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Introductory Research Experience in Molecular Biology PCB 3023L/PCB 3063L Cell Biology & Genetics Laboratory Combined Course Syllabus – Fall 2016 Department of Cell Biology, Microbiology, and Molecular Biology University of South Florida Instructor Dr. Beth Jones-Mason Office : ISA 3008 [email protected] Office Hours : Tues 3-4pm, or by appointment General Information Tues & Thurs, 10:00am-12:45pm ISA 3015 lab This is a 2 credit hour hands-on laboratory course. Students taking this course will receive credit for both the Cell Biology Laboratory course (PCB 3023L) and the General Genetics Laboratory course (PCB 3063L). Registration for this course requires that you enroll in both CRN 92421 and CRN 92422. The single final letter grade you receive upon completion of this course will be reflected twice on your transcript, once for PCB3023L and once for PCB3063L. Students must have taken or be currently enrolled in PCB3023 and PCB3063 to be eligible to take this course. Additionally, students must not have taken Cell Biology Lab or Genetics Lab previously. Registration for this course requires a departmental permit, and because this is a laboratory course, you are charged the lab fee twice, once for each registration. This course offers students an opportunity to also enroll in IDS 4914 (Advanced Undergraduate Research Experience) for 0 credits, S/U. Materials Required Laboratory coat Lab notebook (spiral bound or binder) Safety goggles (wraparound or classic style) Additional Materials will be provided by the instructor and/or available through the Canvas course website Course Objectives This course is designed to complement and reinforce the principles taught in Cell Biology Lecture and Genetics Lecture (PCB 3023 and PCB 3063) and to offer students an introductory research experience in molecular biology. The research questions addressed are aimed at further exploration of several fundamental concepts in genetics and cellular biology. Students will learn to read scientific literature, form hypotheses, design experiments, collect & analyze data, and present their data in notebooks, discussions, lab meeting style presentations, and through writing a scientific research paper. Upon completion of this course, students will have an understanding of developing and carrying out a research project in the lab and will be able to perform several basic laboratory protocols utilized in Cellular Biology and Genetics research.

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Page 1: Introductory Research Experience in Molecular Biology · Introductory Research Experience in Molecular Biology PCB 3023L/PCB 3063L Cell Biology & Genetics Laboratory Combined Course

Introductory Research Experience in Molecular Biology PCB 3023L/PCB 3063L Cell Biology & Genetics Laboratory Combined Course

Syllabus – Fall 2016

Department of Cell Biology, Microbiology, and Molecular Biology University of South Florida

Instructor Dr. Beth Jones-Mason Office : ISA 3008 [email protected] Office Hours : Tues 3-4pm, or by appointment General Information Tues & Thurs, 10:00am-12:45pm ISA 3015 lab This is a 2 credit hour hands-on laboratory course. Students taking this course will receive credit for both the Cell Biology Laboratory course (PCB 3023L) and the General Genetics Laboratory course (PCB 3063L). Registration for this course requires that you enroll in both CRN 92421 and CRN 92422. The single final letter grade you receive upon completion of this course will be reflected twice on your transcript, once for PCB3023L and once for PCB3063L. Students must have taken or be currently enrolled in PCB3023 and PCB3063 to be eligible to take this course. Additionally, students must not have taken Cell Biology Lab or Genetics Lab previously. Registration for this course requires a departmental permit, and because this is a laboratory course, you are charged the lab fee twice, once for each registration. This course offers students an opportunity to also enroll in IDS 4914 (Advanced Undergraduate Research Experience) for 0 credits, S/U. Materials Required

Laboratory coat Lab notebook (spiral bound or binder)

Safety goggles (wraparound or classic style)

Additional Materials will be provided by the instructor and/or available through the Canvas course website

Course Objectives This course is designed to complement and reinforce the principles taught in Cell Biology Lecture and Genetics Lecture (PCB 3023 and PCB 3063) and to offer students an introductory research experience in molecular biology. The research questions addressed are aimed at further exploration of several fundamental concepts in genetics and cellular biology. Students will learn to read scientific literature, form hypotheses, design experiments, collect & analyze data, and present their data in notebooks, discussions, lab meeting style presentations, and through writing a scientific research paper. Upon completion of this course, students will have an understanding of developing and carrying out a research project in the lab and will be able to perform several basic laboratory protocols utilized in Cellular Biology and Genetics research.

