BISC403 Advanced Molecular Biology Fall 2005 Course Syllabus p. 1 of 4
DRAFT 2009, based on 2008
Lectures: TTh 12.30 - 1.50, GFS101
Discussion: Tue 2-3.50, SOSB48
Weds 2-3.50, SOS-B48
Professors:
Prof. Susan Forsburg,
Office: RRI 104C
Office hours: by appointment
Tel/vox: (213) 740-7342,
email: forsburg@usc.edu
Prof. John Tower
Office: RRI 219C
Office hours: Thurs 2-4
Tel/vox: (213) 740-5384
email: jtower@usc.edu
TA: Pao-Chen Li
Office: RRI 108
Office hours: Tue 4-5 (RRI-202)
tel/vox: 740-5558
email: paochenl@usc.edu
Lectures readings and course notes on Blackboard.
Prerequisites: BISC311 or BISC 320L (Molecular Biology) is a firm prerequisite for this course.
Objective: The course objective is to consider a few topics in Molecular Biology in depth. Topics are chosen
by the teaching faculty and generally represent active areas of their current research. The course also requires
reading primary research papers for discussion.
Format: There is no required textbook for this course. You will receive digital copies of lecture handouts and
reading materials. Resources and review articles will also be uploaded to Blackboard (blackboard.usc.edu).
Background reading in any general Genetics, Cell Biology, or Molecular Biology textbook may be helpful.
Discussion Sessions: Participation is required for full points in the course. Each week the professor will
assign a relevant research paper related to that week’s lectures. Students should be prepared to participate in a
journal club about that paper, which will require reading the paper and any background prior to discussion.
Students will be randomly called upon to present background materials, or discuss any figure of the paper or
method employed, and credit will be awarded for this presentation. Additional points will be awarded for
active participation in discussion. This will account for approximately 20% of your grade.
BISC403 Advanced Molecular Biology Fall 2005 Course Syllabus p. 2 of 4
Date
Subject
Professor
SECTION I: EPIGENETICS (Prof Forsburg)
Tues Aug 26
Introduction to Chromosomes
Forsburg
Thurs Aug 28
Histones and nucleosomes
Forsburg
Week 1 Background reading:
Olins DE, Olins AL. Chromatin history: our view from the bridge. Nat Rev Mol Cell Biol. 2003 4:809-14.
Khorasanizadeh S, (2004) The nucleosome: from genomic organization to Genomic regulation. Cell 116: 259.
Read pages 259-262 (we will be using sections of this review throughout the course)
Additional reference: Lall S. Primers on chromatin. Nat Struct Mol Biol. 2007 Nov;14(11):1110-5.
Discussion paper: Randall and Kelly TJ The fate of parental nucleosomes during SV40 DNA replication.
J Biol Chem. 1992 Jul 15;267(20):14259-65.
Wk 2 Tues Sept 2
Nucleosome assembly
Forsburg
Thurs Sept 4
Chromatin remodeling I
Forsburg
Week 2 Background reading
Khorasanizadeh S The nucleosome: from genomic organization to Genomic regulation. Cell 116: 259. (2004)
Read pages 267-269 (ATP remodeling section)
Saha A, Wittmeyer J, Cairns BR Chromatin remodelling: the industrial revolution of DNA around histones.
Nat Rev Mol Cell Biol. 2006 Jun;7(6):437-47. Review
De Koning L, Corpet A, Haber JE, Almouzni G. Histone chaperones: an escort network regulating histone
traffic. Nat Struct Mol Biol. 2007 Nov 5;14(11):997-1007.
.
Discussion paper: Belotserkovskaya R, Oh S, Bondarenko VA, Orphanides G, Studitsky VM, Reinberg D.
FACT facilitates transcription-dependent nucleosome alteration. Science. 2003 Aug 22;301(5636):1090-3.
See comment Svejstrup JQ. Transcription. Histones face the FACT. Science. 2003 Aug 22;301(5636):1053-5.
Wk 3: tues Sept 9
Chromatin remodeling II; histone
Forsburg
modifications I
Thurs Sept 11
Histone Modifications II
Forsburg
Week 3
Background reading
Khorasanizadeh S The nucleosome: from genomic organization to Genomic regulation. Cell 116: 259. (2004)
Read pages 263-267
Peterson CL and Laniel MA Histones and Histone modifications Curr Biol 14: R546-51
Lee KK, Workman JL. Histone acetyltransferase complexes: one size doesn't fit all. Nat Rev Mol Cell Biol.
