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MBG*3350 Laboratory Methods in Molecular BiologyFall 2020
Section(s): C01
Department of Molecular and Cellular BiologyCredit Weight: 0.75
Version 1.00 - September 08, 2020___________________________________________________________________________________________________________________
1 Course Details
1.1 Calendar DescriptionThis course involves laboratory based instruction in the basic methodologies of Molecular Biology. Students will have the opportunity to develop technical skills and practical knowledge sufficient to perform basic procedures independently, and to diagnose and analyze experimental results obtained with these techniques.
BIOC*2580, MCB*2050Pre-Requisites: Registration in BSC.BIOC (major or minor), BIOC:C , BTOX, BTOX:C, BPCH, BPCH:C, MICR(major or minor), MICR:C , MBG (major or minor), PBTC, PLSC (major or minor), TOX, TOX:C
Restrictions:
1.2 TimetableLaboratory: Either Monday & Wednesday or Tuesday & Thursday 1:30-5:20 pm Laboratory will be in a virtual/online format Videos of all experiments will be posted on Courselink, as will protocols, data files, and supporting documentation. Discussion and Q/A sessions with your TA will be online during a portion of the scheduled laboratory hours. Lecture: Friday 2:30-3:50 pm Lectures will be in a virtual/online format delivered through Zoom. Check content page on courselink for links to ZOOM lectures.
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1.3 Final ExamThere is no exam during the exam period, instead there are 2 term exams scheduled during the semester.
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2 Instructional SupportVirtual office hours for TAs will be posted in courselink. Meetings with instructor can be scheduled by email.
2.1 Instructional Support TeamStephen SeahInstructor:[email protected]: +1-519-824-4120 x56750Telephone: SC1 4250Office:
Catrien BouwmanLab Co-ordinator:[email protected]: +1-519-824-4120 x53329Telephone: SSC3503Office:
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3 Learning Resources
3.1 Required ResourcesCourselink (Website)
https://courselink.uoguelph.caThis course will make use of the University of Guelph’s course website on D2L (via Courselink). Consequently, you are responsible for all information posted on the Courselink page for MBG*3350. Please check it regularly.
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4 Learning Outcomes
4.1 Course Learning OutcomesBy the end of this course, you should be able to:
Explain the fundamental principles of practical molecular biology 1. Recognize and interpret experimental results 2. Implement the theoretical principles and apply them in the execution of lab experiments 3. Plan, design, monitor, troubleshoot and optimize experiments 4.
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Use online tools to research a particular topic, and read primary research articles in molecular genetics
5.
Identify skills gained in this course and describe how those skills can be applied in the workforce
6.
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5 Teaching and Learning Activities
5.1 LectureOne lecture per week: Friday 2:30-3:50 pm conducted through Zoom. Links to Microsoft Stream containing audio explanations of slides will be posted in the announcement page on courselink (you will need to sign into your microsoft account using your UofG credentials for access). Powerpoint slides without audio will be posted in the content page of courselink. Lectures will be delivered in a flip classroom format using ZOOM. Check content page in courselink for links to ZOOM lectures. Students are to review slides and audio explanations BEFORE class and be prepared to discuss the topic indicated in the lecture schedule of the courseoutline during lecture time.
5.2 LaboratoryTwo lab sessions per week: Monday/Wednesday or Tuesday/Thursday 1:30-5:20 pm Laboratory will be in a virtual/online format Students are to watch an orientation/introduction video and complete an online survey before Sept 14. "How to" videos, experimental protocols, data files and supporting documentation will be available online at the beginning of each module. There will be scheduled discussion sessions during a portion of the schedule laboratory hours (with a TA over Zoom). These discussions will be recorded and posted on Courselink, along with a discussion board for follow-up questions. Marks will be awarded for participation in discussions during and after tutorials.
5.3 Lecture/Lab Topics and Schedule
Laboratory schedule
Week/Date
Day 1
Day 2
Lecture Topic
Week 1
Orientation and Introduction video
Lecture 1 : Course introduction.
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Sept 7-11 Introduction
Benchling sign-up instructions
Kahoot! quiz for feedback purposes only
Week 2 Sept 14-18 Module 1A
Plasmid mini-prep DNA quantitation Restriction enzyme digests
How to pour an agarose gel How to run and visualize DNA on an agarose gel
Friday Kahoot! quiz•
Lecture 2: Plasmid isolation, DNA analysis and Gene cloning
Week 3 Sept 21-25 Module 1B
Introduce Benchling What are plasmids? Applications Important features Copy number, etc.