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Student Learning Outcomes

Utilize knowledge of basic cell survival, cell proliferation, and cell signaling principles to suggest protein and gene targets of a particular cell signaling event.

Utilize knowledge of molecular genetics principles to design primers and perform gene expression analysis.

Describe and perform basic techniques utilized in cell biology and genetics research, including cell counting, live/dead cell staining, RNA extraction, nucleic acid quantification, cDNA synthesis, gene expression analysis by RT-PCR, and agarose gel electrophoresis.

Perform a literature search and read scientific research articles.

Form hypotheses and identify appropriate controls to include in experiments.

Collect, analyze, and present experimental data in lab meeting style discussions/presentations and through writing a research paper.

Perform statistical analysis to evaluate data sets, distinguishing the use of student’s t-test and ANOVA.

Suggest potential sources of error and troubleshooting strategies based on experimental outcomes.

Communicate and collaborate as a member of a research team to address a current biomedical question.

Class Format The laboratory experiments and activities performed in this course are laid out in the general schedule provided. There is flexibility built into the schedule to allow for troubleshooting and optimization of protocols across the semester, to allow students practice with a process similar to that of a research lab. It is your responsibility to read any assigned reading and to review the previous lab’s exercises before coming to class so that you will be prepared when arriving to lab each week. Keep a written record of all experiments performed in sufficient detail and record all data in your lab notebook. Your TA/Instructor will assist you in succeeding in this course. They will review the concepts and techniques of each lab exercise prior to you doing them, and then observe your work and guide you. They will also keep regular office hours where you are encouraged to ask any questions you have relevant to the lab exercises or material. Attendance Policy The following is a Cell Biology, Microbiology, and Molecular Biology Departmental laboratory course attendance policy. Lab attendance is MANDATORY and arrival to lab must be on time. Students who miss a laboratory without a documented, valid excuse will be penalized 2.5% of the possible total laboratory score for the first occurrence and 5% of the possible total laboratory score for each subsequent occurrence. Due to the hands-on nature of laboratory courses, more than five absences, whether excused or unexcused, will result in a failing grade (F) for this course. Absences are dealt with on a case by case basis and are seldom excusable. Absences will be excused for documented, legitimate reasons according to university guidelines (unforeseen: e.g. medical

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emergency, death in the immediate family; and special circumstances: e.g. jury duty, day of religious observance, USF-sponsored academic conference participation). Documentation may be a medical doctor’s note, hospital admission papers, legal or a funeral notice that documents the specific date & times of the missed lab period. Lab absences due to inclement weather, unless classes are canceled as a result of University closure, do not represent excusable special circumstances. The proper supporting documentation for an excused absence must be presented to the TA/instructor within one week of the absence or the absence will be considered unexcused. The TA/Instructor should be contacted at the beginning of the semester (by the second week of class) for foreseen excusable absences (special circumstances) and within 48 hours of the missed lab period for unforeseen excusable absences to make arrangements for making up the lab exercises where possible and/or turning in assignments due/completed during the missed lab period. Failure to contact your TA/Instructor within this timeframe will result in late penalties for any assignments missed due to excused absences. Laboratories cannot be made up at an alternative time as there is only one section of this lab course. If you find that you are absent for several classes due to illness or other circumstances, it is recommended that you drop the class. Please be aware that absences due to work obligations are not excusable and will result in unexcused absence point penalties. Students who anticipate the necessity of being absent from class due to a major religious observance must provide notice of the date(s) to their TA/Instructor, in writing, by the second week of classes. If an exact date for a major religious observance is not known in advance, the student needs to instead provide notice of the anticipated week of the religious observance by the second week of classes. Late arrival or early departure is disruptive to the class and can often result in students missing important information. Late arrival up to 15 minutes after the lab is scheduled to begin is permitted, but will count against the student’s participation points, as will leaving early prior to completion of that day’s lab work. Students arriving late, but within 15 minutes of the start of class, must check-in with the TA/Instructor prior to participating in lab exercises. If quizzes are given at the beginning of class, late arrivals will be given any remaining time to complete the quiz. No time extensions on quizzes will be granted for students arriving late to class. If students arrive after or as quizzes are being collected, the student will not be allowed to make up the quiz and will thus receive a 0 for that quiz. Students leaving early, within 15 minutes of completion of lab activities, without a valid documented excuse, will lose all participation points for that day. Students arriving 15 minutes or later past the start of class will be turned away and not allowed to complete that day’s exercise. This will count as an unexcused absence. If you encounter an unforeseen circumstance and are going to be late, please notify the TA/Instructor as soon as possible. If you are more than 15 minutes late to class, please do not show up to lab as you will not be permitted to stay unless you have obtained prior permission from your TA/Instructor for an excusable, documented circumstance. Students leaving more than 15 minutes prior to completion of the lab activities without prior permission for an excusable, documented circumstance will also receive the point penalty for an unexcused absence.

