A Celebration of Faculty Achievement
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Single-Molecule Biophysics of Dna Bending: Looping and Unlooping
SINGLE-MOLECULE BIOPHYSICS OF DNA BENDING: LOOPING AND UNLOOPING A Dissertation Presented to The Academic Faculty by Tung T. Le In Partial Fulfillment Of the Requirements for the Degree Doctor of Philosophy in the School of Physics Georgia Institute of Technology August 2015 Copyright © Tung T. Le 2015 SINGLE-MOLECULE BIOPHYSICS OF DNA BENDING: LOOPING AND UNLOOPING Approved by: Professor Harold Kim, Advisor Professor James Gumbart School of Physics School of Physics Georgia Institute of Technology Georgia Institute of Technology Professor Daniel Goldman Professor Loren Williams School of Physics School of Chemistry and Biochemistry Georgia Institute of Technology Georgia Institute of Technology Professor Jennifer Curtis Date Approved: April 09, 2015 School of Physics Georgia Institute of Technology A dedication to my father, with love. ACKNOWLEDGEMENTS First, I would like to give my highest appreciation to my advisor, Dr. Harold D. Kim, for his enduring guidance and generous support to my research during the graduate years. He has given me a unique opportunity to work independently and judge things in a scientific manner. I would like to thank my previous advisor, Dr. Toan Nguyen, for his great mentor and support during my first year at Georgia Tech. I would also like to extend my appreciation to my committee members: Dr. Daniel Goldman, Dr. Jennifer Curtis, Dr. James Gumbart, and Dr. Loren Williams, for reading my thesis and giving me valuable comments. I want to thank Dr. Rasesh Parikh and other members of the Kim's lab for their kindness. Outside the lab, I would like to give thanks to many people, my dear friends (Phuong Doan, Tien Hoang, Phuong Hoang) and many others in the Vietnamese Student Associa- tions (VSA) in Atlanta, and my close friends at home (Vuong Linh Tran, Duy Nguyen) for their love and friendship. -
2019 Annual Report
BECKMAN CENTER 279 Campus Drive West Stanford, CA 94305 650.723.8423 Stanford University | Beckman Center 2019 Annual Report Annual 2019 | Beckman Center University Stanford beckman.stanford.edu 2019 ANNUAL REPORT ARNOLD AND MABEL BECKMAN CENTER FOR MOLECULAR AND GENETIC MEDICINE 30 Years of Innovation, Discovery, and Leadership in the Life Sciences CREDITS: Cover Design: Neil Murphy, Ghostdog Design Graphic Design: Jack Lem, AlphaGraphics Mountain View Photography: Justin Lewis Beckman Center Director Photo: Christine Baker, Lotus Pod Designs MESSAGE FROM THE DIRECTOR Dear Friends and Trustees, It has been 30 years since the Beckman Center for Molecular and Genetic Medicine at Stanford University School of Medicine opened its doors in 1989. The number of translational scientific discoveries and technological innovations derived from the center’s research labs over the course of the past three decades has been remarkable. Equally remarkable have been the number of scientific awards and honors, including Nobel prizes, received by Beckman faculty and the number of young scientists mentored by Beckman faculty who have gone on to prominent positions in academia, bio-technology and related fields. This year we include several featured articles on these accomplishments. In the field of translational medicine, these discoveries range from the causes of skin, bladder and other cancers, to the identification of human stem cells, from the design of new antifungals and antibiotics to the molecular underpinnings of autism, and from opioids for pain -
Journal of Virology Volume 68 * April 1994 * Number 4
JOURNAL OF VIROLOGY VOLUME 68 * APRIL 1994 * NUMBER 4 Arnold J. Levine, Editor in Chief (1994) Vincent R. Racaniello, Editor (1997) Princeton University Columbia University Princeton, N.J. Peter M. Howley, Editor (1998) New York, N.Y Harvard Medical School John M. Coffin, Editor (1996) Boston, Mass. Thomas E. Shenk, Editor (1994) Tufts University Medical School Princeton University Boston, Mass. Michael B. A. Oldstone, Editor (1994) Princeton, N.J. Scripps Clinic & Research Foundation Ronald C. Desrosiers, Editor (1998) La Jolla, Calif. Joseph Sodroski, Editor (1998) Harvard Medical School Dana-Farber Cancer Institute Boston, Mass. Carol Prives, Editor (1996) Boston, Mass. Columbia