Beggs12
Author information Article notes Copyright and License information AbstractDiamond-Blackfan anemia (DBA) a congenital bone-marrow-failure syndrome is characterized by red blood cell aplasia macrocytic anemia clinical heterogeneity and increased risk of malignancy Although anemia is the most prominent feature of DBA the disease is also characterized by growth retardation and congenital anomalies that are present in sim30ndash50 of patients The disease has been associated with mutations in four ribosomal protein (RP) genes RPS19 RPS24 RPS17 and RPL35A in about 30 of patients However the genetic basis of the remaining 70 of cases is still unknown Here we report the second known mutation in RPS17 and probable pathogenic mutations in three more RP genes RPL5 RPL11 and RPS7 In addition we identified rare variants of unknown significance in three other genes RPL36 RPS15 and RPS27A Remarkably careful review of the clinical data showed that mutations in RPL5 are associated with multiple physical abnormalities including craniofacial thumb and heart anomalies whereas isolated thumb malformations are predominantly present in patients carrying mutations in RPL11 We also demonstrate that mutations of RPL5 RPL11 or RPS7 in DBA cells is associated with diverse defects in the maturation of ribosomal RNAs in the large or the small ribosomal subunit production pathway expanding the repertoire of ribosomal RNA processing defects associated with DBA
Develop more inquiry-based lab exercises1 C elegans crosses (Peter Barrett in Genetics lab)
2 Modifications on DNA transformation and lac operon exercises (PB)
3 The lsquotermitersquo experiment in Biol 1230L (Kristal Huggins and SKI)
4 In Cell Biology lab C elegans (endocytosis experiments) experiments with Planaria regeneration (adapted from MITHHMI) and recently with Daphnia (the water flea a small crustacean) adapted from the Nuffield Foundation where students expose the Daphnia to various cardioactive compounds measure changes in heart rate caused by effects on cellular receptors and design follow-up experiments (PB)
Assessment Strategies for Project Scicomp
Formative and summative
General scheme
bull Assessment tasks based on objectives
bull Develop assessment tools and pilot for validation
bull Apply to larger audience
bull Collect and score
bull Share and analyze data
Coordinated course sequences and our curricular design serve as a good platform
for intra and interdepartmental discussions
(weekly meetings lsquoSERGrsquo etc)
Labs
bull General observation on student participationinitiative
bull Data sheets (say 10 collecthellipsay any 4)
bull Midterm skills practical stations and multiple choice (excellent determinant)
bull Quizzes (5-10 depending on the lab)
bull Final exams
Course based research experiencee(CRE)
bull How they design their experiment
bull Notebooks lab techniques
bull Participation in class discussions
bull Ability to troubleshoot
bull Midterm Skills and oral exam along with traditional exam
bull Short answer (non multiple choice) questions
bull Research paper presentations
CREs at Xavier
bull Phage and Genomics
bull lsquoUndergraduate Researchrsquo for credits
bull Introduction to Mammalian Tissue Culture
The SEA-PHAGES ProgramhttpsseaphagesorgThe official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program
SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is a two-semester discovery-based undergraduate research course that begins with simple digging in the soil to find new viruses but progresses through a variety of microbiology techniques and eventually to complex genome annotation and bioinformatic analyses
CBE Life Sci Educ 2016 fall15(3) pii ar38 doi 101187cbe16-01-0078Increasing URM Undergraduate Student Success through Assessment-Driven Interventions A Multiyear Study Using Freshman-Level General Biology as a Model SystemCarmichael MC1 St Clair C1 Edwards AM2 Barrett P1 McFerrin H1 Davenport I1 Awad M1 Kundu A1 Ireland SK3
AbstractXavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students In this multiyear study with sim5500 participants data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course The three hour-long exams were common and administered concurrently to all students New exam questions were developed using Blooms taxonomy and exam results were analyzed statistically with validated assessment tools All but the comprehensive final exam were returned to students for self-evaluation and remediation Among other approaches course rigor was monitored by using an identical set of 60 questions on the final exam across 10 semesters Analysis of the identical sets of 60 final exam questions revealed that overall averages increased from 729 (2010) to 835 (2015) Regression analysis demonstrated a statistically significant correlation between high-risk students and their averages on the 60 questions Additional analysis demonstrated statistically significant improvements for at least one letter grade from midterm to final and a 20 increase in the course pass rates over time also for the high-risk population These results support the hypothesis that our data-driven interventions and assessment techniques are successful in improving student retention particularly for our academically at-risk students
Lecture Biol 1230
bull Competency E4 (chemistry in biology atomic bonds metabolic pathways thermodynamics)
bull Quizzes (formative assessment with Clickers)
bull The coordinator prepares the three lsquoOne hour examsrsquo (questions not from the textbook) instructors again reviewcomment
bull Question types range (content versus applications) and also lsquoBack pagersquo ( 20 of the exam grade) Formative assessment using the LXRtest software (Opscan6 scanner)
Final exam not returned cumulative and has had 60 questions (good discriminators based on the rpbvalues) commonly used on ALL final exams for the past five years Powerful tool for measuring studentsrsquo learning and applications over time and based on academic risk categories
Last Name First Name
Biology 1230 Exam 1 ldquoBack Pagerdquo Score _ 20 pts
I 5 pts Complete the following table for the 3 major components (subatomic particles) of the atom
hint electrical charge = positive negative or neutral and mass = 1 dalton or 11800 dalton 1 pt each
Particle Electrical Charge Mass
1 Proton 1 dalton
2 Electron
3 Neutron
II 5 pts In your own words compare and contrast the following two atoms A and B use the back of the previous page to
make as many observations as you can about similarities (and what they mean) and differences (and what they mean)
between the atoms
A B
III 5 pts Match the following by placing the corresponding in the space provided 1 pt each
_____ tertiary structure 1 produce H2O
_____ two ester linkages 2 is responsible for the 3-dimensional shape of a protein
_____ phosphodiester bonds 3 exist within diglycerides (diacylglyerols) and phospholipids
_____ dehydration synthesis reactions 4 are a type of lipid
_____ steroids 5 are formed when nucleic acids are synthesized
IV 5 pts Circle each of the variable (R) groups in the molecules shown below (3 pts)
a Which lsquoRrsquo group is polar ______ (write the corresponding in the space provided) (1 pt)
b Which lsquoRrsquo group is ionic ______ (write the corresponding in the space provided) (1 pt)
NH3+ OH CH3
1 2 3
12 neutrons
11 protons
10 electrons
13 neutrons
11 protons
11 electrons
Bio1230 Exam 1
Clickers and immediate feedback
Name _____________________________________________________________________________________________
This is a worksheet for your self-evaluation of study habits and exam preparedness Your answers on the corresponding
online exam surveys are confidential
~The average number of hours I spent per week reading the chapters andor reviewingprocessing class notes was (circle the
appropriate response)
zero to one one to two two to four greater than four
~I read the assignment before coming to class (circle the appropriate response)
never sometimes regularly
~I asked my instructor questions when I was confused about textbook material andor lecture material (circle the appropriate
response)
never sometimes regularly
~Overall I spent _____ hours specifically studying for this exam (Please fill in the blank)
~Prior to taking the exam I expected to get an approximate grade of (fill in the blank) _____
~My actual grade was a(n) (fill in the blank) _____
~Check all of the statements that apply to your performance on the exam
____ studied the right information ____ did not study the right information
____ studied the right information but did not ____ studied the right information and
understand it thought I understood it
____ used the class outlines to study ____ thought college would be easier
____ did not know what to study ____ other _____________________
____ did not think I would need to know the information in such detail
Analysis of Missed Questions I answered the question incorrectly because I Insert question number below in the correct category
did not study the information
studied the information but forgot it
did not understand the information in the
summary notes
confused similar concepts or terms (ie
isotopes and isomers)
misread or misunderstood the question
did not consider all of the answer choices
knew the correct answer - but chose an
incorrect answer by mistake
List other reason(s)
List other reason(s)
Please answer additional self-evaluation questions on the back of this page
Self-Evaluation of Study Habits amp Exam Preparedness for Biology 1230 Exam I or II or III (circle one)
Going forwardhellip
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
Alignment of Learning Outcomes
bull 14 + 38 faculty
bull Mapping of learning outcomes with
previous national reports
ndash BIO2010
ndash Vision and Changes
ndash Next Gen Science Standards for Science
and Engineering
ndash Revised AP Biology requirements
ndash Preparing Future Physicians
bull Comparison to previously created
Quantitative Literacy Efforts (eg
QRLA TOSLS)
Mapping Learning Outcomes to National Reports
ContentStudents should
be able to
BIO20
10
Vision
amp
Chang
e
SFFPAP
Bio
NGSS
SampE
Algebra
functions
and
modeling
Carry out basic mathematical
computations (eg proportional reasoning
unit conversion center and variation)
X X X X X
Recognize and use logarithmic or
exponential relationshipsX X
Fit a model such as population growth X X
Use a representation or a model to make
predictionsX X X X X
Describeinfer relationships between
variables (scatterplots regression
network diagrams maps)
X X
Perform logicalalgorithmic reasoning X X X X
Statistics
and
probability
Calculate or use the concept of the
likelihood of an eventX X X
Calculate or use conditional probability X X X
Recognize and interpret what summary
statistics representX X X
Identify different types of error X
Recognize that biological systems are
inherently variable (eg stochastic vs
deterministic)
X X
Formulate hypothesis statements X X X X
Understand what a p-value is X X X X
Understand when causal claims can be
made (eg correlation vs causation)X X X X
Visualizati
on
Choose the appropriate type of graph X X X X X
Interpret a graph (eg functional
relationships logarithmic relationships)X X X X X
Be able to use a table X X X
Use spatial reasoning to interpret
multidimensional numerical and visual
data (geographic information)
X
Stanhope et al (2017) Development of a Biological
Science Quantitative Reasoning Exam (BioSQuaRE)
CBE- Life Science Education Winter edition
December 1 2017
bull identification and validation of learning domains
bull iterative development of BioSQuaRE Instrument
bull evidence of validity
bull discussion of instruments utility for students individual
faculty and departments or programs
Visit wwwmacalestereduhhmibiosquare for more information
BLASTing Human and Other Organisms
bull Our goal is to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus(snake) The objective is to find and precisely map the coding regions using NCBIrsquos BLASTp search tool
bull Answer the following questions for each of the 4 organisms1 Describe the summary distributions2 Interpret the score the percent identity and the E-value If
obtain hit(s) are they likely due to chance If no hits why3 Analyze the alignments
Describe these Summary Distributions
Chimp
Cow
Snake
Chicken
Interpret the Scores E-values and Identities
Chimp
Cow
Snake
Chicken
Analyze the Alignments
Chimp
Cow
Snake
Chicken
Additional Questions of Interest
bull Our goal was to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus (snake) The objective is to find and precisely map the coding regions
bull Answer the following questions1 This presentation is showing only highly significant pairs How
do you think the alignments (scores e-values identities) differ if we analyze low significant pairs
2 Can you infer that this protein does not exist in this organism3 Give alternative explanations for the differences in scores e-
values and identities4 Is there an evolutionary relationship between sequences
Am J Hum Genet 2008 Dec 12 83(6) 769ndash780 Published online 2008 Dec 5 doi 101016jajhg200811004
Ribosomal Protein L5 and L11 Mutations Are Associated with Cleft Palate and Abnormal Thumbs in Diamond-Blackfan Anemia Patients
Hanna T Gazda12lowast
Mee Rie Sheen1
Adrianna Vlachos34
Valerie Choesmel56
Marie-Franccediloise ODonohue
56Hal Schneider
1Natasha Darras
1Catherine Hasman
1Colin A
Sieff27
Peter E Newburger8
Sarah E Ball9
Edyta Niewiadomska10
Michal Matysiak10
Jan M Zaucha
11Bertil Glader
12Charlotte Niemeyer
13Joerg J Meerpohl
13Eva Atsidaftos
34Jeffrey
M Lipton34
Pierre-Emmanuel Gleizes56
and Alan H Beggs12
Author information Article notes Copyright and License information AbstractDiamond-Blackfan anemia (DBA) a congenital bone-marrow-failure syndrome is characterized by red blood cell aplasia macrocytic anemia clinical heterogeneity and increased risk of malignancy Although anemia is the most prominent feature of DBA the disease is also characterized by growth retardation and congenital anomalies that are present in sim30ndash50 of patients The disease has been associated with mutations in four ribosomal protein (RP) genes RPS19 RPS24 RPS17 and RPL35A in about 30 of patients However the genetic basis of the remaining 70 of cases is still unknown Here we report the second known mutation in RPS17 and probable pathogenic mutations in three more RP genes RPL5 RPL11 and RPS7 In addition we identified rare variants of unknown significance in three other genes RPL36 RPS15 and RPS27A Remarkably careful review of the clinical data showed that mutations in RPL5 are associated with multiple physical abnormalities including craniofacial thumb and heart anomalies whereas isolated thumb malformations are predominantly present in patients carrying mutations in RPL11 We also demonstrate that mutations of RPL5 RPL11 or RPS7 in DBA cells is associated with diverse defects in the maturation of ribosomal RNAs in the large or the small ribosomal subunit production pathway expanding the repertoire of ribosomal RNA processing defects associated with DBA
Develop more inquiry-based lab exercises1 C elegans crosses (Peter Barrett in Genetics lab)
2 Modifications on DNA transformation and lac operon exercises (PB)
3 The lsquotermitersquo experiment in Biol 1230L (Kristal Huggins and SKI)
4 In Cell Biology lab C elegans (endocytosis experiments) experiments with Planaria regeneration (adapted from MITHHMI) and recently with Daphnia (the water flea a small crustacean) adapted from the Nuffield Foundation where students expose the Daphnia to various cardioactive compounds measure changes in heart rate caused by effects on cellular receptors and design follow-up experiments (PB)
Assessment Strategies for Project Scicomp
Formative and summative
General scheme
bull Assessment tasks based on objectives
bull Develop assessment tools and pilot for validation
bull Apply to larger audience
bull Collect and score
bull Share and analyze data
Coordinated course sequences and our curricular design serve as a good platform
for intra and interdepartmental discussions
(weekly meetings lsquoSERGrsquo etc)
Labs
bull General observation on student participationinitiative
bull Data sheets (say 10 collecthellipsay any 4)
bull Midterm skills practical stations and multiple choice (excellent determinant)
bull Quizzes (5-10 depending on the lab)
bull Final exams
Course based research experiencee(CRE)
bull How they design their experiment
bull Notebooks lab techniques
bull Participation in class discussions
bull Ability to troubleshoot
bull Midterm Skills and oral exam along with traditional exam
bull Short answer (non multiple choice) questions
bull Research paper presentations
CREs at Xavier
bull Phage and Genomics
bull lsquoUndergraduate Researchrsquo for credits
bull Introduction to Mammalian Tissue Culture
The SEA-PHAGES ProgramhttpsseaphagesorgThe official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program
SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is a two-semester discovery-based undergraduate research course that begins with simple digging in the soil to find new viruses but progresses through a variety of microbiology techniques and eventually to complex genome annotation and bioinformatic analyses
CBE Life Sci Educ 2016 fall15(3) pii ar38 doi 101187cbe16-01-0078Increasing URM Undergraduate Student Success through Assessment-Driven Interventions A Multiyear Study Using Freshman-Level General Biology as a Model SystemCarmichael MC1 St Clair C1 Edwards AM2 Barrett P1 McFerrin H1 Davenport I1 Awad M1 Kundu A1 Ireland SK3
AbstractXavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students In this multiyear study with sim5500 participants data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course The three hour-long exams were common and administered concurrently to all students New exam questions were developed using Blooms taxonomy and exam results were analyzed statistically with validated assessment tools All but the comprehensive final exam were returned to students for self-evaluation and remediation Among other approaches course rigor was monitored by using an identical set of 60 questions on the final exam across 10 semesters Analysis of the identical sets of 60 final exam questions revealed that overall averages increased from 729 (2010) to 835 (2015) Regression analysis demonstrated a statistically significant correlation between high-risk students and their averages on the 60 questions Additional analysis demonstrated statistically significant improvements for at least one letter grade from midterm to final and a 20 increase in the course pass rates over time also for the high-risk population These results support the hypothesis that our data-driven interventions and assessment techniques are successful in improving student retention particularly for our academically at-risk students
Lecture Biol 1230
bull Competency E4 (chemistry in biology atomic bonds metabolic pathways thermodynamics)
bull Quizzes (formative assessment with Clickers)
bull The coordinator prepares the three lsquoOne hour examsrsquo (questions not from the textbook) instructors again reviewcomment
bull Question types range (content versus applications) and also lsquoBack pagersquo ( 20 of the exam grade) Formative assessment using the LXRtest software (Opscan6 scanner)
Final exam not returned cumulative and has had 60 questions (good discriminators based on the rpbvalues) commonly used on ALL final exams for the past five years Powerful tool for measuring studentsrsquo learning and applications over time and based on academic risk categories
Last Name First Name
Biology 1230 Exam 1 ldquoBack Pagerdquo Score _ 20 pts
I 5 pts Complete the following table for the 3 major components (subatomic particles) of the atom
hint electrical charge = positive negative or neutral and mass = 1 dalton or 11800 dalton 1 pt each
Particle Electrical Charge Mass
1 Proton 1 dalton
2 Electron
3 Neutron
II 5 pts In your own words compare and contrast the following two atoms A and B use the back of the previous page to
make as many observations as you can about similarities (and what they mean) and differences (and what they mean)
between the atoms
A B
III 5 pts Match the following by placing the corresponding in the space provided 1 pt each
_____ tertiary structure 1 produce H2O
_____ two ester linkages 2 is responsible for the 3-dimensional shape of a protein
_____ phosphodiester bonds 3 exist within diglycerides (diacylglyerols) and phospholipids
_____ dehydration synthesis reactions 4 are a type of lipid
_____ steroids 5 are formed when nucleic acids are synthesized
IV 5 pts Circle each of the variable (R) groups in the molecules shown below (3 pts)
a Which lsquoRrsquo group is polar ______ (write the corresponding in the space provided) (1 pt)
b Which lsquoRrsquo group is ionic ______ (write the corresponding in the space provided) (1 pt)
NH3+ OH CH3
1 2 3
12 neutrons
11 protons
10 electrons
13 neutrons
11 protons
11 electrons
Bio1230 Exam 1
Clickers and immediate feedback
Name _____________________________________________________________________________________________
This is a worksheet for your self-evaluation of study habits and exam preparedness Your answers on the corresponding
online exam surveys are confidential
~The average number of hours I spent per week reading the chapters andor reviewingprocessing class notes was (circle the
appropriate response)
zero to one one to two two to four greater than four
~I read the assignment before coming to class (circle the appropriate response)
never sometimes regularly
~I asked my instructor questions when I was confused about textbook material andor lecture material (circle the appropriate
response)
never sometimes regularly
~Overall I spent _____ hours specifically studying for this exam (Please fill in the blank)
~Prior to taking the exam I expected to get an approximate grade of (fill in the blank) _____
~My actual grade was a(n) (fill in the blank) _____
~Check all of the statements that apply to your performance on the exam
____ studied the right information ____ did not study the right information
____ studied the right information but did not ____ studied the right information and
understand it thought I understood it
____ used the class outlines to study ____ thought college would be easier
____ did not know what to study ____ other _____________________
____ did not think I would need to know the information in such detail
Analysis of Missed Questions I answered the question incorrectly because I Insert question number below in the correct category
did not study the information
studied the information but forgot it
did not understand the information in the
summary notes
confused similar concepts or terms (ie
isotopes and isomers)
misread or misunderstood the question
did not consider all of the answer choices
knew the correct answer - but chose an
incorrect answer by mistake
List other reason(s)
List other reason(s)
Please answer additional self-evaluation questions on the back of this page
Self-Evaluation of Study Habits amp Exam Preparedness for Biology 1230 Exam I or II or III (circle one)
Going forwardhellip
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
Mapping Learning Outcomes to National Reports
ContentStudents should
be able to
BIO20
10
Vision
amp
Chang
e
SFFPAP
Bio
NGSS
SampE
Algebra
functions
and
modeling
Carry out basic mathematical
computations (eg proportional reasoning
unit conversion center and variation)
X X X X X