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Laboratory Grade

Component Percent of Final Grade

Lab Participation 12%

Laboratory Notebook (2 checks) 8%

In-class Quizzes (6) In-class Activities (6) Lab Meeting Presentations (3)

12% 12% 9%

Research Paper: Rough Draft Assignments (3) 9%

Research Paper: Final Draft 14%

Midterm Exam 10%

Final Exam (Cumulative) 14%

100%

Your TA/Instructor will provide additional details on graded components. All posted grades are final unless they are the result of a miscalculation. If a student wishes to question a grade, he or she must speak with the TA/Instructor within 1 week of receiving the grade. Grading Scale

Letter Grade & %

A 89.5 - 100

B 79.5 - 89.49

C 69.5 - 79.49

D 59.5 - 69.49

F 0 - 59.49

Plus/minus grades will not be used. Late drops, “S/U” and “I” grades will not be granted except under those circumstances specified in the USF undergraduate catalogue. There is no extra credit and no curve provided in this course. Participation: Your TA/Instructor will evaluate your participation during each lab exercise. A total of 5 participation points are possible for each lab period during which you perform laboratory exercises. The total participation score is worth 12% of the final grade and will be determined by the average of the participation scores across the semester. Factors determining participation grades include but are not limited to:

Arriving on time and prepared, with all necessary supplies

Contributing to group work and discussions

Proper conduct, staying on task, and keeping cell phones put away for the duration of lab

Cooperation with other students and your TA/Instructor

Clean-up of your bench space and supplies

Students missing a lab without a valid excuse, as defined in the attendance policy above, will lose their 5 participation points for that day and points for any missed in-class graded component, in addition to an

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additional penalty if needed, to total a loss of 2.5% of the final grade for the first unexcused absence and 5% for subsequent unexcused absences.

Students missing a lab class with a valid excusable absence with proper notification and documentation will receive a participation grade equal to their average participation grade for the remainder of the semester (keeping in mind that even if all absences are excused, a student may miss no more than five lab classes to be able to pass the course).

Lab Notebook: You will need a lab notebook, either a spiral bound or binder with loose-leaf, to record all dates and steps of experiments performed and all data collected. Write as neatly as possible with sufficient details that someone not familiar with the work would need to repeat the experiment as you performed it. Keep any data analysis that you complete outside of lab in this lab notebook as well. Your TA/Instructor will collect and grade your lab notebook during the designated notebook checks. Notebooks are due at the start of each class where notebook checks are assigned. Each notebook check will be graded on completeness, clarity, and accuracy. There will be 2 total notebook checks across the semester, together worth 8% of the final grade (4% each).