University Mary K. Estes, Editor (1998) New N.Y Inder M. Verma, Editor (1998) Baylor College of Medicine York, The Salk Institute Houston, Tex. San Diego, Calif. EDITORIAL BOARD Rafi Ahmed (1994) Harry B. Greenberg (1995) Elizabeth Moran (1996) Priscilla A. Schaffer (1996) Carl C. Baker (1994) Hidesaburo Hanafusa (1995) Bernard Moss (1995) Heinz Schaller (1995) Amiya K. Banerjee (1996) Ed Harlow (1996) Richard W. Moyer (1995) Sondra Schlesinger (1995) Kenneth L. Berns (1994) Gary S. Hayward (1996) James Mullins (1996) Robert J. Schneider (1994) Joseph B. Bolen (1994) Ari H. Helenius (1996) Brian R Murphy (1994) Manfred H. Schubert (1996) Thomas J.'Braciale (1994) Virginia S. Hinshaw (1996) Nicholas A. Muzyczka (1996) Bartholomew M. Sefton (1994) John Brady (1994) David D. Ho (1996) Gerald Myers (1995) Bert L. Semler (1995) Thomas R. Broker (1995) James M. Hogle (1994) Gary J. Nabel (1996) David A. Shafritz (1994) Michael J. Buchmeier (1995) John J. Holland (1996) Opendra Narayan (1994) Yosef Shaul (1995) Robert Callahan (1994) Kathryn V. -
Poliovirus Mutant That Does Not Selectively Inhibit Host Cell Protein Synthesis
MOLECULAR AND CELLULAR BIOLOGY. November 1985. p. 2913-2923 Vol. 5. No. 11 0270-7306/85/112913-11$02.00/0 Copyright © 1985. American Society for Microbiology Poliovirus Mutant That Does Not Selectively Inhibit Host Cell Protein Synthesis HARRIS D. BERNSTEIN,1 NAHUM SONENBERG.~ AND DAVID BALTIMOREh Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, 1 and Department of Biochemistry, McGill Unirersity, Montreal, Quebec, Canada H3G I Y6~ Received 20 May 1985/Accepted 1 August 1985 A poliovirus type I (Mahoney strain) mutant was obtained by inserting three base pairs into an infectious eDNA clone. The extra amino acid encoded by the insertion was in the amino-terminal (protein 8) portion of the P2 segment of the polyprotein. The mutant virus makes small plaques on HeLa and monkey kidney (CV-1) cells at all temperatures. It lost the ability to mediate the selective inhibition of host cell translation which ordinarily occurs in the first few hours after infection. As an apparent consequence, the mutant synthesizes far less protein than does wild-type virus. In mutant-infected CV-1 cells enough protein was produced to permit a normal course of RNA replication, but the yield of progeny virus was very low. In mutant-infected He La cells there was a premature cessation of both cellular and viral protein synthesis followed by a premature halt of viral RNA synthesis. This nonspecific translational inhibition was distinguishable from wild-type-mediated inhibition and did not appear to be part of an interferon or heat shock response. -
Watanabe S, Resch M, Lilyestrom W, Clark N
NIH Public Access Author Manuscript Biochim Biophys Acta. Author manuscript; available in PMC 2010 November 1. NIH-PA Author ManuscriptPublished NIH-PA Author Manuscript in final edited NIH-PA Author Manuscript form as: Biochim Biophys Acta. 2010 ; 1799(5-6): 480±486. doi:10.1016/j.bbagrm.2010.01.009. Structural characterization of H3K56Q nucleosomes and nucleosomal arrays Shinya Watanabe1,*, Michael Resch2,*, Wayne Lilyestrom2, Nicholas Clark2, Jeffrey C. Hansen2, Craig Peterson1, and Karolin Luger2,3 1 Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation St.; Worcester, Massachusetts 01605 2 Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870 3 Howard Hughes Medical Institute Abstract The posttranslational modification of histones is a key mechanism for the modulation of DNA accessibility. Acetylated lysine 56 in histone H3 is associated with nucleosome assembly during replication and DNA repair, and is thus likely to predominate in regions of chromatin containing nucleosome free regions. Here we show by x-ray crystallography that mutation of H3 lysine 56 to glutamine (to mimic acetylation) or glutamate (to cause a charge reversal) has no detectable effects on the structure of the nucleosome. At the level of higher order chromatin structure, the K to Q substitution has no effect on the folding of model nucleosomal arrays in cis, regardless of the degree of nucleosome density. In contrast, defects in array-array interactions in trans (‘oligomerization’) are selectively observed for mutant H3 lysine 56 arrays that contain nucleosome free regions. Our data suggests that H3K56 acetylation is one of the molecular mechanisms employed to keep chromatin with nucleosome free regions accessible to the DNA replication and repair machinery. -
