The Program in Molecular Medicine at the University of Massachusetts Medical School was established in a new research building in 1989. Faculty include both clinical investigators and basic scientists, many of whom focus their research on human disease processes. The laboratory groups and core facilities that compose Molecular Medicine represent many disciplines in the bio-medical sciences: biochemistry and molecular biology, cell biology, medicine, immunology, molecular genetics and microbiology, pediatrics, pharmacology, physiology, genomics, bioinformatics and proteomics. This diverse scientific environment makes the Program an exceptional training ground for graduate students and postdoctoral fellows, who in turn contribute much to its vitality and excitement. This collection showcases publications and presentations written by faculty and researchers of the Program in Molecular Medicine.

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Publications from 2007

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Translational unmasking of Emi2 directs cytostatic factor arrest in meiosis II, Jeffrey J. Tung, Kiran Padmanabhan, David V. Hansen, Joel D. Richter, and Peter K. Jackson

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Transcription factor modularity in a gene-centered C. elegans core neuronal protein-DNA interaction network, Vanessa Vermeirssen, M. Inmaculada Barrasa, Cesar A. Hidalgo, Jenny Aurielle B. Babon, Reynaldo Sequerra, Lynn Doucette-Stamm, Albert-Laszlo Barabasi, and Albertha J. M. Walhout

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Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping, Vanessa Vermeirssen, Bart Deplancke, M. Inmaculada Barrasa, John S. Reece-Hoyes, H. Efsun Arda, Christian A. Grove, Natalia Julia Martinez, Reynaldo Sequerra, Lynn Doucette-Stamm, Michael R. Brent, and Albertha J. M. Walhout

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Human myosin Vc is a low duty ratio nonprocessive motor, Shinya Watanabe, Tomonobu M. Watanabe, Osamu Sato, Junya Awata, Kazuaki Homma, Nobuhisa Umeki, Hideo Higuchi, Reiko Ikebe, and Mitsuo Ikebe

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Msk is required for nuclear import of TGF-{beta}/BMP-activated Smads, Lan Xu, Xiaohao Yao, Xiaochu Chen, Peiyuan Lu, Biliang Zhang, and Y. Tony Ip

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Functional and Structural Dissection of the SWI/SNF Chromatin Remodeling Complex: A Dissertation, Xiaofang Yang

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Swi3p controls SWI/SNF assembly and ATP-dependent H2A-H2B displacement, Xiaofang Yang, Roser Zaurin, Miguel Beato, and Craig L. Peterson

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Mitotic occupancy and lineage-specific transcriptional control of rRNA genes by Runx2, Daniel W. Young, Mohammad Q. Hassan, Jitesh Pratap, Mario Galindo, Sayyed K. Zaidi, Suk Hee Lee, Xiaoqing Yang, Ronglin Xie, Amjad Javed, Jean M. Underwood, Paul S. Furcinitti, Anthony N. Imbalzano, Sheldon Penman, Jeffrey A. Nickerson, Martin A. Montecino, Jane B. Lian, Janet L. Stein, Andre J. Van Wijnen, and Gary S. Stein

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Mitotic retention of gene expression patterns by the cell fate-determining transcription factor Runx2, Daniel W. Young, Mohammad Q. Hassan, Xiaoqing Yang, Mario Galindo, Amjad Javed, Sayyed K. Zaidi, Paul S. Furcinitti, David S. Lapointe, Martin A. Montecino, Jane B. Lian, Janet L. Stein, Andre J. Van Wijnen, and Gary S. Stein

Publications from 2006

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Plasma membrane domains specialized for clathrin-mediated endocytosis in primary cells, Karl D. Bellve, Deborah Leonard, Clive Standley, Lawrence M. Lifshitz, Richard A. Tuft, Akira Hayakawa, Silvia Corvera, and Kevin E. Fogarty

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Gag regulates association of human immunodeficiency virus type 1 envelope with detergent-resistant membranes, Jayanta Bhattacharya, Alexander Repik, and Paul R. Clapham

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Identification of phosphatases for Smad in the BMP/DPP pathway, Hong B. Chen, Jiali Shen, Y. Tony Ip, and Lan Xu

