Biol 101a: Molecular Biotechnology, Fall 2014

Class Meeting Time: Tuesdays and Fridays 9:30-10:50 a.m.

Room: Gerstenzang 122

Instructor: Dr. Rachel Woodruff

Office Hours: see LATTE for updates

TA: Niri Carrol

Office Hours: see LATTE

Summary:

Biol 101 is a course designed for beginning graduate students and advanced undergraduates. This course will focus on the practice application of the tools and processes used to manipulate DNA and proteins in molecular biology.

Course Goals: An overarching goal of this course is to give you the knowledge and skills to research, choose, and interpret the best experimental approaches for answering research questions in molecular biology. More detailed goals are listed in the table on the last page of this syllabus.

Course Format: Classmeetings will involve a mixture of lecture, discussion, group work, and problem-solving. Many challenging in-class activities activities will be graded for effort, to give you a safe place to “fail” on your way to learning and success. You will also need to be an active participant outside of class: reading, working practice problems, and developing your research proposal. Readings will include research articles, reviews, and proposals, as well as excerpts from the textbook. The research proposal project is an important part of this course: you will need to commit substantial amounts of time to this project both during and outside of class time.

Homework assignments: You should read the assigned readings, which will be a mix of textbook readings and research articles, before the class for which they are assigned. In addition, there will be a writing assignment or problem set for each class meeting. Some of these will be due in class; others will be due the day before the class meets (so that I have a response to read them before class).

Exams: To help you assess your learning, there will be one midterm and one finalexam. The final will be cumulative. Note the scheduled exam dates and do not miss either exam! There will be no written make-up exams: in the event that you miss the midterm exam, you will be given an oral exam instead.

Project: Research Proposal! A key component of your learning experience will be writing your own research proposal. The research proposal will involve choosing a scientific question of interest to you, self-directed reading of the scientific literature on this topic, writing, and oral presentation. Each of you will produce your own research proposal, but you will work together in teams during the development of the project. You will begin developing your proposal early in the semester, and your final paper will be due at the end of the semester. I want to see each of you challenge yourself and make improvements in your proposal over the course of the semester.

To avoid plagiarism in your writing, please speak with Dr. Woodruff if you have any questions about how to deal with your sources. (Also see section on Academic Integrity below.)

LATTE: The course website on LATTE is the central point of distribution for lecture slides/notes, practice problems, assignments, schedule updates etc. It is important that you check this site regularly.

Textbook: From Genes to Genomes, By Jeremy Dale and Malcolm von SchantzISBN9780470683859

Additional readings: Assigned research articles and reviewswill be available through LATTE. You will also be responsible for finding research articles to read for your own research proposal.

Disabilities: If you are a student with a documented disability on record at Brandeis University and wish to have a reasonable accommodation made for you in this class, please contact me during the first week of class.

Cell phones and laptops: Use common sense. If I or any of your classmates suspect that you are distracting yourself or anyone else by using these tools in class, you will need to put them away. To state the obvious: No texting or tweeting or skyping in class.

Academic Integrity: You are expected to be familiar with and to follow the University’s policies on academic integrity (see ). Faculty may refer any suspected instances of alleged dishonesty to the Office of Student Development and Conduct. Instances of academic dishonesty may result in sanctions including but not limited to failing grades being issued.

Course Plan: Actual course schedule will differ somewhat from this projected course schedule.

*Objectives: see detailed list of course goals and objectives on last page of syllabus packet.