Recognize and use logarithmic or
exponential relationshipsX X
Fit a model such as population growth X X
Use a representation or a model to make
predictionsX X X X X
Describeinfer relationships between
variables (scatterplots regression
network diagrams maps)
X X
Perform logicalalgorithmic reasoning X X X X
Statistics
and
probability
Calculate or use the concept of the
likelihood of an eventX X X
Calculate or use conditional probability X X X
Recognize and interpret what summary
statistics representX X X
Identify different types of error X
Recognize that biological systems are
inherently variable (eg stochastic vs
deterministic)
X X
Formulate hypothesis statements X X X X
Understand what a p-value is X X X X
Understand when causal claims can be
made (eg correlation vs causation)X X X X
Visualizati
on
Choose the appropriate type of graph X X X X X
Interpret a graph (eg functional
relationships logarithmic relationships)X X X X X
Be able to use a table X X X
Use spatial reasoning to interpret
multidimensional numerical and visual
data (geographic information)
X
Stanhope et al (2017) Development of a Biological
Science Quantitative Reasoning Exam (BioSQuaRE)
CBE- Life Science Education Winter edition
December 1 2017
bull identification and validation of learning domains
bull iterative development of BioSQuaRE Instrument
bull evidence of validity
bull discussion of instruments utility for students individual
faculty and departments or programs
Visit wwwmacalestereduhhmibiosquare for more information
BLASTing Human and Other Organisms
bull Our goal is to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus(snake) The objective is to find and precisely map the coding regions using NCBIrsquos BLASTp search tool
bull Answer the following questions for each of the 4 organisms1 Describe the summary distributions2 Interpret the score the percent identity and the E-value If
obtain hit(s) are they likely due to chance If no hits why3 Analyze the alignments
Describe these Summary Distributions
Chimp
Cow
Snake
Chicken
Interpret the Scores E-values and Identities
Chimp
Cow
Snake
Chicken
Analyze the Alignments
Chimp
Cow
Snake
Chicken
Additional Questions of Interest
bull Our goal was to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus (snake) The objective is to find and precisely map the coding regions
bull Answer the following questions1 This presentation is showing only highly significant pairs How
do you think the alignments (scores e-values identities) differ if we analyze low significant pairs
2 Can you infer that this protein does not exist in this organism3 Give alternative explanations for the differences in scores e-
values and identities4 Is there an evolutionary relationship between sequences
Am J Hum Genet 2008 Dec 12 83(6) 769ndash780 Published online 2008 Dec 5 doi 101016jajhg200811004
Ribosomal Protein L5 and L11 Mutations Are Associated with Cleft Palate and Abnormal Thumbs in Diamond-Blackfan Anemia Patients
Hanna T Gazda12lowast
Mee Rie Sheen1
Adrianna Vlachos34
Valerie Choesmel56
Marie-Franccediloise ODonohue
56Hal Schneider
1Natasha Darras
1Catherine Hasman
1Colin A
Sieff27
Peter E Newburger8
Sarah E Ball9
Edyta Niewiadomska10
Michal Matysiak10
Jan M Zaucha
11Bertil Glader
12Charlotte Niemeyer
13Joerg J Meerpohl
13Eva Atsidaftos
34Jeffrey
M Lipton34
Pierre-Emmanuel Gleizes56
and Alan H Beggs12
Author information Article notes Copyright and License information AbstractDiamond-Blackfan anemia (DBA) a congenital bone-marrow-failure syndrome is characterized by red blood cell aplasia macrocytic anemia clinical heterogeneity and increased risk of malignancy Although anemia is the most prominent feature of DBA the disease is also characterized by growth retardation and congenital anomalies that are present in sim30ndash50 of patients The disease has been associated with mutations in four ribosomal protein (RP) genes RPS19 RPS24 RPS17 and RPL35A in about 30 of patients However the genetic basis of the remaining 70 of cases is still unknown Here we report the second known mutation in RPS17 and probable pathogenic mutations in three more RP genes RPL5 RPL11 and RPS7 In addition we identified rare variants of unknown significance in three other genes RPL36 RPS15 and RPS27A Remarkably careful review of the clinical data showed that mutations in RPL5 are associated with multiple physical abnormalities including craniofacial thumb and heart anomalies whereas isolated thumb malformations are predominantly present in patients carrying mutations in RPL11 We also demonstrate that mutations of RPL5 RPL11 or RPS7 in DBA cells is associated with diverse defects in the maturation of ribosomal RNAs in the large or the small ribosomal subunit production pathway expanding the repertoire of ribosomal RNA processing defects associated with DBA
Develop more inquiry-based lab exercises1 C elegans crosses (Peter Barrett in Genetics lab)
2 Modifications on DNA transformation and lac operon exercises (PB)
3 The lsquotermitersquo experiment in Biol 1230L (Kristal Huggins and SKI)
4 In Cell Biology lab C elegans (endocytosis experiments) experiments with Planaria regeneration (adapted from MITHHMI) and recently with Daphnia (the water flea a small crustacean) adapted from the Nuffield Foundation where students expose the Daphnia to various cardioactive compounds measure changes in heart rate caused by effects on cellular receptors and design follow-up experiments (PB)
Assessment Strategies for Project Scicomp
Formative and summative
General scheme
bull Assessment tasks based on objectives
bull Develop assessment tools and pilot for validation
bull Apply to larger audience
bull Collect and score
bull Share and analyze data
Coordinated course sequences and our curricular design serve as a good platform
for intra and interdepartmental discussions
(weekly meetings lsquoSERGrsquo etc)
Labs
bull General observation on student participationinitiative
bull Data sheets (say 10 collecthellipsay any 4)
bull Midterm skills practical stations and multiple choice (excellent determinant)
bull Quizzes (5-10 depending on the lab)
bull Final exams
Course based research experiencee(CRE)
bull How they design their experiment
bull Notebooks lab techniques
bull Participation in class discussions
bull Ability to troubleshoot
bull Midterm Skills and oral exam along with traditional exam
bull Short answer (non multiple choice) questions
bull Research paper presentations
CREs at Xavier
bull Phage and Genomics
bull lsquoUndergraduate Researchrsquo for credits
bull Introduction to Mammalian Tissue Culture
The SEA-PHAGES ProgramhttpsseaphagesorgThe official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program
SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is a two-semester discovery-based undergraduate research course that begins with simple digging in the soil to find new viruses but progresses through a variety of microbiology techniques and eventually to complex genome annotation and bioinformatic analyses
CBE Life Sci Educ 2016 fall15(3) pii ar38 doi 101187cbe16-01-0078Increasing URM Undergraduate Student Success through Assessment-Driven Interventions A Multiyear Study Using Freshman-Level General Biology as a Model SystemCarmichael MC1 St Clair C1 Edwards AM2 Barrett P1 McFerrin H1 Davenport I1 Awad M1 Kundu A1 Ireland SK3
AbstractXavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students In this multiyear study with sim5500 participants data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course The three hour-long exams were common and administered concurrently to all students New exam questions were developed using Blooms taxonomy and exam results were analyzed statistically with validated assessment tools All but the comprehensive final exam were returned to students for self-evaluation and remediation Among other approaches course rigor was monitored by using an identical set of 60 questions on the final exam across 10 semesters Analysis of the identical sets of 60 final exam questions revealed that overall averages increased from 729 (2010) to 835 (2015) Regression analysis demonstrated a statistically significant correlation between high-risk students and their averages on the 60 questions Additional analysis demonstrated statistically significant improvements for at least one letter grade from midterm to final and a 20 increase in the course pass rates over time also for the high-risk population These results support the hypothesis that our data-driven interventions and assessment techniques are successful in improving student retention particularly for our academically at-risk students
Lecture Biol 1230
bull Competency E4 (chemistry in biology atomic bonds metabolic pathways thermodynamics)
bull Quizzes (formative assessment with Clickers)
bull The coordinator prepares the three lsquoOne hour examsrsquo (questions not from the textbook) instructors again reviewcomment
bull Question types range (content versus applications) and also lsquoBack pagersquo ( 20 of the exam grade) Formative assessment using the LXRtest software (Opscan6 scanner)
Final exam not returned cumulative and has had 60 questions (good discriminators based on the rpbvalues) commonly used on ALL final exams for the past five years Powerful tool for measuring studentsrsquo learning and applications over time and based on academic risk categories
Last Name First Name
Biology 1230 Exam 1 ldquoBack Pagerdquo Score _ 20 pts
I 5 pts Complete the following table for the 3 major components (subatomic particles) of the atom
hint electrical charge = positive negative or neutral and mass = 1 dalton or 11800 dalton 1 pt each
Particle Electrical Charge Mass
1 Proton 1 dalton
2 Electron
3 Neutron
II 5 pts In your own words compare and contrast the following two atoms A and B use the back of the previous page to
make as many observations as you can about similarities (and what they mean) and differences (and what they mean)
between the atoms
A B
III 5 pts Match the following by placing the corresponding in the space provided 1 pt each
_____ tertiary structure 1 produce H2O
_____ two ester linkages 2 is responsible for the 3-dimensional shape of a protein
_____ phosphodiester bonds 3 exist within diglycerides (diacylglyerols) and phospholipids
_____ dehydration synthesis reactions 4 are a type of lipid
_____ steroids 5 are formed when nucleic acids are synthesized
IV 5 pts Circle each of the variable (R) groups in the molecules shown below (3 pts)
a Which lsquoRrsquo group is polar ______ (write the corresponding in the space provided) (1 pt)
b Which lsquoRrsquo group is ionic ______ (write the corresponding in the space provided) (1 pt)
NH3+ OH CH3
1 2 3
12 neutrons
11 protons
10 electrons
13 neutrons
11 protons
11 electrons
Bio1230 Exam 1
Clickers and immediate feedback
Name _____________________________________________________________________________________________
This is a worksheet for your self-evaluation of study habits and exam preparedness Your answers on the corresponding
online exam surveys are confidential
~The average number of hours I spent per week reading the chapters andor reviewingprocessing class notes was (circle the
appropriate response)
zero to one one to two two to four greater than four
~I read the assignment before coming to class (circle the appropriate response)
never sometimes regularly
~I asked my instructor questions when I was confused about textbook material andor lecture material (circle the appropriate
response)
never sometimes regularly
~Overall I spent _____ hours specifically studying for this exam (Please fill in the blank)
~Prior to taking the exam I expected to get an approximate grade of (fill in the blank) _____
~My actual grade was a(n) (fill in the blank) _____
~Check all of the statements that apply to your performance on the exam
____ studied the right information ____ did not study the right information
____ studied the right information but did not ____ studied the right information and
understand it thought I understood it
____ used the class outlines to study ____ thought college would be easier
____ did not know what to study ____ other _____________________
____ did not think I would need to know the information in such detail
Analysis of Missed Questions I answered the question incorrectly because I Insert question number below in the correct category
did not study the information
studied the information but forgot it
did not understand the information in the
summary notes
confused similar concepts or terms (ie
isotopes and isomers)
misread or misunderstood the question
did not consider all of the answer choices
knew the correct answer - but chose an
incorrect answer by mistake
List other reason(s)
List other reason(s)
Please answer additional self-evaluation questions on the back of this page
Self-Evaluation of Study Habits amp Exam Preparedness for Biology 1230 Exam I or II or III (circle one)
Going forwardhellip
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
Stanhope et al (2017) Development of a Biological
Science Quantitative Reasoning Exam (BioSQuaRE)
CBE- Life Science Education Winter edition
December 1 2017
bull identification and validation of learning domains
bull iterative development of BioSQuaRE Instrument
bull evidence of validity
bull discussion of instruments utility for students individual
faculty and departments or programs
Visit wwwmacalestereduhhmibiosquare for more information
BLASTing Human and Other Organisms
bull Our goal is to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus(snake) The objective is to find and precisely map the coding regions using NCBIrsquos BLASTp search tool
bull Answer the following questions for each of the 4 organisms1 Describe the summary distributions2 Interpret the score the percent identity and the E-value If
obtain hit(s) are they likely due to chance If no hits why3 Analyze the alignments
Describe these Summary Distributions
Chimp
Cow
Snake
Chicken
Interpret the Scores E-values and Identities
Chimp
Cow
Snake
Chicken
Analyze the Alignments
Chimp
Cow
Snake
Chicken
Additional Questions of Interest
bull Our goal was to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus (snake) The objective is to find and precisely map the coding regions
bull Answer the following questions1 This presentation is showing only highly significant pairs How
do you think the alignments (scores e-values identities) differ if we analyze low significant pairs
2 Can you infer that this protein does not exist in this organism3 Give alternative explanations for the differences in scores e-
values and identities4 Is there an evolutionary relationship between sequences
Am J Hum Genet 2008 Dec 12 83(6) 769ndash780 Published online 2008 Dec 5 doi 101016jajhg200811004
Ribosomal Protein L5 and L11 Mutations Are Associated with Cleft Palate and Abnormal Thumbs in Diamond-Blackfan Anemia Patients
Hanna T Gazda12lowast
Mee Rie Sheen1
Adrianna Vlachos34
Valerie Choesmel56
Marie-Franccediloise ODonohue
56Hal Schneider
1Natasha Darras
1Catherine Hasman
1Colin A
Sieff27
Peter E Newburger8
Sarah E Ball9
Edyta Niewiadomska10
Michal Matysiak10
Jan M Zaucha
11Bertil Glader
12Charlotte Niemeyer
13Joerg J Meerpohl
13Eva Atsidaftos
34Jeffrey
M Lipton34
Pierre-Emmanuel Gleizes56
and Alan H Beggs12
Author information Article notes Copyright and License information AbstractDiamond-Blackfan anemia (DBA) a congenital bone-marrow-failure syndrome is characterized by red blood cell aplasia macrocytic anemia clinical heterogeneity and increased risk of malignancy Although anemia is the most prominent feature of DBA the disease is also characterized by growth retardation and congenital anomalies that are present in sim30ndash50 of patients The disease has been associated with mutations in four ribosomal protein (RP) genes RPS19 RPS24 RPS17 and RPL35A in about 30 of patients However the genetic basis of the remaining 70 of cases is still unknown Here we report the second known mutation in RPS17 and probable pathogenic mutations in three more RP genes RPL5 RPL11 and RPS7 In addition we identified rare variants of unknown significance in three other genes RPL36 RPS15 and RPS27A Remarkably careful review of the clinical data showed that mutations in RPL5 are associated with multiple physical abnormalities including craniofacial thumb and heart anomalies whereas isolated thumb malformations are predominantly present in patients carrying mutations in RPL11 We also demonstrate that mutations of RPL5 RPL11 or RPS7 in DBA cells is associated with diverse defects in the maturation of ribosomal RNAs in the large or the small ribosomal subunit production pathway expanding the repertoire of ribosomal RNA processing defects associated with DBA
Develop more inquiry-based lab exercises1 C elegans crosses (Peter Barrett in Genetics lab)
2 Modifications on DNA transformation and lac operon exercises (PB)
3 The lsquotermitersquo experiment in Biol 1230L (Kristal Huggins and SKI)
4 In Cell Biology lab C elegans (endocytosis experiments) experiments with Planaria regeneration (adapted from MITHHMI) and recently with Daphnia (the water flea a small crustacean) adapted from the Nuffield Foundation where students expose the Daphnia to various cardioactive compounds measure changes in heart rate caused by effects on cellular receptors and design follow-up experiments (PB)
Assessment Strategies for Project Scicomp
Formative and summative
General scheme
bull Assessment tasks based on objectives
bull Develop assessment tools and pilot for validation
bull Apply to larger audience
bull Collect and score
bull Share and analyze data
Coordinated course sequences and our curricular design serve as a good platform
for intra and interdepartmental discussions
(weekly meetings lsquoSERGrsquo etc)
Labs
bull General observation on student participationinitiative
bull Data sheets (say 10 collecthellipsay any 4)
bull Midterm skills practical stations and multiple choice (excellent determinant)
bull Quizzes (5-10 depending on the lab)
bull Final exams
Course based research experiencee(CRE)
bull How they design their experiment
bull Notebooks lab techniques
bull Participation in class discussions
bull Ability to troubleshoot
bull Midterm Skills and oral exam along with traditional exam
bull Short answer (non multiple choice) questions
bull Research paper presentations
CREs at Xavier
bull Phage and Genomics
bull lsquoUndergraduate Researchrsquo for credits
bull Introduction to Mammalian Tissue Culture
The SEA-PHAGES ProgramhttpsseaphagesorgThe official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program
SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is a two-semester discovery-based undergraduate research course that begins with simple digging in the soil to find new viruses but progresses through a variety of microbiology techniques and eventually to complex genome annotation and bioinformatic analyses
CBE Life Sci Educ 2016 fall15(3) pii ar38 doi 101187cbe16-01-0078Increasing URM Undergraduate Student Success through Assessment-Driven Interventions A Multiyear Study Using Freshman-Level General Biology as a Model SystemCarmichael MC1 St Clair C1 Edwards AM2 Barrett P1 McFerrin H1 Davenport I1 Awad M1 Kundu A1 Ireland SK3
AbstractXavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students In this multiyear study with sim5500 participants data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course The three hour-long exams were common and administered concurrently to all students New exam questions were developed using Blooms taxonomy and exam results were analyzed statistically with validated assessment tools All but the comprehensive final exam were returned to students for self-evaluation and remediation Among other approaches course rigor was monitored by using an identical set of 60 questions on the final exam across 10 semesters Analysis of the identical sets of 60 final exam questions revealed that overall averages increased from 729 (2010) to 835 (2015) Regression analysis demonstrated a statistically significant correlation between high-risk students and their averages on the 60 questions Additional analysis demonstrated statistically significant improvements for at least one letter grade from midterm to final and a 20 increase in the course pass rates over time also for the high-risk population These results support the hypothesis that our data-driven interventions and assessment techniques are successful in improving student retention particularly for our academically at-risk students
Lecture Biol 1230
bull Competency E4 (chemistry in biology atomic bonds metabolic pathways thermodynamics)
bull Quizzes (formative assessment with Clickers)
bull The coordinator prepares the three lsquoOne hour examsrsquo (questions not from the textbook) instructors again reviewcomment
bull Question types range (content versus applications) and also lsquoBack pagersquo ( 20 of the exam grade) Formative assessment using the LXRtest software (Opscan6 scanner)
Final exam not returned cumulative and has had 60 questions (good discriminators based on the rpbvalues) commonly used on ALL final exams for the past five years Powerful tool for measuring studentsrsquo learning and applications over time and based on academic risk categories
Last Name First Name
Biology 1230 Exam 1 ldquoBack Pagerdquo Score _ 20 pts
I 5 pts Complete the following table for the 3 major components (subatomic particles) of the atom
hint electrical charge = positive negative or neutral and mass = 1 dalton or 11800 dalton 1 pt each
Particle Electrical Charge Mass
1 Proton 1 dalton
2 Electron
3 Neutron
II 5 pts In your own words compare and contrast the following two atoms A and B use the back of the previous page to
make as many observations as you can about similarities (and what they mean) and differences (and what they mean)
between the atoms
A B
III 5 pts Match the following by placing the corresponding in the space provided 1 pt each
_____ tertiary structure 1 produce H2O
_____ two ester linkages 2 is responsible for the 3-dimensional shape of a protein
_____ phosphodiester bonds 3 exist within diglycerides (diacylglyerols) and phospholipids
_____ dehydration synthesis reactions 4 are a type of lipid
_____ steroids 5 are formed when nucleic acids are synthesized
IV 5 pts Circle each of the variable (R) groups in the molecules shown below (3 pts)
a Which lsquoRrsquo group is polar ______ (write the corresponding in the space provided) (1 pt)
b Which lsquoRrsquo group is ionic ______ (write the corresponding in the space provided) (1 pt)
NH3+ OH CH3
1 2 3
12 neutrons
11 protons
10 electrons
13 neutrons
11 protons
11 electrons
Bio1230 Exam 1
Clickers and immediate feedback
Name _____________________________________________________________________________________________
This is a worksheet for your self-evaluation of study habits and exam preparedness Your answers on the corresponding
online exam surveys are confidential
~The average number of hours I spent per week reading the chapters andor reviewingprocessing class notes was (circle the
appropriate response)
zero to one one to two two to four greater than four
~I read the assignment before coming to class (circle the appropriate response)
never sometimes regularly
~I asked my instructor questions when I was confused about textbook material andor lecture material (circle the appropriate
response)
never sometimes regularly
~Overall I spent _____ hours specifically studying for this exam (Please fill in the blank)
~Prior to taking the exam I expected to get an approximate grade of (fill in the blank) _____