In-class Quizzes: There will be 6 random pop quizzes during the semester, so you are advised to review the previous lab exercises and read the material for that day’s lab to be prepared. Quizzes may be given at any time during the lab period. Each quiz will consist of 4-5 questions, including but not limited to short answer, fill-in, or multiple choice style questions. Together, the 6 quizzes are worth 12% of the final grade (2% each). Students missing a quiz for an excused, documented absence may schedule to take a makeup quiz during their TA’s/Instructor’s office hours. Makeup quizzes may be different in question style than versions given in class. In-class Activities: There will be a total of 6 in-class activities that together are worth 12% of the final grade (2% each). Specific directions for each will be provided by your TA/Instructor and these in-class activities will help you learn how to calculate volumes and concentrations to make solutions, analyze the contents of a scientific paper, write and reference sources in a scientific research paper, analyze and present data, design primers for gene expression analysis, and communicate with other scientists about their work. Students missing an in-class activity due to an unexcused absence will not be permitted to make up the missed activity. Students missing an in-class activity with an excusable, documented absence may complete a makeup assignment during office hours. Makeup assignments may be different in style and length than the version given in class. Lab Meeting Presentations: There will be a total of 3 lab meeting style class discussions across the semester that total 9% of the final grade (3% each). Each group of 3-4 students will be asked to present and discuss their work in the lab thus far. This includes presenting any data collected, challenges and troubleshooting ideas/efforts, and future directions. Each group will present during each lab meeting and will also have the opportunity to ask questions/provide suggestions for other groups. All group members will participate in each meeting’s presentation. Presentations and discussions in lab meetings will be graded based on clarity, comprehension of the project/work, contribution to discussion, and responsiveness to questions/suggestions. A grading rubric will be provided for you in Canvas.

Research Paper: You will be writing a research paper presenting your semester’s work. Even though experiments will typically be completed in groups of 3-4, research papers (rough and final drafts) will be written and submitted by each individual student. The paper will be written across the semester, with

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rough drafts of individual sections submitted at designated times to be graded and returned with TA/Instructor feedback that will help you write your final draft of the complete paper. A rough draft will be submitted for the Introduction, Materials & Methods, Results & Discussion sections, together totaling 9% of the final grade (3% each). Not all sections will be completed as rough drafts, but you will have the opportunity in class to work on other sections of the paper, including the Abstract and References sections. The final draft of the research paper is worth a total of 14% of the final grade. You must submit a hard-copy and electronic copy of rough and final drafts (see details provided in the Turnitin section below). Specific directions for each component and grading rubrics will be provided on the Canvas course website.

Exams: A midterm and a final exam will be given during this course. The midterm is worth 10% of the final grade and will include questions on material covered prior to the exam. The final exam is worth 14% of the final grade and will be a cumulative exam. Exams will include, but not be limited to, fill-in, multiple choice, short answer, and essay style questions. Students missing an exam with an excused, documented absence may schedule to take a makeup exam during office hours within one week of returning to campus. Makeup exams may be different in question style and length than the version given in-class. Submitting Assignments Notebook checks and research paper components are due at the start of class and will be collected as such. Late assignments will result in a 10% penalty per 24 hours after the start of class. Any assignment being turned in late to the TA’s/Instructor’s mailbox in ISA 2015 MUST receive a departmental timestamp. Research paper components, rough drafts and final draft, are only considered submitted once the hard-copy AND electronic copy are received and WILL NOT BE GRADED (receiving a 0 for the assignment) if not uploaded, in their entirety, to Turnitin (see below) and turned in as a hard-copy. Any dispute with a graded assignment will have a 1 week timeframe to be reviewed. Plagiarism and Academic Dishonesty Plagiarism is a serious offense and will be strictly penalized in this course. During the semester, labs will often be performed in groups of 3-4 students. Discussing & working together with your lab partner or group is allowed and encouraged, but quizzes, exams, notebooks, and research papers, including figures and figure legends, MUST BE COMPLETED BY THE INDIVIDUAL STUDENT. Copying directly from another source (another student, the lab manual materials, the internet, journal articles, text books, or other sources), allowing another student access to copy your work, or using another student’s work, from previous semesters or the current semester, is strictly prohibited. When submitting work, you must always write in your own words AND reference the source of all information utilized. When writing your research paper, references are to be provided both in-text and in the reference section of the report. A copy of USF’s Academic Plagiarism Policies is available in the Undergraduate Handbook. If you are unclear what plagiarism is or are not sure if you have plagiarized, please discuss with your TA/Instructor before turning in your report. If you are found to have plagiarized or cheated you will be penalized to the fullest extent of University Policy. This includes and is not limited to: no credit for the assignment, failure in the course, or a grade of FF (a double FF denotes an F for Academic Dishonesty).