Date / Lecture Topic / Readings and Homework / Ob-jectives*
1 Friday, Aug. 29 / Introduction
Biological Molecules
Challenges in Research / Chapter 1, pp1-13
Optional readings: Pauling and Corey, Watson and Crick
Recommended: Introduce yourselves through the questionnaire on LATTE / 2-1
2 Tuesday, Sept. 2 / DNA Structure and Replication / Read Meselson and Stahl (posted on LATTE)
Written assignment due by 1pm Sept 1. / 1-1,1-2,1-3
3-1, 3-2
3
Friday,
Sept 5 / DNA, Hybridization, and Replication
Introduction to Research Proposals / Strachan, pp 65-70
DePamphilis pp 39-54
Complete miniquiz(zes) on LATTE / 3-1, 3-2
3-3,3-4
5-6
4 Tuesday Sept. 9 / Research Proposals Discussion
DNA structural modeling activity / Textbook, Chapter 1, pp13-23
Read research proposal (on LATTE)
Written assignment due by 1pm Sept. 8 / 3-1, 3-2
5-1, 5-6
5
Friday, Sept. 12 / Central Dogma, with focus on Transcription, Splicing and Translation / Griffiths pp60-64
Reece pp 55-59
Practice Problems, Set1, due in class / 3-1, 3-2
2-2. 2-3,
2-4
6
TuesdaySept 16 / Gene Regulation Analysis:
Overview, gel electrophoresis, Hybridization assays, Western blotting
Discuss Research Areas / Chapter 6, pp169-171 and 174-87
Research article relating to your question by email before 9:30 today. / 5-2
2-2, 2-3,
2-4
4-3, 4-4
7
Friday
Sept 19 / Manipulation (antisense) and analysis of gene expression
Developing Research Questions / Sud et al. 2014 (on LATTE)
Written assignment due by 1pm Sept 18. / 1-2,1-3,1-4
4-4, 5-4
5-1, 5-2
3-1, 3-2
No class Sept 23 Sept 26 / No class
8
Tuesday,Sept 30 / PCR and its applications / Chapter 4, pp110-119 and pp123-130
Chapter 6, pp171-173
Practice Problems due in class today. / 4-1,4-2,4-3
4-5
9
Friday,
Oct 3 / PCR and its applications, II / Read PCR review article (on LATTE)
Research Proposal Intro duein class Oct 3 / 4-1,4-2,4-3
4-5, 5-2
10
Tuesday,
Oct 7 / Sanger Sequencing
Specific AimsDiscussion / Chapter 5: pp131-140
Read specific aims (on LATTE)
Written assignment due by 1pm Oct 6. / 4-1,4-2,4-3
4-5, 5-6
11
Friday, Oct 10 / RNAi / Read 2 articles on RNAi (on LATTE)
Articulate draft of novel research question due by 9:30am Oct 10 (online) / 4-1,4-2,4-3
12
Tuesday,Oct 14 / Exam 1 / Study and Review readings, activities, and practice problems / All so far
13
Friday, Oct 17 / Analysis of Proteins / Textbook reading
Research article (on LATTE)
Written assignment due by 1pm Oct 16 / 1-all
4-4
14
Tuesday, Oct 21 / Gene Cloning, Expression, and Mutagenesis
Experimental Plans Workshop I (rough) / Chapter 2, pp36-61
Chapter 7 pp195-204 and 215-224
Written assignment TBA / 4-1,4-2,4-3
5-1,5-2.5-3
5-4,5-7
15
Friday, Oct 24 / Transgenic organisms: knock-outs, knock-downs, knock-ins / Chapter 11 pp327-353
Chapter 8, pp271-274
Written assignment TBA / 4-1,4-2,4-3
16
Tuesday, Oct 28 / CRISPR
Experimental plans workshop II / Nature News reading (on LATTE)
Written assignment due by 1pm Oct 27
Practice Problems due in class today. / 1-all
4-1,4-2,4-3
17
Friday, Oct 31 / GWAS and Genome Analysis
Next Generation Sequencing / GWASReview Article (on LATTE)
Chapter 8: 8.2, pp229-263
Research Proposal Outline Due Today / 1-all
5-5
18
Tuesday,Nov 4 / DNA Sequencing Technologies / DNA sequencing research: written response due in class today. / 4-1,4-2,4-3
5-3
19
Friday, Nov 7 / Tentative plan:
9:15am tour of genomic sequencing platform at Broad Institute, Cambridge / Reading TBA
Peer and self review of partners Research Outline due today / 4-3
5-3, 5-5
20
Tuesday,Nov 11 / Genetic Variation and analysis / Chapter 9, pp275-298
Read your peer review before class today
Practice Problems due in class / 1-all
5-3,5-4
5-6,5-7
4-1,4-2,4-3
21
Friday, Nov 14 / Gene Therapy / Textbook reading TBA
Research article (on LATTE).
Written assignment due by 1pm Nov 13. / 4-1,4-2,4-3
22
Tuesday,Nov 18 / Clinical Trials and Study Design
Student presentations / Reading TBA. / 5-all
23
Friday,
Nov 21 / Epigenetics revisited
Student presentations / Reading TBA
Draft of full Research Proposal due (unless you are presenting today, in which case yours is due the 25th) / 4-4
2-2, 2-4
24
Tuesday, Nov 25 / Practice Problems,
Student Presentations / Practice Problems Due in class today / 5-2, 5-7
No class Nov 28 / No Class. Happy Thanksgiving!
25
Tuesday,Dec 2 / Student presentations
Some students may visit Broad this day instead of Nov 7. / Peer and self reviews of drafts due today / 5-2, 5-7
26
Friday, Dec 5 / Student presentations Conclusions
and self-assessment / Written assignment due by 1pm Dec 4 / All
Monday Dec 8 / No Class / Final research proposal papers due by Noon
TBA / FINAL EXAM / Study and review notes, readings, practice problems. / All

