BMCB625:Schedule

General Info

• Spring 2007
• Location: BRB 603. Wednesdays from 9:30 - 11:30 (practice session) and Thursdays from 10:30 - 12:30
• How the Class Works

Week-by-Week Schedule Summary

Date	Presenters	Topic	Evaluator/MC/Faculty
April 4	Hoatlin/Dresbeck	Org Meeting	NA
April 12	Chris & Mahta	BMCB625:DNA Replication	JF/CP/(Hoatlin&Thayer)
April 19	Chayne & Larry	BMCB625:DNA Replication (New components)	JL/CS (Hoatlin/Thayer)
April 26	Jeremy & Chayne	BMCB625: noncoding RNA (Xist)	LG/JF (Thayer)
May 17	Jon (Happy Birthday) & Jeremy	Nucleosome Coding	CS/MN(Lundblad?)
May 24	Larry & Jon	Helicases	MN/LG (Hoatlin/Chapman)
May 31	Mahta & Chris	Exon Jxn Complex	CP/JL(Rotwein/Landfear?)
June 7	Chris	Mathematics in Biology	(Chayne, MC) (Shinde?, faculty)
June 7	Chayne	DNA Gyrase	(Chris, MC) (Hoatlin/Thayer/Smolik)
June 13	Mahta	ncRNA (round II)	(Jeremy, MC) (Thayer/Rotwein?)
June 13	Jeremy	ncRNA	(Mahta, MC) (Thayer)
June 14	Larry	pol-Y (Excision Repair)	(Jon, MC) (Hoatlin/Lloyd)
June 14	Jon	Topo	(Larry, MC) (Faculty?)

Proposed Papers

Method

Enlist a faculty mentor

send them the paper

make sure the date works

vote by wiki?

Make sure there is consensus (excitement) among remaining class members about the proposed paper

again, vote can be done on wiki

Suggestions

Proposed Paper for Discussion--Contact Chayne for inquiries

1. Nöllmann M, Stone MD, Bryant Z, Gore J, Crisona NJ, Hong SC, Mitelheiser S, Maxwell A, Bustamante C, and Cozzarelli NR. Multiple modes of Escherichia coli DNA gyrase activity revealed by force and torque. Nat Struct Mol Biol. 2007 Apr;14(4):264-71. DOI:10.1038/nsmb1213 |

Abstract:

E. coli DNA gyrase uses the energy of ATP hydrolysis to introduce essential negative supercoils into the genome, thereby working against the mechanical stresses that accumulate in supercoiled DNA. Using a magnetic-tweezers assay, we demonstrate that small changes in force and torque can switch gyrase among three distinct modes of activity. Under low mechanical stress, gyrase introduces negative supercoils by a mechanism that depends on DNA wrapping. Elevated tension or positive torque suppresses DNA wrapping, revealing a second mode of activity that resembles the activity of topoisomerase IV. This 'distal T-segment capture' mode results in active relaxation of left-handed braids and positive supercoils. A third mode is responsible for the ATP-independent relaxation of negative supercoils. We present a branched kinetic model that quantitatively accounts for all of our single-molecule results and agrees with existing biochemical data.

Gao et al

Proposed Paper(s) for Jon --Contact Jon for inquiries
Evidence that two smaller subunits of RPA bind weakly and preferentially to telomeric DNA. These telomere capping proteins have functional similarities (OB fold) with ssDNA binding proteins and may be involved in the recruitment of telomere maintenance proteins.

2. Gao H, Cervantes RB, Mandell EK, Otero JH, and Lundblad V. RPA-like proteins mediate yeast telomere function. Nat Struct Mol Biol. 2007 Mar;14(3):208-14. DOI:10.1038/nsmb1205 |
3. Miller KM, Rog O, and Cooper JP. Semi-conservative DNA replication through telomeres requires Taz1. Nature. 2006 Apr 6;440(7085):824-8. DOI:10.1038/nature04638 |

Stats

• make sure each of you has a slot as presenter 1 and 2.