Microbiology and Immunology (MI) Courses” Section of This Assistants for Two Courses
National Science Foundation. Program for Graduate Study—The Ph.D. degree requires course MICROBIOLOGY AND work and independent research demonstrating an individual’s creative, scholastic, and intellectual abilities. On entering the department, students meet an advisory faculty member; together they IMMUNOLOGY design a timetable for completion of the degree requirements. Typically, this consists of first identifying gaps in the student’s Emeriti: (Professors) Edward S. Mocarski, Sidney Raffel, Leon T. undergraduate education and determining courses that should be Rosenberg taken. Then, a tentative plan is made for two to four lab rotations Chair: Karla Kirkegaard (one rotation per quarter). During the first year of graduate study in Associate Chair: Hugh O. McDevitt the department, each student also takes six or seven upper-level Professors: Ann Arvin, Helen Blau, John C. Boothroyd, Yueh-Hsiu (200-series) courses. Three of these courses are requirements of the Chien, Mark M. Davis, Stanley Falkow, Stephen J. Galli, Harry department: MI 215, Principles of Biological Techniques; MI 209, B. Greenberg, Karla Kirkegaard, A. C. Matin, Hugh O. Advanced Pathogenesis of Bacteria, Viruses, and Eukaryotic McDevitt, Peter Parham, Phillip Pizzo, Charles Prober, David Parasites, Part I; and MI 210, Advanced Pathogenesis of Bacteria, Relman, Peter Sarnow, Gary K. Schoolnik, Lucy S. Tompkins Viruses, and Eukaryotic Parasites, Part II. Three courses are part of Associate Professors: Christopher Contag, Garry Nolan, David the core curriculum that is required of many graduate students in Schneider, Julie Theriot Stanford Biosciences: BIO 203 /DBIO 203 /GENE 203, Advanced Assistant Professors: Manuel Amieva, Matthew Bogyo, Chang- Genetics; BIO 230, Molecular and Cellular Immunology; and MCP Zheng Chen, Denise Monack, Upinder Singh, Justin Sonnenburg, 221/BIO 214, Cell Biology of Physiological Processes. -
DNA-Mediated Association of Two Histone-Bound
RESEARCH ARTICLE DNA-mediated association of two histone-bound complexes of yeast Chromatin Assembly Factor-1 (CAF-1) drives tetrasome assembly in the wake of DNA replication Francesca Mattiroli1*†, Yajie Gu1,2†, Tejas Yadav3,4, Jeremy L Balsbaugh5, Michael R Harris4, Eileen S Findlay1, Yang Liu1, Catherine A Radebaugh2, Laurie A Stargell2,6, Natalie G Ahn7, Iestyn Whitehouse4, Karolin Luger1,6* 1Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, United States; 2Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States; 3Weill Cornell Graduate School of Medical Sciences, New York, United States; 4Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States; 5Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, United States; 6Institute for Genome Architecture and Function, Colorado State University, Fort Collins, United States; 7Biofrontiers Institute, University of Colorado Boulder, Boulder, United States *For correspondence: francesca. Abstract Nucleosome assembly in the wake of DNA replication is a key process that regulates [email protected] (FM); cell identity and survival. Chromatin assembly factor 1 (CAF-1) is a H3-H4 histone chaperone that [email protected] (KL) associates with the replisome and orchestrates chromatin assembly following DNA synthesis. Little is known about the mechanism and structure of this key complex. Here we investigate the CAF- †These authors contributed 1.H3-H4 binding mode and the mechanism of nucleosome assembly. We show that yeast CAF-1 equally to this work binding to a H3-H4 dimer activates the Cac1 winged helix domain interaction with DNA. This drives Competing interests: The the formation of a transient CAF-1.histone.DNA intermediate containing two CAF-1 complexes, authors declare that no each associated with one H3-H4 dimer. -
Lecture Slides