Note: Each student should attend one additional 50-minute session of student presentations, date and time TBA.

Grading:

Description / Percentage of Final Grade
Homework assignments (including proposal-related homework) / 13%
In-class Activities (including proposal-related activities) / 10%
Midterm Exam / 22%
Final Exam / 25%
Research proposal project:
-Oral Presentation (10%)
-Final written proposal(20%) / 30%
Course Goal
By the end of the course, students should: / Objective
By the end of the course, students should be able to:
  1. Understand how to critically read and evaluate scientific literature
/ 1-1 Identify the key question(s) addressed by a research article
1-2 Identify experiments supporting conclusions in a paper
1-3 Analyze data presented in paper
1-4 Critique authors’ analysis of their results
1-5 Critique study design and/or choice of experiments
  1. Understand the relationships between the molecules and processes central to molecular biology (DNA, RNA, protein, DNA replication, transcription, translation, RNA splicing, gene expression, etc)
/ 2-1 Identify class of molecule by chemical structure
2-2 Explain in detail the relationships between biological molecules and processes
2-3 Understand gene structures
2-4 Explain the significance of multiple levels of regulation of gene expression
  1. Understand the implications of the physical and chemical qualities of DNA and RNA
/ 3-1 Describe structural features of DNA
3-2 Explain how specific features of DNA enable replication and transcription
3-3 Outline the steps of DNA replication
3-4 Diagram a replication bubble
3-5 Interpret hybridization/melting data
3-6 Use your knowledge and research skills to explain DNA/RNA techniques you’ve never seen before.
  1. Understand the use of important molecular biological techniques (for example: PCR, cloning, Sanger sequencing, CRISPR, Western blots, Southerns and Northerns, microarrays, GWAS, transgenic organisms, gene therapy, RNAi knockdown, nextgen sequencing)
/ 4-1 Explain which feature(s) of DNA each technique is dependent upon
4-2 Analyze data resulting from each technique
4-3 Explain what question(s) each technique can be used to address
4-4 Design experiments to determine the level(s) at which a gene’s expression is regulated
4-5 Design DNA oligomers for specific applications
  1. Understand the process and challenges of developing a molecular biology research proposal
/ 5-1 Differentiate high quality biological questions that can answered by observation and experiment
5-2 Develop novel research questions
5-3 Select appropriate molecular techniques to address particular biological question(s)
5-4 Critique the experimental choices of research studies (proposed or completed)
5-5 Differentiate between design and outcome of genome-wide vs. targeted studies
5-6 Understand the purpose and qualities of a good research proposal
5-7 Articulate a research proposal