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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


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


  1. Lopes M, Foiani M, and Sogo JM. . pmid:16387650. PubMed HubMed [Lopes]
  2. Heller RC and Marians KJ. . pmid:16452972. PubMed HubMed [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


  1. Moyer SE, Lewis PW, and Botchan MR. . pmid:16798881. PubMed HubMed [Moyer-PNAS-2006]

Bonus Materials

Lecture slides

Chayne's Intro slides (ppt)

Larry's slides on Moyer (ppt)

Week 4:non-coding RNAs


  1. Chaumeil J, Le Baccon P, Wutz A, and Heard E. . pmid:16912274. PubMed HubMed [Chaumeil-GD-2006]
  2. Pollard KS, Salama SR, Lambert N, Lambot MA, Coppens S, Pedersen JS, Katzman S, King B, Onodera C, Siepel A, Kern AD, Dehay C, Igel H, Ares M Jr, Vanderhaeghen P, and Haussler D. . pmid:16915236. PubMed HubMed [Pollard-Nature-2006]
All Medline abstracts: PubMed HubMed

Bonus Materials

  1. Ponting CP and Lunter G. . pmid:16915234. PubMed HubMed [news-n-views]
  2. Zaratiegui M, Irvine DV, and Martienssen RA. . pmid:17320512. PubMed HubMed [cell-review]
  3. Keohane AM, O'neill LP, Belyaev ND, Lavender JS, and Turner BM. . pmid:8954732. PubMed HubMed [reference]
  4. Heard E and Disteche CM. . pmid:16847345. PubMed HubMed [GenesDev-review]
  5. O'Neill MJ. . pmid:15809263. PubMed HubMed [ncRNAreview]
  6. Avner P and Heard E. . pmid:11253071. PubMed HubMed [Nature-Review]
  7. Seward DJ, Cubberley G, Kim S, Schonewald M, Zhang L, Tripet B, and Bentley DL. . pmid:17310255. PubMed HubMed [NatStrucBiol-Jarid1C]
  8. Diaz-Perez SV, Ferguson DO, Wang C, Csankovszki G, Wang C, Tsai SC, Dutta D, Perez V, Kim S, Eller CD, Salstrom J, Ouyang Y, Teitell MA, Kaltenboeck B, Chess A, Huang S, and Marahrens Y. . pmid:16980402. PubMed HubMed [Genetics]
  9. Chow JC, Yen Z, Ziesche SM, and Brown CJ. . pmid:16124854. PubMed HubMed [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


Bonus Materials

  1. Richmond TJ. . pmid:16915272. PubMed HubMed [Chromatin-code-NewsViews]
  2. Kiyama R and Trifonov EN. . pmid:12123795. PubMed HubMed [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


  1. Enemark EJ and Joshua-Tor L. . pmid:16855583. PubMed HubMed [Enemark]

Bonus Materials

  1. Eichman BF and Fanning E. . pmid:15454074. PubMed HubMed [Power-Pump]
  2. Gai D, Zhao R, Li D, Finkielstein CV, and Chen XS. . pmid:15454080. PubMed HubMed [Gai]
  3. Hanson PI and Whiteheart SW. . pmid:16072036. PubMed HubMed [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. --~~~~


  5. Cozzarelli NR, Cost GJ, Nöllmann M, Viard T, and Stray JE. . pmid:16936698. PubMed HubMed [Gorillas---proteins-that-move-DNA_Maureen-suggested-reading]
All Medline abstracts: PubMed HubMed



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


  1. Bono F, Ebert J, Lorentzen E, and Conti E. . pmid:16923391. PubMed HubMed [Bono]

Bonus Materials

  • Link to Schedule Page and Questions/Comments[[3]]
  1. Tange TØ, Nott A, and Moore MJ. . pmid:15145352. PubMed HubMed [GREAT-EJC-REVIEW]
  2. Andersen CB, Ballut L, Johansen JS, Chamieh H, Nielsen KH, Oliveira CL, Pedersen JS, Séraphin B, Le Hir H, and Andersen GR. . pmid:16931718. PubMed HubMed [Science-crystal-structure]
  3. Stroupe ME, Tange TØ, Thomas DR, Moore MJ, and Grigorieff N. . pmid:16797590. PubMed HubMed [3D-EJC]
  4. Shibuya T, Tange TØ, Sonenberg N, and Moore MJ. . pmid:15034551. PubMed HubMed [eIF4AIII]
  5. Ballut L, Marchadier B, Baguet A, Tomasetto C, Séraphin B, and Le Hir H. . pmid:16170325. PubMed HubMed [EJC-eIF4AIII]
  6. Shi H and Xu RM. . pmid:12704080. PubMed HubMed [Mago-Y14]
  7. Cordin O, Banroques J, Tanner NK, and Linder P. . pmid:16337753. PubMed HubMed [DEADbox]
All Medline abstracts: PubMed HubMed


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


  • 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.)

