Seminars and Journal Club
Speakers in the biophysics seminar program have focused on molecular and cellular structure, and interactions between molecules. Outstanding speakers from leading laboratories in the US and abroad speak weekly, and students have the opportunity to meet with them on an informal basis over lunch. Student Research Talks and Journal Clubs are held weekly. In the course of the year each student presents at least one journal article outside of his or her immediate study and a discussion of current work. These seminars are open to faculty and other interested colleagues. This activity serves two purposes, both broadening the interests of students and giving them the opportunity for oral presentations.
Twice monthly first and second year students invite a member of the faculty to speak informally, followed by dinner. In this way, students can be assured of meeting every faculty member associated with the group and learn about his or her research in a substantive way.
In addition to the formal seminar program and informal faculty dinners, individual faculty hold weekly group meetings in which group members present their own results or plan new projects. These sessions are among the most critical and rigorous aspects of graduate training with much give and take for all participants. Even after completion of their formal rotation schedule, students are encouraged to attend all group meetings of interest.
Journal Club & Research Talks
Mondays at noon, Genentech Hall Room S201
Academic Year 2010: | ||
| Date | Speaker | Topic |
| 9/14/09 | Molly Darragh | TBA |
| 9/21/09 | Matt Eames | TBA |
| 9/28/09 | Ian Harwood | TBA |
Academic Year 2009: | ||
| Date | Speaker | Topic |
| 9/8/08 | Brittany Belin | A Role for Confined Water in Chaperonin Function |
| 9/15/08 | Hannes Braberg and David Burkhardt | Braberg: High-resolution mapping of meiotic crossovers and non-crossovers in yeast; Burkhardt: Metabolic gene regulation in a dynamically changing environment |
| 9/22/08 | Kiyoshi Egami and Jaline Gerardin | Egami: Structural basis for the activation of PPARgamma by oxidized fatty acids; Gerardin: Bacteria Subsisting on Antibiotics |
| 9/29/08 | Jenny Hsiao and Heather Newman | Hsiao: Actin restricts FcepsilonRI diffusion and facilitates antigen-induced receptor immobilization; Newman: Misfolded proteins partition between two distinct quality control compartments |
| 10/6/08 | Joe Kliegman and George Peterson | Joe Kliegman: Orientation and structure of the Ndc80 complex on the microtubule lattice. George Peterson: Accurate Coarse-Grained Modeling of Red Blood Cells |
| 10/13/08 | Elaine Kirschke and Gabe Rocklin | Elaine Kirschke: An inhibitor of FtsZ with potent and selective anti-staphylococcal activity. Gabe Rocklin: AMPK and PPARdelta Agonists are Exercise Mimetics |
| 10/20/08 | Monica Tremont and David Booth | Monica Tremont: Packaging Double-Helical DNA into Viral Capsids: Structures, Forces and Energetics David Booth: Structure of the 30S translation initiation complex. |
| 10/27/08 | Christian Cunningham | Conformational Dynamics of Hsp90 |
| 11/3/08 | Liz Clarke | A Eukaryotic-like Ser/Thr kinase signals bacteria to exit dormancy in response to peptidoglycan fragments. |
| 11/17/08 | Morris Feldman | The fragile X syndrome protein represses activity-dependent translation through CYFIP1, a new 4E-BP |
| 12/1/08 | Anselm Levskaya | TBA |
| 12/15/08 | Arjun Narayanan | Surface Sites for Engineering Allosteric Control in Proteins. |
| 1/12/09 | Molly Darragh | Specific Targeting of Cancer-Associated Proteolytic Activity for Tumor Detection in vivo |
| 1/26/09 | Matt Eames | Evolution. |
| 2/2/09 | Ian Harwood | Crystallographic Insight into Neurotransmitter Transporter Inhibition |
| 2/9/09 | Elisabeth Humphris | Rediction of Protein-Protein Interface Sequence Diversity Using Flexible Backbone Computational Protein Design |
| 2/23/09 | Peretz Partensky | How chromatin remodelers and DNA sequence cooperate to position nucleosomes |
| 3/2/09 | Bryant Chhun | Super-Resolution Video Microscopy of Live Cells by Structured Illumination |
| 3/9/09 | Deb Datta | Real-time DNA sequencing from single polymerase molecules. |
| 3/16/09 | Stephen Floor | A Coupling between Cap Recognition and Conformational Dynamics Drives Catalysis by the mRNA Decapping Enzyme Dcp2 |
| 3/23/09 | Chris McClendon | Computational Models of Allostery |
| 3/30/09 | Ethan Mirsky | Artificial nanopores that mimic the transport selectivity of the nuclear pore complex |
| 4/6/09 | Liz Montabana | Understanding Form and Function of Monomeric Tubulin Family Members |
| 4/13/09 | Rich Oberdorf | TBA |
| 4/20/09 | Ben Rhau | Symmetry-breaking polarization driven by a Cdc42p GEF-PAK complex. |
| 4/27/09 | Charles Biddle-Snead | Stretching Single Talin Rod Molecules Activates Vinculin Binding |
| 5/4/09 | Laura Lavery | TBA |
| 5/11/09 | Rebeca Choy | AAA+ Ring and Linker Swing Mechanism in the Dynein Motor |
| 5/18/09 | Sheel Dandekar | Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy. |
| 6/1/09 | Sai Duriseti | Protease-Triggered Unveiling of Bioactive Nanoparticles |
| 6/8/09 | Kris Kuchenbecker | TBA |
| 6/15/09 | Maya Chandru | TBA |
| 6/22/09 | Reid Williams | TBA |
| 6/29/09 | David Stanley | TBA |
| 7/6/09 | Dan Lu | TBA |
| 7/13/09 | Ryan Ritterson | TBA |
| 7/20/09 | Geoff Rollins | TBA |
| 7/27/09 | Edwin Rodriguez | TBA |
| 8/3/09 | James Kraemer | TBA |
| 8/10/09 | Anthony Shiver | TBA |
Academic Year 2008: | ||
| Date | Speaker | Topic |
| 9/17/07 | Caleb Bashor | Exploiting a Scaffold Protein as a Platform to Generate Diverse I/O Dynamics in a MAP Kinase Pathway |
| 9/24/07 | Clement Chu | TBA |
| 10/1/07 | Morris Feldman | POSTPONED |
| 10/8/07 | Eli Groban | Space flight alters bacterial gene expression and virulence and reveals a role for global regulator Hfq |
| 10/15/07 | Quincey Justman | TBA |
| 10/22/07 | Sam Pfaff | How to make your very own nuclear pore |
| 11/5/07 | Neema Salimi | New Insights into Alpha-lytic Unfolding |
| 11/19/07 | Jeremy Wilbur | Structure and regulatory roles of clathrin light chain determined by a low resolution crystal structure |
| 11/26/07 | Elizabeth Clarke | A Common Mechanism of Cellular Death Induced by Bactericidal Antibiotics |
| 12/10/07 | David Eramian | Can the accuracy of comparative protein structure models be predicted? |
| 12/17/07 | Morris Feldman | ATP competitive inhibition of mTOR |
| 1/14/08 | Anselm Levskaya | Controlling Signaling Pathways with Light |
| 1/28/08 | Arjun Narayanan | AH Bonding at the Helix-Bundle Crossing Controls Gating in Kir Potassium Channels |
| 2/4/08 | Greg Friedland | A simple model of backbone flexibility improves modeling of side-chain conformational variability |
| 2/11/08 | Christian Cunningham | Elephants, Rats, and Bacteria...Oh my! |
| 2/25/08 | Molly Darragh | Designed Protein-Protein Association |