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Keystone meeting summary: 'Adipogenesis, obesity, and inflammation' and 'Diabetes mellitus and the control of cellular energy metabolism, ' January 21-26, 2006, Vancouver, Canada, Silvia Corvera, Alison Burkart, Ja-Young Kim, Jennifer L. Christianson, Zhao Wang, and Philipp E. Scherer

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Global analysis of hematopoietic and vascular endothelial gene expression by tissue specific microarray profiling in zebrafish, Laurence D. Covassin, Julio D. Amigo, Kana Suzuki, Viktor Teplyuk, Juerg R. Straubhaar, and Nathan D. Lawson

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A gene-centered C. elegans protein-DNA interaction network, Bart Deplancke, Arnab Mukhopadhyay, Wanyuan Ao, Ahmed M. Elewa, Christian A. Grove, Natalia Julia Martinez, Reynaldo Sequerra, Lynn Doucette-Stamm, John S. Reece-Hoyes, Ian A. Hope, Heidi A. Tissenbaum, Susan E. Mango, and Albertha J. M. Walhout

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Gateway-Compatible Yeast One-Hybrid Screens, Bart Deplancke, Vanessa Vermeirssen, H. Efsun Arda, Albertha J. M. Walhout, and Natalia Julia Martinez

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Deficiency of the zinc finger protein ZPR1 causes neurodegeneration, Beth Doran, Norberto G. Gherbesi, Gregory M. Hendricks, Richard A. Flavell, Roger J. Davis, and Laxman Gangwani

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Functional proteomics reveals the biochemical niche of C. elegans DCR-1 in multiple small-RNA-mediated pathways, Thomas F. Duchaine, James A. Wohlschlegel, Scott Kennedy, Yanxia Bei, Darryl Conte, Ka Ming Pang, Daniel R. Brownell, Sandra Harding, Shohei Mitani, Gary Ruvkun, John R. Yates, and Craig C. Mello

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The intraflagellar transport protein IFT20 is associated with the Golgi complex and is required for cilia assembly, John A. Follit, Richard A. Tuft, Kevin E. Fogarty, and Gregory J. Pazour

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The Intraflagellar Transport Protein IFT20 Is Associated with the Golgi Complex and Is Required for Cilia Assembly, John A. Follit, Richard A. Tuft, Kevin E. Fogarty, and Gregory J. Pazour

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The LRS and SIN domains: two structurally equivalent but functionally distinct nucleosomal surfaces required for transcriptional silencing, Christopher J. Fry, Anne Norris, Michael S. Cosgrove, Jef D. Boeke, and Craig L. Peterson

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Facioscapulohumeral muscular dystrophy in mice overexpressing FRG1, Davide Gabellini, Giuseppe D'Antona, Maurizio Moggio, Alessandro Prelle, Chiara Zecca, Raffaella Adami, Barbara Angeletti, Patrizia Ciscato, Maria Antonietta Pellegrino, Roberto Bottinelli, Michael R. Green, and Rossella Tupler

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Deficiency of the zinc finger protein ZPR1 causes defects in transcription and cell cycle progression, Laxman Gangwani

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Control of cellular senescence by CPEB, Irina Groisman, Maria Ivshina, Veronica Marin, Norman J. Kennedy, Roger J. Davis, and Joel D. Richter

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The WD40 and FYVE domain containing protein 2 defines a class of early endosomes necessary for endocytosis, Akira Hayakawa, Deborah Marie Leonard, Stephanie Murphy, Susan J. Hayes, Martha C. Soto, Kevin E. Fogarty, Clive Standley, Karl D. Bellve, David G. Lambright, Craig C. Mello, and Silvia Corvera

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Apoptin nucleocytoplasmic shuttling is required for cell type-specific localization, apoptosis, and recruitment of the anaphase-promoting complex/cyclosome to PML bodies, Destin W. Heilman, Jose G. Teodoro, and Michael R. Green

