Biochemistry 201

Advanced Molecular Biology

January 14 Literature Review on Chromatin Remodeling

Cairns, B. R., Lorch, Y., Li, Y., Zhang, M., Lacomis, L., Erdjument-Bromage, H., Tempst, P., Du, J., Laurent, B. and Kornberg, R. D. (1996). RSC, an essential, abundant chromatin-remodeling complex. Cell, 87(7), 1249-60.

Section A: Seth Stratton

Section B:Michael Buckley

Lorch, Y., Zhang, M. and Kornberg, R. D. (1999). Histone Octamer Transfer by a Chromatin-Remodeling Complex. Cell 96: 389-392.

Section A; Joe Dan Dunn

Section B: Jake Lai

January 28 Literature Review on Repair

C. Masutani et al. (1999) The XPV (xeroderma pigmentosum variant) gene encodes human DNA polymerase eta. Nature 399: 700.

Section A: Prasanthi Bhagavatula

Section B: Carrie Arnold

K. Leuther et al. (1999) Structure of DNA-dependent protein kinase: implications for its regulation by DNA. EMBO J. 18: 1114.

Section A: Joe Budman

Section B: Mike Ginsberg

February 4 Literature Review on Transcription & Regulation

Callaci S, Heyduk E, Heyduk T. (1999) Core RNA polymerase from E. coli induces a major change in the domain arrangement of the sigma 70 subunit. Mol Cell 3(2):229-38.

Section A & B: Kaman Chan

Sharp MM, Chan CL, Lu CZ, Marr MT, Nechaev S, Merritt EW, Severinov K, Roberts JW, Gross CA (1999) The interface of sigma with core RNA polymerase is extensive, conserved, and functionally specialized. Genes Dev 13(22):3015-26.

Section A & B: Christopher Sundberg

 

February 11 Literature Review on Eukaryotic Transcription factors

Myers, L.C., Gustafsson, C.M., Hayashibara, K.C., Brown, P.O., and Kornberg, R.D. (1999) Mediator protein mutations that selectively abolish activated transcription PNAS 96:67-72

Section A: Sunny Chin

Section B: Mike Cleary

Apone, et al., (1999) Broad, but Not Universal, Transcriptional Requirement for yTAFII17, a Histone H3-like TAFII Present in TFIID and SAGA Molecular Cell, 2, 653-661.

Section A: Vivian Thruong

Section B: Tom Purcell

February 18 Literature review on RNA structure, catalysis, and processing

Ferré-D’Amaré, A. R., Zhou, K. and Doudna, J.A.,(1998) Crystal Structure of a hepatitis delta virus ribozyme. Nature 395, 567-574.

Section A: Jungie Liu

Section B: Katrin Karbstein

Herschlag, D. (1998) Ribozyme crevices and catalysis. Nature 395, 548-549.

Raghunathan, P. L, Guthrie, C. (1998) A spliceosomal recycling factor that reanneals U4 and U6 small nuclear ribonucleoprotein particles.Science 279, 857-860.

Section A: Rebecca Vega

Section B: Frauke Rees 

March 3 Literature Review on Gene Expression

Wang, D. G., et al. (1998) Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 280, 1077-82 .

Section A: Kathryn Hunkapiller

Section B: Evan Hurowitz

Eisen. M. B., Spellman, P.T., Brown, P. O., Botstein, D. (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 95, 14863-8

Section A: Jomaquai Jenkins

Section B: Caroline Uhlik

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The following questions should be considered in writing your two-page report on each of the papers presented in the literature reviews. Everyone will be required to turn in their reports at the time of the literature review except those presenting papers. Reviews must be brought to the review session. One set of reviews can be up to week late with no academic penalty. However, if a subsequent set of reviews are turned in late without a written medical excuse, the score for those reviews will be penalized one point per week late. Papers turned in more than 5 weeks late will receive no credit.

Introduction and Background:

What hypotheses are being tested in this paper?

What information induced the authors to perform the experiments?

What new methods or insights brought to bear on the problem?

Methods:

What are the critical methods of the paper?

What enabling technologies are used?

What are the weaknesses of the methods used?

Are there other or better approaches that could be used?

If this is a genetics approach, what would be a biochemical or molecular approach?

If this is a biochemical or molecular approach, what genetics methods could be used?

Results and Discussion

What are the primary conclusions of the paper?

Did the authors prove their hypotheses?

What novel information or directions come from this work?

What control experiments were performed?

What assumptions still remain in the work?

How could these assumptions be tested?

What other explanations for the observations are still possible?

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