| 3/3/08 | Matt Eames | Post-op introns going under the knife |
| 3/10/08 | Ben Sellers | Synthetic antibodies for specific recognition and crystallization of structured RNA |
| 3/17/08 | Ian Harwood | TBA |
| 3/24/08 | Peretz Partensky | Caught in the act of swapping genetic material: Direct Visualization of Horizontal Gene Transfer |
| 3/31/08 | Bryant Chhun | Microtubule polymerase XMAP215 |
| 4/7/08 | Elisabeth Humphris | Interconversion between two unrelated protein folds in the lymphotactin native state |
| 4/14/08 | Deb Datta | Coiled-coil irregularities and instabilities in group A Streptococcus M1 are required for virulence |
| 4/21/08 | Stephen Floor | Intrinsic motions along an enzymatic reaction trajectory |
| 4/28/08 | Chris McClendon | A Cholesterol Biosynthesis Inhibitor Blocks Staphylococcus aureus Virulence |
| 5/5/08 | Ethan Mirsky | Evolvability and hierarchy in rewired bacterial gene networks |
| 5/12/08 | Liz Montabana | In Vitro Reconstitution of a Bacterial Pilus: Insights into Macromolecular Assembly |
| 5/19/08 | Richard Oberdorf | Predictive Behavior Within Microbial Genetic Networks |
| 6/2/08 | Hesper Rego | Ultra-high resolution light microscopy with photoswitchable molecules |
| 6/9/08 | Ben Rhau | Spatial regulators for bacterial cell division self organize into surface waves in vitro |
| 6/23/08 | Maya Chandru | Sliding Pores, Article: Surface mobility of postsynaptic AMPARs tunes synaptic transmission |
| 6/30/08 | Rebeca Choy | Monolayer purification: a rapid method for isolating protein complexes for single-particle electron microscopy |
| 7/7/08 | Laura Lavery | Social Integration of Robots into Groups of Cockroaches to Control Self-Organized Choices |
| 7/14/08 | Sai Duriseti | Nanoparticle-mediated cellular response is size-dependent |
| 7/21/08 | David Stanley | Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution |
| 7/28/08 | Sheel Dandekar | Robust, tunable biological oscillations from interlinked positive and negative feedback loops |
| 8/4/08 | Ryan Ritterson | Perceptual accuracy and conflicting effects of certainty on risk-taking behavior |
| 8/11/08 | Kris Kuchenbecker | Whispering-gallery-mode biosensing: Label-free detection down to single molecules |
| 8/18/08 | Reid Williams | TBA |
| 8/25/08 | Charles Biddle-Snead | TBA |
Academic Year 2007: | ||
| Date | Speaker | Topic |
| 9/25/06 | Chris Farady | The mechanism of inhibition of novel macromolecular inhibitors of membrane-type serine protease 1(MT-SP1) |
| 10/2/06 | Eli Groban | Towards a better understanding of two component systems: A mishmash of protein purification, genetic manipulation, and kinetics |
| 10/9/06 | Quincey Justman | Is bistability necessary to produce sustained oscillations? |
| 10/16/06 | Jeremy Nilmeier | Multiscale Monte Carlo Modeling: theory |
| 10/23/06 | Sam Pfaff | Biochemistry and structure of glucocorticoid receptor activation |
| 10/30/06 | Neema Salimi | Promiscuous PolyQ Proteins: Say that three times fast |
| 11/6/06 | Ben Sellers | Improving protein structure prediction using model systems |
| 11/13/06 | Jeremy Wilbur | Clathrin Assembly requires flexibility in the HIPs |
| 11/20/06 | Randy Wu | Nucleosome positions predicted through comparative genomics |
| 12/11/06 | Eli Zunder | A screen in yeast for inhibitor-resistant mutations in the P13K family |
| 12/18/06 | Alan Graves | Probing the boundaries of molecular docking with decoys and model systems |
| 1/8/07 | Caleb Bashor | TBA |
| 1/29/07 | Dave Eramian | Protein model building based on distantly related structures |
| 2/5/07 | Christian Cunningham | A Tale of Two DNAs: Single molecule studies on bacterial chromatin organization by H-NS protein |
| 2/12/07 | Liz Clarke | Getting along: Evolution of species interactions |
| 2/26/07 | Morri Feldman | A Pharmacology of translational balance |
| 3/5/07 | Molly Darragh | Broadening antibody specificity while maintaining optimal affinity |
| 3/12/07 | Peretz Partensky | A "silent" polymorphism in the MDR1 gene changes substrate specificity |
| 3/19/07 | Arjun Narayanan | Quantitative analysis of the activation mechanism of the multicomponent growth-factor receptor Ret |
| 3/26/07 | Greg Friedland | Some predictions left behind: Using computational protein design as input to experimental library selection |
| 4/2/07 | Matt Eames | Kirkland Brand Codons: Why? |
| 4/23/07 | Stephen Floor | Cypoviruses hide inside self-assembling polyhedra waiting for insects |
| 4/30/07 | Anselm Levskaya | Soluble Time: the three-protein circadian clock KaiABC |
| 5/7/07 | Bryant Chhun | Optical interrogation of neural circuitry using light-driven ion pumps |
| 5/14/07 | Deb Datta | An SCN9A channelopathy causes congenital inability to experience pain |
| 5/21/07 | Elisabeth Humphris | Selection Inversion: Forcing Antibiotic Interactions to Select Against Resistance |
| 6/4/07 | Liz Montabana | How Synaptotagmin Promotes Membrane Fusion |
| 6/11/07 | Chris McClendon | Dance of the Pin1 Domains: Dynamical NMR |
| 6/18/07 | Richard Oberdorf | Why Have Costly Sex? |
| 6/25/07 | Hesper Rego | Molecule by molecule: Light microscopy with subdiffraction resolution |
| 7/2/07 | Benjamin Rhau | A universal RNAi-based logic evaluator that operates in mammalian cells |
| 7/9/07 | Ian Harwood | Hooking Up In Sin |
| 7/16/07 | Ethan Mirsky | Advanced Counting |
| 7/23/07 | Charles Biddle-Snead & Maya Chandru | Avoid Probing the Brobe: Delivery of siRNA across the blood-brain barrier (Biddle-Snead) & Are you a Man or a Monkey? A rapidly evolved human RNA gene (Chandru) |
| 7/30/07 | Rebeca Choy & Sheel Dandekar | Electron cryotomography of immature HIV-1 virions reveals the structure of the CA and SP1 Gag shells (Choy) & Experimental and theoretical study of mitotic spindle orientation (Dandekar) |
| 8/6/07 | Sai Duriseti & Kris Kuchenbecker | SP1 as a novel scaffold building block for self-assembly nanofabrication of submicron enzymatic structures (Duriseti) & Picking Up the Pieces: A new fragment-based strategy for small molecule development (Kuchenbecker) |
| 8/13/07 | Laura Lavery & Ryan Ritterson | Probing transcription factor dynamics at the single-molecule level in a living cell (Lavery) & Beyond transfection to trans-speciation: Is your genome all it takes to re-create you? (Ritterson) |
| 8/20/07 | Reid Williams, Lim Lab | Adaptive mutations in bacteria: high rate and small effects |
BBC Journal Club
Academic Year 2009: | |||
| Date | Speaker 1 | Speaker 2 | |
| 9/23/08 | BBC Journal Club Organizational Meeting | ||
| 9/30/08 | Monica Tremont (Biophysics) | Michael Lopez (CCB) | Details |
Monica Tremont Electron Relay in Proteins Tryptophan-Accelerated Electron Flow Through Proteins. Shih C, Museth AK, Abrahamsson M, Blanco-Rodriguez AM, Di Bilio AJ, Sudhamsu J, Crane BR, Ronayne KL, Towrie M, Vlcek A, Richards JH, Winkler JR, Gray HB. Science 2008 Jun 27 320(5884):1760-2 Michael Lopez S-nitrosylation of the histone deacetylase 2 induces chromatin remodelling in neurons Nott, Alexi et al. S-nitrosylation of the histone deacetylase 2 induces chromatin remodelling in neurons. Nature. Advanced online publication, (2008). | |||
