BMCB625:Materials

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BMCB625 Advanced Topics in Molecular Biology

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Biochemistry Dep’t and course “quick” Links:

“This week’s tasks” Course web-page BMCB625
BMB Seminar Series
"Universal Slide Template" BMCB625:Discussion_Univ_template
Protein Crystallography Tutorial
Amazing page of links for all of your structural biology needs
A brief intro to crystallographic model analysis
MolProbity structure validation server
Gerard Kleywegt's model validation tutorial
Glossary of crystallography terms--Very nice!
Nicholas Cozzarelli (1938-2006) obituary in Cell


Contents

Class Focus, Spring 2007

  1. Organization Meeting and Rules of Engagement
  2. Biochemistry and Structure of Replicating Machines at the Protein-DNA Interface
  3. Molecular Mechanisms of Genomic Information Expansion
  4. A Revealing Structure of the Exon Junction Complex

Week 1: Introduction and Scheduling

Presentation Zen

  1. Slide Zen
  2. Delivery Zen
  3. Feel free to add links that help you

Evaluation Forms

Week 2: Rewrite the textbooks on DNA Replication

Papers

Error fetching PMID 16387650:
Error fetching PMID 16452972:
  1. Error fetching PMID 16387650: [Lopes]
  2. Error fetching PMID 16452972: [Heller]
All Medline abstracts: PubMed HubMed

Bonus Materials

  1. Review: Replisome assembly and the direct restart of stalled replication forks. Heller RC, & Marians KJ. Nat Rev Mol Cell Biol. 2006 Dec;7(12):932-43. Epub 2006 Nov 8. [1] [REVIEW]

BND Cellulose Protocol [1]

Using Caffeine to Elute Replication Intermediates with Single Stranded Regions [2]

Lecture Slides

DNA Replication Slides (pdf)‎

Chris and Mahta's Slides (ppt)

Supplemental Slides (ppt)‎


BMCB625:DNA Replication


Week 3: Go, Ichi, Nii, and San;New Components of DNA Replication

Papers

Error fetching PMID 16798881:
  1. Error fetching PMID 16798881: [Moyer-PNAS-2006]

Bonus Materials

Lecture slides

Chayne's Intro slides (ppt)

Larry's slides on Moyer (ppt)

Week 4:non-coding RNAs

Papers

Error fetching PMID 16912274:
Error fetching PMID 16915236:
  1. Error fetching PMID 16912274: [Chaumeil-GD-2006]
  2. Error fetching PMID 16915236: [Pollard-Nature-2006]
All Medline abstracts: PubMed HubMed

Bonus Materials

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  1. Error fetching PMID 16915234: [news-n-views]
  2. Error fetching PMID 17320512: [cell-review]
  3. Error fetching PMID 8954732: [reference]
  4. Error fetching PMID 16847345: [GenesDev-review]
  5. Error fetching PMID 15809263: [ncRNAreview]
  6. Error fetching PMID 11253071: [Nature-Review]
  7. Error fetching PMID 17310255: [NatStrucBiol-Jarid1C]
  8. Error fetching PMID 16980402: [Genetics]
  9. Error fetching PMID 16124854: [Annualreview]
All Medline abstracts: PubMed HubMed

Nature podcast on Pollard paper

Summary ppt of Chaumeil, et al

X Inactivation Intro Slides

Week 5: Consolidating weeks 2, 3 and 4 (Wed May 2 10AM)

Review of Methods/papers, answering questions from non-coding RNA and DNA Replication papers

Week 6: Student Research Forum

SRF 2007

Week 7: Nucleosome positioning and Chromatin Structure

Papers

Bonus Materials

Error fetching PMID 16915272:
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  1. Error fetching PMID 16915272: [Chromatin-code-NewsViews]
  2. Error fetching PMID 12123795: [What-Positions_Nucleosomes]
All Medline abstracts: PubMed HubMed
  • link to Eran Segal's Lab page where you can test your favorite sequence for predicted nucleosome occupancy

Lecture Slides

Nucleosome Coding Introduction

Nucleosome Coding Paper



Nucleosome Coding- student Q&A

Week 8: Structure function of DNA Helicases

Papers

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  1. Error fetching PMID 16855583: [Enemark]

Bonus Materials

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  1. Error fetching PMID 15454074: [Power-Pump]
  2. Error fetching PMID 15454080: [Gai]
  3. Error fetching PMID 16072036: [AAA-type-ATPase-review]
  4.  :PCNA, the Maestro of the Replication Fork [[1]] A recent addition to Cell that looks at a critical component of the replication fork. --~~~~

    [Review]

  5. Error fetching PMID 16936698: [Gorillas---proteins-that-move-DNA_Maureen-suggested-reading]
All Medline abstracts: PubMed HubMed

BMCB625:Helicases

Helicase_DNA_Replication.ppt

Week 9: A gripping story about the RNA exon junction complex

Papers

Error fetching PMID 16923391:
  1. Error fetching PMID 16923391: [Bono]

Bonus Materials

  • Link to Schedule Page and Questions/Comments[[3]]
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  1. Error fetching PMID 15145352: [GREAT-EJC-REVIEW]
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  3. Error fetching PMID 16797590: [3D-EJC]
  4. Error fetching PMID 15034551: [eIF4AIII]
  5. Error fetching PMID 16170325: [EJC-eIF4AIII]
  6. Error fetching PMID 12704080: [Mago-Y14]
  7. Error fetching PMID 16337753: [DEADbox]
All Medline abstracts: PubMed HubMed