(J. American Chemical Association, 78, 3458-3459) The Secondary Structure of Complementary RNA E. Peter Geiduschek, John W. Moohr, and Smauel B. Weiss, Proceedings of The National Academy of Sciences, 48, 1078-1086, 1962. R.H. DOI RH, and S. SPIEGELMAN Homology test between the nucleic acid of an RNA virus and the DNA in the host cell. Science 1962 Dec 14 1270-2. MONTAGNIER L, SANDERS FK. REPLICATIVE FORM OF ENCEPHALOMYOCARDITIS VIRUS RIBONUCLEIC ACID. Nature. 1963 Aug 17;199:664-7. (Science 143, 1034-1036, March 6, 1964) WARNER RC, SAMUELS HH, ABBOTT MT, KRAKOW JS. (1963) Ribonucleic acid polymerase of Azotobacter vinelandii, II. Formation of DNA- RNA hybrids with single-stranded DNA as primer. Proc Natl Acad Sci U S A. 49:533-8. Double Stranded RNA as a Specific Biological Effector December 8, 2006 Karolinska Institute, Stockholm, Sweden Viral interference (Interferon) effects in animals M. Hoskins (1935) A protective action of neurotropic against viscerotropic yellow fever virus in Macacus rhesus. American Journal of Tropical Medicine, 15, 675-680 G. Findlay and F. MacCallum (1937) An interference phenomenon in relation to yellow fever and other viruses. J. Path. Bact. 44, 405-424. A. Isaacs and J. Lindenmann (1957) Virus Interference. I. The Interferon Proc. Royal Soc. B 147, 268-273. Proceedings of the National Academy of Sciences, USA, Volume 58, Pages 782-789. 1967 Promoter Make transgenic worms geneX Antisense Transcripts Interference (Development 113:503 [1991]) geneX Promoter Make transgeneic worms geneX SENSE Transcripts Also Interference! (Development 113:503 [1991]) In Vitro Promoter Make RNA in vitro geneX Antisense RNA Inject worm gonad Interference! (Guo and Kemphues, 1995) In Vitro geneX Promoter Make RNA in vitro geneX SENSE RNA Inject worm gonad Also Interference! (Guo and Kemphues, 1995) Craig Mello's RNAi Workshop: 1997 C. -
Surrender, Avoidance and Subversion by Microorganisms
REVIEWS CELLULAR AUTOPHAGY: SURRENDER, AVOIDANCE AND SUBVERSION BY MICROORGANISMS Karla Kirkegaard, Matthew P.Taylor and William T. Jackson Intracellular bacteria and viruses must survive the vigorous antimicrobial responses of their hosts to replicate successfully. The cellular process of autophagy — in which compartments bound by double membranes engulf portions of the cytosol and then mature to degrade their cytoplasmic contents — is likely to be one such host-cell response. Several lines of evidence show that both bacteria and viruses are vulnerable to autophagic destruction and that successful pathogens have evolved strategies to avoid autophagy, or to actively subvert its components, to promote their own replication. The molecular mechanisms of the avoidance and subversion of autophagy by microorganisms will be the subject of much future research, not only to study their roles in the replication of these microorganisms, but also because they will provide — as bacteria and viruses so often have — unique tools to study the cellular process itself. 6,7 4 DAUER Cellular autophagy involves the sequestration of thaliana and C. elegans ,wild-type autophagy genes An arrested stage in regions of the cytosol within double-membrane-bound are required to prevent premature senescence. Caenorhabditis elegans compartments that then mature and degrade their cyto- One attractive hypothesis is that the degradation of development that can be formed plasmic contents. It is a highly regulated process, the cytosolic structures by autophagy might have -
Nucleosome Eviction and Activated Transcription Require P300 Acetylation of Histone H3 Lysine 14
Nucleosome eviction and activated transcription require p300 acetylation of histone H3 lysine 14 Whitney R. Luebben1, Neelam Sharma1, and Jennifer K. Nyborg2 Department of Biochemistry and Molecular Biology, Campus Box 1870, Colorado State University, Fort Collins, CO 80523 Edited by Mark T. Groudine, Fred Hutchinson Cancer Research Center, Seattle, WA, and approved September 9, 2010 (received for review July 6, 2010) Histone posttranslational modifications and chromatin dynamics include H4 acetylation-dependent relaxation of the chromatin are inextricably linked to eukaryotic gene expression. Among fiber and recruitment of ATP-dependent chromatin-remodeling the many modifications that have been characterized, histone tail complexes via acetyl-lysine binding bromodomains (12–17). acetylation is most strongly correlated with transcriptional activa- However, the mechanism by which histone tail acetylation elicits tion. In Metazoa, promoters of transcriptionally active genes are chromatin reconfiguration and coupled transcriptional activation generally devoid of physically repressive nucleosomes, consistent is unknown (6). with the contemporaneous binding of the large RNA polymerase II In recent years, numerous high profile mapping studies of transcription machinery. The histone acetyltransferase p300 is also nucleosomes and their modifications identified nucleosome-free detected at active gene promoters, flanked by regions of histone regions (NFRs) at the promoters of transcriptionally active genes hyperacetylation. Although the correlation -