| 10/7/08 | Noah Ollikainen (Bioinformatics) | Gabe Rocklin (Biophysics) | Details |
Noah Ollikainen In vivo reprogramming of adult pancreatic exocrine cells to beta-cells Zhou Q, Brown J, Kanarek A, Rajagopal J, Melton DA. In vivo reprogramming of adult pancreatic exocrine cells to beta-cells. Nature advance online publication 27 August 2008. Gabe Rocklin Crowded, cell-like environment induces shape changes in aspherical protein Crowded, cell-like environment induces shape changes in aspherical protein. Dirar Homouz, Michael Perham, Antonios Samiotakis, Margaret S. Cheung, and Pernilla Wittung-Stafshede, PNAS August 19, 2008 vol. 105 no. 33 11754-11759 | |||
| 10/14/08 | Nicholas Hertz (CCB) | Adam Marko (Bioinformatics) | Details |
Nicholas Hertz A double S Shape Provides the Structural Basis for the Extraordinary Binding Specificity of Dscam Isoforms Michael R. Sawaya, Wof M. Wojtowicz, Ingemar Andre, Bin Qian, Wei Wu, David Baker, David Eisenberg, S. Lawrence Zipursky (2008). A double S Shape Provides the Structural Basis for the Extraordinary Binding Specificity of Dscam Isoforms. Cell 134, 1007-1018 Adam Marko It's all in your head: The Drosophila pheromone cVA activates a sexually dimorphic neural circuit Sandeep Robert Datta, Maria Luisa Vasconcelos, Vanessa Ruta, Sean Luo, Allan Wong, Ebru Demir, Jorge Flores, Karen Balonze, Barry J. Dickson & Richard Axel. The Drosophila pheromone cVA activates a sexually dimorphic neural circuit. Nature 452, 473-477 (27 March 2008) doi:10.1038/nature06808. http://www.nature.com/nature/journal/v452/n7186/full/nature06808.html | |||
| 10/21/08 | Cheryl Tajon (CCB) | Jennifer Hsiao (Biophysics) | Details |
Cheryl Tajon The effect of particle design on cellular internalization pathways Stephanie E. A. Gratton, Patricia A. Ropp, Patrick D. Pohlhaus, J. Christopher Luft, Victoria J. Madden, Mary E. Napier, and Joseph M. DeSimone. The effect of particle design on cellular internalization pathways. PNAS August 29, 2008 vol. 105 no. 33 1161311618. Jennifer Hsiao Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions "Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions." Guelen L, Pagie L, Brasset E, Meuleman W, Faza MB, Talhout W, Eussen BH, de Klein A, Wessels L, de Laat W, van Steensel B. Nature. 2008 Jun 12;453(7197):948-51. Epub 2008 May 7. | |||
| 10/28/08 | David Burkhardt (Biophysics) | Rebecca Maglathlin (CCB) | Details |
David Burkhardt The 3D Structure of the Immunoglobulin Heavy-Chain Locus: Implications for Long-Range Genomic Interactions S. Jhunjhunwala, M. van Zelm, M. Peak, S. Cutchin, R. Riblet, J. van Dongen, F. Grosveld, T. Knoch, C. Mur. The 3D Structure of the Immunoglobulin Heavy-Chain Locus: Implications for Long-Range Genomic Interactions. Cell, Volume 133, Issue 2, Pages 265-279. Rebecca Maglathlin "An Alternative Menaqinone Biosynthetic Pathway Operating in Microorganisms" "An Alternative Menaqinone Biosynthetic Pathway Operating in Microorganisms" Hiratsuka, et. al., Science, 321, 1670 (2008):DOI: 10.1126/science.1160446 | |||
| 11/4/08 | Bethany Simmons (Bioinformatics) | Jaline Gerardin (Biophysics) | Details |
Bethany Simmons Tissue deformation modulates twist expression to determine anterior midgut differentiation in Drosophila embryos Tissue deformation modulates twist expression to determine anterior midgut differentiation in Drosophila embryos. Desprat N, Supatto W, Pouille PA, Beaurepaire E, Farge E Dev Cell 2008 Sep 15(3):470-7 Jaline Gerardin A mechanism for asymmetric segregation of age during yeast budding Shcheprova Z, Baldi S, Frei SB, Gonnet G, Barral Y. A mechanism for asymmetric segregation of age during yeast budding. Nature. 2008 Aug 7;454(7205):728-34. | |||
| 11/18/08 | Brandon Butler (CCB) | Elaine Kirschke (Biophysics) | Details |
Brandon Butler Cathepsin L Proteolytically Processes Histone H3 During Mouse Embryonic Stem Cell Differentiation EM Duncan, TL Muratore-Schroeder, RG Cook, BA Garcia, J Shabanowitz, DF Hunt, and CD Allis. Cathepsin L Proteolytically Processes Histone H3 During Mouse Embryonic Stem Cell Differentiation. Cell, Volume 135, Issue 2, 284-294, 17 October 2008. doi:10.1016/j.cell.2008.09.055 Elaine Kirschke XPD Helicase Structures and Activities: Insights into the Cancer and Aging Phenotypes from XPD Mutations XPD Helicase Structures and Activities: Insights into the Cancer and Aging Phenotypes from XPD Mutations. Li Fan, Jill O. Fuss, Quen J. Cheng, Andrew S. Arvai, Michal Hammel, Victoria A. Roberts, Priscilla K. Cooper and John A. Taine. Cell, Vol 133, Issue 5, 30 May 2008 | |||
| 11/25/08 | Hannes Braberg (Biophysics) | Robin Aglietti (CCB) | Details |
Hannes Braberg Stepwise chromatin remodelling by a cascade of transcription initiation of non-coding RNA "Stepwise chromatin remodelling by a cascade of transcription initiation of non-coding RNAs". Kouji Hirota, Tomoichiro Miyoshi, Kazuto Kugou, Charles S. Hoffman, Takehiko Shibata & Kunihiro Ohta. Nature, Vol 456, 6 November 2008, doi:10.1038/nature07348. Robin Aglietti The Acidic Repetitive Domain of the Magnetospirillum gryphiswaldense MamJ Protein Displays Hypervariability but Is Not Required for Magnetosome Chain Assembly The Acidic Repetitive Domain of the Magnetospirillum gryphiswaldense MamJ Protein Displays Hypervariability but Is Not Required for Magnetosome Chain Assembly. André Scheffel and Dirk Schüler. Journal of Bacteriology, September 2007, p. 6437-6446, Vol. 189, No. 17. doi:10.1128/JB.00421-07 | |||
| 1/6/09 | Rand Miller (CCB) | Details | |
Rand Miller CASK Functions as a Mg2+-independent Neurexin Kinase CASK Functions as a Mg2+-independent Neurexin Kinase. Mukherjee, M. et al. Cell, Vol. 133, No. 2, April 18, 2008, p. 328-339 | |||
| 1/13/09 | Heather Newman (Biophysics) | Charlie Kehoe (Bioinformatics) | Details |
Heather Newman Label-Free Biomedical Imaging with High Sensitivity by Stimulated Raman Scattering Microscopy Christian W. Freudiger, Wei Min, Brian G. Saar, Sijia Lu, Gary R. Holtom, Chengwei He, Jason C. Tsai, Jing X. Kang, and X. Sunney Xie. Label-Free Biomedical Imaging with High Sensitivity by Stimulated Raman Scattering Microscopy. Science 322 (5909), 1857. (19 December 2008) [DOI:10.1126/science.1165758] Charlie Kehoe Structure and function of an RNase H domain at the heart of the spliceosome Vladimir Pena, Alexey Rozov, Patrizia Fabrizio, Reinhard Lührmann, and Markus C Wahl. Structure and function of an RNase H domain at the heart of the spliceosome. The EMBO Journal (2008) 27, 29292940, doi:10.1038/emboj.2008.209 Published online 9 October 2008 | |||
| 1/20/09 | George Peterson (Biophysics) | Xiuming Wong (CCB) | Details |