~My actual grade was a(n) (fill in the blank) _____
~Check all of the statements that apply to your performance on the exam
____ studied the right information ____ did not study the right information
____ studied the right information but did not ____ studied the right information and
understand it thought I understood it
____ used the class outlines to study ____ thought college would be easier
____ did not know what to study ____ other _____________________
____ did not think I would need to know the information in such detail
Analysis of Missed Questions I answered the question incorrectly because I Insert question number below in the correct category
did not study the information
studied the information but forgot it
did not understand the information in the
summary notes
confused similar concepts or terms (ie
isotopes and isomers)
misread or misunderstood the question
did not consider all of the answer choices
knew the correct answer - but chose an
incorrect answer by mistake
List other reason(s)
List other reason(s)
Please answer additional self-evaluation questions on the back of this page
Self-Evaluation of Study Habits amp Exam Preparedness for Biology 1230 Exam I or II or III (circle one)
Going forwardhellip
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
BLASTing Human and Other Organisms
bull Our goal is to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus(snake) The objective is to find and precisely map the coding regions using NCBIrsquos BLASTp search tool
bull Answer the following questions for each of the 4 organisms1 Describe the summary distributions2 Interpret the score the percent identity and the E-value If
obtain hit(s) are they likely due to chance If no hits why3 Analyze the alignments
Describe these Summary Distributions
Chimp
Cow
Snake
Chicken
Interpret the Scores E-values and Identities
Chimp
Cow
Snake
Chicken
Analyze the Alignments
Chimp
Cow
Snake
Chicken
Additional Questions of Interest
bull Our goal was to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus (snake) The objective is to find and precisely map the coding regions
bull Answer the following questions1 This presentation is showing only highly significant pairs How
do you think the alignments (scores e-values identities) differ if we analyze low significant pairs
2 Can you infer that this protein does not exist in this organism3 Give alternative explanations for the differences in scores e-
values and identities4 Is there an evolutionary relationship between sequences
Am J Hum Genet 2008 Dec 12 83(6) 769ndash780 Published online 2008 Dec 5 doi 101016jajhg200811004
Ribosomal Protein L5 and L11 Mutations Are Associated with Cleft Palate and Abnormal Thumbs in Diamond-Blackfan Anemia Patients
Hanna T Gazda12lowast
Mee Rie Sheen1
Adrianna Vlachos34
Valerie Choesmel56
Marie-Franccediloise ODonohue
56Hal Schneider
1Natasha Darras
1Catherine Hasman
1Colin A
Sieff27
Peter E Newburger8
Sarah E Ball9
Edyta Niewiadomska10
Michal Matysiak10
Jan M Zaucha
11Bertil Glader
12Charlotte Niemeyer
13Joerg J Meerpohl
13Eva Atsidaftos
34Jeffrey
M Lipton34
Pierre-Emmanuel Gleizes56
and Alan H Beggs12
Author information Article notes Copyright and License information AbstractDiamond-Blackfan anemia (DBA) a congenital bone-marrow-failure syndrome is characterized by red blood cell aplasia macrocytic anemia clinical heterogeneity and increased risk of malignancy Although anemia is the most prominent feature of DBA the disease is also characterized by growth retardation and congenital anomalies that are present in sim30ndash50 of patients The disease has been associated with mutations in four ribosomal protein (RP) genes RPS19 RPS24 RPS17 and RPL35A in about 30 of patients However the genetic basis of the remaining 70 of cases is still unknown Here we report the second known mutation in RPS17 and probable pathogenic mutations in three more RP genes RPL5 RPL11 and RPS7 In addition we identified rare variants of unknown significance in three other genes RPL36 RPS15 and RPS27A Remarkably careful review of the clinical data showed that mutations in RPL5 are associated with multiple physical abnormalities including craniofacial thumb and heart anomalies whereas isolated thumb malformations are predominantly present in patients carrying mutations in RPL11 We also demonstrate that mutations of RPL5 RPL11 or RPS7 in DBA cells is associated with diverse defects in the maturation of ribosomal RNAs in the large or the small ribosomal subunit production pathway expanding the repertoire of ribosomal RNA processing defects associated with DBA
Develop more inquiry-based lab exercises1 C elegans crosses (Peter Barrett in Genetics lab)
2 Modifications on DNA transformation and lac operon exercises (PB)
3 The lsquotermitersquo experiment in Biol 1230L (Kristal Huggins and SKI)
4 In Cell Biology lab C elegans (endocytosis experiments) experiments with Planaria regeneration (adapted from MITHHMI) and recently with Daphnia (the water flea a small crustacean) adapted from the Nuffield Foundation where students expose the Daphnia to various cardioactive compounds measure changes in heart rate caused by effects on cellular receptors and design follow-up experiments (PB)
Assessment Strategies for Project Scicomp
Formative and summative
General scheme
bull Assessment tasks based on objectives
bull Develop assessment tools and pilot for validation
bull Apply to larger audience
bull Collect and score
bull Share and analyze data
Coordinated course sequences and our curricular design serve as a good platform
for intra and interdepartmental discussions
(weekly meetings lsquoSERGrsquo etc)
Labs
bull General observation on student participationinitiative
bull Data sheets (say 10 collecthellipsay any 4)
bull Midterm skills practical stations and multiple choice (excellent determinant)
bull Quizzes (5-10 depending on the lab)
bull Final exams
Course based research experiencee(CRE)
bull How they design their experiment
bull Notebooks lab techniques
bull Participation in class discussions
bull Ability to troubleshoot
bull Midterm Skills and oral exam along with traditional exam
bull Short answer (non multiple choice) questions
bull Research paper presentations
CREs at Xavier
bull Phage and Genomics
bull lsquoUndergraduate Researchrsquo for credits
bull Introduction to Mammalian Tissue Culture
The SEA-PHAGES ProgramhttpsseaphagesorgThe official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program
SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is a two-semester discovery-based undergraduate research course that begins with simple digging in the soil to find new viruses but progresses through a variety of microbiology techniques and eventually to complex genome annotation and bioinformatic analyses
CBE Life Sci Educ 2016 fall15(3) pii ar38 doi 101187cbe16-01-0078Increasing URM Undergraduate Student Success through Assessment-Driven Interventions A Multiyear Study Using Freshman-Level General Biology as a Model SystemCarmichael MC1 St Clair C1 Edwards AM2 Barrett P1 McFerrin H1 Davenport I1 Awad M1 Kundu A1 Ireland SK3
AbstractXavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students In this multiyear study with sim5500 participants data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course The three hour-long exams were common and administered concurrently to all students New exam questions were developed using Blooms taxonomy and exam results were analyzed statistically with validated assessment tools All but the comprehensive final exam were returned to students for self-evaluation and remediation Among other approaches course rigor was monitored by using an identical set of 60 questions on the final exam across 10 semesters Analysis of the identical sets of 60 final exam questions revealed that overall averages increased from 729 (2010) to 835 (2015) Regression analysis demonstrated a statistically significant correlation between high-risk students and their averages on the 60 questions Additional analysis demonstrated statistically significant improvements for at least one letter grade from midterm to final and a 20 increase in the course pass rates over time also for the high-risk population These results support the hypothesis that our data-driven interventions and assessment techniques are successful in improving student retention particularly for our academically at-risk students
Lecture Biol 1230
bull Competency E4 (chemistry in biology atomic bonds metabolic pathways thermodynamics)
bull Quizzes (formative assessment with Clickers)
bull The coordinator prepares the three lsquoOne hour examsrsquo (questions not from the textbook) instructors again reviewcomment
bull Question types range (content versus applications) and also lsquoBack pagersquo ( 20 of the exam grade) Formative assessment using the LXRtest software (Opscan6 scanner)
Final exam not returned cumulative and has had 60 questions (good discriminators based on the rpbvalues) commonly used on ALL final exams for the past five years Powerful tool for measuring studentsrsquo learning and applications over time and based on academic risk categories
Last Name First Name
Biology 1230 Exam 1 ldquoBack Pagerdquo Score _ 20 pts
I 5 pts Complete the following table for the 3 major components (subatomic particles) of the atom
hint electrical charge = positive negative or neutral and mass = 1 dalton or 11800 dalton 1 pt each
Particle Electrical Charge Mass
1 Proton 1 dalton
2 Electron
3 Neutron
II 5 pts In your own words compare and contrast the following two atoms A and B use the back of the previous page to
make as many observations as you can about similarities (and what they mean) and differences (and what they mean)
between the atoms
A B
III 5 pts Match the following by placing the corresponding in the space provided 1 pt each
_____ tertiary structure 1 produce H2O
_____ two ester linkages 2 is responsible for the 3-dimensional shape of a protein
_____ phosphodiester bonds 3 exist within diglycerides (diacylglyerols) and phospholipids
_____ dehydration synthesis reactions 4 are a type of lipid
_____ steroids 5 are formed when nucleic acids are synthesized
IV 5 pts Circle each of the variable (R) groups in the molecules shown below (3 pts)
a Which lsquoRrsquo group is polar ______ (write the corresponding in the space provided) (1 pt)
b Which lsquoRrsquo group is ionic ______ (write the corresponding in the space provided) (1 pt)
NH3+ OH CH3
1 2 3
12 neutrons
11 protons
10 electrons
13 neutrons
11 protons
11 electrons
Bio1230 Exam 1
Clickers and immediate feedback
Name _____________________________________________________________________________________________
This is a worksheet for your self-evaluation of study habits and exam preparedness Your answers on the corresponding
online exam surveys are confidential
~The average number of hours I spent per week reading the chapters andor reviewingprocessing class notes was (circle the
appropriate response)
zero to one one to two two to four greater than four
~I read the assignment before coming to class (circle the appropriate response)
never sometimes regularly
~I asked my instructor questions when I was confused about textbook material andor lecture material (circle the appropriate
response)
never sometimes regularly
~Overall I spent _____ hours specifically studying for this exam (Please fill in the blank)
~Prior to taking the exam I expected to get an approximate grade of (fill in the blank) _____
~My actual grade was a(n) (fill in the blank) _____
~Check all of the statements that apply to your performance on the exam
____ studied the right information ____ did not study the right information
____ studied the right information but did not ____ studied the right information and
understand it thought I understood it
____ used the class outlines to study ____ thought college would be easier
____ did not know what to study ____ other _____________________
____ did not think I would need to know the information in such detail
Analysis of Missed Questions I answered the question incorrectly because I Insert question number below in the correct category
did not study the information
studied the information but forgot it
did not understand the information in the
summary notes
confused similar concepts or terms (ie
isotopes and isomers)
misread or misunderstood the question
did not consider all of the answer choices
knew the correct answer - but chose an
incorrect answer by mistake
List other reason(s)
List other reason(s)
Please answer additional self-evaluation questions on the back of this page
Self-Evaluation of Study Habits amp Exam Preparedness for Biology 1230 Exam I or II or III (circle one)
Going forwardhellip
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
Describe these Summary Distributions
Chimp
Cow
Snake
Chicken
Interpret the Scores E-values and Identities
Chimp
Cow
Snake
Chicken
Analyze the Alignments
Chimp
Cow
Snake
Chicken
Additional Questions of Interest
bull Our goal was to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus (snake) The objective is to find and precisely map the coding regions
bull Answer the following questions1 This presentation is showing only highly significant pairs How
do you think the alignments (scores e-values identities) differ if we analyze low significant pairs
2 Can you infer that this protein does not exist in this organism3 Give alternative explanations for the differences in scores e-
values and identities4 Is there an evolutionary relationship between sequences
Am J Hum Genet 2008 Dec 12 83(6) 769ndash780 Published online 2008 Dec 5 doi 101016jajhg200811004
Ribosomal Protein L5 and L11 Mutations Are Associated with Cleft Palate and Abnormal Thumbs in Diamond-Blackfan Anemia Patients
Hanna T Gazda12lowast
Mee Rie Sheen1
Adrianna Vlachos34
Valerie Choesmel56
Marie-Franccediloise ODonohue
56Hal Schneider
1Natasha Darras
1Catherine Hasman
1Colin A
Sieff27
Peter E Newburger8
Sarah E Ball9
Edyta Niewiadomska10
Michal Matysiak10
Jan M Zaucha
11Bertil Glader
12Charlotte Niemeyer
13Joerg J Meerpohl
13Eva Atsidaftos
34Jeffrey
M Lipton34
Pierre-Emmanuel Gleizes56
and Alan H Beggs12
Author information Article notes Copyright and License information AbstractDiamond-Blackfan anemia (DBA) a congenital bone-marrow-failure syndrome is characterized by red blood cell aplasia macrocytic anemia clinical heterogeneity and increased risk of malignancy Although anemia is the most prominent feature of DBA the disease is also characterized by growth retardation and congenital anomalies that are present in sim30ndash50 of patients The disease has been associated with mutations in four ribosomal protein (RP) genes RPS19 RPS24 RPS17 and RPL35A in about 30 of patients However the genetic basis of the remaining 70 of cases is still unknown Here we report the second known mutation in RPS17 and probable pathogenic mutations in three more RP genes RPL5 RPL11 and RPS7 In addition we identified rare variants of unknown significance in three other genes RPL36 RPS15 and RPS27A Remarkably careful review of the clinical data showed that mutations in RPL5 are associated with multiple physical abnormalities including craniofacial thumb and heart anomalies whereas isolated thumb malformations are predominantly present in patients carrying mutations in RPL11 We also demonstrate that mutations of RPL5 RPL11 or RPS7 in DBA cells is associated with diverse defects in the maturation of ribosomal RNAs in the large or the small ribosomal subunit production pathway expanding the repertoire of ribosomal RNA processing defects associated with DBA
Develop more inquiry-based lab exercises1 C elegans crosses (Peter Barrett in Genetics lab)
2 Modifications on DNA transformation and lac operon exercises (PB)
3 The lsquotermitersquo experiment in Biol 1230L (Kristal Huggins and SKI)
4 In Cell Biology lab C elegans (endocytosis experiments) experiments with Planaria regeneration (adapted from MITHHMI) and recently with Daphnia (the water flea a small crustacean) adapted from the Nuffield Foundation where students expose the Daphnia to various cardioactive compounds measure changes in heart rate caused by effects on cellular receptors and design follow-up experiments (PB)
Assessment Strategies for Project Scicomp
Formative and summative
General scheme
bull Assessment tasks based on objectives
bull Develop assessment tools and pilot for validation
bull Apply to larger audience
bull Collect and score
bull Share and analyze data
Coordinated course sequences and our curricular design serve as a good platform
for intra and interdepartmental discussions
(weekly meetings lsquoSERGrsquo etc)
Labs
bull General observation on student participationinitiative
bull Data sheets (say 10 collecthellipsay any 4)
bull Midterm skills practical stations and multiple choice (excellent determinant)
bull Quizzes (5-10 depending on the lab)
bull Final exams
Course based research experiencee(CRE)
bull How they design their experiment
bull Notebooks lab techniques
bull Participation in class discussions
bull Ability to troubleshoot
bull Midterm Skills and oral exam along with traditional exam
bull Short answer (non multiple choice) questions
bull Research paper presentations
CREs at Xavier
bull Phage and Genomics
bull lsquoUndergraduate Researchrsquo for credits
bull Introduction to Mammalian Tissue Culture
The SEA-PHAGES ProgramhttpsseaphagesorgThe official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program
SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is a two-semester discovery-based undergraduate research course that begins with simple digging in the soil to find new viruses but progresses through a variety of microbiology techniques and eventually to complex genome annotation and bioinformatic analyses
CBE Life Sci Educ 2016 fall15(3) pii ar38 doi 101187cbe16-01-0078Increasing URM Undergraduate Student Success through Assessment-Driven Interventions A Multiyear Study Using Freshman-Level General Biology as a Model SystemCarmichael MC1 St Clair C1 Edwards AM2 Barrett P1 McFerrin H1 Davenport I1 Awad M1 Kundu A1 Ireland SK3
AbstractXavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students In this multiyear study with sim5500 participants data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course The three hour-long exams were common and administered concurrently to all students New exam questions were developed using Blooms taxonomy and exam results were analyzed statistically with validated assessment tools All but the comprehensive final exam were returned to students for self-evaluation and remediation Among other approaches course rigor was monitored by using an identical set of 60 questions on the final exam across 10 semesters Analysis of the identical sets of 60 final exam questions revealed that overall averages increased from 729 (2010) to 835 (2015) Regression analysis demonstrated a statistically significant correlation between high-risk students and their averages on the 60 questions Additional analysis demonstrated statistically significant improvements for at least one letter grade from midterm to final and a 20 increase in the course pass rates over time also for the high-risk population These results support the hypothesis that our data-driven interventions and assessment techniques are successful in improving student retention particularly for our academically at-risk students
Lecture Biol 1230
bull Competency E4 (chemistry in biology atomic bonds metabolic pathways thermodynamics)
bull Quizzes (formative assessment with Clickers)
bull The coordinator prepares the three lsquoOne hour examsrsquo (questions not from the textbook) instructors again reviewcomment
bull Question types range (content versus applications) and also lsquoBack pagersquo ( 20 of the exam grade) Formative assessment using the LXRtest software (Opscan6 scanner)
Final exam not returned cumulative and has had 60 questions (good discriminators based on the rpbvalues) commonly used on ALL final exams for the past five years Powerful tool for measuring studentsrsquo learning and applications over time and based on academic risk categories
Last Name First Name
Biology 1230 Exam 1 ldquoBack Pagerdquo Score _ 20 pts
I 5 pts Complete the following table for the 3 major components (subatomic particles) of the atom
hint electrical charge = positive negative or neutral and mass = 1 dalton or 11800 dalton 1 pt each
Particle Electrical Charge Mass
1 Proton 1 dalton
2 Electron
3 Neutron
II 5 pts In your own words compare and contrast the following two atoms A and B use the back of the previous page to
make as many observations as you can about similarities (and what they mean) and differences (and what they mean)
between the atoms
A B
III 5 pts Match the following by placing the corresponding in the space provided 1 pt each
_____ tertiary structure 1 produce H2O
_____ two ester linkages 2 is responsible for the 3-dimensional shape of a protein
_____ phosphodiester bonds 3 exist within diglycerides (diacylglyerols) and phospholipids
_____ dehydration synthesis reactions 4 are a type of lipid
_____ steroids 5 are formed when nucleic acids are synthesized
IV 5 pts Circle each of the variable (R) groups in the molecules shown below (3 pts)
a Which lsquoRrsquo group is polar ______ (write the corresponding in the space provided) (1 pt)
b Which lsquoRrsquo group is ionic ______ (write the corresponding in the space provided) (1 pt)
NH3+ OH CH3
1 2 3
12 neutrons
11 protons
10 electrons
13 neutrons
11 protons
11 electrons
Bio1230 Exam 1
Clickers and immediate feedback
Name _____________________________________________________________________________________________
This is a worksheet for your self-evaluation of study habits and exam preparedness Your answers on the corresponding
online exam surveys are confidential
~The average number of hours I spent per week reading the chapters andor reviewingprocessing class notes was (circle the
appropriate response)
zero to one one to two two to four greater than four
~I read the assignment before coming to class (circle the appropriate response)
never sometimes regularly
~I asked my instructor questions when I was confused about textbook material andor lecture material (circle the appropriate
response)
never sometimes regularly
~Overall I spent _____ hours specifically studying for this exam (Please fill in the blank)
~Prior to taking the exam I expected to get an approximate grade of (fill in the blank) _____
~My actual grade was a(n) (fill in the blank) _____
~Check all of the statements that apply to your performance on the exam
____ studied the right information ____ did not study the right information
____ studied the right information but did not ____ studied the right information and
understand it thought I understood it
____ used the class outlines to study ____ thought college would be easier
____ did not know what to study ____ other _____________________
____ did not think I would need to know the information in such detail
Analysis of Missed Questions I answered the question incorrectly because I Insert question number below in the correct category
did not study the information
studied the information but forgot it
did not understand the information in the
summary notes
confused similar concepts or terms (ie
isotopes and isomers)
misread or misunderstood the question
did not consider all of the answer choices
knew the correct answer - but chose an
incorrect answer by mistake
List other reason(s)
List other reason(s)
