BMCB625:Schedule: Difference between revisions
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==General Info== | ==General Info== | ||
*Spring 2007 | *Spring 2007 | ||
*Location: BRB 603. Wednesdays from 9:30 - 11:30 (practice session) and Thursdays from 10:30 - 12:30 | *Location: BRB 603. Wednesdays from 9:30 - 11:30 (practice and review session) and Thursdays (The Real Thang) from 10:30 - 12:30 | ||
*[[BMCB625:How the class works|How the Class Works]] | *[[BMCB625:How the class works|How the Class Works]] | ||
==Week-by-Week Schedule Summary== | ==Week-by-Week Schedule Summary== | ||
| Line 13: | Line 14: | ||
| align="center" style="background:#f0f0f0;"|'''Presenters''' | | align="center" style="background:#f0f0f0;"|'''Presenters''' | ||
| align="center" style="background:#f0f0f0;"|'''Topic''' | | align="center" style="background:#f0f0f0;"|'''Topic''' | ||
| align="center" style="background:#f0f0f0;"|'''Evaluator/MC | | align="center" style="background:#f0f0f0;"|'''Evaluator/MC/Faculty''' | ||
|-- | |-- | ||
| Line 22: | Line 23: | ||
|-- | |-- | ||
| April 12 | | April 12 | ||
| Chris & | | Chris & Maureen | ||
| [[DNA Replication]] | | [[BMCB625:DNA Replication]] | ||
| JF/CP/ | | JF/CP/(Hoatlin&Thayer) | ||
|-- | |-- | ||
| April 19 | | April 19 | ||
| Chayne & Larry | | Chayne & Larry | ||
| DNA Replication (New components) | | [[BMCB625:DNA Replication (New components)]] | ||
|JL/CS/ | | JL/CS (Hoatlin/Thayer) | ||
|-- | |-- | ||
| April 26 | | April 26 | ||
| Jeremy & Chayne | | Jeremy & Chayne | ||
| Xist | | [[BMCB625: noncoding RNA (Xist)]] | ||
| LG/JF | | LG/JF (Thayer) | ||
|-- | |-- | ||
| May 2 (Wed) | |||
| | |||
| BMCB625: Bringing it all together - DNA replication and NC RNA | |||
| | |||
|-- | |||
| May 17 | | May 17 | ||
| Jon (Happy Birthday) & Jeremy | | Jon (Happy Birthday) & Jeremy | ||
| Nucleosome Coding | | [[BMCB625:Nucleosome Coding]] | ||
| CS/MN | | CS/MN(Lundblad?) | ||
|-- | |-- | ||
| May 24 | | May 24 | ||
| | | Larry & Jon | ||
| | | [[BMCB625:Helicases]] | ||
| | | MN/JL (Hoatlin/Chapman) | ||
|-- | |-- | ||
| May 31 | | May 31 | ||
| | | Mahta & Chris | ||
| | | [[BMCB625:Exon Jxn Complex]] | ||
| | | CP/LG(Rotwein/Landfear?) | ||
|-- | |-- | ||
| June 7 | | June 7 | ||
| Chris | | Chris | ||
| Mathematics in Biology ( | | [[BMCB625:Mathematics in Biology]] | ||
| (Chayne, MC) (Shinde?, Farrens?) | |||
|-- | |-- | ||
|June 7 | |June 7 | ||
| Chayne | | Chayne | ||
| [[ | | [[BMCB625:DNA Gyrase]] | ||
|(Chris, MC) (Hoatlin/Thayer/Smolik) | |||
|-- | |-- | ||
| June 13 | | June 13 | ||
| Mahta | | Mahta | ||
| | | [[BMCB625:Noncoding Y RNA]] | ||
| (Jeremy, MC) (Thayer/Rotwein?) | |||
|-- | |-- | ||
| June 13 | | June 13 | ||
| | | Jeremy | ||
| | | [[BMCB625:ncRNA]] | ||
| | | (Mahta, MC) (Thayer) | ||
|-- | |-- | ||
|June 14 | | June 14 | ||
| | | Larry | ||
|pol-Y (Excision Repair) ( | | [[BMCB625:pol-Y (Excision Repair)]] | ||
|(Jon, MC) (Hoatlin/Lloyd/McCullough) | |||
|-- | |-- | ||
|June 14 | |June 14 | ||
|Jon | |Jon | ||
|[[BMCB625:Topo]] | |||
|[[ | |(Larry, MC) | ||
|-- | |-- | ||
|} | |} | ||
| Line 85: | Line 91: | ||
==Proposed Papers== | ==Proposed Papers== | ||
;Enlist a faculty mentor | ===Method=== | ||
;Enlist a faculty mentor | |||
:send them the paper | :send them the paper | ||
:make sure the date works | :make sure the date works | ||
:vote by wiki? | :vote by wiki? | ||
;Make sure there is consensus (excitement) among remaining class members about the proposed paper | ;Make sure there is consensus (excitement) among remaining class members about the proposed paper | ||
:again, vote can be done on wiki | :again, vote can be done on wiki | ||
===Suggestions=== | |||
<span id="DNA Gyrase"> | <span id="DNA Gyrase"> | ||
'''Proposed Paper for Discussion'''--Contact Chayne for inquiries | '''Proposed Paper for Discussion'''--Contact Chayne for inquiries | ||
| Line 106: | Line 111: | ||
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. | 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. | ||
==Stats== | ==Stats== | ||
*make sure each of you has a slot as presenter 1 and 2. | *make sure each of you has a slot as presenter 1 and 2. | ||
Latest revision as of 15:12, 23 July 2007
General Info
- Spring 2007
- Location: BRB 603. Wednesdays from 9:30 - 11:30 (practice and review session) and Thursdays (The Real Thang) 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 & Maureen | 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 2 (Wed) | BMCB625: Bringing it all together - DNA replication and NC RNA | ||
| May 17 | Jon (Happy Birthday) & Jeremy | BMCB625:Nucleosome Coding | CS/MN(Lundblad?) |
| May 24 | Larry & Jon | BMCB625:Helicases | MN/JL (Hoatlin/Chapman) |
| May 31 | Mahta & Chris | BMCB625:Exon Jxn Complex | CP/LG(Rotwein/Landfear?) |
| June 7 | Chris | BMCB625:Mathematics in Biology | (Chayne, MC) (Shinde?, Farrens?) |
| June 7 | Chayne | BMCB625:DNA Gyrase | (Chris, MC) (Hoatlin/Thayer/Smolik) |
| June 13 | Mahta | BMCB625:Noncoding Y RNA | (Jeremy, MC) (Thayer/Rotwein?) |
| June 13 | Jeremy | BMCB625:ncRNA | (Mahta, MC) (Thayer) |
| June 14 | Larry | BMCB625:pol-Y (Excision Repair) | (Jon, MC) (Hoatlin/Lloyd/McCullough) |
| June 14 | Jon | BMCB625:Topo | (Larry, MC) |
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
- 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.
Stats
- make sure each of you has a slot as presenter 1 and 2.