George Peterson Tomas-Loba A, Flores I, Fernandez-Marcos PJ, Cayuela ML, Maraver A, Tejera A, Borras C, Matheu A, Klatt P, Flores JM, Vina J, Serrano M, Blasco MA. Telomerase Reverse Transcriptase Delays Aging in Cancer-Resistant Mice. Cell 135 (2008), 609-622. Xiuming Wong Structural and Mechanistic Insights into STIM1-Mediated Initiation of Store-Operated Calcium Entry Structural and Mechanistic Insights into STIM1-Mediated Initiation of Store-Operated Calcium Entry. P Li, MJ Plevin, M Ikura. Cell, Volume 135, Issue 1, 110-122, 3 October 2008 | |||
| 1/27/09 | Peter Skewes-Cox (Bioinformatics) | Carrie Shiau (CCB) | Details |
Peter Skewes-Cox Antigenic variation in Giardia lamblia is regulated by RNA interference. Nature. 2008 Dec 11;456(7223):750-4 Carrie Shiau DNA Demethylation in Zebrafish Involves the Coupling of a Deaminase, a Glycosylase, and Gadd45. Rai, K. et al. Cell, Vol 135, No. 7, December 26, 2008, p. 1201-1212. | |||
| 2/3/09 | Joe Kliegman (Biophysics) | Chris Wen (Bioinformatics) | Details |
Joe Kliegman Sun et al. The structure of the phage T4 DNA packaging motor suggests a mechanism dependent on electrostatic forces. Cell (2008) vol. 135 (7) pp. 1251-62 Chris Wen Ashok Prasada,Julie Zikhermanb, Jayajit Dasa, Jeroen P. Roosec, Arthur Weissbd1 and Arup K. Chakrabortyaef1. Origin of the sharp boundary that discriminates positive and negative selection of thymocytes. PNAS January 13, 2009 vol. 106 no. 2 528-533 | |||
| 2/10/09 | Brittany Belin (Biophysics) | Jennifer Liu (CCB) | Details |
Brittany Belin Scott Smukalla, Marina Caldara, Nathalie Pochet, Anne Beauvais, Stephanie Guadagnini, Chen Yan, Marcelo D. Vinces, An Jansen, Marie Christine Prevost, Jean-Paul Latge, Gerald R. Fink, Kevin R. Foster, and Kevin J. Verstrepen. (2008) FLO1 Is a Variable Green Beard Gene that Drives Biofilm-like Cooperation in Budding Yeast. Cell 135(4), 726-737. Jennifer Liu A tunable synthetic mammalian oscillator. Nature 457, 309-312 (15 January 2009) | |||
| 2/17/09 | David Booth (Biophysics) | Jonathan Choy (CCB) | Details |
David Booth Byres E, et al. (4 Dec 2008) "Incorporation of a non-human glycan mediates human susceptibility to a bacterial toxin." Nature 456: 648-52. Jonathan Choy AMPK and PPARδ Agonists Are Exercise Mimetics. Narkar, V. A., et al (2008). AMPK and PPARδ Agonists Are Exercise Mimetics. Cell 134, 405-415. doi:10.1016/j.cell.2008.06.051 | |||
| 2/24/09 | Daniel Le (CCB) | Chris Fuller (Bioinformatics) | Details |
Daniel Le Yamagata K, Daitoku H, Takahashi Y, Namiki K, Hisatake K, Kako K, Mukai H, Kasuya Y, Fukamizu A. Arginine methylation of FOXO transcription factors inhibits their phosphorylation by Akt. Mol Cell. 2008 Oct 24;32(2):221-31. Chris Fuller Genotype, haplotype and copy-number variation in worldwide human populations. Jakobsson, M. et al. Nature vol 451, 908-1002. 2008 | |||
| 3/3/09 | Megan Riel-Mehan (CCB) | Geoffrey Rollins (Biophysics) | Details |
Megan Riel-Mehan Science 28 November 2008: Vol. 322. no. 5906, pp. 1387 - 1392. An Epigenetic Role for Maternally Inherited piRNAs in Transposon Silencing. Julius Brennecke, Colin D. Malone, Alexei A. Aravin, Ravi Sachidanandam, Alexander Stark, Gregory J. Hannon. Geoffrey Rollins Intersubunit coordination in a homomeric ring ATPase. Moffitt et al. Nature 457, 446-450 (2009). | |||
| 3/10/09 | Genevieve Erwin (Bioinformatics) | Charles Morgan (CCB) | Details |
Genevieve Erwin ChIP-seq accurately predicts tissue-specific activity of enhancers. Axel Visel, Matthew J. Blow, Zirong Li, Tao Zhang, Jennifer A. Akiyama, Amy Holt, Ingrid Plajzer-Frick, Malak Shoukry, Crystal Wright, Feng Chen, Veena Afzal, Bing Ren, Edward M. Rubin & Len A. Pennacchio. Nature Vol 457| 12 February 2009| doi:10.1038/nature07730 Charles Morgan Quantitive exploration of the catalytic landscape separating divergent plant sesquiterpene synthases". Nature Chemical Biology. October(2008) Vol. 4 Number 10. pg. 617-623. O'Maille et. al. | |||
| 3/31/09 | Russell Spitzer (Bioinformatics) | Edwin Rodriguez (Biophysics) | Details |
Russell Spitzer A stress-responsive RNA switch regulates VEGFA expression. Partho Sarothi Ray, Jie Jia, Peng Yao, Mithu Majumder, Maria Hatzoglou & Paul L. Fox Nature. 457. 915-919. 2009 Edwin Rodriguez Self-Sustained Replication of an RNA Enzyme. Science 323, 1229 (2009) Tracey A. Lincoln et al. | |||
| 4/7/09 | Emmanuel Yera (Bioinformatics) | Details | |
Emmanuel Yera A TARBP2 mutation in human cancer impairs microRNA processing and DICER1 function. Sonia A Melo, Santiago Ropero, Catia Moutinho, Lauri A Aaltonen, Hiroyuki Yamamoto, George A Calin, Simona Rossi, Agustin F Fernandez, Fatima Carneiro, Carla Oliveira, Bibiana Ferreira, Chang-Gong Liu, Alberto Villanueva, Gabriel Capella, Simo Schwartz Jr, Ramin Shiekhattar & Manel Esteller. Nature Genetics 41, 365 - 370 (2009) Published online: 15 February 2009 | doi:10.1038/ng.317 | |||
| 4/14/09 | Dan Lu (Biophysics) | Roxana Ordonez (Bioinformatics) | Details |
Dan Lu Julien F Ayroles et al. Systems genetics of complex traits in Drosophila melanogaster. Nat Genet (2009) vol. 41 (3) pp. 299 Roxana Ordonez Cohen et al. Dynamic proteomics of individual cancer cells in response to a drug. Science (2008) vol. 322 (5907) pp. 1511-6 | |||
| 4/21/09 | Andrew Wiser (CCB) | Henry Lin (Bioinformatics) | Details |
Andrew Wiser "Monomeric fluorescent timers that change color from blue to red report on cellular trafficking". Subach et al. Nature Chemical Biology (2009) Volume 5 Number 2 February 2009 118-126 Henry Lin Variants of the Antibody Herceptin That Interact with HER2 and VEGF at the Antigen Binding Site. Jenny Bostrom, Shang-Fan Yu, David Kan, Brent A. Appleton, Chingwei V. Lee, Karen Billeci, Wenyan Man, Franklin Peale, Sarajane Ross, Christian Wiesmann, Germaine Fuh. Science 323, 1610 (2009) | |||
| 4/28/09 | Samuel Myers (CCB) | Anthony Shiver (Biophysics) | Details |
Samuel Myers Histone h3 lysine 56 acetylation is linked to the core transcriptional network in human embryonic stem cells. Xie W, Song C, Young NL, Sperling AS, Xu F, Sridharan R, Conway AE, Garcia BA, Plath K, Clark AT, Grunstein M. Mol Cell. 2009 Feb 27;33(4):417-27. Anthony Shiver Nature Structural & Molecular Biology. Helix Sliding in the stalk coiled coil of dynein couples ATPase and microtubule binding Takashide Kon et al. Vol 16 numb 3 march 2009 | |||
| 5/5/09 | Joanna Lipinski (Bioinformatics) | Idelisse Ortiz Torres (CCB) | Details |
Joanna Lipinski Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis. Sabrina L. Spencer, Suzanne Gaudet, John G. Albeck, John M. Burke & Peter K. Sorger. (doi:10.1038/nature08012) Idelisse Ortiz Torres Selective Erasure of a Fear Memory Jin-Hee Han, Steven A. Kushner, Adelaide P. Yiu, Hwa-Lin (Liz) Hsiang, Thorsten Buch, Ari Waisman, Bruno Bontempi, Rachael L. Neve, Paul W. Frankland, and Sheena A. Josselyn (13 March 2009) Science 323 (5920), 1492. [DOI: 10.1126/science.1164139] | |||
| 5/12/09 | Ryan Gile (Bioinformatics) | Details | |