Please answer additional self-evaluation questions on the back of this page
Self-Evaluation of Study Habits amp Exam Preparedness for Biology 1230 Exam I or II or III (circle one)
Going forwardhellip
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
Interpret the Scores E-values and Identities
Chimp
Cow
Snake
Chicken
Analyze the Alignments
Chimp
Cow
Snake
Chicken
Additional Questions of Interest
bull Our goal was to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus (snake) The objective is to find and precisely map the coding regions
bull Answer the following questions1 This presentation is showing only highly significant pairs How
do you think the alignments (scores e-values identities) differ if we analyze low significant pairs
2 Can you infer that this protein does not exist in this organism3 Give alternative explanations for the differences in scores e-
values and identities4 Is there an evolutionary relationship between sequences
Am J Hum Genet 2008 Dec 12 83(6) 769ndash780 Published online 2008 Dec 5 doi 101016jajhg200811004
Ribosomal Protein L5 and L11 Mutations Are Associated with Cleft Palate and Abnormal Thumbs in Diamond-Blackfan Anemia Patients
Hanna T Gazda12lowast
Mee Rie Sheen1
Adrianna Vlachos34
Valerie Choesmel56
Marie-Franccediloise ODonohue
56Hal Schneider
1Natasha Darras
1Catherine Hasman
1Colin A
Sieff27
Peter E Newburger8
Sarah E Ball9
Edyta Niewiadomska10
Michal Matysiak10
Jan M Zaucha
11Bertil Glader
12Charlotte Niemeyer
13Joerg J Meerpohl
13Eva Atsidaftos
34Jeffrey
M Lipton34
Pierre-Emmanuel Gleizes56
and Alan H Beggs12
Author information Article notes Copyright and License information AbstractDiamond-Blackfan anemia (DBA) a congenital bone-marrow-failure syndrome is characterized by red blood cell aplasia macrocytic anemia clinical heterogeneity and increased risk of malignancy Although anemia is the most prominent feature of DBA the disease is also characterized by growth retardation and congenital anomalies that are present in sim30ndash50 of patients The disease has been associated with mutations in four ribosomal protein (RP) genes RPS19 RPS24 RPS17 and RPL35A in about 30 of patients However the genetic basis of the remaining 70 of cases is still unknown Here we report the second known mutation in RPS17 and probable pathogenic mutations in three more RP genes RPL5 RPL11 and RPS7 In addition we identified rare variants of unknown significance in three other genes RPL36 RPS15 and RPS27A Remarkably careful review of the clinical data showed that mutations in RPL5 are associated with multiple physical abnormalities including craniofacial thumb and heart anomalies whereas isolated thumb malformations are predominantly present in patients carrying mutations in RPL11 We also demonstrate that mutations of RPL5 RPL11 or RPS7 in DBA cells is associated with diverse defects in the maturation of ribosomal RNAs in the large or the small ribosomal subunit production pathway expanding the repertoire of ribosomal RNA processing defects associated with DBA
Develop more inquiry-based lab exercises1 C elegans crosses (Peter Barrett in Genetics lab)
2 Modifications on DNA transformation and lac operon exercises (PB)
3 The lsquotermitersquo experiment in Biol 1230L (Kristal Huggins and SKI)
4 In Cell Biology lab C elegans (endocytosis experiments) experiments with Planaria regeneration (adapted from MITHHMI) and recently with Daphnia (the water flea a small crustacean) adapted from the Nuffield Foundation where students expose the Daphnia to various cardioactive compounds measure changes in heart rate caused by effects on cellular receptors and design follow-up experiments (PB)
Assessment Strategies for Project Scicomp
Formative and summative
General scheme
bull Assessment tasks based on objectives
bull Develop assessment tools and pilot for validation
bull Apply to larger audience
bull Collect and score
bull Share and analyze data
Coordinated course sequences and our curricular design serve as a good platform
for intra and interdepartmental discussions
(weekly meetings lsquoSERGrsquo etc)
Labs
bull General observation on student participationinitiative
bull Data sheets (say 10 collecthellipsay any 4)
bull Midterm skills practical stations and multiple choice (excellent determinant)
bull Quizzes (5-10 depending on the lab)
bull Final exams
Course based research experiencee(CRE)
bull How they design their experiment
bull Notebooks lab techniques
bull Participation in class discussions
bull Ability to troubleshoot
bull Midterm Skills and oral exam along with traditional exam
bull Short answer (non multiple choice) questions
bull Research paper presentations
CREs at Xavier
bull Phage and Genomics
bull lsquoUndergraduate Researchrsquo for credits
bull Introduction to Mammalian Tissue Culture
The SEA-PHAGES ProgramhttpsseaphagesorgThe official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program
SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is a two-semester discovery-based undergraduate research course that begins with simple digging in the soil to find new viruses but progresses through a variety of microbiology techniques and eventually to complex genome annotation and bioinformatic analyses
CBE Life Sci Educ 2016 fall15(3) pii ar38 doi 101187cbe16-01-0078Increasing URM Undergraduate Student Success through Assessment-Driven Interventions A Multiyear Study Using Freshman-Level General Biology as a Model SystemCarmichael MC1 St Clair C1 Edwards AM2 Barrett P1 McFerrin H1 Davenport I1 Awad M1 Kundu A1 Ireland SK3
AbstractXavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students In this multiyear study with sim5500 participants data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course The three hour-long exams were common and administered concurrently to all students New exam questions were developed using Blooms taxonomy and exam results were analyzed statistically with validated assessment tools All but the comprehensive final exam were returned to students for self-evaluation and remediation Among other approaches course rigor was monitored by using an identical set of 60 questions on the final exam across 10 semesters Analysis of the identical sets of 60 final exam questions revealed that overall averages increased from 729 (2010) to 835 (2015) Regression analysis demonstrated a statistically significant correlation between high-risk students and their averages on the 60 questions Additional analysis demonstrated statistically significant improvements for at least one letter grade from midterm to final and a 20 increase in the course pass rates over time also for the high-risk population These results support the hypothesis that our data-driven interventions and assessment techniques are successful in improving student retention particularly for our academically at-risk students
Lecture Biol 1230
bull Competency E4 (chemistry in biology atomic bonds metabolic pathways thermodynamics)
bull Quizzes (formative assessment with Clickers)
bull The coordinator prepares the three lsquoOne hour examsrsquo (questions not from the textbook) instructors again reviewcomment
bull Question types range (content versus applications) and also lsquoBack pagersquo ( 20 of the exam grade) Formative assessment using the LXRtest software (Opscan6 scanner)
Final exam not returned cumulative and has had 60 questions (good discriminators based on the rpbvalues) commonly used on ALL final exams for the past five years Powerful tool for measuring studentsrsquo learning and applications over time and based on academic risk categories
Last Name First Name
Biology 1230 Exam 1 ldquoBack Pagerdquo Score _ 20 pts
I 5 pts Complete the following table for the 3 major components (subatomic particles) of the atom
hint electrical charge = positive negative or neutral and mass = 1 dalton or 11800 dalton 1 pt each
Particle Electrical Charge Mass
1 Proton 1 dalton
2 Electron
3 Neutron
II 5 pts In your own words compare and contrast the following two atoms A and B use the back of the previous page to
make as many observations as you can about similarities (and what they mean) and differences (and what they mean)
between the atoms
A B
III 5 pts Match the following by placing the corresponding in the space provided 1 pt each
_____ tertiary structure 1 produce H2O
_____ two ester linkages 2 is responsible for the 3-dimensional shape of a protein
_____ phosphodiester bonds 3 exist within diglycerides (diacylglyerols) and phospholipids
_____ dehydration synthesis reactions 4 are a type of lipid
_____ steroids 5 are formed when nucleic acids are synthesized
IV 5 pts Circle each of the variable (R) groups in the molecules shown below (3 pts)
a Which lsquoRrsquo group is polar ______ (write the corresponding in the space provided) (1 pt)
b Which lsquoRrsquo group is ionic ______ (write the corresponding in the space provided) (1 pt)
NH3+ OH CH3
1 2 3
12 neutrons
11 protons
10 electrons
13 neutrons
11 protons
11 electrons
Bio1230 Exam 1
Clickers and immediate feedback
Name _____________________________________________________________________________________________
This is a worksheet for your self-evaluation of study habits and exam preparedness Your answers on the corresponding
online exam surveys are confidential
~The average number of hours I spent per week reading the chapters andor reviewingprocessing class notes was (circle the
appropriate response)
zero to one one to two two to four greater than four
~I read the assignment before coming to class (circle the appropriate response)
never sometimes regularly
~I asked my instructor questions when I was confused about textbook material andor lecture material (circle the appropriate
response)
never sometimes regularly
~Overall I spent _____ hours specifically studying for this exam (Please fill in the blank)
~Prior to taking the exam I expected to get an approximate grade of (fill in the blank) _____
~My actual grade was a(n) (fill in the blank) _____
~Check all of the statements that apply to your performance on the exam
____ studied the right information ____ did not study the right information
____ studied the right information but did not ____ studied the right information and
understand it thought I understood it
____ used the class outlines to study ____ thought college would be easier
____ did not know what to study ____ other _____________________
____ did not think I would need to know the information in such detail
Analysis of Missed Questions I answered the question incorrectly because I Insert question number below in the correct category
did not study the information
studied the information but forgot it
did not understand the information in the
summary notes
confused similar concepts or terms (ie
isotopes and isomers)
misread or misunderstood the question
did not consider all of the answer choices
knew the correct answer - but chose an
incorrect answer by mistake
List other reason(s)
List other reason(s)
Please answer additional self-evaluation questions on the back of this page
Self-Evaluation of Study Habits amp Exam Preparedness for Biology 1230 Exam I or II or III (circle one)
Going forwardhellip
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
Analyze the Alignments
Chimp
Cow
Snake
Chicken
Additional Questions of Interest
bull Our goal was to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus (snake) The objective is to find and precisely map the coding regions
bull Answer the following questions1 This presentation is showing only highly significant pairs How
do you think the alignments (scores e-values identities) differ if we analyze low significant pairs
2 Can you infer that this protein does not exist in this organism3 Give alternative explanations for the differences in scores e-
values and identities4 Is there an evolutionary relationship between sequences
Am J Hum Genet 2008 Dec 12 83(6) 769ndash780 Published online 2008 Dec 5 doi 101016jajhg200811004
Ribosomal Protein L5 and L11 Mutations Are Associated with Cleft Palate and Abnormal Thumbs in Diamond-Blackfan Anemia Patients
Hanna T Gazda12lowast
Mee Rie Sheen1
Adrianna Vlachos34
Valerie Choesmel56
Marie-Franccediloise ODonohue
56Hal Schneider
1Natasha Darras
1Catherine Hasman
1Colin A
Sieff27
Peter E Newburger8
Sarah E Ball9
Edyta Niewiadomska10
Michal Matysiak10
Jan M Zaucha
11Bertil Glader
12Charlotte Niemeyer
13Joerg J Meerpohl
13Eva Atsidaftos
34Jeffrey
M Lipton34
Pierre-Emmanuel Gleizes56
and Alan H Beggs12
Author information Article notes Copyright and License information AbstractDiamond-Blackfan anemia (DBA) a congenital bone-marrow-failure syndrome is characterized by red blood cell aplasia macrocytic anemia clinical heterogeneity and increased risk of malignancy Although anemia is the most prominent feature of DBA the disease is also characterized by growth retardation and congenital anomalies that are present in sim30ndash50 of patients The disease has been associated with mutations in four ribosomal protein (RP) genes RPS19 RPS24 RPS17 and RPL35A in about 30 of patients However the genetic basis of the remaining 70 of cases is still unknown Here we report the second known mutation in RPS17 and probable pathogenic mutations in three more RP genes RPL5 RPL11 and RPS7 In addition we identified rare variants of unknown significance in three other genes RPL36 RPS15 and RPS27A Remarkably careful review of the clinical data showed that mutations in RPL5 are associated with multiple physical abnormalities including craniofacial thumb and heart anomalies whereas isolated thumb malformations are predominantly present in patients carrying mutations in RPL11 We also demonstrate that mutations of RPL5 RPL11 or RPS7 in DBA cells is associated with diverse defects in the maturation of ribosomal RNAs in the large or the small ribosomal subunit production pathway expanding the repertoire of ribosomal RNA processing defects associated with DBA
Develop more inquiry-based lab exercises1 C elegans crosses (Peter Barrett in Genetics lab)
2 Modifications on DNA transformation and lac operon exercises (PB)
3 The lsquotermitersquo experiment in Biol 1230L (Kristal Huggins and SKI)
4 In Cell Biology lab C elegans (endocytosis experiments) experiments with Planaria regeneration (adapted from MITHHMI) and recently with Daphnia (the water flea a small crustacean) adapted from the Nuffield Foundation where students expose the Daphnia to various cardioactive compounds measure changes in heart rate caused by effects on cellular receptors and design follow-up experiments (PB)
Assessment Strategies for Project Scicomp
Formative and summative
General scheme
bull Assessment tasks based on objectives
bull Develop assessment tools and pilot for validation
bull Apply to larger audience
bull Collect and score
bull Share and analyze data
Coordinated course sequences and our curricular design serve as a good platform
for intra and interdepartmental discussions
(weekly meetings lsquoSERGrsquo etc)
Labs
bull General observation on student participationinitiative
bull Data sheets (say 10 collecthellipsay any 4)
bull Midterm skills practical stations and multiple choice (excellent determinant)
bull Quizzes (5-10 depending on the lab)
bull Final exams
Course based research experiencee(CRE)
bull How they design their experiment
bull Notebooks lab techniques
bull Participation in class discussions
bull Ability to troubleshoot
bull Midterm Skills and oral exam along with traditional exam
bull Short answer (non multiple choice) questions
bull Research paper presentations
CREs at Xavier
bull Phage and Genomics
bull lsquoUndergraduate Researchrsquo for credits
bull Introduction to Mammalian Tissue Culture
The SEA-PHAGES ProgramhttpsseaphagesorgThe official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program
SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is a two-semester discovery-based undergraduate research course that begins with simple digging in the soil to find new viruses but progresses through a variety of microbiology techniques and eventually to complex genome annotation and bioinformatic analyses
CBE Life Sci Educ 2016 fall15(3) pii ar38 doi 101187cbe16-01-0078Increasing URM Undergraduate Student Success through Assessment-Driven Interventions A Multiyear Study Using Freshman-Level General Biology as a Model SystemCarmichael MC1 St Clair C1 Edwards AM2 Barrett P1 McFerrin H1 Davenport I1 Awad M1 Kundu A1 Ireland SK3
AbstractXavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students In this multiyear study with sim5500 participants data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course The three hour-long exams were common and administered concurrently to all students New exam questions were developed using Blooms taxonomy and exam results were analyzed statistically with validated assessment tools All but the comprehensive final exam were returned to students for self-evaluation and remediation Among other approaches course rigor was monitored by using an identical set of 60 questions on the final exam across 10 semesters Analysis of the identical sets of 60 final exam questions revealed that overall averages increased from 729 (2010) to 835 (2015) Regression analysis demonstrated a statistically significant correlation between high-risk students and their averages on the 60 questions Additional analysis demonstrated statistically significant improvements for at least one letter grade from midterm to final and a 20 increase in the course pass rates over time also for the high-risk population These results support the hypothesis that our data-driven interventions and assessment techniques are successful in improving student retention particularly for our academically at-risk students
Lecture Biol 1230
bull Competency E4 (chemistry in biology atomic bonds metabolic pathways thermodynamics)
bull Quizzes (formative assessment with Clickers)
bull The coordinator prepares the three lsquoOne hour examsrsquo (questions not from the textbook) instructors again reviewcomment
bull Question types range (content versus applications) and also lsquoBack pagersquo ( 20 of the exam grade) Formative assessment using the LXRtest software (Opscan6 scanner)
Final exam not returned cumulative and has had 60 questions (good discriminators based on the rpbvalues) commonly used on ALL final exams for the past five years Powerful tool for measuring studentsrsquo learning and applications over time and based on academic risk categories
Last Name First Name
Biology 1230 Exam 1 ldquoBack Pagerdquo Score _ 20 pts
I 5 pts Complete the following table for the 3 major components (subatomic particles) of the atom
hint electrical charge = positive negative or neutral and mass = 1 dalton or 11800 dalton 1 pt each
Particle Electrical Charge Mass
1 Proton 1 dalton
2 Electron
3 Neutron
II 5 pts In your own words compare and contrast the following two atoms A and B use the back of the previous page to
make as many observations as you can about similarities (and what they mean) and differences (and what they mean)
between the atoms
A B
III 5 pts Match the following by placing the corresponding in the space provided 1 pt each
_____ tertiary structure 1 produce H2O
_____ two ester linkages 2 is responsible for the 3-dimensional shape of a protein
_____ phosphodiester bonds 3 exist within diglycerides (diacylglyerols) and phospholipids
_____ dehydration synthesis reactions 4 are a type of lipid
_____ steroids 5 are formed when nucleic acids are synthesized
IV 5 pts Circle each of the variable (R) groups in the molecules shown below (3 pts)
a Which lsquoRrsquo group is polar ______ (write the corresponding in the space provided) (1 pt)
b Which lsquoRrsquo group is ionic ______ (write the corresponding in the space provided) (1 pt)
NH3+ OH CH3
1 2 3
12 neutrons
11 protons
10 electrons
13 neutrons
11 protons
11 electrons
Bio1230 Exam 1
Clickers and immediate feedback
Name _____________________________________________________________________________________________
This is a worksheet for your self-evaluation of study habits and exam preparedness Your answers on the corresponding
online exam surveys are confidential
~The average number of hours I spent per week reading the chapters andor reviewingprocessing class notes was (circle the
appropriate response)
zero to one one to two two to four greater than four
~I read the assignment before coming to class (circle the appropriate response)
never sometimes regularly
~I asked my instructor questions when I was confused about textbook material andor lecture material (circle the appropriate
response)
never sometimes regularly
~Overall I spent _____ hours specifically studying for this exam (Please fill in the blank)
~Prior to taking the exam I expected to get an approximate grade of (fill in the blank) _____
~My actual grade was a(n) (fill in the blank) _____
~Check all of the statements that apply to your performance on the exam
____ studied the right information ____ did not study the right information
____ studied the right information but did not ____ studied the right information and
understand it thought I understood it
____ used the class outlines to study ____ thought college would be easier
____ did not know what to study ____ other _____________________
____ did not think I would need to know the information in such detail
Analysis of Missed Questions I answered the question incorrectly because I Insert question number below in the correct category
did not study the information
studied the information but forgot it
did not understand the information in the
summary notes
confused similar concepts or terms (ie
isotopes and isomers)
misread or misunderstood the question
did not consider all of the answer choices
knew the correct answer - but chose an
incorrect answer by mistake
List other reason(s)
List other reason(s)
Please answer additional self-evaluation questions on the back of this page
Self-Evaluation of Study Habits amp Exam Preparedness for Biology 1230 Exam I or II or III (circle one)
Going forwardhellip
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
Additional Questions of Interest
bull Our goal was to determine if a 297 length sequence of homo sapiens ribosomal protein L5 (RPL5) contains region(s) with sequence similarity to gallus gallus (chicken) pan troglodytes (chimp) bos taurus (cow) and python molurus (snake) The objective is to find and precisely map the coding regions
bull Answer the following questions1 This presentation is showing only highly significant pairs How
do you think the alignments (scores e-values identities) differ if we analyze low significant pairs
2 Can you infer that this protein does not exist in this organism3 Give alternative explanations for the differences in scores e-
values and identities4 Is there an evolutionary relationship between sequences
Am J Hum Genet 2008 Dec 12 83(6) 769ndash780 Published online 2008 Dec 5 doi 101016jajhg200811004
Ribosomal Protein L5 and L11 Mutations Are Associated with Cleft Palate and Abnormal Thumbs in Diamond-Blackfan Anemia Patients
Hanna T Gazda12lowast
Mee Rie Sheen1
Adrianna Vlachos34
Valerie Choesmel56
Marie-Franccediloise ODonohue
56Hal Schneider
1Natasha Darras
1Catherine Hasman
1Colin A
Sieff27
Peter E Newburger8
Sarah E Ball9
Edyta Niewiadomska10
Michal Matysiak10
Jan M Zaucha
11Bertil Glader
12Charlotte Niemeyer
13Joerg J Meerpohl
13Eva Atsidaftos
34Jeffrey
M Lipton34
Pierre-Emmanuel Gleizes56
and Alan H Beggs12