  1. Nöllmann M, Stone MD, Bryant Z, Gore J, Crisona NJ, Hong SC, Mitelheiser S, Maxwell A, Bustamante C, and Cozzarelli NR. . pmid:17334374. PubMed HubMed [Nollman]

Chayne - Bonus Materials

  1. Maxwell A, Costenaro L, Mitelheiser S, and Bates AD. . pmid:16246146. PubMed HubMed [TopoII_review]
  2. Schoeffler AJ and Berger JM. . pmid:16246147. PubMed HubMed [TopoII_review]
  3. Corbett KD and Berger JM. . pmid:15139806. PubMed HubMed [Great_overview_of_Topos]
  4. Gellert M, Mizuuchi K, O'Dea MH, and Nash HA. . pmid:186775. PubMed HubMed [The_original_gyrase_paper]
  5. Espeli O and Marians KJ. . pmid:15130115. PubMed HubMed [single_molecule_plus_topology_review]
  6. Wasserman SA and Cozzarelli NR. . pmid:3010458. PubMed HubMed [DNA_topology_review]
  7. Nöllmann M, Crisona NJ, and Arimondo PB. . pmid:17397985. PubMed HubMed [New_Review]
All Medline abstracts: PubMed HubMed
Nicholas Cozzarelli (1938-2006) obituary in Cell----

Week 11: Individual Presentations

Mahta - Papers

  1. Christov CP, Gardiner TJ, Szüts D, and Krude T. . pmid:16943439. PubMed HubMed [Christov-MCB-2006]

Mahta -Bonus Materials

  1. Chen X and Wolin SL. . pmid:15168680. PubMed HubMed [Ro60-autoimmunity]
  2. Green CD, Long KS, Shi H, and Wolin SL. . pmid:9671049. PubMed HubMed [Ro-binding-Y]
  3. Pruijn GJ, Wingens PA, Peters SL, Thijssen JP, and van Venrooij WJ. . pmid:7505620. PubMed HubMed [Y-RNA_conservation]
  4. van Gelder CW, Thijssen JP, Klaassen EC, Sturchler C, Krol A, van Venrooij WJ, and Pruijn GJ. . pmid:8041611. PubMed HubMed [hY-structure]
All Medline abstracts: PubMed HubMed

Image:BMCB625 Y RNA 061307.ppt

BMCB625:Noncoding Y RNA

Jeremy - Papers

  1. Zalfa F, Giorgi M, Primerano B, Moro A, Di Penta A, Reis S, Oostra B, and Bagni C. . pmid:12581522. PubMed HubMed [Zalfa]

FMRP and BC1 RNA Slides

Jeremy-Bonus Materials

  1. Zalfa F, Achsel T, and Bagni C. . pmid:16707258. PubMed HubMed [Zalfa]
  1. Bagni C and Greenough WT. . pmid:15861180. PubMed HubMed [Bagni]
  1. Klann E and Dever TE. . pmid:15550948. PubMed HubMed [Klann]
  1. Martignetti JA and Brosius J. . pmid:8265590. PubMed HubMed [Martignetti]
  1. Tiedge H, Chen W, and Brosius J. . pmid:7684772. PubMed HubMed [Tiedge]
  1. Bourne J and Harris KM. . pmid:17498943. PubMed HubMed [Dendritic_spine_shape_in_learning_and_memory]
  1. Darnell JC, Warren ST, and Darnell RB. . pmid:14994288. PubMed HubMed [lit_review]

Larry - Papers

  1. Ogi T and Lehmann AR. . pmid:16738703. PubMed HubMed [Ogi-NCB-2006]

Larry-Bonus Materials

News and Views

  1. Lehmann AR. . pmid:17188030. PubMed HubMed [review]
  2. Haracska L, Prakash L, and Prakash S. . pmid:12444249. PubMed HubMed [polk_kinetics]
  3. Einolf HJ and Guengerich FP. . pmid:10748013. PubMed HubMed [poldelta_kinetics]
  4. Trincao J, Johnson RE, Escalante CR, Prakash S, Prakash L, and Aggarwal AK. . pmid:11545743. PubMed HubMed [pol-eta_structure]
  5. Bebenek K and Kunkel TA. . pmid:15588842. PubMed HubMed [Function_of_DNA_Polymerases_Review]
All Medline abstracts: PubMed HubMed

Pol Kappa Presentation

Jon - Papers

  1. Gao H, Cervantes RB, Mandell EK, Otero JH, and Lundblad V. . pmid:17293872. PubMed HubMed [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

  1. Haring SJ and Wold MS. . pmid:17334404. PubMed HubMed [2]
  2. Miller KM, Rog O, and Cooper JP. . pmid:16598261. PubMed HubMed [1]
  3. Suck D. . pmid:9164449. PubMed HubMed [3]
  4. Eggleston A. . pmid:10655599. PubMed HubMed [4]
All Medline abstracts: PubMed HubMed

cool RPA discussion



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

  1. Olaussen KA, Dunant A, Fouret P, Brambilla E, André F, Haddad V, Taranchon E, Filipits M, Pirker R, Popper HH, Stahel R, Sabatier L, Pignon JP, Tursz T, Le Chevalier T, Soria JC, and IALT Bio Investigators. . pmid:16957145. PubMed HubMed [Olaussen-NEJM-2006]
  2. Kumagai A, Lee J, Yoo HY, and Dunphy WG. . pmid:16530042. PubMed HubMed [Kumagai-Cell-2006]
  3. Zegerman P and Diffley JF. . pmid:17167417. PubMed HubMed [Zegerman]
  4. Botchan M. . pmid:17230184. PubMed HubMed [comment-Zegerman]
  5. Kitamura E, Blow JJ, and Tanaka TU. . pmid:16814716. PubMed HubMed [Kitamura]
  6. Meister P, Taddei A, and Gasser SM. . pmid:16814710. PubMed HubMed [comment-Kitamura]
All Medline abstracts: PubMed HubMed

Overlapping coverage but Podcast is interesting

  1. Zhou T, Xu L, Dey B, Hessell AJ, Van Ryk D, Xiang SH, Yang X, Zhang MY, Zwick MB, Arthos J, Burton DR, Dimitrov DS, Sodroski J, Wyatt R, Nabel GJ, and Kwong PD. . pmid:17301785. PubMed HubMed [Zhou]
Nature podcast on Zhou paper
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