Ryan Gile Stretching Single Talin Rod Molecules Activates Vinculin Binding. Armando del Rio. Science (January 2009). | |||
| 5/19/09 | Linh Ho (CCB) | James Kraemer (Biophysics) | Details |
Linh Ho Linh Ho: AMPK regulates energy expenditure by modulating NAD+ metabolism and SIRT1 activity Nature 458, 1056-1060, 2009. James Kraemer Ligand-Dependent Equilibrium Fluctuations of Single Calmodulin Molecules. Jan Philipp Junker, Fabian Ziegler, and Matthias Rief. Science 30 January 2009: 633-637. | |||
| 5/26/09 | Rocco Varela (Bioinformatics) | Kiyoshi Egami (Biophysics) | Details |
Rocco Varela Rocco Varela: An inhibitor of NEDD8-activating enzyme as a new approach to treat cancer Nature. 2009 Apr 9;458(7239):732-6 | |||
| 6/2/09 | Make-Up Day | ||
Academic Year 2008: | |||
| Date | Speaker 1 | Speaker 2 | |
| 10/9/07 | Maya Chandru (Biophysics) | Brianna Burden (CCB) | Details |
Maya Chandru Multi-step pericellular proteolysis controls the transition from individual to collective cancer cell invasion. Wolf et al, Nat Cell Biol 2007 Aug 9 Brianna Burden Aptamer Displacement Identifies Alternative Small-Molecule Target Sites that Escape Viral Resistance amazaki et al, Cell: Chemistry and Biology 14, 804-812, 2007. | |||
| 10/16/07 | Jeremy Phillips (Bioinformatics) | Reid Williams (Biophysics) | Details |
Jeremy Phillips Two distinct modes of guidance signalling during collective migration of border cells. Bianco A, Poukkula M, Cliffe A, Mathieu J, Luque CM, Fulga TA, Rorth P. Nature. 2007 Jul 19;448(7151):362-5. Reid Williams Selection and evolution of enzymes from a partially randomized non-catalytic scaffold Seelig B, Szostak JW. Nature. 2007 Aug 16;448(7155):828-31. | |||
| 10/23/07 | Daniel Gray (CCB) | Rebeca Choy (Biophysics) | Details |
Daniel Gray Crystal Structure of an Ancient Protein: Evolution by Conformational Epistasis. Ortlund, Bridgham, Redinbo, Thornton. Science. 2007 Sep 14;317(5844):1544-8. Epub 2007 Aug 16. http://www.nature.com/nsmb/journal/v14/n9/abs/nsmb1280.html Rebeca Choy In vivo dynamics of RNA polymerase II transcription Xavier Darzacq, Yaron Shav-Tal, Valeria de Turris, Yehuda Brody, Shailesh M Shenoy, Robert D Phair & Robert H Singer. Nature Structural & Molecular Biology - 14, 796 - 806 (2007). | |||
| 10/30/07 | Charles Biddle-Snead (Biophysics) | Iana Serafimova (CCB) | Details |
Charles Biddle-Snead Array Tomography: A New Tool for Imaging the Molecular Architecture and Ultrastructure of Neural Circuits Kristina D. Micheva and Stephen J Smith. Neuron 55, 25â36, July 5, 2007 ª2007 Elsevier Inc. 25 Iana Serafimova Splicing factor SF3b as a target of the antitumor natural product pladienolide Yoshihiko Kotake1, Koji Sagane1, Takashi Owa, Yuko Mimori-Kiyosue, Hajime Shimizu, Mai Uesugi, Yasushi Ishihama, Masao Iwata & Yoshiharu Mizui. Nature Chemical Biology, Vol 3, Number 9, September 2007, p570 - 575. | |||
| 11/6/07 | Daniele Canzio (CCB) | David Stanley (Biophysics) | Details |
Daniele Canzio A motor that makes his own track: helicase unwinding of DNA: Single-Molecule Studies Reveal Dynamics of DNA unwinding by the Ring-Shaped T7 Helicase Cell 129, 1299-1309, June 29, 2007 David Stanley Dynamic Scaffolding of a G Protein-Coupled Signaling System Prashant Mishra, Michael Socolich, Mark A. Wall, Jennifer Graves, ZiFen Wang, and Rama Ranganathan. Cell, Vol 131, 80-92, 05 October 2007 | |||
| 11/13/07 | Kris Kuchenbecker (Biophysics) | Details | |
Kris Kuchenbecker Energetics and dynamics of SNAREpin folding across lipid bilayers. Nature Structural and Molecular biology. October 2007. | |||
| 11/20/07 | Laura Lavery (Biophysics) | Sheel Dandekar (Biophysics) | Details |
Laura Lavery High-afinity single-domain binding proteins with a binary-code interface. Akiko Koidea, Ryan N. Gilbreth, Kaori Esaki, Valentina Tershko, Shohei Koide. PNAS, Vol 104, No. 16. April 17, 2007. http://www.pnas.org/cgi/content/full/104/16/6632 Sheel Dandekar Ordered phosphorylation governs oscillation of a three-protein circadian clock Rust MJ, Markson JS, Lane WS, Fisher DS, O'Shea EK. Science. 2007 Nov 2;318(5851):809-12. Epub 2007 Oct 4. | |||
| 1/8/08 | Jonathan Choy (CCB) | Sai Duriseti (Biophysics) | Details |
Jonathan Choy Design of Cyclic Peptides That Bind Protein Surfaces with Antibody-Like Affinity Steven W. Millward, Stephen Fiacco, Ryan J. Austin, and Richard W. Roberts (2007) ACS Chem. Biol. 2, 625-634. Sai Duriseti A Simple DNA-Based Translation System Alejandra V. Garibotti, Shiping Liao, and Nadrian C. Seeman. Nano Letters 2007 Vol. 7, No. 2. 480-483. | |||
| 1/15/08 | Ryan Ritterson (Biophysics) | Charles Kehoe (Bioinformatics) | Details |
Ryan Ritterson Retroposons: DNA parasites or facilitators? A CORE-SINE retroposon as a highly conserved neuronal enhancer. Ancient Exaptation of a CORE-SINE Retroposon into a Highly Conserved Mammalian Neuronal Enhancer of the Proopiomelanocortin Gene. Santangelo AM, de Souza FSJ, Franchini LF, Bumaschny VF, Low MJ, et al. PLoS Genetics Vol. 3, No. 10, e166doi:10.1371/journal.pgen.0030166 http://genetics.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pgen.0030166 Charles Kehoe Functional specificity among ribosomal proteins regulates gene expression. Komili S, Farny NG, Roth FP, Silver PA.Cell. 2007 Nov 2;131(3):450-1. | |||
| 1/22/08 | David Booth (Biophysics) | Details | |
David Booth Solvent Tuning of Electrochemical Potentials in the Active Sites of HiPIP Versus Ferredoxin Solvent Tuning of Electrochemical Potentials in the Active Sites of HiPIP Versus Ferredoxin Abhishek Dey, Francis E. Jenney, Jr., Michael W. W. Adams, Elena Babini, Yasuhiro Takahashi, Keiichi Fukuyama, Keith O. Hodgson, Britt Hedman, Edward I. Solomon, Science, 318, 1464-8, 2007 | |||
| 1/29/08 | Joseph Kliegman (Biophysics) | Michael Lopez (CCB) | Details |
Joseph Kliegman Minor Details of Transcription Factor Specificity Rohit Joshi, Jonathan M. Passner, Remo Rohs, Rinku Jain, Alona Sosinsky, Michael A. Crickmore, Vinitha Jacob, Aneel K. Aggarwal, Barry Honig and Richard S. Mann. Functional Specificity of a Hox Protein Mediated by the Recognition of Minor Groove Structure, CellVolume 131, Issue 3, , 2 November 2007, Pages 530-543. Michael Lopez A GluR1-cGKII Interaction Regulates AMPA Receptor Trafficking Yafell Serulle, Shuang Zhang, Ipe Ninan, Daniela Puzzo, Maria McCarthy, Latika Khatri, Ottavio Arancio, and Edward B. Ziff Neuron 56, 670�âïÿýïÿý688, November 21, 2007 | |||
| 2/5/08 | Noah Ollikainen (Bioinformatics) | George Peterson (Biophysics) | Details |
Noah Ollikainen Somewhere over the brainbow Jean Livet, Tamily A. Weissman, Hyuno Kang, Ryan W. Draft, Ju Lu, Robyn A. Bennis, Joshua R. Sanes & Jeff W. Lichtman. Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system. Nature. 450, 56-62 (2007). http://www.nature.com/nature/journal/v450/n7166/abs/nature06293.html George Peterson Nicotinamide Riboside Promotes Sir2 Silencing and Extends Lifespan via Nrk and Urh1/Pnp1/Meu1 Pathways to NAD+ Belenky P, Racette FG, Bogan KL, McClure JM, Smith JS, Brenner C. Cell 129: 473-84 (2007) http://www.cell.com/content/article/abstract?uid=PIIS009286740700390X | |||