Author information Article notes Copyright and License information AbstractDiamond-Blackfan anemia (DBA) a congenital bone-marrow-failure syndrome is characterized by red blood cell aplasia macrocytic anemia clinical heterogeneity and increased risk of malignancy Although anemia is the most prominent feature of DBA the disease is also characterized by growth retardation and congenital anomalies that are present in sim30ndash50 of patients The disease has been associated with mutations in four ribosomal protein (RP) genes RPS19 RPS24 RPS17 and RPL35A in about 30 of patients However the genetic basis of the remaining 70 of cases is still unknown Here we report the second known mutation in RPS17 and probable pathogenic mutations in three more RP genes RPL5 RPL11 and RPS7 In addition we identified rare variants of unknown significance in three other genes RPL36 RPS15 and RPS27A Remarkably careful review of the clinical data showed that mutations in RPL5 are associated with multiple physical abnormalities including craniofacial thumb and heart anomalies whereas isolated thumb malformations are predominantly present in patients carrying mutations in RPL11 We also demonstrate that mutations of RPL5 RPL11 or RPS7 in DBA cells is associated with diverse defects in the maturation of ribosomal RNAs in the large or the small ribosomal subunit production pathway expanding the repertoire of ribosomal RNA processing defects associated with DBA
Develop more inquiry-based lab exercises1 C elegans crosses (Peter Barrett in Genetics lab)
2 Modifications on DNA transformation and lac operon exercises (PB)
3 The lsquotermitersquo experiment in Biol 1230L (Kristal Huggins and SKI)
4 In Cell Biology lab C elegans (endocytosis experiments) experiments with Planaria regeneration (adapted from MITHHMI) and recently with Daphnia (the water flea a small crustacean) adapted from the Nuffield Foundation where students expose the Daphnia to various cardioactive compounds measure changes in heart rate caused by effects on cellular receptors and design follow-up experiments (PB)
Assessment Strategies for Project Scicomp
Formative and summative
General scheme
bull Assessment tasks based on objectives
bull Develop assessment tools and pilot for validation
bull Apply to larger audience
bull Collect and score
bull Share and analyze data
Coordinated course sequences and our curricular design serve as a good platform
for intra and interdepartmental discussions
(weekly meetings lsquoSERGrsquo etc)
Labs
bull General observation on student participationinitiative
bull Data sheets (say 10 collecthellipsay any 4)
bull Midterm skills practical stations and multiple choice (excellent determinant)
bull Quizzes (5-10 depending on the lab)
bull Final exams
Course based research experiencee(CRE)
bull How they design their experiment
bull Notebooks lab techniques
bull Participation in class discussions
bull Ability to troubleshoot
bull Midterm Skills and oral exam along with traditional exam
bull Short answer (non multiple choice) questions
bull Research paper presentations
CREs at Xavier
bull Phage and Genomics
bull lsquoUndergraduate Researchrsquo for credits
bull Introduction to Mammalian Tissue Culture
The SEA-PHAGES ProgramhttpsseaphagesorgThe official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program
SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is a two-semester discovery-based undergraduate research course that begins with simple digging in the soil to find new viruses but progresses through a variety of microbiology techniques and eventually to complex genome annotation and bioinformatic analyses
CBE Life Sci Educ 2016 fall15(3) pii ar38 doi 101187cbe16-01-0078Increasing URM Undergraduate Student Success through Assessment-Driven Interventions A Multiyear Study Using Freshman-Level General Biology as a Model SystemCarmichael MC1 St Clair C1 Edwards AM2 Barrett P1 McFerrin H1 Davenport I1 Awad M1 Kundu A1 Ireland SK3
AbstractXavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students In this multiyear study with sim5500 participants data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course The three hour-long exams were common and administered concurrently to all students New exam questions were developed using Blooms taxonomy and exam results were analyzed statistically with validated assessment tools All but the comprehensive final exam were returned to students for self-evaluation and remediation Among other approaches course rigor was monitored by using an identical set of 60 questions on the final exam across 10 semesters Analysis of the identical sets of 60 final exam questions revealed that overall averages increased from 729 (2010) to 835 (2015) Regression analysis demonstrated a statistically significant correlation between high-risk students and their averages on the 60 questions Additional analysis demonstrated statistically significant improvements for at least one letter grade from midterm to final and a 20 increase in the course pass rates over time also for the high-risk population These results support the hypothesis that our data-driven interventions and assessment techniques are successful in improving student retention particularly for our academically at-risk students
Lecture Biol 1230
bull Competency E4 (chemistry in biology atomic bonds metabolic pathways thermodynamics)
bull Quizzes (formative assessment with Clickers)
bull The coordinator prepares the three lsquoOne hour examsrsquo (questions not from the textbook) instructors again reviewcomment
bull Question types range (content versus applications) and also lsquoBack pagersquo ( 20 of the exam grade) Formative assessment using the LXRtest software (Opscan6 scanner)
Final exam not returned cumulative and has had 60 questions (good discriminators based on the rpbvalues) commonly used on ALL final exams for the past five years Powerful tool for measuring studentsrsquo learning and applications over time and based on academic risk categories
Last Name First Name
Biology 1230 Exam 1 ldquoBack Pagerdquo Score _ 20 pts
I 5 pts Complete the following table for the 3 major components (subatomic particles) of the atom
hint electrical charge = positive negative or neutral and mass = 1 dalton or 11800 dalton 1 pt each
Particle Electrical Charge Mass
1 Proton 1 dalton
2 Electron
3 Neutron
II 5 pts In your own words compare and contrast the following two atoms A and B use the back of the previous page to
make as many observations as you can about similarities (and what they mean) and differences (and what they mean)
between the atoms
A B
III 5 pts Match the following by placing the corresponding in the space provided 1 pt each
_____ tertiary structure 1 produce H2O
_____ two ester linkages 2 is responsible for the 3-dimensional shape of a protein
_____ phosphodiester bonds 3 exist within diglycerides (diacylglyerols) and phospholipids
_____ dehydration synthesis reactions 4 are a type of lipid
_____ steroids 5 are formed when nucleic acids are synthesized
IV 5 pts Circle each of the variable (R) groups in the molecules shown below (3 pts)
a Which lsquoRrsquo group is polar ______ (write the corresponding in the space provided) (1 pt)
b Which lsquoRrsquo group is ionic ______ (write the corresponding in the space provided) (1 pt)
NH3+ OH CH3
1 2 3
12 neutrons
11 protons
10 electrons
13 neutrons
11 protons
11 electrons
Bio1230 Exam 1
Clickers and immediate feedback
Name _____________________________________________________________________________________________
This is a worksheet for your self-evaluation of study habits and exam preparedness Your answers on the corresponding
online exam surveys are confidential
~The average number of hours I spent per week reading the chapters andor reviewingprocessing class notes was (circle the
appropriate response)
zero to one one to two two to four greater than four
~I read the assignment before coming to class (circle the appropriate response)
never sometimes regularly
~I asked my instructor questions when I was confused about textbook material andor lecture material (circle the appropriate
response)
never sometimes regularly
~Overall I spent _____ hours specifically studying for this exam (Please fill in the blank)
~Prior to taking the exam I expected to get an approximate grade of (fill in the blank) _____
~My actual grade was a(n) (fill in the blank) _____
~Check all of the statements that apply to your performance on the exam
____ studied the right information ____ did not study the right information
____ studied the right information but did not ____ studied the right information and
understand it thought I understood it
____ used the class outlines to study ____ thought college would be easier
____ did not know what to study ____ other _____________________
____ did not think I would need to know the information in such detail
Analysis of Missed Questions I answered the question incorrectly because I Insert question number below in the correct category
did not study the information
studied the information but forgot it
did not understand the information in the
summary notes
confused similar concepts or terms (ie
isotopes and isomers)
misread or misunderstood the question
did not consider all of the answer choices
knew the correct answer - but chose an
incorrect answer by mistake
List other reason(s)
List other reason(s)
Please answer additional self-evaluation questions on the back of this page
Self-Evaluation of Study Habits amp Exam Preparedness for Biology 1230 Exam I or II or III (circle one)
Going forwardhellip
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
Am J Hum Genet 2008 Dec 12 83(6) 769ndash780 Published online 2008 Dec 5 doi 101016jajhg200811004
Ribosomal Protein L5 and L11 Mutations Are Associated with Cleft Palate and Abnormal Thumbs in Diamond-Blackfan Anemia Patients
Hanna T Gazda12lowast
Mee Rie Sheen1
Adrianna Vlachos34
Valerie Choesmel56
Marie-Franccediloise ODonohue
56Hal Schneider
1Natasha Darras
1Catherine Hasman
1Colin A
Sieff27
Peter E Newburger8
Sarah E Ball9
Edyta Niewiadomska10
Michal Matysiak10
Jan M Zaucha
11Bertil Glader
12Charlotte Niemeyer
13Joerg J Meerpohl
13Eva Atsidaftos
34Jeffrey
M Lipton34
Pierre-Emmanuel Gleizes56
and Alan H Beggs12
Author information Article notes Copyright and License information AbstractDiamond-Blackfan anemia (DBA) a congenital bone-marrow-failure syndrome is characterized by red blood cell aplasia macrocytic anemia clinical heterogeneity and increased risk of malignancy Although anemia is the most prominent feature of DBA the disease is also characterized by growth retardation and congenital anomalies that are present in sim30ndash50 of patients The disease has been associated with mutations in four ribosomal protein (RP) genes RPS19 RPS24 RPS17 and RPL35A in about 30 of patients However the genetic basis of the remaining 70 of cases is still unknown Here we report the second known mutation in RPS17 and probable pathogenic mutations in three more RP genes RPL5 RPL11 and RPS7 In addition we identified rare variants of unknown significance in three other genes RPL36 RPS15 and RPS27A Remarkably careful review of the clinical data showed that mutations in RPL5 are associated with multiple physical abnormalities including craniofacial thumb and heart anomalies whereas isolated thumb malformations are predominantly present in patients carrying mutations in RPL11 We also demonstrate that mutations of RPL5 RPL11 or RPS7 in DBA cells is associated with diverse defects in the maturation of ribosomal RNAs in the large or the small ribosomal subunit production pathway expanding the repertoire of ribosomal RNA processing defects associated with DBA
Develop more inquiry-based lab exercises1 C elegans crosses (Peter Barrett in Genetics lab)
2 Modifications on DNA transformation and lac operon exercises (PB)
3 The lsquotermitersquo experiment in Biol 1230L (Kristal Huggins and SKI)
4 In Cell Biology lab C elegans (endocytosis experiments) experiments with Planaria regeneration (adapted from MITHHMI) and recently with Daphnia (the water flea a small crustacean) adapted from the Nuffield Foundation where students expose the Daphnia to various cardioactive compounds measure changes in heart rate caused by effects on cellular receptors and design follow-up experiments (PB)
Assessment Strategies for Project Scicomp
Formative and summative
General scheme
bull Assessment tasks based on objectives
bull Develop assessment tools and pilot for validation
bull Apply to larger audience
bull Collect and score
bull Share and analyze data
Coordinated course sequences and our curricular design serve as a good platform
for intra and interdepartmental discussions
(weekly meetings lsquoSERGrsquo etc)
Labs
bull General observation on student participationinitiative
bull Data sheets (say 10 collecthellipsay any 4)
bull Midterm skills practical stations and multiple choice (excellent determinant)
bull Quizzes (5-10 depending on the lab)
bull Final exams
Course based research experiencee(CRE)
bull How they design their experiment
bull Notebooks lab techniques
bull Participation in class discussions
bull Ability to troubleshoot
bull Midterm Skills and oral exam along with traditional exam
bull Short answer (non multiple choice) questions
bull Research paper presentations
CREs at Xavier
bull Phage and Genomics
bull lsquoUndergraduate Researchrsquo for credits
bull Introduction to Mammalian Tissue Culture
The SEA-PHAGES ProgramhttpsseaphagesorgThe official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program
SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is a two-semester discovery-based undergraduate research course that begins with simple digging in the soil to find new viruses but progresses through a variety of microbiology techniques and eventually to complex genome annotation and bioinformatic analyses
CBE Life Sci Educ 2016 fall15(3) pii ar38 doi 101187cbe16-01-0078Increasing URM Undergraduate Student Success through Assessment-Driven Interventions A Multiyear Study Using Freshman-Level General Biology as a Model SystemCarmichael MC1 St Clair C1 Edwards AM2 Barrett P1 McFerrin H1 Davenport I1 Awad M1 Kundu A1 Ireland SK3
AbstractXavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students In this multiyear study with sim5500 participants data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course The three hour-long exams were common and administered concurrently to all students New exam questions were developed using Blooms taxonomy and exam results were analyzed statistically with validated assessment tools All but the comprehensive final exam were returned to students for self-evaluation and remediation Among other approaches course rigor was monitored by using an identical set of 60 questions on the final exam across 10 semesters Analysis of the identical sets of 60 final exam questions revealed that overall averages increased from 729 (2010) to 835 (2015) Regression analysis demonstrated a statistically significant correlation between high-risk students and their averages on the 60 questions Additional analysis demonstrated statistically significant improvements for at least one letter grade from midterm to final and a 20 increase in the course pass rates over time also for the high-risk population These results support the hypothesis that our data-driven interventions and assessment techniques are successful in improving student retention particularly for our academically at-risk students
Lecture Biol 1230
bull Competency E4 (chemistry in biology atomic bonds metabolic pathways thermodynamics)
bull Quizzes (formative assessment with Clickers)
bull The coordinator prepares the three lsquoOne hour examsrsquo (questions not from the textbook) instructors again reviewcomment
bull Question types range (content versus applications) and also lsquoBack pagersquo ( 20 of the exam grade) Formative assessment using the LXRtest software (Opscan6 scanner)
Final exam not returned cumulative and has had 60 questions (good discriminators based on the rpbvalues) commonly used on ALL final exams for the past five years Powerful tool for measuring studentsrsquo learning and applications over time and based on academic risk categories
Last Name First Name
Biology 1230 Exam 1 ldquoBack Pagerdquo Score _ 20 pts
I 5 pts Complete the following table for the 3 major components (subatomic particles) of the atom
hint electrical charge = positive negative or neutral and mass = 1 dalton or 11800 dalton 1 pt each
Particle Electrical Charge Mass
1 Proton 1 dalton
2 Electron
3 Neutron
II 5 pts In your own words compare and contrast the following two atoms A and B use the back of the previous page to
make as many observations as you can about similarities (and what they mean) and differences (and what they mean)
between the atoms
A B
III 5 pts Match the following by placing the corresponding in the space provided 1 pt each
_____ tertiary structure 1 produce H2O
_____ two ester linkages 2 is responsible for the 3-dimensional shape of a protein
_____ phosphodiester bonds 3 exist within diglycerides (diacylglyerols) and phospholipids
_____ dehydration synthesis reactions 4 are a type of lipid
_____ steroids 5 are formed when nucleic acids are synthesized
IV 5 pts Circle each of the variable (R) groups in the molecules shown below (3 pts)
a Which lsquoRrsquo group is polar ______ (write the corresponding in the space provided) (1 pt)
b Which lsquoRrsquo group is ionic ______ (write the corresponding in the space provided) (1 pt)
NH3+ OH CH3
1 2 3
12 neutrons
11 protons
10 electrons
13 neutrons
11 protons
11 electrons
Bio1230 Exam 1
Clickers and immediate feedback
Name _____________________________________________________________________________________________
This is a worksheet for your self-evaluation of study habits and exam preparedness Your answers on the corresponding
online exam surveys are confidential
~The average number of hours I spent per week reading the chapters andor reviewingprocessing class notes was (circle the
appropriate response)
zero to one one to two two to four greater than four
~I read the assignment before coming to class (circle the appropriate response)
never sometimes regularly
~I asked my instructor questions when I was confused about textbook material andor lecture material (circle the appropriate
response)
never sometimes regularly
~Overall I spent _____ hours specifically studying for this exam (Please fill in the blank)
~Prior to taking the exam I expected to get an approximate grade of (fill in the blank) _____
~My actual grade was a(n) (fill in the blank) _____
~Check all of the statements that apply to your performance on the exam
____ studied the right information ____ did not study the right information
____ studied the right information but did not ____ studied the right information and
understand it thought I understood it
____ used the class outlines to study ____ thought college would be easier
____ did not know what to study ____ other _____________________
____ did not think I would need to know the information in such detail
Analysis of Missed Questions I answered the question incorrectly because I Insert question number below in the correct category
did not study the information
studied the information but forgot it
did not understand the information in the
summary notes
confused similar concepts or terms (ie
isotopes and isomers)
misread or misunderstood the question
did not consider all of the answer choices
knew the correct answer - but chose an
incorrect answer by mistake
List other reason(s)
List other reason(s)
Please answer additional self-evaluation questions on the back of this page
Self-Evaluation of Study Habits amp Exam Preparedness for Biology 1230 Exam I or II or III (circle one)
Going forwardhellip
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
Develop more inquiry-based lab exercises1 C elegans crosses (Peter Barrett in Genetics lab)
2 Modifications on DNA transformation and lac operon exercises (PB)
3 The lsquotermitersquo experiment in Biol 1230L (Kristal Huggins and SKI)
4 In Cell Biology lab C elegans (endocytosis experiments) experiments with Planaria regeneration (adapted from MITHHMI) and recently with Daphnia (the water flea a small crustacean) adapted from the Nuffield Foundation where students expose the Daphnia to various cardioactive compounds measure changes in heart rate caused by effects on cellular receptors and design follow-up experiments (PB)
Assessment Strategies for Project Scicomp
Formative and summative
General scheme
bull Assessment tasks based on objectives
bull Develop assessment tools and pilot for validation
bull Apply to larger audience
bull Collect and score
bull Share and analyze data
Coordinated course sequences and our curricular design serve as a good platform
for intra and interdepartmental discussions
(weekly meetings lsquoSERGrsquo etc)
Labs
bull General observation on student participationinitiative
bull Data sheets (say 10 collecthellipsay any 4)
bull Midterm skills practical stations and multiple choice (excellent determinant)
bull Quizzes (5-10 depending on the lab)
bull Final exams
Course based research experiencee(CRE)
bull How they design their experiment
bull Notebooks lab techniques
bull Participation in class discussions
bull Ability to troubleshoot
bull Midterm Skills and oral exam along with traditional exam
bull Short answer (non multiple choice) questions
bull Research paper presentations
CREs at Xavier
bull Phage and Genomics
bull lsquoUndergraduate Researchrsquo for credits
bull Introduction to Mammalian Tissue Culture
The SEA-PHAGES ProgramhttpsseaphagesorgThe official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program
SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is a two-semester discovery-based undergraduate research course that begins with simple digging in the soil to find new viruses but progresses through a variety of microbiology techniques and eventually to complex genome annotation and bioinformatic analyses
CBE Life Sci Educ 2016 fall15(3) pii ar38 doi 101187cbe16-01-0078Increasing URM Undergraduate Student Success through Assessment-Driven Interventions A Multiyear Study Using Freshman-Level General Biology as a Model SystemCarmichael MC1 St Clair C1 Edwards AM2 Barrett P1 McFerrin H1 Davenport I1 Awad M1 Kundu A1 Ireland SK3
AbstractXavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students In this multiyear study with sim5500 participants data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course The three hour-long exams were common and administered concurrently to all students New exam questions were developed using Blooms taxonomy and exam results were analyzed statistically with validated assessment tools All but the comprehensive final exam were returned to students for self-evaluation and remediation Among other approaches course rigor was monitored by using an identical set of 60 questions on the final exam across 10 semesters Analysis of the identical sets of 60 final exam questions revealed that overall averages increased from 729 (2010) to 835 (2015) Regression analysis demonstrated a statistically significant correlation between high-risk students and their averages on the 60 questions Additional analysis demonstrated statistically significant improvements for at least one letter grade from midterm to final and a 20 increase in the course pass rates over time also for the high-risk population These results support the hypothesis that our data-driven interventions and assessment techniques are successful in improving student retention particularly for our academically at-risk students