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A regulatory CD4+ T cell subset in the BB rat model of autoimmune diabetes expresses neither CD25 nor Foxp3, Jan-Luuk Hillebrands, Barbara J. Whalen, Jeroen T. J. Visser, Jasper Koning, Kenneth D. Bishop, Jean Leif, Jan Rozing, John P. Mordes, Dale L. Greiner, and Aldo A. Rossini

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CPEB3 and CPEB4 in neurons: analysis of RNA-binding specificity and translational control of AMPA receptor GluR2 mRNA, Yi-Shuian Huang, Ming-Chung Kan, Chien-Ling Lin, and Joel D. Richter

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Translational control by neuroguidin, a eukaryotic initiation factor 4E and CPEB binding protein, Mi-Young Jung, Lori J. Lorenz, and Joel D. Richter

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Mechanisms of Endocytic Sorting: A Dissertation, Deborah Marie Leonard

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Development of the pancreas and pancreatic cancer, Brian C. Lewis

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Vaccines to prevent transmission of HIV-1 via breastmilk: scientific and logistical priorities, Katherine Luzuriaga, Marie-Louise Newell, Francios Dabis, Jean-Louis Excler, and John L. Sullivan

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Latent membrane protein 1 suppresses RASSF1A expression, disrupts microtubule structures and induces chromosomal aberrations in human epithelial cells, Cornelia Man, Jack Rosa, Leo T. O. Lee, Vien H. Y. Lee, Billy K. C. Chow, Kwok-Wai Lo, Stephen J. Doxsey, Z G Wu, Yok-Lam Kwong, Dong-Yan Jin, Annie Lai-Man Cheung, and Sai Wah Tsao

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Homologous recombination prevents methylation-induced toxicity in Escherichia coli, Anetta Nowosielska, Stephen A. Smith, Bevin P. Engelward, and Martin G. Marinus

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Autophagy is activated for cell survival after endoplasmic reticulum stress, Maiko Ogata, Shin-ichiro Hino, Atsushi Saito, Keisuke Morikawa, Shinichi Kondo, Soshi Kanemoto, Tomohiko Murakami, Manabu Taniguchi, Ichiro Tanii, Kazuya Yoshinaga, Sadao Shiosaka, James A. Hammarback, Fumihiko Urano, and Kazunori Imaizumi

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Identification of direct DAF-16 targets controlling longevity, metabolism and diapause by chromatin immunoprecipitation, Seung Wook Oh, Arnab Mukhopadhyay, Bharat L. Dixit, Tamal Raha, Michael R. Green, and Heidi A. Tissenbaum

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Epigenetic telomere protection by Drosophila DNA damage response pathways, Sarah R. Oikemus, Joana Queiroz-Machado, KuanJu Lai, Nadine Schultz, Claudio E. Sunkel, and Michael H. Brodsky

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Dynamic expression of LIM cofactors in the developing mouse neural tube, Heather P. Ostendorff, Baris Tursun, Kerstin Cornils, Anne Schluter, Alexander Drung, Cenap Gungor, and Ingolf Bach

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Regulated Pumilio-2 binding controls RINGO/Spy mRNA translation and CPEB activation, Kiran Padmanabhan and Joel D. Richter

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Interplay between Ino80 and Swr1 chromatin remodeling enzymes regulates cell cycle checkpoint adaptation in response to DNA damage, Manolis Papamichos-Chronakis, Jocelyn E. Krebs, and Craig L. Peterson

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The DNA helicase ChlR1 is required for sister chromatid cohesion in mammalian cells, Joanna L. Parish, Jack Rosa, Xiaoyu Wang, Jill M. Lahti, Stephen J. Doxsey, and Elliot J. Androphy

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Identification of predicted human outer dynein arm genes: candidates for primary ciliary dyskinesia genes, Gregory J. Pazour, Nathan S. Agrin, Bethany L. Walker, and George B. Witman (Journal of medical genetics)

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Non-macrophage-tropic human immunodeficiency virus type 1 R5 envelopes predominate in blood, lymph nodes, and semen: implications for transmission and pathogenesis, Paul J. Peters, W. Matthew Sullivan, Maria J. Duenas-Decamp, Jayanta Bhattacharya, Chiambah Ankghuambom, Richard J. P. Brown, Katherine Luzuriaga, Jeanne E. Bell, Peter Simmonds, K. Jonathan Ball, and Paul R. Clapham