Presentations:

Link to Schedule page: BMCB625:Exon Jxn Complex


Week 10: Individual Presentations

Chris - Papers

Outline of Talk and Discussion

  1. Introduction: Perspectives between disciplines and establishing common languages
  2. "Classic Paper" (as reference): Luria and Delbruck Fluctuation Test, trends via statistical arguements
  3. "Main Paper" : Lactose Utilization as a model for Bistability
  4. Discussion

PAPERS:

  • MAIN PAPER: "Multistability in the lactose utilization network of Escherichia coli"

EM Ozbudak, et al, Nature 427, 737-740 (19 February 2004) Main Paper

  • CLASSIC: "Mutations of Bacteria from Virus Sensitivity to Virus Resistance"

S. E. Luria and M. Delbrück, Genetics. 1943 November; 28(6): 491–511 Classic Paper

  • See Below: "Biologists Fixing Radios"
  • Presentation: Presentation

Chris - Bonus Materials

A good primer on how biologists and engineers look at a problem in different ways; while many comments do not address the complexity of biochemistry and genetics, it does provide an interesting perspective on what we consider "important." Also, of importance, in my opinion, is developing a common language by which numerous disciplines can communicate. I'll touch more on this particular topic during my talk. Y. Lazebnik, "Can a Biologist Fix a Radio? or, What I Learned while Studying Apoptosis" Bio fixing Radios


Chayne - Papers

  • Presentation slides:

DNA Gyrase ppt lecture (Nollmann, et al.)

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  1. Error fetching PMID 17334374: [Nollman]

Chayne - Bonus Materials

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  1. Error fetching PMID 16246146: [TopoII_review]
  2. Error fetching PMID 16246147: [TopoII_review]
  3. Error fetching PMID 15139806: [Great_overview_of_Topos]
  4. Error fetching PMID 186775: [The_original_gyrase_paper]
  5. Error fetching PMID 15130115: [single_molecule_plus_topology_review]
  6. Error fetching PMID 3010458: [DNA_topology_review]
  7. Error fetching PMID 17397985: [New_Review]
All Medline abstracts: PubMed HubMed
Nicholas Cozzarelli (1938-2006) obituary in Cell----

Week 11: Individual Presentations

Mahta - Papers

Error fetching PMID 16943439:
  1. Error fetching PMID 16943439: [Christov-MCB-2006]

Mahta -Bonus Materials

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  1. Error fetching PMID 15168680: [Ro60-autoimmunity]
  2. Error fetching PMID 9671049: [Ro-binding-Y]
  3. Error fetching PMID 7505620: [Y-RNA_conservation]
  4. Error fetching PMID 8041611: [hY-structure]
All Medline abstracts: PubMed HubMed

Image:BMCB625 Y RNA 061307.ppt

BMCB625:Noncoding Y RNA


Jeremy - Papers

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  1. Error fetching PMID 12581522: [Zalfa]

FMRP and BC1 RNA Slides

Jeremy-Bonus Materials

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  1. Error fetching PMID 16707258: [Zalfa]
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  1. Error fetching PMID 15861180: [Bagni]
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  1. Error fetching PMID 15550948: [Klann]
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  1. Error fetching PMID 8265590: [Martignetti]
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  1. Error fetching PMID 7684772: [Tiedge]
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  1. Error fetching PMID 17498943: [Dendritic_spine_shape_in_learning_and_memory]
Error fetching PMID 14994288:
  1. Error fetching PMID 14994288: [lit_review]

Larry - Papers

Error fetching PMID 16738703:
  1. Error fetching PMID 16738703: [Ogi-NCB-2006]

Larry-Bonus Materials

News and Views

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  1. Error fetching PMID 17188030: [review]
  2. Error fetching PMID 12444249: [polk_kinetics]
  3. Error fetching PMID 10748013: [poldelta_kinetics]
  4. Error fetching PMID 11545743: [pol-eta_structure]
  5. Error fetching PMID 15588842: [Function_of_DNA_Polymerases_Review]
All Medline abstracts: PubMed HubMed

Pol Kappa Presentation

Jon - Papers

Error fetching PMID 17293872:
  1. Error fetching PMID 17293872: [2]


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.


Telomere Presentation

Jon - Bonus Materials

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  1. Error fetching PMID 17334404: [2]
  2. Error fetching PMID 16598261: [1]
  3. Error fetching PMID 9164449: [3]
  4. Error fetching PMID 10655599: [4]
All Medline abstracts: PubMed HubMed

cool RPA discussion

G4_Antibody

EMBO REPORTS

So many papers, so little time: Papers we would have liked to cover (note podcast link below)

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  1. Error fetching PMID 16957145: [Olaussen-NEJM-2006]
  2. Error fetching PMID 16530042: [Kumagai-Cell-2006]
  3. Error fetching PMID 17167417: [Zegerman]
  4. Error fetching PMID 17230184: [comment-Zegerman]
  5. Error fetching PMID 16814716: [Kitamura]
  6. Error fetching PMID 16814710: [comment-Kitamura]
All Medline abstracts: PubMed HubMed

Overlapping coverage but Podcast is interesting

Error fetching PMID 17301785:
  1. Error fetching PMID 17301785: [Zhou]
Nature podcast on Zhou paper
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