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Academic dishonesty in any form will not be tolerated. This includes, but is not limited to, cheating, plagiarism, fabrication, complicity, and multiple submissions. If you are uncertain as to what constitutes academic dishonesty, please consult the University of South Florida's Student Handbook for further details. Turnitin This course utilizes Turnitin. Turnitin is an anti-plagiarism program integrated into Canvas. You must submit a hard-copy AND upload your research paper components through Turnitin, which will then compare your paper to a wide range of sources, including Internet sources, the lab manual, & all other student papers submitted. A detailed originality report will be provided to your TA/Instructor showing any sources that have high degrees of similarity (i.e. have been plagiarized). Your assignment WILL NOT BE GRADED unless it has been uploaded to Turnitin in Canvas by the beginning of the class period when it is due. Failure to upload your assignment to Turnitin will result in a 0 for the assignment. For the research paper, students must submit the same word doc file as submitted in hard-copy, as a single submission to Turnitin through Canvas. In order to comply with privacy laws, students are not required to include personal identifying information, such as name, in the body of the document submitted to turnitin. However, your name must be included on the hard-copy printout submitted. Please follow your TA's/Instructor’s instructions and research paper guidelines carefully regarding what identifying information to include. Conduct in the lab Any activity that is a disruption of the academic process in the lab will not be tolerated. This includes, but is not limited to: (a) any general conduct that directs attention away from the academic matters at hand, such as noisy distractions, use of disrespectful/offensive language, cell phones, (b) any conduct that presents a danger to the health or safety of either the student or people in the lab and/or (c) not following the lab safety rules. The student will first receive a warning from the TA/Instructor. If the behavior continues, the punishment will be based on University regulations as set forth in the Undergraduate Handbook. If the conduct is serious enough that the TA/Instructor feels the behavior endangers themselves and/or other students present, the TA/Instructor will have the right to ask the student to leave the lab, which will be considered an unexcused absence & could lead to dismissal from the course. Please refer to the following website for course & University polices regarding conduct: http://regulationspolicies.usf.edu/ . Be advised that you could potentially be under video surveillance while in the laboratory. Laboratory Safety Some of the reagents that are used in the lab are toxic. Follow all instructions carefully. Those students who do not follow all safety rules endanger themselves and their fellow students. Flagrant violations of safety rules will result in expulsion from the lab. If you are asked to leave, you will not receive credit for that lab and will receive the point penalty for an unexcused absence. Closed-toe shoes must be worn in the laboratory and feet and legs must be entirely covered. No open-toed or open back shoes or sandals are permitted. Shorts and short skirts are not allowed! Students should wear long pants or jeans, which provide better protection for the legs in case of a spill. Gloves must be

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worn at all times unless noted by the TA/Instructor. The fume hood must be used when appropriate under direction of your lab instructor. You must wear a lab coat at all times and wear safety goggles to protect yourself when working with corrosive or toxic chemicals and when there is any risk of splash or objects impacting the eye. No eating, drinking, or smoking is permitted in the lab at any time. No friends or children are permitted in the lab. Wash your hands after lab to prevent carrying any contamination home with you. If a student has any kind of mishap in the lab, an accident or near miss, the student is to immediately inform the TA. Disposal of Used Materials Regular trash receptacles are available for general non-hazardous lab waste such as paper towels, used gloves, etc. However, the following special receptacles should be used:

Broken glassware must be disposed of promptly in the designated glass waste container.