Analyze data, label a gel, how to write a figure legend, virtual digests using Benchling
Lecture 3: E. coli as a heterologous host for gene cloning
Week 4 Sept 28-Oct 2 Module 2A
PCR for molecular cloning Cleaning a PCR product DNA ligation
DNA transformation, selection of recombinant bacteria (colony PCR) qPCR
Assignment 1 due 12pm
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Friday Kahoot! quiz•
Lecture 4: PCR
Primer design principles Design primers, virtual PCR using Benchling PCR result troubleshooting
Clone PCR product into appropriate vector (Benchling) using appropriate restriction enzymes, antibiotics
Week 5 Oct 5-9 Module 2B
Lecture 5 qRTPCR
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Import DNA sequence into Benchling
qPCR data analysis
Week 6 Oct 12-16 Thanksgiving Week
No Lab
No Lab
Term exam # 1 on lectures 2-4 & labs of week 1-5 (21%).
Week 7 Oct 19-23 Module 3A
Protein purification: start cultures, induce, harvest and lyse, affinity purification of GFP protein
SDS-PAGE: how to pour a gel How to load and run protein on SDS-PAGE Visualize protein with Coomassie Western blot
Assignment 2 due 12pm
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Friday Kahoot! quiz•
Lecture 6: Recombinant protein expression and purification
Week 8 Oct 26-30 Module 3B
protein purification strategies. Discuss C-terminal vs N-terminal tags
Analyze data Examine Methods sections of Journal articles
Lecture 7: Protein quantification and analysis by SDS-PAGE
Online tools GenBank NCBI-blast
Online tools multiple sequence alignments
Assignment 3 due 12pm
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Week 9 Nov 2-6 Module 4A
Lecture 8: Western, Northern and Southern blotting
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Friday Kahoot! quiz•
Week 10 Nov 9-13 Module 4B
Online tools Conserved regions in homologous proteins
Online tools Protein structure predictions
Self Reflection Assignment due 12 pm (4%). Check courselink for instructions.
Week 11 Nov 16-20
No Lab
No Lab Assignment 4 due 12pm
Week 12 Nov 23-27
No Lab
No Lab Culminating report due 12pm
Final exam on all lectures and labs (25%).
Week 13 Nov 30 -Dec 4
No Lab
No Lab
No Lecture
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6 Assessments
6.1 Methods of Assessment
Assessment
Form of Assessment
Weight of Assessment (% of final)
Due Date of Assessment
Course Content /Activity
Learning Outcome (see above)
Virtual Lab activities Kahoots! Quiz: 4 x 2% = 8%
See lab topics and schedule in the
50 %
Lab weeks 1-10
1, 2, 3, 4, 5 and 6
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Form of Assessment
Weight of Assessment (% of final)
Due Date of Assessment
Course Content /Activity
Learning Outcome (see above)
Module assignments 4 x 6% = 24% Cumulative assignment 15% Discussion participation 3%
courseoutline for deadlines
Self reflection assignment
4% Nov 13 6
Term exam 1 21% Oct16 Lectures and Labs weeks 1-5
1,2,3,4 and 6
Term exam 2
25%
Nov 27
Lectures and Labs cumulative (all materials covered in course
1,2,3,4 and 6
6.2 NoteTerm Exams Term exams 1 and 2 will be held during regular lecture time online on courselink. Respondus lockdown and monitor may be used. Students are advised to access the practice test on courselink in advance of the exam dates to ensure that Respondus is working on their computer systems. If you fail to write Term exam 1, a grade of 0% will be assigned unless an
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acceptable cause such as sickness or family emergency is documented. In the situation where academic consideration is given, Term exam 2 will be adjusted to 46 %. For missed Term exam 2 an Incomplete grade will be submitted with a recommendation of 0% unless academic consideration is granted for a deferred exam. Assigments Assignments and reports must be typed, double-spaced, 12-point font. All assignments are due at 12pm (noon) on their noted due date. Assignments must be uploaded to the relevant folder in the dropbox of courselink. Late assignments will be accepted without penalty only for medical or compassionate reasons with documentation. Late assignments without valid reasons will be penalized 10% per day up to 50%. A grade of zero is assigned after 5 days late. ALL lab assignments and reports are an important part of the course. Missing two or more of these assessment will lead to an “incomplete” for the course at the end of the semester. Kahoot! Quizzes
Kahoot! quizzes are on Fridays of week 1 for each Module (check “Lecture/Lab Topics and Schedule” in this courseoutline for dates, you will receive an invitation for each quiz via your university email account). You can complete each Quiz anytime during the scheduled date from 12 am to 11.59 pm. There will be no make up quiz.
