BIOL 162 2017
DNA Mechanisms and Research
BIOL 162b Spring 2017
Tuesdays and Fridays, 9:30-10:50 am
Room SSC-LL16
Instructor: Dr. Rachel Woodruff ()
Office hours: in Bassine 202. Drop-in Fridays 2-3pm, or by appointment
This is an experiential learning course. You might prefer to think of it as a workshop, and you are an active participant. Those of you who registered early know this already, as you had the opportunity to participate in the selection of topics for the course.
Through discussion, questioning, reading, and shared projects, we will work together to develop in every member of the group a deeper understanding of some of the most important and highly conserved molecular mechanisms in biology: mechanisms that affect the copying, protection, and alteration of genomes. We will also practice key skills which will serve you well in a variety of future endeavors: reading and analysis of complex information (specifically, review and research articles); and communication of advanced ideas through written or oral presentation.
By using free online PDF annotation software (Perusall), you will be able to initiate discussions of the readings before we even get to class, and help each other to delve deep into each research article or review that we read.
In the second half of the semester, you and a small team of classmates will be engaged in co-authoring a review of recent DNA research. We will all work together to optimize each review paper. The authors of particularly high-quality review papers will be encouraged and assisted in submission of their papers to an undergraduate research journal for possible publication.
Course Goals:
By the end of the course, students should…
- Know DNA structure and chemistry at a deep level.
- Understand mechanisms involved in genome duplication and copy-number maintenance.
- Understand mechanisms of mutagenesis
- Understand the significance and mechanisms of protein interactions with DNA, both specific and non-specific
- Understand the mechanisms underlying epigenetics.
- Understand the process of developing and interpreting models/theories of complex molecular processes.
- Have the essential research-related experience of identifying an area which is of interest to themselves, and digging deep into that area to understand thoroughly what is known and unknown in that area of research
- Develop their skills in scientific thinking and writing of their own ideas
- Improve their scientific reading skills
Course format:
This is a seminar, relying on readings from scientific review articles, primary research articles, and some textbook excerpts. Class meetings will include a mixture of discussion and small projects to help students achieve course goals.
The class will involve work in small groups: I know that this is hard and sometimes uncomfortable, but group work is the norm in most career paths you may find yourselves on later in life, so I aim to give you more practice in it now, while you are a still student. I will help and support you in formation of appropriate groups, and in finding your most productive ways to work together.
Final Project: Students will write and revise a review article.
Homework: There will be regular and frequent homework assignments based on the readings. One common class of homework assignment will be to add to our class’ online discussion of scientific articles through Perusall. Homework will typically be due online by 8:30pm on the day before a class meeting.
Quizzes and Exams: Several short quizzes will be given over the course of the semester to assess student progress and needs. Tentative quiz dates are given in the schedule below. Because there is a final paper, there will not be a final exam, but we may use the scheduled final exam period for presentations: stay tuned!
Readings. Research and review articles and excerpts will be posted on LATTE or on Perusall. Students will also need to find and read additional articles as part of their project (writing a review article).
Final grade determination:
Homework: 20%
Work and participation in class: 20%
Presentations: 10%
Quizzes: 24%
Literature review Paper (final paper and assignments leading up to it): 26%
Topics:
- DNA structure and chemistry
- Protein-DNA interactions
- DNA replication
- Telomeres and Telomerase
- Chromatin and 3D genome structure
- Epigenetics
- Cell cycle regulation
- CRISPR (in native systems)
- Transposable elements
- DNA damage
- DNA damage responses, repair and damage tolerance
- Student-selected topic(s)
See LATTE site for specific reading assignments, homework assignments, and updates to the schedule.
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