Micro-pipette tips should be placed in the designated waste buckets provided on the bench top to ultimately be disposed of in a box lined with a plastic bag or should be placed in the sharps containers provided, as directed by your TA/Instructor.

Any used serological plastic pipettes should be placed in the designated plastic-lined box for disposal.

Solid waste coming in contact with or containing hazardous materials (including ethidium bromide, 2-mercaptoethanol, guanidinium thiocyanate, and trypan blue) must be disposed of in labeled hazardous waste buckets.

Liquid waste containing hazardous materials must be disposed of in labeled hazardous liquid waste receptacles.

Solid biohazardous waste containing or coming in contact with cell culture (cells or media) must be disposed of in red biohazard bags provided or in biomedical sharps bins for any sharps items or pipettes utilized with biohazardous materials.

Liquid biohazardous waste must be properly disinfected and disposed of per TA/Instructor instructions.

Lecture/Lab drop policy When taken together with the Genetics lecture (PCB 3063) and/or Cell Biology lecture (PCB 3023), the lecture serves as a co-requisite for the corresponding lab component. Withdrawal from the lecture component will therefore automatically drop you from the lab as well. However, a student who is passing the lab, with a grade of C or higher, at the time of the withdrawal deadline may request departmental approval for a permit to withdraw from the lecture and remain in the lab. Your TA/Instructor can provide a petition form for this purpose that will need to be submitted to the Biology Undergrad Advising Office. You may only request the petition form and submit it during the last week available to drop courses online. Once the form has been submitted and the permit has been issued, it is the student’s responsibility to process the drop online before the withdrawal deadline. The department will not grant permits to drop a lab and remain in the lecture.

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Religious Observances Students who anticipate the necessity of being absent from class due to the observance of a major religious observance must provide notice of the date(s) to the TA/instructor in writing, by the second class meeting per University guidelines. If an exact date for a major religious observance is not known in advance, the student needs to instead provide notice of the anticipated week of the religious observance by the second week of classes. Disabilities Students in need of academic accommodations for a disability may consult with the office of Students with Disabilities Services to arrange appropriate accommodations. Students are required to give reasonable notice prior to requesting an accommodation. Additional University Deadlines, Policies, and Procedures: Withdrawal Deadline for the Fall 2016 semester: October 29, 2016 It is the student’s responsibility to be aware of their academic standing and grade status. In an attempt to assist the student in evaluating his/her academic status mid-term, instructors will submit midterm grades electronically for each student enrolled in 1000, 2000, and 3000 level courses. All classes at USF make use of an online system for students to provide feedback to the University regarding the course. These surveys will be made available at the end of the semester, and the University will notify you by email when the response window opens. Your participation is highly encouraged and valued. The results of student feedback are sent to departments and faculty members after semester grades are already submitted, and student responses are reported only anonymously and in the aggregate to faculty. USF is committed to providing an environment free from sex discrimination, including sexual harassment and sexual violence (USF System Policy 0-004). The USF Center for Victim Advocacy and Violence Prevention is a confidential resource where you can talk about incidents of sexual harassment and gender-based crimes including sexual assault, stalking, and domestic/relationship violence. This confidential resource can help you without having to report your situation to either the Office of Student Rights and Responsibilities (OSSR) or the Office of Diversity, Inclusion, and Equal Opportunity (DIEO), unless you request that they make a report. Please be aware that in compliance with Title IX and under the USF System Policy, educators must report incidents of sexual harassment and gender-based crimes including sexual assault, stalking, and domestic/relationship violence. If you disclose any of these situations in class, in papers, or personally, instructors and teaching assistants are required to report it to OSSR or DIEO for investigation. Contact the USF Center for Victim Advocacy and Violence Prevention: (813) 974-5757. In the event of an emergency, it may be necessary for USF to suspend normal operations. During this time, USF may opt to continue delivery of instruction through methods that include but are not limited to: Canvas, Skype, and email messaging and/or an alternate schedule. It’s the responsibility of the student to monitor the Canvas course website for each class for course specific communication, and

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the main USF, College, and department websites, emails, and MoBull messages for important general information. Finally, please note that I reserve the right to make changes to this syllabus, with notification to the students, during the course of the semester as situation(s) may dictate.