Lecture Biol 1230
bull Competency E4 (chemistry in biology atomic bonds metabolic pathways thermodynamics)
bull Quizzes (formative assessment with Clickers)
bull The coordinator prepares the three lsquoOne hour examsrsquo (questions not from the textbook) instructors again reviewcomment
bull Question types range (content versus applications) and also lsquoBack pagersquo ( 20 of the exam grade) Formative assessment using the LXRtest software (Opscan6 scanner)
Final exam not returned cumulative and has had 60 questions (good discriminators based on the rpbvalues) commonly used on ALL final exams for the past five years Powerful tool for measuring studentsrsquo learning and applications over time and based on academic risk categories
Last Name First Name
Biology 1230 Exam 1 ldquoBack Pagerdquo Score _ 20 pts
I 5 pts Complete the following table for the 3 major components (subatomic particles) of the atom
hint electrical charge = positive negative or neutral and mass = 1 dalton or 11800 dalton 1 pt each
Particle Electrical Charge Mass
1 Proton 1 dalton
2 Electron
3 Neutron
II 5 pts In your own words compare and contrast the following two atoms A and B use the back of the previous page to
make as many observations as you can about similarities (and what they mean) and differences (and what they mean)
between the atoms
A B
III 5 pts Match the following by placing the corresponding in the space provided 1 pt each
_____ tertiary structure 1 produce H2O
_____ two ester linkages 2 is responsible for the 3-dimensional shape of a protein
_____ phosphodiester bonds 3 exist within diglycerides (diacylglyerols) and phospholipids
_____ dehydration synthesis reactions 4 are a type of lipid
_____ steroids 5 are formed when nucleic acids are synthesized
IV 5 pts Circle each of the variable (R) groups in the molecules shown below (3 pts)
a Which lsquoRrsquo group is polar ______ (write the corresponding in the space provided) (1 pt)
b Which lsquoRrsquo group is ionic ______ (write the corresponding in the space provided) (1 pt)
NH3+ OH CH3
1 2 3
12 neutrons
11 protons
10 electrons
13 neutrons
11 protons
11 electrons
Bio1230 Exam 1
Clickers and immediate feedback
Name _____________________________________________________________________________________________
This is a worksheet for your self-evaluation of study habits and exam preparedness Your answers on the corresponding
online exam surveys are confidential
~The average number of hours I spent per week reading the chapters andor reviewingprocessing class notes was (circle the
appropriate response)
zero to one one to two two to four greater than four
~I read the assignment before coming to class (circle the appropriate response)
never sometimes regularly
~I asked my instructor questions when I was confused about textbook material andor lecture material (circle the appropriate
response)
never sometimes regularly
~Overall I spent _____ hours specifically studying for this exam (Please fill in the blank)
~Prior to taking the exam I expected to get an approximate grade of (fill in the blank) _____
~My actual grade was a(n) (fill in the blank) _____
~Check all of the statements that apply to your performance on the exam
____ studied the right information ____ did not study the right information
____ studied the right information but did not ____ studied the right information and
understand it thought I understood it
____ used the class outlines to study ____ thought college would be easier
____ did not know what to study ____ other _____________________
____ did not think I would need to know the information in such detail
Analysis of Missed Questions I answered the question incorrectly because I Insert question number below in the correct category
did not study the information
studied the information but forgot it
did not understand the information in the
summary notes
confused similar concepts or terms (ie
isotopes and isomers)
misread or misunderstood the question
did not consider all of the answer choices
knew the correct answer - but chose an
incorrect answer by mistake
List other reason(s)
List other reason(s)
Please answer additional self-evaluation questions on the back of this page
Self-Evaluation of Study Habits amp Exam Preparedness for Biology 1230 Exam I or II or III (circle one)
Going forwardhellip
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
Assessment Strategies for Project Scicomp
Formative and summative
General scheme
bull Assessment tasks based on objectives
bull Develop assessment tools and pilot for validation
bull Apply to larger audience
bull Collect and score
bull Share and analyze data
Coordinated course sequences and our curricular design serve as a good platform
for intra and interdepartmental discussions
(weekly meetings lsquoSERGrsquo etc)
Labs
bull General observation on student participationinitiative
bull Data sheets (say 10 collecthellipsay any 4)
bull Midterm skills practical stations and multiple choice (excellent determinant)
bull Quizzes (5-10 depending on the lab)
bull Final exams
Course based research experiencee(CRE)
bull How they design their experiment
bull Notebooks lab techniques
bull Participation in class discussions
bull Ability to troubleshoot
bull Midterm Skills and oral exam along with traditional exam
bull Short answer (non multiple choice) questions
bull Research paper presentations
CREs at Xavier
bull Phage and Genomics
bull lsquoUndergraduate Researchrsquo for credits
bull Introduction to Mammalian Tissue Culture
The SEA-PHAGES ProgramhttpsseaphagesorgThe official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program
SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is a two-semester discovery-based undergraduate research course that begins with simple digging in the soil to find new viruses but progresses through a variety of microbiology techniques and eventually to complex genome annotation and bioinformatic analyses
CBE Life Sci Educ 2016 fall15(3) pii ar38 doi 101187cbe16-01-0078Increasing URM Undergraduate Student Success through Assessment-Driven Interventions A Multiyear Study Using Freshman-Level General Biology as a Model SystemCarmichael MC1 St Clair C1 Edwards AM2 Barrett P1 McFerrin H1 Davenport I1 Awad M1 Kundu A1 Ireland SK3
AbstractXavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students In this multiyear study with sim5500 participants data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course The three hour-long exams were common and administered concurrently to all students New exam questions were developed using Blooms taxonomy and exam results were analyzed statistically with validated assessment tools All but the comprehensive final exam were returned to students for self-evaluation and remediation Among other approaches course rigor was monitored by using an identical set of 60 questions on the final exam across 10 semesters Analysis of the identical sets of 60 final exam questions revealed that overall averages increased from 729 (2010) to 835 (2015) Regression analysis demonstrated a statistically significant correlation between high-risk students and their averages on the 60 questions Additional analysis demonstrated statistically significant improvements for at least one letter grade from midterm to final and a 20 increase in the course pass rates over time also for the high-risk population These results support the hypothesis that our data-driven interventions and assessment techniques are successful in improving student retention particularly for our academically at-risk students
Lecture Biol 1230
bull Competency E4 (chemistry in biology atomic bonds metabolic pathways thermodynamics)
bull Quizzes (formative assessment with Clickers)
bull The coordinator prepares the three lsquoOne hour examsrsquo (questions not from the textbook) instructors again reviewcomment
bull Question types range (content versus applications) and also lsquoBack pagersquo ( 20 of the exam grade) Formative assessment using the LXRtest software (Opscan6 scanner)
Final exam not returned cumulative and has had 60 questions (good discriminators based on the rpbvalues) commonly used on ALL final exams for the past five years Powerful tool for measuring studentsrsquo learning and applications over time and based on academic risk categories
Last Name First Name
Biology 1230 Exam 1 ldquoBack Pagerdquo Score _ 20 pts
I 5 pts Complete the following table for the 3 major components (subatomic particles) of the atom
hint electrical charge = positive negative or neutral and mass = 1 dalton or 11800 dalton 1 pt each
Particle Electrical Charge Mass
1 Proton 1 dalton
2 Electron
3 Neutron
II 5 pts In your own words compare and contrast the following two atoms A and B use the back of the previous page to
make as many observations as you can about similarities (and what they mean) and differences (and what they mean)
between the atoms
A B
III 5 pts Match the following by placing the corresponding in the space provided 1 pt each
_____ tertiary structure 1 produce H2O
_____ two ester linkages 2 is responsible for the 3-dimensional shape of a protein
_____ phosphodiester bonds 3 exist within diglycerides (diacylglyerols) and phospholipids
_____ dehydration synthesis reactions 4 are a type of lipid
_____ steroids 5 are formed when nucleic acids are synthesized
IV 5 pts Circle each of the variable (R) groups in the molecules shown below (3 pts)
a Which lsquoRrsquo group is polar ______ (write the corresponding in the space provided) (1 pt)
b Which lsquoRrsquo group is ionic ______ (write the corresponding in the space provided) (1 pt)
NH3+ OH CH3
1 2 3
12 neutrons
11 protons
10 electrons
13 neutrons
11 protons
11 electrons
Bio1230 Exam 1
Clickers and immediate feedback
Name _____________________________________________________________________________________________
This is a worksheet for your self-evaluation of study habits and exam preparedness Your answers on the corresponding
online exam surveys are confidential
~The average number of hours I spent per week reading the chapters andor reviewingprocessing class notes was (circle the
appropriate response)
zero to one one to two two to four greater than four
~I read the assignment before coming to class (circle the appropriate response)
never sometimes regularly
~I asked my instructor questions when I was confused about textbook material andor lecture material (circle the appropriate
response)
never sometimes regularly
~Overall I spent _____ hours specifically studying for this exam (Please fill in the blank)
~Prior to taking the exam I expected to get an approximate grade of (fill in the blank) _____
~My actual grade was a(n) (fill in the blank) _____
~Check all of the statements that apply to your performance on the exam
____ studied the right information ____ did not study the right information
____ studied the right information but did not ____ studied the right information and
understand it thought I understood it
____ used the class outlines to study ____ thought college would be easier
____ did not know what to study ____ other _____________________
____ did not think I would need to know the information in such detail
Analysis of Missed Questions I answered the question incorrectly because I Insert question number below in the correct category
did not study the information
studied the information but forgot it
did not understand the information in the
summary notes
confused similar concepts or terms (ie
isotopes and isomers)
misread or misunderstood the question
did not consider all of the answer choices
knew the correct answer - but chose an
incorrect answer by mistake
List other reason(s)
List other reason(s)
Please answer additional self-evaluation questions on the back of this page
Self-Evaluation of Study Habits amp Exam Preparedness for Biology 1230 Exam I or II or III (circle one)
Going forwardhellip
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
General scheme
bull Assessment tasks based on objectives
bull Develop assessment tools and pilot for validation
bull Apply to larger audience
bull Collect and score
bull Share and analyze data
Coordinated course sequences and our curricular design serve as a good platform
for intra and interdepartmental discussions
(weekly meetings lsquoSERGrsquo etc)
Labs
bull General observation on student participationinitiative
bull Data sheets (say 10 collecthellipsay any 4)
bull Midterm skills practical stations and multiple choice (excellent determinant)
bull Quizzes (5-10 depending on the lab)
bull Final exams
Course based research experiencee(CRE)
bull How they design their experiment
bull Notebooks lab techniques
bull Participation in class discussions
bull Ability to troubleshoot
bull Midterm Skills and oral exam along with traditional exam
bull Short answer (non multiple choice) questions
bull Research paper presentations
CREs at Xavier
bull Phage and Genomics
bull lsquoUndergraduate Researchrsquo for credits
bull Introduction to Mammalian Tissue Culture
The SEA-PHAGES ProgramhttpsseaphagesorgThe official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program
SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is a two-semester discovery-based undergraduate research course that begins with simple digging in the soil to find new viruses but progresses through a variety of microbiology techniques and eventually to complex genome annotation and bioinformatic analyses
CBE Life Sci Educ 2016 fall15(3) pii ar38 doi 101187cbe16-01-0078Increasing URM Undergraduate Student Success through Assessment-Driven Interventions A Multiyear Study Using Freshman-Level General Biology as a Model SystemCarmichael MC1 St Clair C1 Edwards AM2 Barrett P1 McFerrin H1 Davenport I1 Awad M1 Kundu A1 Ireland SK3
AbstractXavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students In this multiyear study with sim5500 participants data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course The three hour-long exams were common and administered concurrently to all students New exam questions were developed using Blooms taxonomy and exam results were analyzed statistically with validated assessment tools All but the comprehensive final exam were returned to students for self-evaluation and remediation Among other approaches course rigor was monitored by using an identical set of 60 questions on the final exam across 10 semesters Analysis of the identical sets of 60 final exam questions revealed that overall averages increased from 729 (2010) to 835 (2015) Regression analysis demonstrated a statistically significant correlation between high-risk students and their averages on the 60 questions Additional analysis demonstrated statistically significant improvements for at least one letter grade from midterm to final and a 20 increase in the course pass rates over time also for the high-risk population These results support the hypothesis that our data-driven interventions and assessment techniques are successful in improving student retention particularly for our academically at-risk students
Lecture Biol 1230
bull Competency E4 (chemistry in biology atomic bonds metabolic pathways thermodynamics)
bull Quizzes (formative assessment with Clickers)
bull The coordinator prepares the three lsquoOne hour examsrsquo (questions not from the textbook) instructors again reviewcomment
bull Question types range (content versus applications) and also lsquoBack pagersquo ( 20 of the exam grade) Formative assessment using the LXRtest software (Opscan6 scanner)
Final exam not returned cumulative and has had 60 questions (good discriminators based on the rpbvalues) commonly used on ALL final exams for the past five years Powerful tool for measuring studentsrsquo learning and applications over time and based on academic risk categories
Last Name First Name
Biology 1230 Exam 1 ldquoBack Pagerdquo Score _ 20 pts
I 5 pts Complete the following table for the 3 major components (subatomic particles) of the atom
hint electrical charge = positive negative or neutral and mass = 1 dalton or 11800 dalton 1 pt each
Particle Electrical Charge Mass
1 Proton 1 dalton
2 Electron
3 Neutron
II 5 pts In your own words compare and contrast the following two atoms A and B use the back of the previous page to
make as many observations as you can about similarities (and what they mean) and differences (and what they mean)
between the atoms
A B
III 5 pts Match the following by placing the corresponding in the space provided 1 pt each
_____ tertiary structure 1 produce H2O
_____ two ester linkages 2 is responsible for the 3-dimensional shape of a protein
_____ phosphodiester bonds 3 exist within diglycerides (diacylglyerols) and phospholipids
_____ dehydration synthesis reactions 4 are a type of lipid
_____ steroids 5 are formed when nucleic acids are synthesized
IV 5 pts Circle each of the variable (R) groups in the molecules shown below (3 pts)
a Which lsquoRrsquo group is polar ______ (write the corresponding in the space provided) (1 pt)
b Which lsquoRrsquo group is ionic ______ (write the corresponding in the space provided) (1 pt)
NH3+ OH CH3
1 2 3
12 neutrons
11 protons
10 electrons
13 neutrons
11 protons
11 electrons
Bio1230 Exam 1
Clickers and immediate feedback
Name _____________________________________________________________________________________________
This is a worksheet for your self-evaluation of study habits and exam preparedness Your answers on the corresponding
online exam surveys are confidential
~The average number of hours I spent per week reading the chapters andor reviewingprocessing class notes was (circle the
appropriate response)
zero to one one to two two to four greater than four
~I read the assignment before coming to class (circle the appropriate response)
never sometimes regularly
~I asked my instructor questions when I was confused about textbook material andor lecture material (circle the appropriate
response)
never sometimes regularly
~Overall I spent _____ hours specifically studying for this exam (Please fill in the blank)
~Prior to taking the exam I expected to get an approximate grade of (fill in the blank) _____
~My actual grade was a(n) (fill in the blank) _____
~Check all of the statements that apply to your performance on the exam
____ studied the right information ____ did not study the right information
____ studied the right information but did not ____ studied the right information and
understand it thought I understood it
____ used the class outlines to study ____ thought college would be easier
____ did not know what to study ____ other _____________________
____ did not think I would need to know the information in such detail
Analysis of Missed Questions I answered the question incorrectly because I Insert question number below in the correct category
did not study the information
studied the information but forgot it
did not understand the information in the
summary notes
confused similar concepts or terms (ie
isotopes and isomers)
misread or misunderstood the question
did not consider all of the answer choices
knew the correct answer - but chose an
incorrect answer by mistake
List other reason(s)
List other reason(s)
Please answer additional self-evaluation questions on the back of this page
Self-Evaluation of Study Habits amp Exam Preparedness for Biology 1230 Exam I or II or III (circle one)
Going forwardhellip
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
Labs
bull General observation on student participationinitiative
bull Data sheets (say 10 collecthellipsay any 4)
bull Midterm skills practical stations and multiple choice (excellent determinant)
bull Quizzes (5-10 depending on the lab)
bull Final exams
Course based research experiencee(CRE)
bull How they design their experiment
bull Notebooks lab techniques
bull Participation in class discussions
bull Ability to troubleshoot
bull Midterm Skills and oral exam along with traditional exam
bull Short answer (non multiple choice) questions
bull Research paper presentations
CREs at Xavier
bull Phage and Genomics
bull lsquoUndergraduate Researchrsquo for credits
bull Introduction to Mammalian Tissue Culture
The SEA-PHAGES ProgramhttpsseaphagesorgThe official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program
SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is a two-semester discovery-based undergraduate research course that begins with simple digging in the soil to find new viruses but progresses through a variety of microbiology techniques and eventually to complex genome annotation and bioinformatic analyses
CBE Life Sci Educ 2016 fall15(3) pii ar38 doi 101187cbe16-01-0078Increasing URM Undergraduate Student Success through Assessment-Driven Interventions A Multiyear Study Using Freshman-Level General Biology as a Model SystemCarmichael MC1 St Clair C1 Edwards AM2 Barrett P1 McFerrin H1 Davenport I1 Awad M1 Kundu A1 Ireland SK3
AbstractXavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students In this multiyear study with sim5500 participants data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course The three hour-long exams were common and administered concurrently to all students New exam questions were developed using Blooms taxonomy and exam results were analyzed statistically with validated assessment tools All but the comprehensive final exam were returned to students for self-evaluation and remediation Among other approaches course rigor was monitored by using an identical set of 60 questions on the final exam across 10 semesters Analysis of the identical sets of 60 final exam questions revealed that overall averages increased from 729 (2010) to 835 (2015) Regression analysis demonstrated a statistically significant correlation between high-risk students and their averages on the 60 questions Additional analysis demonstrated statistically significant improvements for at least one letter grade from midterm to final and a 20 increase in the course pass rates over time also for the high-risk population These results support the hypothesis that our data-driven interventions and assessment techniques are successful in improving student retention particularly for our academically at-risk students
Lecture Biol 1230
bull Competency E4 (chemistry in biology atomic bonds metabolic pathways thermodynamics)
bull Quizzes (formative assessment with Clickers)
bull The coordinator prepares the three lsquoOne hour examsrsquo (questions not from the textbook) instructors again reviewcomment
bull Question types range (content versus applications) and also lsquoBack pagersquo ( 20 of the exam grade) Formative assessment using the LXRtest software (Opscan6 scanner)
Final exam not returned cumulative and has had 60 questions (good discriminators based on the rpbvalues) commonly used on ALL final exams for the past five years Powerful tool for measuring studentsrsquo learning and applications over time and based on academic risk categories
Last Name First Name
Biology 1230 Exam 1 ldquoBack Pagerdquo Score _ 20 pts
I 5 pts Complete the following table for the 3 major components (subatomic particles) of the atom
hint electrical charge = positive negative or neutral and mass = 1 dalton or 11800 dalton 1 pt each
Particle Electrical Charge Mass
1 Proton 1 dalton
2 Electron
3 Neutron
II 5 pts In your own words compare and contrast the following two atoms A and B use the back of the previous page to
make as many observations as you can about similarities (and what they mean) and differences (and what they mean)
between the atoms
A B
III 5 pts Match the following by placing the corresponding in the space provided 1 pt each