Self reflection
Details on how to complete the self reflection assignment will be posted on courselink.
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7 Course Statements
7.1 GradingAll assignments are due at 12:00pm (noon). When assignment grades are released, take your time to review the assignment and the comments that were made. After 24h you may contact the Lab Coordinator. if you have questions. Students who wish to have their assignments re-graded must submit them to the Lab Coordinator. within 5 class days of their return. The entire assingment will be re-graded so the mark may go up, down or remain unchanged.
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7.2 TurnitinIn this course, your instructor will be using Turnitin, integrated with the CourseLink Dropbox tool, to detect possible plagiarism, unauthorized collaboration or copying as part of the ongoing efforts to maintain academic integrity at the University of Guelph. All submitted assignments will be included as source documents in the Turnitin.com reference database solely for the purpose of detecting plagiarism of such papers. Use of the Turnitin.com service is subject to the Usage Policy posted on the Turnitin.com site. A major benefit of using Turnitin is that students will be able to educate and empower themselves in preventing academic misconduct. In this course, you may screen your own assignments through Turnitin as many times as you wish before the due date. You will be able to see and print reports that show you exactly where you have properly and improperly referenced the outside sources and materials in your assignment.
8 Department of Molecular and Cellular Biology Statements
8.1 Academic AdvisorsIf you are concerned about any aspect of your academic program:
Make an appointment with a program counsellor in your degree program. B.Sc. Academic Advising or Program Counsellors
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8.2 Academic SupportIf you are struggling to succeed academically:
Learning Commons: There are numerous academic resources offered by the Learning Commons including, Supported Learning Groups for a variety of courses, workshops related to time management, taking multiple choice exams, and general study skills. You can also set up individualized appointments with a learning specialist. http://www.learningcommons.uoguelph.ca/
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Science Commons: Located in the library, the Science Commons provides support for physics, mathematic/statistics, and chemistry. Details on their hours of operations can be found at: http://www.lib.uoguelph.ca/get-assistance/studying/chemistry-physics-help and http://www.lib.uoguelph.ca/get-assistance/studying/math-stats-help
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8.3 WellnessIf you are struggling with personal or health issues:
Counselling services offers individualized appointments to help students work through personal struggles that may be impacting their academic performance.
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https://www.uoguelph.ca/counselling/Student Health Services is located on campus and is available to provide medical attention. https://www.uoguelph.ca/studenthealthservices/clinic
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For support related to stress and anxiety, besides Health Services and Counselling Services, Kathy Somers runs training workshops and one-on-one sessions related to stress management and high performance situations. http://www.selfregulationskills.ca/
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8.4 Personal informationPersonal information is collected under the authority of the University of Guelph Act (1964), and in accordance with Ontario's Freedom of Information and Protection of Privacy Act (FIPPA) http://www.e-laws.gov.on.ca/index.html. This information is used by University officials in order to carry out their authorized academic and administrative responsibilities and also to establish a relationship for alumni and development purposes. For more information regarding the Collection, Use and Disclosure of Personal Information policies please see the Undergraduate Calendar. (https://www.uoguelph.ca/registrar/calendars/undergraduate/current/intro/index.shtml)
9 University Statements
9.1 Email CommunicationAs per university regulations, all students are required to check their e-mail account regularly: e-mail is the official route of communication between the University and its students.