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PCB3023L/PCB3063L Combined Lab Fall 2016 Schedule Actual laboratory experiment schedule may vary from that shown

Day Exercise What’s Due 8/23 Course Intro and Lab Safety

8/25 Introduction to Research Model System Workshop: Literature Search

Bring laptops*

8/30 Research Question and Forming Hypotheses In-class activity: Pipetting and Calculations

Bring laptops*

9/1 Data From Last Semester

9/6 Experimental Design In-class activity: Research Paper Analysis

Bring laptops*

9/8 Investigation of gene targets Experimental Design

Cell counting and live/dead cell staining

Bring laptops* Bring safety goggles

9/13 In-class activity: Writing and Citing Investigation of gene targets

Cell counting and live/dead cell staining

Bring laptops* Bring safety goggles

9/15 Cell counting and live/dead cell staining Lab Meeting 1

Bring safety goggles

9/20 Cell counting and live/dead cell staining Introduction to genome databases and primer design

Intro to RNA extraction protocol

Rough Draft: Intro Bring laptops*

Bring safety goggles

9/22 RNA extraction practice Bring safety goggles

9/27 RNA extraction practice Introduction to RNA quantification

In-class activity: Primer Design

Notebook Check 1 Bring laptops*

Bring safety goggles

9/29 Proliferation and Survival Assay RNA extraction

RNA quantification

Bring safety goggles

10/4 Proliferation and Survival Assay RNA extraction

RNA quantification

Bring safety goggles

10/6 Complete primer design Lab Meeting 2

Rough Draft: Materials & Methods

Bring laptops*

10/11 Midterm Proliferation and Survival Assay

Bring safety goggles

10/13 Proliferation and Survival Assay RNA extraction

RNA quantification

Bring safety goggles

10/18 DNase I treatment In-class activity: Data Analysis

Workshop: Statistics

Bring laptops* Bring safety goggles

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10/20 cDNA synthesis Intro to agarose gel electrophoresis

RT-PCR – Primer test and optimization

Bring safety goggles

10/25 cDNA quality check Serial dilution of cDNA samples

RT-PCR – Primer test and optimization

Bring safety goggles

10/27 cDNA quality check Serial dilution of cDNA samples

RT-PCR – Primer test and optimization

Rough Draft: Results & Discussion

Bring safety goggles

11/1 RT-PCR - Analysis of gene targets Bring safety goggles

11/3 RT-PCR - Analysis of gene targets Lab Meeting 3

Bring safety goggles

11/8 RT-PCR - Analysis of gene targets Bring safety goggles

11/10 RT-PCR - Analysis of gene targets In-class activity: Data Discussion

Workshop: How to write an Abstract

Notebook Check 2 Bring safety goggles

Bring laptops*

11/15 Final Data Analysis Bring safety goggles

11/17 Discussion of Future Directions Final Review

Research Paper: Final Draft

11/22 NO LAB MEETING – Thanksgiving Break

11/24 NO LAB MEETING – Thanksgiving Break

11/29 Final Exam

12/1 NO LAB MEETING – Reading Days *Days when we will likely be using laptops – bring laptops if you have them, otherwise you can share

with other group members.