| 2/12/08 | Rebecca Maglathlin (CCB) | Heather Newman (Biophysics) | Details |
Rebecca Maglathlin Structural Rearrangements of NR1/NR2A NMDA Receptors during Allosteric Inhibition Marc Gielen, Anne Le Goff, David Stroebel, Jon W. Johnson, Jacques Neyton, and Pierre Paoletti. Neuron 57, 80�93, January 10, 2008 Heather Newman Multicolor Super-Resolution Imagining with Photo-switchable Fluorescent Probes Multicolor Super-Resolution Imagining with Photo-switchable Fluorescent Probes Mark Bates et al., Science 317, 1749 (2007). | |||
| 2/19/08 | Peter Skewes-Cox (Bioinformatics) | David Burkhardt (Biophysics) | Details |
Peter Skewes-Cox Will newly identified host factors exploited by HIV make good drug targets? "Identification of Host Proteins Required for HIV Infection Through a Functional Genomic Screen," Abraham L. Brass, Derek M. Dykxhoorn, Yair Benita, Nan Yan, Alan Engelman, Ramnik J. Xavier, Judy Lieberman, Stephen J. Elledge. Science, 2008 Jan 10 http://www.sciencemag.org/cgi/content/abstract/1152725v David Burkhardt Switching from repression to activation: microRNAs can up-regulate translation. Vasudevan S, Tong Y, Steitz JA, " Switching from repression to activation: microRNAs can up-regulate translation.", Science 2007 Dec 21 | |||
| 2/26/08 | Hannes Braberg (Biophysics) | Rand Miller (CCB) | Details |
Hannes Braberg High-content single-cell drug screening with phosphospecific flow cytometry Peter O Krutzik, Janelle M Crane, Matthew R Clutter and Garry P Nolan. Nature Chemical Biology 4, 132-142 (2007) doi:10.1038/nchembio.2007.59 Rand Miller Systemic Leukocyte-Directed siRNA Delivery Revealing Cyclin D1 as an Anti-Inflammatory Target Peer, D., Park, E. J., Morishita, Y., Carman, C. V., Shimaoka, M, "Systemic Leukocyte-Directed siRNA Delivery Revealing Cyclin D1 as an Anti-Inflammatory Target," /Science/, 319, 627-630, (2008). DOI: 10.1126/science.1149859 | |||
| 3/4/08 | Nicholas Hertz (CCB) | Elaine Kirschke (Biophysics) | Details |
Nicholas Hertz A Comprehensive Profile of Brain Enzymes that Hydrolyze the Endocannabinoid 2-Arachidonoylglycerol Blankman, J.L., Simon, G.M., Cravatt, B.F. (2007). A Comprehensive Profile of Brain Enzymes that Hydrolyze the Endocannabinoid 2-Arachidonoylglycerol. Chem. Biol. 14, 1347-1356 Elaine Kirschke Activation of the Chaperone Hsp26 Is Controlled by the Rearrangement of Its Thermosensor Domain T. Franzmann, P. Menhorn, S. Walter, and J. Buchner. (2008) Activation of the Chaperone Hsp26 Is Controlled by the Rearrangement of Its Thermosensor Domain. Molecular Cell, Vol 29, 207-216, 01 | |||
| 3/11/08 | Bethany Simmons (Bioinformatics) | Kiyoshi Egami (Biophysics) | Details |
Bethany Simmons Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function. Lecuyer E, Yoshida H, ..., Tomancak P, Krause HM Cell 2007 Oct 5 131(1):174-87 Kiyoshi Egami Glycan topology determines human adaptation of avian H5N1 virus hemagglutinin. Chandrasekaran A, Srinivasan A, Raman R, Viswanathan K, Raguram S, Tumpey TM, Sasisekharan V, Sasisekharan R. Nat Biotechnol. 2008 Jan;26(1):107-13. Epub 2008 Jan 6. | |||
| 4/1/08 | Brandon Butler (CCB) | Jaline Gerardin (Biophysics) | Details |
Brandon Butler A beta-arrestin 2 Signalling Complex Mediates Lithium Action on Behavior Jean-Martin Beaulieu et al. Cell, 132, 125-136, Jan 11, 2008. Jaline Gerardin Direct observation of hierarchical folding in single riboswitch aptamers Greenleaf WJ, Frieda KL, Foster DAN, Woodside MT, Block SM. Direct observation of hierarchical folding in single riboswitch aptamers. Science. 2008 Feb 1;319(5863):630-3. | |||
| 4/8/08 | Carrie Shiau (CCB) | Adam Marko (Bioinformatics) | Details |
Carrie Shiau Transcriptional repression mediated by repositioning of genes to the nuclear lamina Reddy, K. L. et al. Transcriptional repression mediated by repositioning of genes to the nuclear lamina. Nature 452, 243 247 (2008). Adam Marko Computational Enzyme Design Lin Jiang, Eric A. Althoff, Fernando R. Clemente, Lindsey Doyle, Daniela Röthlisberger, Alexandre Zanghellini, Jasmine L. Gallaher, Jamie L. Betker, Fujie Tanaka, Carlos F. Barbas, III, Donald Hilvert, Kendall N. Houk, Barry L. Stoddard, David Baker. De Novo Computational Design of Retro-Aldol Enzymes. Science 7 March 2008: Vol. 319. no. 5868, pp. 1387 - 139. DOI: 10.1126/science.1152692 | |||
| 4/15/08 | Jennifer Hsiao (Biophysics) | Jennifer Liu (CCB) | Details |
Jennifer Hsiao Hydrodynamic Flow-Mediated Protein Sorting on the Cell Surface of Trypanosomes Markus Engstler, Thomas Pfohl, Stephan Herminghaus, Michael Boshart, Geert Wiegertjes, Niko Heddergott, and Peter Overath. Cell 131, 505515, November 2, 2007 Jennifer Liu Preserving cell shape under environmental stress Boaz Cook, Robert W Hardy, William B McConnaughey, Charles S Zuker. Nature 452, 361-364 (20 March 2008), doi:10.1038/nature06603 | |||
| 4/22/08 | Gabriel Rocklin (Biophysics) | Cheryl Tajon (CCB) | Details |
Gabriel Rocklin Integrating high-content screening and ligand-target prediction to identify mechanism of action Young, DW et al. Integrating high-content screening and ligand-target prediction to identify mechanism of action. Nature Chemical Biology 4:1 Jan 2008 Cheryl Tajon Near-Infrared Resonant Nanoshells for Combined Optical Imaging and Photothermal Cancer Therapy Andre´ M. Gobin, Min Ho Lee, Naomi J. Halas, William D. James, Rebekah A. Drezek, and Jennifer L. West. Near-Infrared Resonant Nanoshells for Combined Optical Imaging and Photothermal Cancer Therapy. Nano Letters, 2007, vol. 7, no. 7, 1929-34. | |||
| 4/29/08 | Brittany Belin (Biophysics) | Xiu Ming Wong (CCB) | Details |
Brittany Belin Structural basis of membrane invagination by F-BAR domains Frost A, Perera R, Roux A, Spasov K, Destaing O, Egelman EH, De Camilli P, Unger VM. (2008) Structural basis of membrane invagination by F-BAR domains. Cell 132(5):807-17. Xiu Ming Wong Ran-Binding Protein 3 Phosphorylation Links the Ras and PI3-Kinase Pathways to Nucleocytoplasmic Transport. Sang-Oh Yoon, Sejeong Shin, Yuzhen Liu, Bryan A. Ballif, Michele S. Woo, Steven P. Gygi, and John Blenis, Ran-Binding Protein 3 Phosphorylation Links the Ras and PI3-Kinase Pathways to Nucleocytoplasmic Transport. Molecular Cell, Volume 29, Issue 3, 15 February 2008, Pages 362-375. | |||
| 5/6/08 | Monica Tremont (Biophysics) | Christopher Wen (Bioinformatics) | Details |
Monica Tremont Allosteric cooperativity in protein kinase A Masterson, L. Rl et al. Allosteric cooperativity in protein kinase A. Proc. Nat. Acad. Sci. U.S.A. 105(2), 506-511 (2008). http://www.pnas.org/cgi/reprint/105/2/506 Christopher Wen 1. Membrane proteins of the endoplasmic reticulum induce high-curvature tubules. Hu J, Shibata Y, Voss C, Shemesh T, Li Z, Coughlin M, Kozlov MM, Rapoport TA, Prinz WA. Membrane proteins of the endoplasmic reticulum induce high-curvature tubules. Science. 2008 Feb 29;319(5867):1247-50 | |||