2007 Apr;8(4):284-95Background. Review.
Discussion paper: Allfrey VG, Faulkner R, Mirsky AE. Acetylation and methylation of histones and their
possible role in the regulation of RNA synthesis. Proc Natl Acad Sci U S A. 1964 May;51:786-94.
Wk 4: Tues Sept 16
Recognition of Histone
Forsburg
modifications. Histone variants.
Thurs Sept 18
Midterm I
Forsburg
Background reading Week 4
Khorasanizadeh S The nucleosome: from genomic organization to Genomic regulation. Cell 116: 259. (2004)
Read pages 269-270
BISC403 Advanced Molecular Biology Fall 2005 Course Syllabus p. 3 of 4
Sarma K and Reinberg D, Histone Variants meet their match. Nat Rev Mol Cell Biol 6:139-149 (2005)
De la Cruz X, Lois S, Sanchez-Molina S, Martinez-Balbas MA (2005) Do protein motifs read the histone
code? Bioessays 27:164-175
Discussion paper: week 4
Bannister AJ, Zegerman P, Partridge JF, Miska EA, Thomas JO, Allshire RC, Kouzarides T.
Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain.
Nature. 2001 Mar 1;410(6824):120-4.
Wk 5 Tues Sept 23
Case study: DNA damage response Forsburg
Thurs Sept 25
Case study: heterochromatin and
Forsburg
silencing
Background reading Week 5
Downs JA, Nussenzweig MC, Nussenzweig A.Chromatin dynamics and the preservation of genetic
information. Nature. 2007 Jun 21;447(7147):951-8. Review.
Grewal SI, Jia S. Heterochromatin revisited. Nat Rev Genet. 2007 Jan;8(1):35-46. Review.
Discussion paper: Lan F, Zaratiegui M, Villen J, Vaughn MW, Verdel A, Huarte M, Shi Y, Gygi SP, Moazed
D, Martienssen RA, Shi Y. S. pombe LSD1 homologs regulate heterochromatin propagation and euchromatic
gene transcription. Mol Cell. 2007 Apr 13;26(1):89-101.
Wk 6: Tues Sept 30
Case study: Centromeres and
Forsburg
chromosome segregation
Thurs Oct 2
RNAi
Background reading Week 6
Grewal SI, Elgin SC. Transcription and RNA interference in the formation of heterochromatin.
Nature. 2007 May 24;447(7143):399-406. Review.
Discussion paper: Mizuguchi G, Xiao H, Wisniewski J, Smith MM, Wu C. Nonhistone Scm3 and histones
CenH3-H4 assemble the core of centromere-specific nucleosomes. Cell. 2007 Jun 15;129(6):1153-64.
Wk 7: Tues Oct 7
DNA methylation
Forsburg
Thurs Oct 9
MIDTERM II
Forsburg
Background reading Week 7
Khorasanizadeh S The nucleosome: from genomic organization to Genomic regulation. Cell 116: 259. (2004)
Read pages 267
Klose RJ, Bird AP. Genomic DNA methylation: the mark and its mediators Trends Biochem Sci. 2006
Feb;31(2):89-97.
Discussion paper: Lehnertz B, Ueda Y, Derijck AA, Braunschweig U, Perez-Burgos L, Kubicek S, Chen T, Li
E, Jenuwein T, Peters AH. Suv39h-mediated histone H3 lysine 9 methylation directs DNA methylation to major
satellite repeats at pericentric heterochromatin. Curr Biol. 2003 Jul 15;13(14):1192-200.
SECTION II: AGING (Prof Tower)
Wk 8: Tues Oct 14
Models of aging
Tower
Thurs Oct 16
Models of aging
Tower
Week 8 Background reading:
Hughes, K. A. and R. M. Reynolds, 2005. Evolutionary and mechanistic theories of aging. Annu Rev Entomol
50, 421-45.
BISC403 Advanced Molecular Biology Fall 2005 Course Syllabus p. 4 of 4
Muller, F. L., M. S. Lustgarten, Y. Jang, A. Richardson and H. Van Remmen, 2007. Trends in oxidative aging
theories. Free Radic Biol Med 43, 477-503.
Week 8 Discussion paper: Yoshida, K., T. Fujisawa, J. S. Hwang, K. Ikeo and T. Gojobori, 2006.
Degeneration after sexual differentiation in hydra and its relevance to the evolution of aging. Gene 385,
64-70.
Wk 9: Tues Oct 21
Mortality
Tower
Thurs Oct 23
Gene expression during aging
Tower
Week 9 Background reading: Partridge et al (2005) Dietary restriction, mortality trajectories, risk and
damage. Mech Age Dev 126:35-41.