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PCB 3023L/PCB 3063L Cell Biology and Genetics Combined Laboratory Policies:

Attendance in this class is Mandatory. Students who anticipate the necessity of being absent from class due to the observation of a major religious observance or other foreseen excusable absence must provide notice of the date(s) to their TA/Instructor, in writing, by the second week of classes. Your TA/Instructor must be contacted within 48 hrs of an unforeseen excusable absence. Excused absences (as described in the syllabus) must have supporting documentation. Unexcused absences will result in a 2.5-5% reduction of the total possible points in the course per occurrence as detailed in the syllabus. More than five absences in the course will result in a failing grade, whether they are excused or unexcused. Failure to come to class on time, prepared, and/or not following the safety rules will lead to Lab Participation points being deducted and/or dismissal from class, as outlined in the syllabus. Notebook checks and research paper assignments are due at the beginning of you lab section. Any notebooks or assignments that are handed in after the beginning of your lab section will be subject to a 10% deduction in points for every day they are late. Research paper components MUST be submitted electronically to Turnitin AND as a hard copy to the lab TA/Instructor and are subject to plagiarism checking. Both electronic and hard copy must be submitted by the deadline to avoid late penalties. I understand that plagiarism is a serious offense & if I am caught cheating/plagiarizing I will be punished by receiving no credit for the assignment, failure in the course, or a FF. The following are not permitted in the lab at any time: Eating/drinking, smoking, and cell phone use. Children are also not allowed in the lab at any time. By signing below, you acknowledge that you understand the policies for this course and agree to abide by them: I understand the Laboratory Polices that have been explained to me today. Your signature____________________________________ Date_____________

Your name (print) __________________________________ Section #__________

STUDENT COPY: Please sign & return to your TA/Instructor the duplicate copy provided to you. This copy serves as your record of the policies you are signing.

Page 14: Introductory Research Experience in Molecular Biology · Introductory Research Experience in Molecular Biology PCB 3023L/PCB 3063L Cell Biology & Genetics Laboratory Combined Course

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Teaching Laboratory Safety Guidelines The following Safety Guidelines are to be strictly adhered to in all teaching laboratories. These rules apply to students, teaching assistants, and instructors. The Teaching Lab Manager must maintain records of all the signed documents.

No food, drinks, smoking, chewing gum, or applying cosmetics and contact lenses in labs/studios/shops or clinics.

Splash goggles are to be worn when there is a risk of chemical or biological material splashing. Eye protection needs to be worn when there is the possibility of an object impacting the eye.

Footwear that covers the entire foot must be worn at all times. Therefore sandals, flip-flops, ballet-flats, backless and open-toed shoes are not acceptable.

Clothing appropriate for laboratory safety must be worn. Clothing (pants or skirt) must be worn which completely covers the entire leg from the waist to the ankle. Clothing (shirt, blouse, etc.) must be worn which completely covers the torso from the waist to the neck. Shoulders must be completely covered and sleeves must be worn that cover the arm from the shoulder to at least halfway to the elbow. Therefore, tank tops, halters, shorts, cutoffs, etc. are not acceptable. Some lab courses may require the use of a lab coat/apron and/or gloves.

Long hair should be tied back.

Long, dangling jewelry, such as necklaces or earrings with the potential to interfere with or be contaminated by an experiment, should not be worn.

Backpacks should be placed in the shelving units provided and not in the walkway. Safety Suggestions

Waste materials are to be disposed of immediately after use in the designated containers.

All containers are to be labeled completely with full chemical names and a hazard description. For example: “6M Hydrochloric Acid: CORROSSIVE”

Never leave an experiment unattended.

Never leave a solution on a hot plate unattended.

Hotplates that have been turned off, but are still hot, should have a warning note in front of them.

Working alone is not recommended. IF THERE IS A SERIOUS ACCIDENT, CALL 911 OR UNIVERSITY POLICE IMMEDIATELY. NOTIFY THE TEACHING

LAB MANAGER. I have read the safety guidelines listed above and understand that non-compliance will result in my dismissal from the laboratory until I do comply, and I will not be allowed to make-up missed work resulting from that dismissal. Sign___________________________________________ Course #_______________ Print Name______________________________________ Section #_______________

STUDENT COPY: Please sign & return to your TA the duplicate copy provided to you. This copy serves as your record of the policies you are signing.