| 5/13/08 | Marlisa Pillsbury (CCB) | Robin Aglietti (CCB) | Details |
Marlisa Pillsbury Concurrent Fast and Slow Cycling of a Transcriptional Activator at an Endogenous Promoter Karpova,T, Kim, MJ, Spriet, C, Nalley, K, Stasevich, TJ, Kherrouche, Z, Heliot, L, McNally JG. Concurrent Fast and Slow Cycling of a Transcriptional Activator at an Endogenous Promoter. Science 25 January 2008: Vol. 319. no. 5862, pp. 466 - 469. DOI: 10.1126/science.1150559 Robin Aglietti Structural Basis for Signal-Sequence Recognition by the Translocase Motor SecA as Determined by NMR Ioannis Gelis, Alexandre M.J.J. Bonvin, Dimitra Keramisanou, Marina Koukaki, Giorgos Gouridis, Spyridoula Karamanou, Anastassios Economou, and Charalampos G. Kalodimos. Structural Basis for Signal-Sequence Recognition by the Translocase Motor SecA as Determined by NMR. Cell, Vol 131, 756-769, 16 November 2007 | |||
Academic Year 2007: | |||
| Date | Speaker 1 | Speaker 2 | |
| 10/10/06 | Segun Williams (CCB) | Stephen Floor (Biophysics) | |
| 10/17/06 | Michelle Dimon (Bioinformatics) | Ethan Mirsky (Biophysics) | Details |
Michelle Dimon DNA Sequences Predict Packaging Segal E, Fondufe-Mittendorf Y, Chen L, Thastrom AC, Field Y, Moore IK, Wang JPZ, Widome J. A genomic code for nucleosome positioning. Nature 17:442 (7104), 772 (2006) Ethan Mirsky Oceanic Gene Pooling Lindell, D. et al.â¯Photosynthesis genes in marine viruses yield proteins during host infection. Nature. 438(7064): 86 (2005) | |||
| 10/24/06 | Hesper Rego (Biophysics) | Karin Buser (CCB) | |
| 10/31/06 | Rafaela Ferreira (CCB) | Michael Cary (Bioinformatics) | Details |
Michael Cary The first genome-wide map of DNA methylation Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SW, Chen H, Henderson IR, Shinn P, Pellegrini M, Jacobsen SE, Ecker JR. Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. Cell 126(6): 1189 (2006) | |||
| 11/7/06 | Benjamin Rhau (Biophysics) | Andy MacKinnon (CCB) | Details |
Benjamin Rhau Computational redesign of endonuclease DNA binding and cleavage specificity. Ashworth J, Hayranek JJ, Duarte CM, Sussman D, Monnat RJ Jr., Stoddard BL, Baker D. Nature. 2006 Jun 1;441(7093):656-9. Andy MacKinnon A Proposed Twisting Mechanism of Dynamin During Membrane Fission Roux, Aurelien, Uyhazi, Katherine, Frost, Adam, De Camilli, Pietro. GTP-dependent twisting of dynamin implicates constriction and tension in membrane fission. Nature.⯠441: 528 (2006) | |||
| 11/14/06 | Colin Smith (Bioinformatics) | Bryant Chhun (Biophysics) | Details |
Colin Smith Taking turns with the whip Leake MC, Chandler JH, Wadhams GH, Bai F, Berry RM, Armitage JP. Stoichiometry and turnover in single, functioning membrane protein complexes. Nature 443(7109):355 (2006) | |||
| 11/21/06 | Chris McClendon (Biophysics) | Mark Borja (CCB) | |
| 1/9/07 | Liz Montabana (Biophysics) | David Barkan (Bioinformatics) | Details |
David Barkan Imitation by epidermal growth factor receptor is the sincerest form of flattery Zhang et al. An allosteric mechanism for activation of the kinase domain of epidermal growth factor receptor. Cell. 125 (6):1137-49. (2006) | |||
| 1/16/07 | Julie Zorn (CCB) | Richard Oberdorf (Biophysics) | |
| 1/23/07 | Deb Datta (Biophysics) | Brandon Tavshanjian (CCB) | |
| 1/30/07 | Beth Apsel (CCB) | Leonard Apeltsin (Bioinformatics) | Details |
Leonard Apeltsin Computer Tobacco Mosaic Viruses: Engineering a Digital Memory Device from Biological Parts Tseng, R.J. Tsai, C. Ma, L. Ouyang, J. Ozkan C.S. Yang, Y. Digitalmemory device based on tobacco mosaic virus conjugated with nanoparticles. Nature Nanotechnology. 1, 72-77. (2006) | |||
| 2/6/07 | Emily Crawford (CCB) | Charles Biddle-Snead (Biophysics) | |
| 2/13/07 | Jeremy Phillips (Bioinformatics) | Maya Chandru (Biophysics) | Details |
Jeremy Phillips A noise-excitable circuit induces competence in B. subtilis Suel GM, Garcia-Ojalvo J, Liberman LM, Elowitz MB. An excitable gene regulatory circuit induces transient cellular differentiation. Nature. 440(7083):545-50. (2006) | |||
| 2/20/07 | Ryan Ritterson (Biophysics) | Briana Burden (CCB) | |
| 2/27/07 | Daniel Gray (CCB) | David Stanley (Biophysics) | |
| 3/6/07 | Marlisa Pillsbury (CCB) | David Stanley (Biophysics) | |
| 3/13/07 | Reid Williams (Biophysics) | Daniele Canzio (CCB) | |
| 3/20/07 | Laura Lavery (Biophysics) | Kimberly Erickson (CCB) | |
| 4/3/07 | Iana Serafimova (CCB) | Kris Kuchenbecker (Biophysics) | Details |
Iana Serafimova Live-cell imaging of enzyme-substrate interaction reveals spatial regulation of PTP1B. Yudushkin IA, Schleifenbaum A., Kinkhabwala A, Neel BG, Schultz C, Bastiaens PI. European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, D-69117 Heidelberg, Germany. Kris Kuchenbecker Coupling substrate and ion binding to extracellular gate of a sodium-dependent aspartate transporter. Boudker O, Ryan RM, Yernool D, Shimamoto K, Gouaux E. Science. 2007 Jan 5;315(5808):115-9. | |||
| 4/10/07 | Sheel Dandekar (Biophysics) | Rebeca Choy (Biophysics) | Details |
Rebeca Choy From Swimming to Walking with a Salamander Robot Driven by a Spinal Cord Model Auke Jan Ijspeert,1* Alessandro Crespi,1 Dimitri Ryczko,2,3 Jean-Marie Cabelguen2,3. Science 9 March 2007: Vol. 315. no. 5817, pp. 1416 - 1420 DOI: 10.1126/science.1138353 | |||
Biophysics / CCB Formal Seminars
Thursdays, GH Auditorium 12:00-1:00, Simulcast to S161 Parnassus
Academic Year 2009: | |||
| Date | Speaker | Topic | Host |
| 10/2/08 | David Savage | Clements Talk: The Carbon Cycle at a Molecular Level: Design Principles of Cyanobacterial and Yeast Metabolism | TBA |
| 10/16/08 | Jamie Williamson, Scripps | Ribosome assembly: watching a machine assemble in vitro and in cells using mass spectrometry | S. Floor |
| 10/23/08 | Bruce Cohen, LBNL-Biological Nanostructures Facility of the Molecular Foundry | Smart Nanoparticles and the Future of Bioimaging | Lily Jan |
| 10/30/08 | Ruben Gonzalez, Columbia | Coupling of ribosome and tRNA dynamics during translation elongation | TBA |
| 11/13/08 | Sharad Ramanthan, Harvard | "Deforming signaling networks: using evolutionary analyses to re-wire kinase pathways." | H. El-Samad |
| 11/20/08 | Jean-Louis Reymond, Univ. of Berne Switzerland | "Exploration of Chemical Space for Drug Discovery by Database Generation" | B. Shoichet |
| 12/11/08 | A. Joshua Wand, University of Pennsylvania | The dark energy of proteins: Conformational entropy and its contribution to molecular recognition by proteins | C. Mcclendon |
| 1/15/09 | James Chou, Harvard | The Proton Channels of Influenza Virus | John Gross |
| 1/22/09 | Anand Asthagiri, Cal Tech | "From molecular networks to multicellular phenotypes" | Hana El-Samad |
| 1/29/09 | Tom Muir, Rockefeller | Testing the Histone Code Hypothesis Using Synthesis | TBA |