_____ tertiary structure 1 produce H2O
_____ two ester linkages 2 is responsible for the 3-dimensional shape of a protein
_____ phosphodiester bonds 3 exist within diglycerides (diacylglyerols) and phospholipids
_____ dehydration synthesis reactions 4 are a type of lipid
_____ steroids 5 are formed when nucleic acids are synthesized
IV 5 pts Circle each of the variable (R) groups in the molecules shown below (3 pts)
a Which lsquoRrsquo group is polar ______ (write the corresponding in the space provided) (1 pt)
b Which lsquoRrsquo group is ionic ______ (write the corresponding in the space provided) (1 pt)
NH3+ OH CH3
1 2 3
12 neutrons
11 protons
10 electrons
13 neutrons
11 protons
11 electrons
Bio1230 Exam 1
Clickers and immediate feedback
Name _____________________________________________________________________________________________
This is a worksheet for your self-evaluation of study habits and exam preparedness Your answers on the corresponding
online exam surveys are confidential
~The average number of hours I spent per week reading the chapters andor reviewingprocessing class notes was (circle the
appropriate response)
zero to one one to two two to four greater than four
~I read the assignment before coming to class (circle the appropriate response)
never sometimes regularly
~I asked my instructor questions when I was confused about textbook material andor lecture material (circle the appropriate
response)
never sometimes regularly
~Overall I spent _____ hours specifically studying for this exam (Please fill in the blank)
~Prior to taking the exam I expected to get an approximate grade of (fill in the blank) _____
~My actual grade was a(n) (fill in the blank) _____
~Check all of the statements that apply to your performance on the exam
____ studied the right information ____ did not study the right information
____ studied the right information but did not ____ studied the right information and
understand it thought I understood it
____ used the class outlines to study ____ thought college would be easier
____ did not know what to study ____ other _____________________
____ did not think I would need to know the information in such detail
Analysis of Missed Questions I answered the question incorrectly because I Insert question number below in the correct category
did not study the information
studied the information but forgot it
did not understand the information in the
summary notes
confused similar concepts or terms (ie
isotopes and isomers)
misread or misunderstood the question
did not consider all of the answer choices
knew the correct answer - but chose an
incorrect answer by mistake
List other reason(s)
List other reason(s)
Please answer additional self-evaluation questions on the back of this page
Self-Evaluation of Study Habits amp Exam Preparedness for Biology 1230 Exam I or II or III (circle one)
Going forwardhellip
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
Course based research experiencee(CRE)
bull How they design their experiment
bull Notebooks lab techniques
bull Participation in class discussions
bull Ability to troubleshoot
bull Midterm Skills and oral exam along with traditional exam
bull Short answer (non multiple choice) questions
bull Research paper presentations
CREs at Xavier
bull Phage and Genomics
bull lsquoUndergraduate Researchrsquo for credits
bull Introduction to Mammalian Tissue Culture
The SEA-PHAGES ProgramhttpsseaphagesorgThe official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program
SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is a two-semester discovery-based undergraduate research course that begins with simple digging in the soil to find new viruses but progresses through a variety of microbiology techniques and eventually to complex genome annotation and bioinformatic analyses
CBE Life Sci Educ 2016 fall15(3) pii ar38 doi 101187cbe16-01-0078Increasing URM Undergraduate Student Success through Assessment-Driven Interventions A Multiyear Study Using Freshman-Level General Biology as a Model SystemCarmichael MC1 St Clair C1 Edwards AM2 Barrett P1 McFerrin H1 Davenport I1 Awad M1 Kundu A1 Ireland SK3
AbstractXavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students In this multiyear study with sim5500 participants data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course The three hour-long exams were common and administered concurrently to all students New exam questions were developed using Blooms taxonomy and exam results were analyzed statistically with validated assessment tools All but the comprehensive final exam were returned to students for self-evaluation and remediation Among other approaches course rigor was monitored by using an identical set of 60 questions on the final exam across 10 semesters Analysis of the identical sets of 60 final exam questions revealed that overall averages increased from 729 (2010) to 835 (2015) Regression analysis demonstrated a statistically significant correlation between high-risk students and their averages on the 60 questions Additional analysis demonstrated statistically significant improvements for at least one letter grade from midterm to final and a 20 increase in the course pass rates over time also for the high-risk population These results support the hypothesis that our data-driven interventions and assessment techniques are successful in improving student retention particularly for our academically at-risk students
Lecture Biol 1230
bull Competency E4 (chemistry in biology atomic bonds metabolic pathways thermodynamics)
bull Quizzes (formative assessment with Clickers)
bull The coordinator prepares the three lsquoOne hour examsrsquo (questions not from the textbook) instructors again reviewcomment
bull Question types range (content versus applications) and also lsquoBack pagersquo ( 20 of the exam grade) Formative assessment using the LXRtest software (Opscan6 scanner)
Final exam not returned cumulative and has had 60 questions (good discriminators based on the rpbvalues) commonly used on ALL final exams for the past five years Powerful tool for measuring studentsrsquo learning and applications over time and based on academic risk categories
Last Name First Name
Biology 1230 Exam 1 ldquoBack Pagerdquo Score _ 20 pts
I 5 pts Complete the following table for the 3 major components (subatomic particles) of the atom
hint electrical charge = positive negative or neutral and mass = 1 dalton or 11800 dalton 1 pt each
Particle Electrical Charge Mass
1 Proton 1 dalton
2 Electron
3 Neutron
II 5 pts In your own words compare and contrast the following two atoms A and B use the back of the previous page to
make as many observations as you can about similarities (and what they mean) and differences (and what they mean)
between the atoms
A B
III 5 pts Match the following by placing the corresponding in the space provided 1 pt each
_____ tertiary structure 1 produce H2O
_____ two ester linkages 2 is responsible for the 3-dimensional shape of a protein
_____ phosphodiester bonds 3 exist within diglycerides (diacylglyerols) and phospholipids
_____ dehydration synthesis reactions 4 are a type of lipid
_____ steroids 5 are formed when nucleic acids are synthesized
IV 5 pts Circle each of the variable (R) groups in the molecules shown below (3 pts)
a Which lsquoRrsquo group is polar ______ (write the corresponding in the space provided) (1 pt)
b Which lsquoRrsquo group is ionic ______ (write the corresponding in the space provided) (1 pt)
NH3+ OH CH3
1 2 3
12 neutrons
11 protons
10 electrons
13 neutrons
11 protons
11 electrons
Bio1230 Exam 1
Clickers and immediate feedback
Name _____________________________________________________________________________________________
This is a worksheet for your self-evaluation of study habits and exam preparedness Your answers on the corresponding
online exam surveys are confidential
~The average number of hours I spent per week reading the chapters andor reviewingprocessing class notes was (circle the
appropriate response)
zero to one one to two two to four greater than four
~I read the assignment before coming to class (circle the appropriate response)
never sometimes regularly
~I asked my instructor questions when I was confused about textbook material andor lecture material (circle the appropriate
response)
never sometimes regularly
~Overall I spent _____ hours specifically studying for this exam (Please fill in the blank)
~Prior to taking the exam I expected to get an approximate grade of (fill in the blank) _____
~My actual grade was a(n) (fill in the blank) _____
~Check all of the statements that apply to your performance on the exam
____ studied the right information ____ did not study the right information
____ studied the right information but did not ____ studied the right information and
understand it thought I understood it
____ used the class outlines to study ____ thought college would be easier
____ did not know what to study ____ other _____________________
____ did not think I would need to know the information in such detail
Analysis of Missed Questions I answered the question incorrectly because I Insert question number below in the correct category
did not study the information
studied the information but forgot it
did not understand the information in the
summary notes
confused similar concepts or terms (ie
isotopes and isomers)
misread or misunderstood the question
did not consider all of the answer choices
knew the correct answer - but chose an
incorrect answer by mistake
List other reason(s)
List other reason(s)
Please answer additional self-evaluation questions on the back of this page
Self-Evaluation of Study Habits amp Exam Preparedness for Biology 1230 Exam I or II or III (circle one)
Going forwardhellip
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
CREs at Xavier
bull Phage and Genomics
bull lsquoUndergraduate Researchrsquo for credits
bull Introduction to Mammalian Tissue Culture
The SEA-PHAGES ProgramhttpsseaphagesorgThe official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program
SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is a two-semester discovery-based undergraduate research course that begins with simple digging in the soil to find new viruses but progresses through a variety of microbiology techniques and eventually to complex genome annotation and bioinformatic analyses
CBE Life Sci Educ 2016 fall15(3) pii ar38 doi 101187cbe16-01-0078Increasing URM Undergraduate Student Success through Assessment-Driven Interventions A Multiyear Study Using Freshman-Level General Biology as a Model SystemCarmichael MC1 St Clair C1 Edwards AM2 Barrett P1 McFerrin H1 Davenport I1 Awad M1 Kundu A1 Ireland SK3
AbstractXavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students In this multiyear study with sim5500 participants data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course The three hour-long exams were common and administered concurrently to all students New exam questions were developed using Blooms taxonomy and exam results were analyzed statistically with validated assessment tools All but the comprehensive final exam were returned to students for self-evaluation and remediation Among other approaches course rigor was monitored by using an identical set of 60 questions on the final exam across 10 semesters Analysis of the identical sets of 60 final exam questions revealed that overall averages increased from 729 (2010) to 835 (2015) Regression analysis demonstrated a statistically significant correlation between high-risk students and their averages on the 60 questions Additional analysis demonstrated statistically significant improvements for at least one letter grade from midterm to final and a 20 increase in the course pass rates over time also for the high-risk population These results support the hypothesis that our data-driven interventions and assessment techniques are successful in improving student retention particularly for our academically at-risk students
Lecture Biol 1230
bull Competency E4 (chemistry in biology atomic bonds metabolic pathways thermodynamics)
bull Quizzes (formative assessment with Clickers)
bull The coordinator prepares the three lsquoOne hour examsrsquo (questions not from the textbook) instructors again reviewcomment
bull Question types range (content versus applications) and also lsquoBack pagersquo ( 20 of the exam grade) Formative assessment using the LXRtest software (Opscan6 scanner)
Final exam not returned cumulative and has had 60 questions (good discriminators based on the rpbvalues) commonly used on ALL final exams for the past five years Powerful tool for measuring studentsrsquo learning and applications over time and based on academic risk categories
Last Name First Name
Biology 1230 Exam 1 ldquoBack Pagerdquo Score _ 20 pts
I 5 pts Complete the following table for the 3 major components (subatomic particles) of the atom
hint electrical charge = positive negative or neutral and mass = 1 dalton or 11800 dalton 1 pt each
Particle Electrical Charge Mass
1 Proton 1 dalton
2 Electron
3 Neutron
II 5 pts In your own words compare and contrast the following two atoms A and B use the back of the previous page to
make as many observations as you can about similarities (and what they mean) and differences (and what they mean)
between the atoms
A B
III 5 pts Match the following by placing the corresponding in the space provided 1 pt each
_____ tertiary structure 1 produce H2O
_____ two ester linkages 2 is responsible for the 3-dimensional shape of a protein
_____ phosphodiester bonds 3 exist within diglycerides (diacylglyerols) and phospholipids
_____ dehydration synthesis reactions 4 are a type of lipid
_____ steroids 5 are formed when nucleic acids are synthesized
IV 5 pts Circle each of the variable (R) groups in the molecules shown below (3 pts)
a Which lsquoRrsquo group is polar ______ (write the corresponding in the space provided) (1 pt)
b Which lsquoRrsquo group is ionic ______ (write the corresponding in the space provided) (1 pt)
NH3+ OH CH3
1 2 3
12 neutrons
11 protons
10 electrons
13 neutrons
11 protons
11 electrons
Bio1230 Exam 1
Clickers and immediate feedback
Name _____________________________________________________________________________________________
This is a worksheet for your self-evaluation of study habits and exam preparedness Your answers on the corresponding
online exam surveys are confidential
~The average number of hours I spent per week reading the chapters andor reviewingprocessing class notes was (circle the
appropriate response)
zero to one one to two two to four greater than four
~I read the assignment before coming to class (circle the appropriate response)
never sometimes regularly
~I asked my instructor questions when I was confused about textbook material andor lecture material (circle the appropriate
response)
never sometimes regularly
~Overall I spent _____ hours specifically studying for this exam (Please fill in the blank)
~Prior to taking the exam I expected to get an approximate grade of (fill in the blank) _____
~My actual grade was a(n) (fill in the blank) _____
~Check all of the statements that apply to your performance on the exam
____ studied the right information ____ did not study the right information
____ studied the right information but did not ____ studied the right information and
understand it thought I understood it
____ used the class outlines to study ____ thought college would be easier
____ did not know what to study ____ other _____________________
____ did not think I would need to know the information in such detail
Analysis of Missed Questions I answered the question incorrectly because I Insert question number below in the correct category
did not study the information
studied the information but forgot it
did not understand the information in the
summary notes
confused similar concepts or terms (ie
isotopes and isomers)
misread or misunderstood the question
did not consider all of the answer choices
knew the correct answer - but chose an
incorrect answer by mistake
List other reason(s)
List other reason(s)
Please answer additional self-evaluation questions on the back of this page
Self-Evaluation of Study Habits amp Exam Preparedness for Biology 1230 Exam I or II or III (circle one)
Going forwardhellip
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
The SEA-PHAGES ProgramhttpsseaphagesorgThe official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program
SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is a two-semester discovery-based undergraduate research course that begins with simple digging in the soil to find new viruses but progresses through a variety of microbiology techniques and eventually to complex genome annotation and bioinformatic analyses
CBE Life Sci Educ 2016 fall15(3) pii ar38 doi 101187cbe16-01-0078Increasing URM Undergraduate Student Success through Assessment-Driven Interventions A Multiyear Study Using Freshman-Level General Biology as a Model SystemCarmichael MC1 St Clair C1 Edwards AM2 Barrett P1 McFerrin H1 Davenport I1 Awad M1 Kundu A1 Ireland SK3
AbstractXavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students In this multiyear study with sim5500 participants data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course The three hour-long exams were common and administered concurrently to all students New exam questions were developed using Blooms taxonomy and exam results were analyzed statistically with validated assessment tools All but the comprehensive final exam were returned to students for self-evaluation and remediation Among other approaches course rigor was monitored by using an identical set of 60 questions on the final exam across 10 semesters Analysis of the identical sets of 60 final exam questions revealed that overall averages increased from 729 (2010) to 835 (2015) Regression analysis demonstrated a statistically significant correlation between high-risk students and their averages on the 60 questions Additional analysis demonstrated statistically significant improvements for at least one letter grade from midterm to final and a 20 increase in the course pass rates over time also for the high-risk population These results support the hypothesis that our data-driven interventions and assessment techniques are successful in improving student retention particularly for our academically at-risk students
Lecture Biol 1230
bull Competency E4 (chemistry in biology atomic bonds metabolic pathways thermodynamics)
bull Quizzes (formative assessment with Clickers)
bull The coordinator prepares the three lsquoOne hour examsrsquo (questions not from the textbook) instructors again reviewcomment
bull Question types range (content versus applications) and also lsquoBack pagersquo ( 20 of the exam grade) Formative assessment using the LXRtest software (Opscan6 scanner)
Final exam not returned cumulative and has had 60 questions (good discriminators based on the rpbvalues) commonly used on ALL final exams for the past five years Powerful tool for measuring studentsrsquo learning and applications over time and based on academic risk categories
Last Name First Name
Biology 1230 Exam 1 ldquoBack Pagerdquo Score _ 20 pts
I 5 pts Complete the following table for the 3 major components (subatomic particles) of the atom
hint electrical charge = positive negative or neutral and mass = 1 dalton or 11800 dalton 1 pt each
Particle Electrical Charge Mass
1 Proton 1 dalton
2 Electron
3 Neutron
II 5 pts In your own words compare and contrast the following two atoms A and B use the back of the previous page to
make as many observations as you can about similarities (and what they mean) and differences (and what they mean)
between the atoms
A B
III 5 pts Match the following by placing the corresponding in the space provided 1 pt each
_____ tertiary structure 1 produce H2O
_____ two ester linkages 2 is responsible for the 3-dimensional shape of a protein
_____ phosphodiester bonds 3 exist within diglycerides (diacylglyerols) and phospholipids
_____ dehydration synthesis reactions 4 are a type of lipid
_____ steroids 5 are formed when nucleic acids are synthesized
IV 5 pts Circle each of the variable (R) groups in the molecules shown below (3 pts)
a Which lsquoRrsquo group is polar ______ (write the corresponding in the space provided) (1 pt)
b Which lsquoRrsquo group is ionic ______ (write the corresponding in the space provided) (1 pt)
NH3+ OH CH3
1 2 3
12 neutrons
11 protons
10 electrons
13 neutrons
11 protons
11 electrons
Bio1230 Exam 1
Clickers and immediate feedback
Name _____________________________________________________________________________________________
This is a worksheet for your self-evaluation of study habits and exam preparedness Your answers on the corresponding
online exam surveys are confidential
~The average number of hours I spent per week reading the chapters andor reviewingprocessing class notes was (circle the
appropriate response)
zero to one one to two two to four greater than four
~I read the assignment before coming to class (circle the appropriate response)
never sometimes regularly
~I asked my instructor questions when I was confused about textbook material andor lecture material (circle the appropriate
response)
never sometimes regularly
~Overall I spent _____ hours specifically studying for this exam (Please fill in the blank)
~Prior to taking the exam I expected to get an approximate grade of (fill in the blank) _____
~My actual grade was a(n) (fill in the blank) _____
~Check all of the statements that apply to your performance on the exam
____ studied the right information ____ did not study the right information
____ studied the right information but did not ____ studied the right information and
understand it thought I understood it
____ used the class outlines to study ____ thought college would be easier
____ did not know what to study ____ other _____________________
____ did not think I would need to know the information in such detail
Analysis of Missed Questions I answered the question incorrectly because I Insert question number below in the correct category
did not study the information
studied the information but forgot it
did not understand the information in the
summary notes
confused similar concepts or terms (ie
isotopes and isomers)
misread or misunderstood the question
did not consider all of the answer choices
knew the correct answer - but chose an
incorrect answer by mistake
List other reason(s)
List other reason(s)
Please answer additional self-evaluation questions on the back of this page
Self-Evaluation of Study Habits amp Exam Preparedness for Biology 1230 Exam I or II or III (circle one)
Going forwardhellip
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
CBE Life Sci Educ 2016 fall15(3) pii ar38 doi 101187cbe16-01-0078Increasing URM Undergraduate Student Success through Assessment-Driven Interventions A Multiyear Study Using Freshman-Level General Biology as a Model SystemCarmichael MC1 St Clair C1 Edwards AM2 Barrett P1 McFerrin H1 Davenport I1 Awad M1 Kundu A1 Ireland SK3
AbstractXavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students In this multiyear study with sim5500 participants data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course The three hour-long exams were common and administered concurrently to all students New exam questions were developed using Blooms taxonomy and exam results were analyzed statistically with validated assessment tools All but the comprehensive final exam were returned to students for self-evaluation and remediation Among other approaches course rigor was monitored by using an identical set of 60 questions on the final exam across 10 semesters Analysis of the identical sets of 60 final exam questions revealed that overall averages increased from 729 (2010) to 835 (2015) Regression analysis demonstrated a statistically significant correlation between high-risk students and their averages on the 60 questions Additional analysis demonstrated statistically significant improvements for at least one letter grade from midterm to final and a 20 increase in the course pass rates over time also for the high-risk population These results support the hypothesis that our data-driven interventions and assessment techniques are successful in improving student retention particularly for our academically at-risk students
Lecture Biol 1230
bull Competency E4 (chemistry in biology atomic bonds metabolic pathways thermodynamics)
bull Quizzes (formative assessment with Clickers)
bull The coordinator prepares the three lsquoOne hour examsrsquo (questions not from the textbook) instructors again reviewcomment
bull Question types range (content versus applications) and also lsquoBack pagersquo ( 20 of the exam grade) Formative assessment using the LXRtest software (Opscan6 scanner)
Final exam not returned cumulative and has had 60 questions (good discriminators based on the rpbvalues) commonly used on ALL final exams for the past five years Powerful tool for measuring studentsrsquo learning and applications over time and based on academic risk categories
Last Name First Name
Biology 1230 Exam 1 ldquoBack Pagerdquo Score _ 20 pts
I 5 pts Complete the following table for the 3 major components (subatomic particles) of the atom
hint electrical charge = positive negative or neutral and mass = 1 dalton or 11800 dalton 1 pt each
Particle Electrical Charge Mass
1 Proton 1 dalton
2 Electron
3 Neutron
II 5 pts In your own words compare and contrast the following two atoms A and B use the back of the previous page to
make as many observations as you can about similarities (and what they mean) and differences (and what they mean)
between the atoms
A B
III 5 pts Match the following by placing the corresponding in the space provided 1 pt each
_____ tertiary structure 1 produce H2O
_____ two ester linkages 2 is responsible for the 3-dimensional shape of a protein
_____ phosphodiester bonds 3 exist within diglycerides (diacylglyerols) and phospholipids
_____ dehydration synthesis reactions 4 are a type of lipid
_____ steroids 5 are formed when nucleic acids are synthesized
IV 5 pts Circle each of the variable (R) groups in the molecules shown below (3 pts)
a Which lsquoRrsquo group is polar ______ (write the corresponding in the space provided) (1 pt)
b Which lsquoRrsquo group is ionic ______ (write the corresponding in the space provided) (1 pt)
NH3+ OH CH3
1 2 3
12 neutrons
11 protons
10 electrons
13 neutrons
11 protons
11 electrons
Bio1230 Exam 1
Clickers and immediate feedback
Name _____________________________________________________________________________________________
This is a worksheet for your self-evaluation of study habits and exam preparedness Your answers on the corresponding
online exam surveys are confidential
~The average number of hours I spent per week reading the chapters andor reviewingprocessing class notes was (circle the
appropriate response)
zero to one one to two two to four greater than four
~I read the assignment before coming to class (circle the appropriate response)
never sometimes regularly
~I asked my instructor questions when I was confused about textbook material andor lecture material (circle the appropriate
response)
never sometimes regularly
~Overall I spent _____ hours specifically studying for this exam (Please fill in the blank)
~Prior to taking the exam I expected to get an approximate grade of (fill in the blank) _____
~My actual grade was a(n) (fill in the blank) _____
~Check all of the statements that apply to your performance on the exam
____ studied the right information ____ did not study the right information
____ studied the right information but did not ____ studied the right information and
understand it thought I understood it
____ used the class outlines to study ____ thought college would be easier
____ did not know what to study ____ other _____________________
____ did not think I would need to know the information in such detail
Analysis of Missed Questions I answered the question incorrectly because I Insert question number below in the correct category
did not study the information
studied the information but forgot it
did not understand the information in the
summary notes
confused similar concepts or terms (ie
isotopes and isomers)
misread or misunderstood the question
did not consider all of the answer choices
knew the correct answer - but chose an
incorrect answer by mistake
List other reason(s)
List other reason(s)
Please answer additional self-evaluation questions on the back of this page
Self-Evaluation of Study Habits amp Exam Preparedness for Biology 1230 Exam I or II or III (circle one)
Going forwardhellip
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
Lecture Biol 1230
bull Competency E4 (chemistry in biology atomic bonds metabolic pathways thermodynamics)
bull Quizzes (formative assessment with Clickers)
bull The coordinator prepares the three lsquoOne hour examsrsquo (questions not from the textbook) instructors again reviewcomment
bull Question types range (content versus applications) and also lsquoBack pagersquo ( 20 of the exam grade) Formative assessment using the LXRtest software (Opscan6 scanner)
Final exam not returned cumulative and has had 60 questions (good discriminators based on the rpbvalues) commonly used on ALL final exams for the past five years Powerful tool for measuring studentsrsquo learning and applications over time and based on academic risk categories
Last Name First Name
Biology 1230 Exam 1 ldquoBack Pagerdquo Score _ 20 pts
I 5 pts Complete the following table for the 3 major components (subatomic particles) of the atom
hint electrical charge = positive negative or neutral and mass = 1 dalton or 11800 dalton 1 pt each
Particle Electrical Charge Mass
1 Proton 1 dalton
2 Electron
3 Neutron
II 5 pts In your own words compare and contrast the following two atoms A and B use the back of the previous page to
make as many observations as you can about similarities (and what they mean) and differences (and what they mean)
between the atoms
A B
III 5 pts Match the following by placing the corresponding in the space provided 1 pt each
_____ tertiary structure 1 produce H2O
_____ two ester linkages 2 is responsible for the 3-dimensional shape of a protein
_____ phosphodiester bonds 3 exist within diglycerides (diacylglyerols) and phospholipids
_____ dehydration synthesis reactions 4 are a type of lipid
_____ steroids 5 are formed when nucleic acids are synthesized
IV 5 pts Circle each of the variable (R) groups in the molecules shown below (3 pts)
a Which lsquoRrsquo group is polar ______ (write the corresponding in the space provided) (1 pt)
b Which lsquoRrsquo group is ionic ______ (write the corresponding in the space provided) (1 pt)
NH3+ OH CH3
1 2 3
12 neutrons
11 protons
10 electrons
13 neutrons
11 protons
11 electrons
Bio1230 Exam 1
Clickers and immediate feedback
Name _____________________________________________________________________________________________
This is a worksheet for your self-evaluation of study habits and exam preparedness Your answers on the corresponding
online exam surveys are confidential
~The average number of hours I spent per week reading the chapters andor reviewingprocessing class notes was (circle the
appropriate response)
zero to one one to two two to four greater than four
~I read the assignment before coming to class (circle the appropriate response)
never sometimes regularly
~I asked my instructor questions when I was confused about textbook material andor lecture material (circle the appropriate
response)
never sometimes regularly
~Overall I spent _____ hours specifically studying for this exam (Please fill in the blank)
~Prior to taking the exam I expected to get an approximate grade of (fill in the blank) _____
~My actual grade was a(n) (fill in the blank) _____
~Check all of the statements that apply to your performance on the exam
____ studied the right information ____ did not study the right information
____ studied the right information but did not ____ studied the right information and
understand it thought I understood it
____ used the class outlines to study ____ thought college would be easier
____ did not know what to study ____ other _____________________
____ did not think I would need to know the information in such detail
Analysis of Missed Questions I answered the question incorrectly because I Insert question number below in the correct category
did not study the information
studied the information but forgot it
did not understand the information in the
summary notes
confused similar concepts or terms (ie
isotopes and isomers)
misread or misunderstood the question
did not consider all of the answer choices
knew the correct answer - but chose an
incorrect answer by mistake
List other reason(s)
List other reason(s)
Please answer additional self-evaluation questions on the back of this page
Self-Evaluation of Study Habits amp Exam Preparedness for Biology 1230 Exam I or II or III (circle one)
Going forwardhellip
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
Final exam not returned cumulative and has had 60 questions (good discriminators based on the rpbvalues) commonly used on ALL final exams for the past five years Powerful tool for measuring studentsrsquo learning and applications over time and based on academic risk categories
Last Name First Name
Biology 1230 Exam 1 ldquoBack Pagerdquo Score _ 20 pts
I 5 pts Complete the following table for the 3 major components (subatomic particles) of the atom
hint electrical charge = positive negative or neutral and mass = 1 dalton or 11800 dalton 1 pt each
Particle Electrical Charge Mass
1 Proton 1 dalton
2 Electron
3 Neutron
II 5 pts In your own words compare and contrast the following two atoms A and B use the back of the previous page to
make as many observations as you can about similarities (and what they mean) and differences (and what they mean)
between the atoms
A B
III 5 pts Match the following by placing the corresponding in the space provided 1 pt each
_____ tertiary structure 1 produce H2O
_____ two ester linkages 2 is responsible for the 3-dimensional shape of a protein
_____ phosphodiester bonds 3 exist within diglycerides (diacylglyerols) and phospholipids
_____ dehydration synthesis reactions 4 are a type of lipid
_____ steroids 5 are formed when nucleic acids are synthesized
IV 5 pts Circle each of the variable (R) groups in the molecules shown below (3 pts)
a Which lsquoRrsquo group is polar ______ (write the corresponding in the space provided) (1 pt)
b Which lsquoRrsquo group is ionic ______ (write the corresponding in the space provided) (1 pt)
NH3+ OH CH3
1 2 3
12 neutrons
11 protons
10 electrons
13 neutrons
11 protons
11 electrons
Bio1230 Exam 1
Clickers and immediate feedback
Name _____________________________________________________________________________________________
This is a worksheet for your self-evaluation of study habits and exam preparedness Your answers on the corresponding
online exam surveys are confidential
~The average number of hours I spent per week reading the chapters andor reviewingprocessing class notes was (circle the
appropriate response)
zero to one one to two two to four greater than four
~I read the assignment before coming to class (circle the appropriate response)
never sometimes regularly
~I asked my instructor questions when I was confused about textbook material andor lecture material (circle the appropriate
response)
never sometimes regularly
~Overall I spent _____ hours specifically studying for this exam (Please fill in the blank)
~Prior to taking the exam I expected to get an approximate grade of (fill in the blank) _____
~My actual grade was a(n) (fill in the blank) _____
~Check all of the statements that apply to your performance on the exam
____ studied the right information ____ did not study the right information
____ studied the right information but did not ____ studied the right information and
understand it thought I understood it
____ used the class outlines to study ____ thought college would be easier
____ did not know what to study ____ other _____________________
____ did not think I would need to know the information in such detail
Analysis of Missed Questions I answered the question incorrectly because I Insert question number below in the correct category
did not study the information
studied the information but forgot it
did not understand the information in the
summary notes
confused similar concepts or terms (ie
isotopes and isomers)
misread or misunderstood the question
did not consider all of the answer choices
knew the correct answer - but chose an
incorrect answer by mistake
List other reason(s)
List other reason(s)
Please answer additional self-evaluation questions on the back of this page
Self-Evaluation of Study Habits amp Exam Preparedness for Biology 1230 Exam I or II or III (circle one)
Going forwardhellip
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
Last Name First Name
Biology 1230 Exam 1 ldquoBack Pagerdquo Score _ 20 pts
I 5 pts Complete the following table for the 3 major components (subatomic particles) of the atom
hint electrical charge = positive negative or neutral and mass = 1 dalton or 11800 dalton 1 pt each
Particle Electrical Charge Mass
1 Proton 1 dalton
2 Electron
3 Neutron
II 5 pts In your own words compare and contrast the following two atoms A and B use the back of the previous page to
make as many observations as you can about similarities (and what they mean) and differences (and what they mean)
between the atoms
A B
III 5 pts Match the following by placing the corresponding in the space provided 1 pt each
_____ tertiary structure 1 produce H2O
_____ two ester linkages 2 is responsible for the 3-dimensional shape of a protein
_____ phosphodiester bonds 3 exist within diglycerides (diacylglyerols) and phospholipids
_____ dehydration synthesis reactions 4 are a type of lipid
_____ steroids 5 are formed when nucleic acids are synthesized
IV 5 pts Circle each of the variable (R) groups in the molecules shown below (3 pts)
a Which lsquoRrsquo group is polar ______ (write the corresponding in the space provided) (1 pt)
b Which lsquoRrsquo group is ionic ______ (write the corresponding in the space provided) (1 pt)
NH3+ OH CH3
1 2 3
12 neutrons
11 protons
10 electrons
13 neutrons
11 protons
11 electrons
Bio1230 Exam 1
Clickers and immediate feedback
Name _____________________________________________________________________________________________
This is a worksheet for your self-evaluation of study habits and exam preparedness Your answers on the corresponding
online exam surveys are confidential
~The average number of hours I spent per week reading the chapters andor reviewingprocessing class notes was (circle the
appropriate response)
zero to one one to two two to four greater than four
~I read the assignment before coming to class (circle the appropriate response)
never sometimes regularly
~I asked my instructor questions when I was confused about textbook material andor lecture material (circle the appropriate
response)
never sometimes regularly
~Overall I spent _____ hours specifically studying for this exam (Please fill in the blank)
~Prior to taking the exam I expected to get an approximate grade of (fill in the blank) _____
~My actual grade was a(n) (fill in the blank) _____
~Check all of the statements that apply to your performance on the exam
____ studied the right information ____ did not study the right information
____ studied the right information but did not ____ studied the right information and
understand it thought I understood it
____ used the class outlines to study ____ thought college would be easier
____ did not know what to study ____ other _____________________
____ did not think I would need to know the information in such detail
Analysis of Missed Questions I answered the question incorrectly because I Insert question number below in the correct category
did not study the information
studied the information but forgot it
did not understand the information in the
summary notes
confused similar concepts or terms (ie
isotopes and isomers)
misread or misunderstood the question
did not consider all of the answer choices
knew the correct answer - but chose an
incorrect answer by mistake
List other reason(s)
List other reason(s)
Please answer additional self-evaluation questions on the back of this page
Self-Evaluation of Study Habits amp Exam Preparedness for Biology 1230 Exam I or II or III (circle one)
Going forwardhellip
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
Clickers and immediate feedback
Name _____________________________________________________________________________________________
This is a worksheet for your self-evaluation of study habits and exam preparedness Your answers on the corresponding
online exam surveys are confidential
~The average number of hours I spent per week reading the chapters andor reviewingprocessing class notes was (circle the
appropriate response)
zero to one one to two two to four greater than four
~I read the assignment before coming to class (circle the appropriate response)
never sometimes regularly
~I asked my instructor questions when I was confused about textbook material andor lecture material (circle the appropriate
response)
never sometimes regularly
~Overall I spent _____ hours specifically studying for this exam (Please fill in the blank)
~Prior to taking the exam I expected to get an approximate grade of (fill in the blank) _____
~My actual grade was a(n) (fill in the blank) _____
~Check all of the statements that apply to your performance on the exam
____ studied the right information ____ did not study the right information
____ studied the right information but did not ____ studied the right information and
understand it thought I understood it
____ used the class outlines to study ____ thought college would be easier
____ did not know what to study ____ other _____________________
____ did not think I would need to know the information in such detail
Analysis of Missed Questions I answered the question incorrectly because I Insert question number below in the correct category
did not study the information
studied the information but forgot it
did not understand the information in the
summary notes
confused similar concepts or terms (ie
isotopes and isomers)
misread or misunderstood the question
did not consider all of the answer choices
knew the correct answer - but chose an
incorrect answer by mistake
List other reason(s)
List other reason(s)
Please answer additional self-evaluation questions on the back of this page
Self-Evaluation of Study Habits amp Exam Preparedness for Biology 1230 Exam I or II or III (circle one)
Going forwardhellip
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
Name _____________________________________________________________________________________________
This is a worksheet for your self-evaluation of study habits and exam preparedness Your answers on the corresponding
online exam surveys are confidential
~The average number of hours I spent per week reading the chapters andor reviewingprocessing class notes was (circle the
appropriate response)
zero to one one to two two to four greater than four
~I read the assignment before coming to class (circle the appropriate response)
never sometimes regularly
~I asked my instructor questions when I was confused about textbook material andor lecture material (circle the appropriate
response)
never sometimes regularly
~Overall I spent _____ hours specifically studying for this exam (Please fill in the blank)
~Prior to taking the exam I expected to get an approximate grade of (fill in the blank) _____
~My actual grade was a(n) (fill in the blank) _____
~Check all of the statements that apply to your performance on the exam
____ studied the right information ____ did not study the right information
____ studied the right information but did not ____ studied the right information and
understand it thought I understood it
____ used the class outlines to study ____ thought college would be easier
____ did not know what to study ____ other _____________________
____ did not think I would need to know the information in such detail
Analysis of Missed Questions I answered the question incorrectly because I Insert question number below in the correct category
did not study the information
studied the information but forgot it
did not understand the information in the
summary notes
confused similar concepts or terms (ie
isotopes and isomers)
misread or misunderstood the question
did not consider all of the answer choices
knew the correct answer - but chose an
incorrect answer by mistake
List other reason(s)
List other reason(s)
Please answer additional self-evaluation questions on the back of this page
Self-Evaluation of Study Habits amp Exam Preparedness for Biology 1230 Exam I or II or III (circle one)
Going forwardhellip
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
Going forwardhellip
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
bull Track randomly selected students from the FR cohort based on academic risk categories and follow their progression through the curriculum
bull Adapt these validated assessment tools in as many courses as possible (faculty lsquobuy inrsquo)
bull Continue the competency-based approach of teaching to help all students perform better and reach their goals
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
Strengths
bull Curricular design amp recommended course sequence
bull Coordinated introductory science courses with defined learning objectives and common exams
bull Dedicated faculty to bring about real change
bull Students eager to join STEM particularly Biology
bull Overall receptive and appreciative student body
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
Areas we are addressing
bull Teachersrsquo willingness to work and change themselves
bull Increasing student engagement in lectures amp labsbull Classroom based researchmore open ended labsbull Early exposure of to scientific literaturebull Early introduction to interdisciplinary conceptsbull More effective teaching and testingbull Developing newer assessment techniques bull Assessing beyond the routineminimum and
actually using the data to improve
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback
AcknowledgmentsSupported by the Howard Hughes Medical Institutebull Candace St Clair (HHMI technician)
bull Mary Carmichael (Biol 1230 coordinator amp departmental assessment person)
bull Harris McFerrin Hector Biliran Harish Ratnayaka Peter Martinat and Cecily DeFreece (Biol 1210L and Biol 1220L)
bull Peter Barrett (Genetics lab coordinator and Cell Bio lecture and labs)
bull Joseph Ross (Phage Genomics)
bull Xavier undergraduate serving as TAs
bull David Hanauer Professor Indiana Univ of Pennsylvania Assessment Consultant
bull University Administration
bull The BioSQuaRE team members
bull Undergraduate students providing formal and informal feedback