Topical Collection on Chromatin Biology and Epigenetics
J Biosci (2020)45:1 Ó Indian Academy of Sciences DOI: 10.1007/s12038-019-9988-x (0123456789().,-volV)(0123456789().,-volV) Editorial Topical collection on Chromatin Biology and Epigenetics At an Indo–US conference held in Bengaluru in 2018, we were discussing the many opportunities for collabo- rations between scientists in the US and India. We realized that having a regular meeting in India akin to a Gordon conference would provide the continuity to foster such collaborations and also enable experimental workshops and courses analogous to those at Woodshole and CSHL, USA. As a first step, a hands-on laboratory based course on ‘Phase Separation in Genome Organization’ was conducted by Geeta during July-August 2019 at IISER Pune. This course was attended by 15 participants that included PhD students and postdoctoral fellows from various institutions in India. As another step we felt it would be useful to put together a special issue of the Journal of Biosciences centered around the theme of Chromatin Biology and Epigenetic Regulation. The Editors of the journal enthusiastically supported this initiative. Our aim was to assemble a collection that consisted of topical reviews by leaders in the field as well as reports of original research or analysis. This issue represents the results of these efforts and includes contributions primarily from scientists in US and India. Below we provide a brief preview of the collection. Among the diverse modes of transcriptional regulation, regulation dictated by chromatin organisation is immensely critical, albeit insufficiently understood. The reorganisation of chromatin in three dimensional space inside a eukaryotic nucleus can allow discrete regulatory regions of the genome to make or break contacts leading to formation of transient regulatory hubs wherein supramolecular complexes can assemble and regulate gene expression patterns. -
Live-Cell Epigenome Manipulation by Synthetic Histone Acetylation Catalyst System
Live-cell epigenome manipulation by synthetic histone acetylation catalyst system Yusuke Fujiwaraa, Yuki Yamanashia, Akiko Fujimuraa, Yuko Satob, Tomoya Kujiraic, Hitoshi Kurumizakac, Hiroshi Kimurab, Kenzo Yamatsugua,1, Shigehiro A. Kawashimaa,1, and Motomu Kanaia,1 aGraduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan; bCell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan; and cInstitute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0033, Japan Edited by Tom W. Muir, Princeton University, Princeton, NJ, and accepted by Editorial Board Member Karolin Luger December 5, 2020 (received for review September 16, 2020) Chemical modifications of histones, such as lysine acetylation and lysine residues on histone tails. Interestingly, synthetic histone ubiquitination, play pivotal roles in epigenetic regulation of gene acetylation of Xenopus chromatin by 16DMAP with PAc-gly pre- expression. Methods to alter the epigenome thus hold promise as vented DNA replication in cell-free Xenopus egg extract system, tools for elucidating epigenetic mechanisms and as therapeutics. providing a novel link between histone acetylation and cell cycle However, an entirely chemical method to introduce histone modifi- (12). However, oligoDMAP-based catalysts did not work in live cations in living cells without genetic manipulation is unprecedented. cells, probably due to inactivation of the catalytically active species Here, we developed a chemical catalyst, PEG-LANA-DSSMe 11, that (i.e., acetyl pyridinium ion) under highly reductive and nucleo- ’ binds with nucleosome s acidic patch and promotes regioselective, philic environment in cells (e.g., the presence of glutathione synthetic histone acetylation at H2BK120 in living cells.