Week 9 Discussion paper: Mair et al (2003) Demography of Dietary Restriction and Death in Drosophila.
Science 301:1731
Wk 10: Oct 28
Oxidative stress and damage
Tower
Thurs Oct 30
Oxidative stress and damage
Tower
Week 10 Background reading: Partridge et al (2005) Sex and Death: What is the Connection? Cell 120:461472.
Week 10 Discussion paper: Giannakou et al (2007) Dynamics of the action of dFOXO on adult mortality in
Drosophila. Aging Cell 6:429-438.
Wk 11: Tues Nov 4
Mitochondria
Tower
Thurs Nov 6
MIDTERM III
Tower
Week 11 Background reading: Kujoth and Prolla (2008) Evolving insight into the role of mitochondrial
mutations in aging. Exp Gero 43:20-23.
Week 11 Discussion paper: Vermulst et al (2008) DNA deletions and clonal mutations drive premature aging
in mitochondrial mutator mice. Nature Genetics 40:392
Wk 12: Tues Nov 11
Stem cells
Tower
Thurs Nov 13
Cellular senescence, telomeres
Week 12 Background reading: Brack and Rando (2007) Intrinsic Changes and Extrinsic Influences of
Myogenic Stem Cell Function During aging. Stem Cell Rev 3:2260237.
Week 12 Discussion paper: Conboy et al (2005) Rejuvenation of aged progenitor cells by exposure to a young
systemic environment. Nature 433:760-764.
Wk 13: Tues Nov 18
Cellular senescence, telomeres
Tower
Thurs Tues Nov 20
Progerias
Tower
Week 13 Background reading: Martin et al (2007) Genetic determinants of human health span and life span:
progress and new opportunities. PLOS Genetics 3:e125.
Discussion paper: Scaffidi, P. and T. Misteli, 2006. Lamin A-dependent nuclear defects in human aging.
Science 312, 1059-63.
Wk 14: Tues Nov 25
Sirtuins, DR and IIS
Tower
Thurs Nov 27
THANKSGIVING
Week 14 Background reading:
Kondratov, R. V. 2007 A role of the circadian system and circadian proteins in aging. Ageing Research
Reviews 6:12-27.Week 14 Discussion paper: Chen, Z., E. A. Odstrcil, B. P. Tu and S. L. McKnight, 2007.
Restriction of DNA replication to the reductive phase of the metabolic cycle protects genome integrity. Science
316, 1916-9.
Wk 15: Tues Dec 2
Replicators and Game theory, SAP
Tower
Thurs Dec 4
Circadian Rhythms
BISC403 Advanced Molecular Biology Fall 2005 Course Syllabus p. 5 of 4
Week 15 Discussion paper: Koh, K., J. M. Evans, J. C. Hendricks and A. Sehgal, 2006. A Drosophila model
for age-associated changes in sleep:wake cycles. Proc Natl Acad Sci U S A 103, 13843-7.
Dec XXX
FINAL
BISC403 Advanced Molecular Biology Fall 2005 Course Syllabus p. 6 of 4
Grading:
Midterm I 100 pts
Midterm II 100 pts
Midterm III 100 pts
Final 100pts
Discussion participation: 100 pts
TOTAL = 500 pts
Letter grades are determined by a curve based upon total points.
Other Policies:
1. Exam dates are firm. If a student misses an exam due to a true emergency(with an acceptable written excuse;
written information concerning a death in the family must be provided), we MAY schedule a make-up exam, or
at our discretion MAY permit the use of the average of other exams in determining the course grade. No one
will be admitted to an exam after the first student has left the exam.
2. Regrading of exams will be done only by the professor who wrote the question. Regrading can only be done
within one week of the day the exam is initially returned to the class.
3. No special assignments for extra credit are given.
4. Final exams will be kept in Dr. Forsburg’s office for the required period.
5. Academic integrity policies of the university will be strictly followed. Infractions can result in severe
penalties. See SCampus for these policies.
6. It may be necessary to make some adjustments in the syllabus during the semester.
7. Disability: Students requesting academic accommodations based on a disability are required to register with
Disability Services and Programs (DSP) each semester. A letter of verification for approved accommodations
can be obtained from DSP when adequate documentation is filed. Please be sure the letter is delivered to Dr.
Tower or Dr. Forsburg as early in the semester as possible. DSP is open Mon-Fri, 8:30-5:00. The office is in
Student Union 301 and their phone number is 740-0776.