BMCB625:Materials

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

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

Presentation Zen

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

Evaluation Forms

 * [[Media:BMCB625MC Eval.pdf|Evaluation Form MC]]
 * [[Media:BMCB625Intro Eval.pdf|Evaluation Form Presenter 1(Intro)]]
 * [[Media:BMCB625P2 Evaluation.pdf|Evaluation Form Presenter 2]]
 * [[Media:Hoatlin_Dept_Eval.pdf|Dept. Evaluation Form]]

Papers

 * 1) Lopes pmid=16387650
 * 2) Heller pmid=16452972

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

Using Caffeine to Elute Replication Intermediates with Single Stranded Regions

Lecture Slides
[[Media:04122007_DNA_Replication.pdf|DNA Replication Slides (pdf)‎]]

[[Media:BMCB625DNARep.ppt|Chris and Mahta's Slides (ppt)]]

[[Media:BMCB625_BND_2D RI supp.ppt|Supplemental Slides (ppt)‎]]

BMCB625:DNA Replication

Papers
Moyer-PNAS-2006 pmid=16798881 Pacek-MC-2006 pmid=16483939

Lecture slides
[[Media:CMGcomplex-intro-17apr07clp.ppt|Chayne's Intro slides (ppt) ]]

[[Media:Moyer.ppt|Larry's slides on Moyer (ppt)]]

Papers

 * 1) Chaumeil-GD-2006 pmid=16912274
 * 2) Pollard-Nature-2006 pmid=16915236

Bonus Materials

 * 1) news-n-views pmid=16915234
 * 2) cell-review pmid=17320512
 * 3) reference pmid=8954732
 * 4) GenesDev-review pmid=16847345
 * 5) ncRNAreview pmid=15809263
 * 6) Nature-Review pmid=11253071
 * 7) NatStrucBiol-Jarid1C pmid=17310255
 * 8) Genetics pmid=16980402
 * 9) Annualreview pmid=16124854

Nature podcast on Pollard paper

[[Media:bcmb625-XistPaper-26apr07clp.ppt|Summary ppt of Chaumeil, et al]]

[[Media:X_Chromosome_Inactivation_and_ncRNA_Intro.ppt|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

Bonus Materials

 * 1) Chromatin-code-NewsViews pmid=16915272
 * 2) What-Positions_Nucleosomes pmid=12123795


 * link to Eran Segal's Lab page where you can test your favorite sequence for predicted nucleosome occupancy

Lecture Slides
Nucleosome Coding Introduction

[[Media:BMCM625Genomic code.ppt | Nucleosome Coding Paper]]

Nucleosome Coding- student Q&A

Papers

 * 1) Enemark pmid=16855583

Bonus Materials
Power-Pump pmid=15454074
 * 1) Gai pmid=15454080


 * 1) AAA-type-ATPase-review pmid=16072036


 * 1) Review
 * PCNA, the Maestro of the Replication Fork []

A recent addition to Cell that looks at a critical component of the replication fork. --~


 * 1) Gorillas---proteins-that-move-DNA_Maureen-suggested-reading pmid=16936698

BMCB625:Helicases

[[Media:Helicase_DNA_Replication.ppt | Helicase_DNA_Replication.ppt]]

Papers

 * 1) Bono pmid=16923391

Bonus Materials

 * Link to Schedule Page and Questions/Comments[]
 * 1) GREAT-EJC-REVIEW pmid=15145352
 * 2) Science-crystal-structure pmid=16931718
 * 3) 3D-EJC pmid=16797590
 * 4) eIF4AIII pmid=15034551
 * 5) EJC-eIF4AIII pmid=16170325
 * 6) Mago-Y14 pmid=12704080
 * 7) DEADbox pmid=16337753

Presentations:
 * Introduction:[[Image:053107_EJC.ppt]]
 * Paper: [[Image:EJC_Presentation_May2007.ppt]] (Note: 33MB File)

Link to Schedule page: BMCB625:Exon Jxn Complex

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: EM Ozbudak, et al, Nature 427, 737-740 (19 February 2004) Main Paper S. E. Luria and M. Delbrück, Genetics. 1943 November; 28(6): 491–511 Classic Paper
 * MAIN PAPER: "Multistability in the lactose utilization network of Escherichia coli"
 * CLASSIC: "Mutations of Bacteria from Virus Sensitivity to Virus Resistance"
 * 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
[[Media:Bcmb625-7jun07-DNAGyrase-piscitelli.ppt | DNA Gyrase ppt lecture (Nollmann, et al.)]]
 * Presentation slides:


 * 1) Nollman pmid=17334374

Chayne - Bonus Materials

 * A good "News & Views" on the [|DNA Gyrase Article]


 * 1) TopoII_review pmid=16246146
 * 2) TopoII_review pmid=16246147
 * 3) Great_overview_of_Topos pmid=15139806
 * 4) The_original_gyrase_paper pmid=186775
 * 5) single_molecule_plus_topology_review pmid=15130115
 * 6) DNA_topology_review pmid=3010458
 * 7) New_Review pmid=17397985
 * Nicholas Cozzarelli (1938-2006) obituary in Cell

Mahta - Papers

 * 1) Christov-MCB-2006 pmid=16943439

Mahta -Bonus Materials

 * 1) Ro60-autoimmunity pmid=15168680
 * 2) Ro-binding-Y pmid=9671049
 * 3) Y-RNA_conservation pmid=7505620
 * 4) hY-structure pmid=8041611



BMCB625:Noncoding Y RNA

Jeremy - Papers

 * 1) Zalfa pmid=12581522

[[Media:FMRP_and_BC1_RNA.ppt|FMRP and BC1 RNA Slides]]

Jeremy-Bonus Materials

 * 1) Zalfa pmid=16707258


 * 1) Bagni pmid=15861180


 * 1) Klann pmid=15550948


 * 1) Martignetti pmid=8265590


 * 1) Tiedge pmid=7684772


 * 1) Dendritic_spine_shape_in_learning_and_memory pmid=17498943


 * 1) lit_review pmid=14994288

Larry - Papers

 * 1) Ogi-NCB-2006 pmid=16738703

Larry-Bonus Materials
News and Views


 * 1) review pmid=17188030
 * 2) polk_kinetics pmid=12444249
 * 3) poldelta_kinetics pmid=10748013
 * 4) pol-eta_structure pmid=11545743
 * 5) Function_of_DNA_Polymerases_Review pmid=15588842

[[Media:Final.ppt|Pol Kappa Presentation]]

Jon - Papers
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.
 * 1) 2 pmid=17293872

[[Media:Telomere.ppt| Telomere Presentation]]

Jon - Bonus Materials
cool RPA discussion
 * 1) 1 pmid=16598261
 * 2) 2 pmid=17334404
 * 3) 3 pmid=9164449
 * 4) 4 pmid=10655599

G4_Antibody

EMBO REPORTS

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

 * 1) Olaussen-NEJM-2006 pmid=16957145
 * 2) Kumagai-Cell-2006 pmid=16530042
 * 3) Zegerman pmid=17167417
 * 4) comment-Zegerman pmid=17230184
 * 5) Kitamura pmid=16814716,
 * 6) comment-Kitamura pmid=16814710

Overlapping coverage but Podcast is interesting
Nature podcast on Zhou paper
 * 1) Zhou pmid=17301785 (see podcast link below)