| 2/12/09 | Richard Friesner, Columbia | Computational Modeling of Protein-Ligand Interactions: Successes, Challenges, and Prospects. | Matt Jacobson |
| 2/19/09 | Chris Miller, Brandeis | Chloride transporters and chloride channels all mixed up | Dan Minor |
| 3/12/09 | Bryan Roth, UNC, Chapel Hill | Synthetic and chemical biological approaches for modulating neuronal signaling in vivo | Brian Shoichet |
| 3/19/09 | James Chen, Stanford | Chemical probes of embryonic signaling and patterning | TBA |
| 4/2/09 | Joachim Frank, NYU | Ribosomal Dynamics during Translation | Rebeca Choy |
| 4/16/09 | Wes Sundquist, University of Utah | The Biochemistry of HIV Budding | Alkan Frankel |
| 4/23/09 | Vern Schramm, Albert Einstein College of Medicine | Enzymatic Transition States: Drugs and Dynamics. | Danica Galanic Fujimori |
| 4/30/09 | Deborah Hung, Harvard | TBA | TBA |
| 5/14/09 | TBA | Braisted Lecture | TBA |
| 5/21/09 | Annelise Barron, Stanford | Robust, non-natural peptoid mimics of antimicrobial peptides for potent, selective bacterial pathogen killing | Ken Dill |
| 5/28/09 | Andy McCammon, UCSD | TBA | TBA |
Academic Year 2008: | |||
| Date | Speaker | Topic | Host |
| 10/11/07 | Nick Endres, UC Berkeley | Clements Talk: Using artificial lipid membranes to gain insights into the structure and function of signaling proteins in the EGFR/Ras signaling network | D. Agard |
| 10/18/07 | Justin Gallivan, Emory University | Reprogramming Bacteria with Small Molecules and RNA | P. England |
| 10/25/07 | Jack Szostak, Harvard Medical School |
Braisted Lecture: Towards the Design and Synthesis of an Artificial Cell Please note: this talk will be held at 4:00pm |
C. Craik and J. Wells |
| 11/1/07 | Peter Wright, Scripps | Exploring the protein energy landscape: Disorder, dynamics, and protein function | S. Miller |
| 11/15/07 | Paul Hergenrother, University of Illinois | Using small molecules to identify novel targets for the treatment of cancer | J. Taunton |
| 11/29/07 | David Baker, U Washington | Novel enzyme catalysts, rapid structure determination, and pushing the limits of folding and design with a multiplayer online computer game | J. Wells |
| 12/13/07 | David Deamer, UC Santa Cruz | Nanopore analysis of DNA | K. Dill |
| 12/20/07 | Lewis Kay, University of Toronto | Seeing the invisible by solution NMR spectroscopy | T. James |
| 1/3/08 | Rob Phillips, Caltech | How Cells Decide What to Eat and Where to Go | W. Marshall |
| 1/10/08 | Tom Knight, MIT | TBA | R. Williams |
| 1/17/08 | Tom Wandless, Stanford | A General Solution to the "Problem" of Chemical Genetics | J. Taunton |
| 1/24/08 | Gaudenz Danuser, Scripps | Integration of mechanical and chemical signals in cell migration deciphered by global fluctuation analysis | W. Marshall |
| 2/14/08 | Eric Siggia, Rockefeller University | Predicting the course of evolution | H. Li |
| 2/21/08 | Susan Marqusee, UC Berkeley | TBA | K. Dill |
| 2/28/08 | James Inglese, NIH Chemical Genomics Center | Integrative Technologies Enabling Chemistry and Biology as a Public Resource for Chemical Probe and Drug Discovery | B. Shoichet |
| 3/13/08 | Gavin MacBeath, Harvard University | TBA | TBA |
| 3/20/08 | Ned Wingreen, Princeton | Modeling the chemotaxis network of E. coli | C. Tang |
| 4/17/08 | Tudor Oprea, University of New Mexico | From Digital to Experimental Bioactivity: Exploring novel estrogen receptors | B. Shoichet |
| 4/24/08 | Richard Ebright, Rutgers | Single-molecule analysis of transcription | G. Narlikar |
| 5/1/08 | Vishva Dixit, Genentech, Inc. | The Inflammasome & Deubiquitinases in Innate Immune Signaling | J. Wells |
| 5/15/08 | Rachel Brem, UC Berkeley | Expression variation and regulatory feedback | K. Dill |
| 5/22/08 | Jagesh Shah, Harvard Medical School | Biophysical measurements of mitotic checkpoint signaling: How cells prevent chromosome loss | W. Marshall |
| 5/27/08 | Gary Ruvkun, Harvard University | TBA | TBA |
| 5/29/08 | Brian Chait, Rockefeller University | Protein Interactions as a Window into Cellular Function | A. Krutchinsky |
| 6/5/08 | Gerald Crabtree, Stanford | Designing small molecules to regulate protein interactions | TBA |
Academic Year 2007: | |||
| Date | Speaker | Topic | Host |
| 10/12/06 | Mathew Francis, UC Berkeley | New chemical tools for site-selective protein modification | P. England |
| 10/19/06 | Adrian Keatinge-Clay, UCSF | Dissecting, deciphering, and designing polyketide assembly lines | R. Stroud |
| 10/26/06 | Christopher Walsh, Harvard | Andrew Braisted Lecture, Halogenases: Natural product tailoring enzymes | C. Craik |
| 11/2/06 | Ron Weiss, Princeton | Synthetic biology: from bacteria to stem cells | C. Voigt |
| 11/16/06 | Jay Keasling, UC Berkeley | Engineering microorganisms for production of inexpensive, effective, anti-malarial drugs | C. Craik |
| 11/30/06 | Sarah O'Connor, MIT | Biosynthesis of new alkaloids in periwinkle | K. Shokat |
| 12/14/06 | Maurizio Pellecchia, Burnham Institute | A million little pieces: Fragment based approaches to drug discovery | M. Jacobson |
| 1/11/07 | David Weitz, Harvard | Reconstituted networks as models of cell mechanics | W. Marshall |
| 1/18/07 | Richard H. Kramer, UC Berkeley | Engineering light-activated ion channels for remote control of neuronal activity | R. Edwards |
| 1/25/07 | Edward Egelman, University of Virginia | Polymorphic perversity in polymers: The biological role of multiple subunit interfaces in helical filaments | D. Mullins |
| 2/1/07 | Christina Smolke, Caltech | Engineering molecular sensors for probing and programming cellular systems | H. El-Samad |
| 2/22/07 | Alice Ting, MIT | New protein labeling methodology and application to single molecule imaging of receptor trafficking with quantum dots | J. Wells |
| 3/1/07 | Lorena Beese, Duke | An integrated view of DNA polymerization and repair | R. Stroud |
| 3/15/07 | Wilfred van der Donk, University of Illinois | Chemistry and biology of ianthionine synthesis | J. Taunton |
| 4/12/07 | David Tirrell, California Institute of Technology | Non-canonical amino acids in protein engineering and proteomic analysis | P. England |
| 4/19/07 | Brenda Bass, University of Utah | dsRNA binding proteins in RNA editing and RNA interference | J. Gross |
| 4/26/07 | Adrian Gross, Northwestern | Structural aspects of potassium channel function | B. Shoichet |
| 5/10/07 | Pei Zhou, Duke University Medical Center | From novel antibiotics to fast NMR | J. Gross |
| 5/17/07 | Melissa Jurica, UCSC | Spliceosome structure by cryo-EM reconstruction | G. Narlikar |
| 5/24/07 | Phil Baran, Scripps | The catalytic cycle of discovery in total synthesis | A. Renslo |
| 5/31/07 | William Bialek, Princeton | Physics problems in early embryonic development | R. Fletterick |
| 6/7/07 | Luc Jaeger, UC Santa Barbara | Exploring folding, assembly and design principles of RNA as a proto-language | A. Frankel |