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Revision as of 19:04, 15 January 2013 by Ilya J. Finkelstein (talk | contribs) (Topics)

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


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.


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.


Index of All CH391/S2013 Pages

View Recent Changes to CH391/S2013 Pages

Week 1 (Jan 16): Introduction

  • Introduction.
  • Wiki editing tutorial.
  • Overview of course structure and topics.

Week 2 (Jan 23): Double Strand Break (DSB) Repair

Suggested Topics

  • DSB repair mechanisms in prokaryotes
    • Homologous Recombination
    • SOS Response
  • DSB repair in eukaryotes
    • Homologous Recombination
    • Non-Homologous End Joining
    • Alternative End-Joining

Week 3 (Jan 30): Double Strand Break (DSB) & Associated Diseases

Suggested Topics

  • DSB Repair: Pathway Choice
  • DSB-related diseases:
    • Seckel & Jawad Syndromes
    • Nijmegen Breakage Syndrome
    • Ataxia - telangiectasia
    • Werner & Bloom Syndromes

Week 4 (Feb 6): DNA Replication as a Source of Genomic Instability

Suggested Topics

  • Replicating Aberrant Structures
    • DNA Hairpins
    • Z-DNA
    • G-Quadruplex DNA
    • Chromosome Fragile Sites
  • Replication-Transcription Conflicts
  • Replication-Collapse at Interstrand Cross Links

Week 5 (Feb 13): Mechanisms of DNA Mismatch Repair

Suggested Topics

  • Mismatch Repair in Prokaryotes
  • Very short patch repair
  • Mismatch Repair in Eukaryotes
    • How is a Mismatch Recognized?
    • How is a Mismatch Removed?

Week 6 (Feb 20): Mismatch Repair, Adaptation & Diseases

Suggested Topics

  • Mismatch repair and adaptation
    • Mutagenesis in Bacteria
    • Mutagenesis in Eukaryotes
  • Meiotic-specific Roles of Mismatch Repair Proteins
  • Diseases
    • Lynch Syndrome

Week 7 (Feb 27): Mitochondrial DNA Damage

Suggested Topics

  • Structure of Mitochondrial DNA
  • Mechanisms of DNA Repair
  • Mitochondrial DNA repair and aging
  • Diseases Associated with Mitochondrial DNA Damage

Week 8 (Mar 6): Special Topics Lecture

Week 9 (Mar 20: Nucleotide Excision Repair

Week 10 (Mar 27): Base Excision Repair

Week 11 (Apr 3): Damage Tolerance and Mutagenesis — Prokaryotes

Week 12 (Apr 10): Damage Tolerance and Mutagenesis — Eukaryotes

Week 13 (Apr 17): Cell-cycle response to DNA damage

Week 14 (Apr 24): p53 -- The Guardian of the Genome

Week 15 (May 1): Student-selected topic

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.