CH391L/2013

Molecular Mechanisms of Genome Maintenance

CH 391L (Spring 2013)

Unique # 52955

Wednesdays 2–5 PM, WEL 3.422, Professor: Finkelstein

Instructor: Dr. Ilya Finkelstein

Office Hours: by appointment only

Office: MBB 3.422AA

Introduction

Topics: This course will focus on current developments in understanding the molecular mechanisms of genome maintenance and cancerogenesis. A strong emphasis of the course will be to understand the methods and techniques that have enabled modern breakthroughs in understanding genome stability. The course will rely heavily on primary literature and class presentations.

Prerequisite: Biochemistry (CH339K and CH339L) or equivalent. Undergraduate students must have the instructor's permission to register for this course.

Course web page: The course web site on the OpenWetWare (OWW) Wiki will be used to complete assignments. Participants will be required to register an account on OWW and learn to edit this Wiki.

Grading

Final grades will be assigned by a straight scale (no curve) based on how many points you accumulate. Grades will be assigned based on the following ruberick:

| Topic | Points | | :------------ | -------------------: | | Written Reports (wiki) | 400| | Oral Presentations | 300| | Participation (Class/Wiki) | 300| | Total | 1000|

| Points | Grade | | :------------ | -------------------: | | >900 | A| | 801-900 | B| | 701-800 | C| | 601-700 | D| | <600 | F|

Class Structure

Each class time will be split into two halves with a 10-15 minute break between them.

First Section — New Topics

In the first half of each class, 3-5 participants will have 15 to 20 minutes each to individually present new topics. To prepare for these oral presentations, you are required to complete a written report by creating a new page on the course web site that is an in-depth discussion of the topic (aim for ~1000 words, ≥3 citations to scientific reviews and research papers, and explanatory figures.)

This Wiki report should be finished by the day of your presentation. Presentations should be kept simple. They may contain figures from the literature (with proper attribution) and a verbal description of the background, experimental methods, results, and future directions in a research area.

Be brief and consise. The PowerPoint presentation should contain no more than ten slides. You are encouranged to follow the outline of your written Wiki report. Other members of the class are expected to provide feedback by asking questions during your presentation and by editing the Talk pages for your written Wiki report after your presentation. Comments should be constructive, with proper citations were applicable. Your classmates will ask you interesting questions or bring up issues that you may not immediately answer, and that all of us will all learn from the feedback and revision cycle! You are encouraged (but not required) to bring a laptop / tablet / smart-phone to view Wiki pages and related scientific papers during in-class presentations.

Second Section — Topic Updates.

In the second half of the class period, students who presented new topics the previous time will present their answers to questions that were raised during the in-class discussion of their topic or on the Wiki talk pages since they presented. You may need to add additional citations to research papers to expand on the background.

To keep a record of your changes, you should keep track of your point-by-point responses and the Wiki edits that you made to your written report on your topic's Talk page as if you were responding to reviewers of a scientific paper.

Topic Choice

Topic choices should be discussed with the instructor and class at least one week prior to the scheduled presentation. A list of [topics] can be found below, but there is significant leeway to tailor the papers and topics toward your specific interests.

The goal of the topic component of the class is to create a reference work that you can come back to after completing the class to remember key details.

Scholastic Dishonesty

If you are caught in some form of scholastic dishonesty you will receive an F in the course, and you will be reported to Student Judicial Services (Office of the Dean of Students). You will receive no warning before these actions are taken. Be particularly careful when editing OWW Wiki pages— include references to all copyrighted material (such as figures from papers) that are not in the public domain.

Special Accomodations

The University of Austin provides appropriate academic accommodations for qualified students with disabilities upon request. For more information, contact the Office of the Dean of Students at 471-6259, 471-6441 TTY.

It is the policy of The University of Texas at Austin that the student must notify each instructor at least fourteen days prior to the classes scheduled on dates he or she will be absent to observe a religious holy day. For religious holidays that fall within the first two weeks of the semester, the notice should be given on the first day of the semester. The student may not be penalized for these excused absences but the instructor may appropriately respond if the student fails to complete satisfactorily the missed assignment or examination within a reasonable time after the excused absence.

Topics

| Week Number | Date | Topic | |---------|--------- |--------- | | 1 | January 16 | Introduction: DNA repair and replication in the context of human desease. Survey of types of DNA damage. Wiki editing tutorial. Overview of course structure and topics. | | 2 | January 23 | Endogenous and Exogenous sources of DNA damage. | | 3 | January 30 | Repairing altered bases in DNA.| | 4 |February 6 | Mismatch repair. | | 5 | February 13 | Nucleotide Excision Repair (NER) | | 6 | February 20 | Double-strand break (DSB) repair | | 7 | February 27 | Mitochondrial DNA repair | | 8 | March 6 | Special Topics Lecture | | | March 13 | No class: Spring Break | | 9 | March 20 | Damage Tolerance and Mutagenesis — Prokaryotes | | 10 | March 27 | Damage Tolerance and Mutagenesis — Eukaryotes | | 11 | April 3 | Cell-cycle response to DNA damage | | 12 | April 10 | Transcriptional response to DNA damage | | 13 | April 17 | Diseases associated with mismach repair | | 14 | April 24 | Diseases associated with DSB repair | | 15 | May 1 | Diseases associated with aberrant repair |

The above schedule and topics may be modified at the instructor's discretion. The class will be notified of any changes in class and on the OpenWetWare course web site.