9.2 When You Cannot Meet a Course RequirementWhen you find yourself unable to meet an in-course requirement because of illness or compassionate reasons please advise the course instructor (or designated person, such as a teaching assistant) in writing, with your name, id#, and e-mail contact. The grounds for Academic Consideration are detailed in the Undergraduate and Graduate Calendars. Undergraduate Calendar - Academic Consideration and Appeals https://www.uoguelph.ca/registrar/calendars/undergraduate/current/c08/c08-ac.shtml Graduate Calendar - Grounds for Academic Consideration https://www.uoguelph.ca/registrar/calendars/graduate/current/genreg/index.shtml Associate Diploma Calendar - Academic Consideration, Appeals and Petitions https://www.uoguelph.ca/registrar/calendars/diploma/current/index.shtml
9.3 Drop DateStudents will have until the last day of classes to drop courses without academic penalty. The
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deadline to drop two-semester courses will be the last day of classes in the second semester. This applies to all students (undergraduate, graduate and diploma) except for Doctor of Veterinary Medicine and Associate Diploma in Veterinary Technology (conventional and alternative delivery) students. The regulations and procedures for course registration are available in their respective Academic Calendars. Undergraduate Calendar - Dropping Courses https://www.uoguelph.ca/registrar/calendars/undergraduate/current/c08/c08-drop.shtml Graduate Calendar - Registration Changes https://www.uoguelph.ca/registrar/calendars/graduate/current/genreg/genreg-reg-regchg.shtml Associate Diploma Calendar - Dropping Courses https://www.uoguelph.ca/registrar/calendars/diploma/current/c08/c08-drop.shtml
9.4 Copies of Out-of-class AssignmentsKeep paper and/or other reliable back-up copies of all out-of-class assignments: you may be asked to resubmit work at any time.
9.5 AccessibilityThe University promotes the full participation of students who experience disabilities in their academic programs. To that end, the provision of academic accommodation is a shared responsibility between the University and the student. When accommodations are needed, the student is required to first register with Student Accessibility Services (SAS). Documentation to substantiate the existence of a disability is required; however, interim accommodations may be possible while that process is underway. Accommodations are available for both permanent and temporary disabilities. It should be noted that common illnesses such as a cold or the flu do not constitute a disability. Use of the SAS Exam Centre requires students to book their exams at least 7 days in advance and not later than the 40th Class Day. For Guelph students, information can be found on the SAS website https://www.uoguelph.ca/sas For Ridgetown students, information can be found on the Ridgetown SAS website https://www.ridgetownc.com/services/accessibilityservices.cfm
9.6 Academic IntegrityThe University of Guelph is committed to upholding the highest standards of academic integrity, and it is the responsibility of all members of the University community-faculty, staff, and students-to be aware of what constitutes academic misconduct and to do as much as possible to prevent academic offences from occurring. University of Guelph students have
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the responsibility of abiding by the University's policy on academic misconduct regardless of their location of study; faculty, staff, and students have the responsibility of supporting an environment that encourages academic integrity. Students need to remain aware that instructors have access to and the right to use electronic and other means of detection. Please note: Whether or not a student intended to commit academic misconduct is not relevant for a finding of guilt. Hurried or careless submission of assignments does not excuse students from responsibility for verifying the academic integrity of their work before submitting it. Students who are in any doubt as to whether an action on their part could be construed as an academic offence should consult with a faculty member or faculty advisor. Undergraduate Calendar - Academic Misconduct https://www.uoguelph.ca/registrar/calendars/undergraduate/current/c08/c08-amisconduct.shtml Graduate Calendar - Academic Misconduct https://www.uoguelph.ca/registrar/calendars/graduate/current/genreg/index.shtml
9.7 Recording of MaterialsPresentations that are made in relation to course work - including lectures - cannot be recorded or copied without the permission of the presenter, whether the instructor, a student, or guest lecturer. Material recorded with permission is restricted to use for that course unless further permission is granted.
9.8 ResourcesThe Academic Calendars are the source of information about the University of Guelph’s procedures, policies, and regulations that apply to undergraduate, graduate, and diploma programs. Academic Calendars https://www.uoguelph.ca/academics/calendars
9.9 DisclaimerPlease note that the ongoing COVID-19 pandemic may necessitate a revision of the format of course offerings and academic schedules. Any such changes will be announced via CourseLink and/or class email. All University-wide decisions will be posted on the COVID-19 website (https://news.uoguelph.ca/2019-novel-coronavirus-information/) and circulated by email.
9.10 IllnessThe University will not normally require verification of illness (doctor's notes) for fall 2020 or winter 2021 semester courses. However, requests for Academic Consideration may still require medical documentation as appropriate.
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