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MicroRNA-206 colocalizes with ribosome-rich regions in both the nucleolus and cytoplasm of rat myogenic cells, Joan C. Ritland Politz, Fan Zhang, and Thoru Pederson

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RNAi-based gene silencing in primary mouse and human adipose tissues, Vishwajeet Puri, Abhijit Chakladar, Joseph V. Virbasius, Silvana Konda, Aimee M. Powelka, My T. Chouinard, G. Nana Hagan, Richard A. Perugini, and Michael P. Czech

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A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks, John S. Reece-Hoyes, Bart Deplancke, Jane Shingles, Christian A. Grove, Ian A. Hope, and Albertha J. M. Walhout

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Therapy with a severe acute respiratory syndrome-associated coronavirus-neutralizing human monoclonal antibody reduces disease severity and viral burden in golden Syrian hamsters, Anjeanette Roberts, William D. Thomas, Jeannette Guarner, Elaine W. Lamirande, Gregory J. Babcock, Thomas C. Greenough, Leatrice Vogel, Norman Hayes, John L. Sullivan, Sherif Zaki, Kanta Subbarao, and Donna M. Ambrosino

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Perturbation and Modulation of Microtubule Cytoskeletal Elements in Response to the Potentially Oncogenic Molecules, Survivin and P53, and Cytokinesis: A Dissertation, Jack Rosa

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Survivin modulates microtubule dynamics and nucleation throughout the cell cycle, Jack Rosa, Pedro Canovas, Ashraful Islam, Dario C. Altieri, and Stephen J. Doxsey

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Histone H4-K16 acetylation controls chromatin structure and protein interactions, Michael Shogren-Knaak, Haruhiko Ishii, Jian-Min Sun, Michael J. Pazin, James R. Davie, and Craig L. Peterson

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Switching on chromatin: mechanistic role of histone H4-K16 acetylation, Michael Shogren-Knaak and Craig L. Peterson

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Probing SWI/SNF remodeling of the nucleosome by unzipping single DNA molecules, Alla Shundrovsky, Corey Lewis Smith, John T. Lis, Craig L. Peterson, and Michelle D. Wang

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Developments in basic science research, Mario Stevenson

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Quantitative Analysis of Hedgehog Gradient Formation Using an Inducible Expression System: a Dissertation, Vivian F. Su

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Supervillin modulation of focal adhesions involving TRIP6/ZRP-1, Norio Takizawa, Tara C. Smith, Thomas Nebl, Jessica Lynn Crowley, Stephen J. Palmieri, Lawrence M. Lifshitz, Anka G. Ehrhardt, Laura M. Hoffman, Mary C. Beckerle, and Elizabeth J. Luna

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An RNA interference-based screen identifies MAP4K4/NIK as a negative regulator of PPARgamma, adipogenesis, and insulin-responsive hexose transport, Xiaoqing Tang, Adilson L. Guilherme, Abhijit Chakladar, Aimee M. Powelka, Silvana Konda, Joseph V. Virbasius, Sarah M. Nicoloro, Juerg R. Straubhaar, and Michael P. Czech

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p53-mediated inhibition of angiogenesis through up-regulation of a collagen prolyl hydroxylase, Jose G. Teodoro, Albert E. Parker, Xiaochun Zhu, and Michael R. Green

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IFN-α/β Induction by dsRNA and Toll-Like Receptors Shortens Allograft Survival Induced by Costimulation Blockade: A Dissertation, Thomas B. Thornley

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Protein-tyrosine kinase and GTPase signals cooperate to phosphorylate and activate Wiskott-Aldrich syndrome protein (WASP)/neuronal WASP, Eduardo M. Torres and Michael K. Rosen

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Light Intermediate Chain 1: a Multifunctional Cargo Binder for Cytoplasmic Dynein 1: a Dissertation, Thomas Wadzinski

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CPEB controls oocyte growth and follicle development in the mouse, Racki J. Waldemar and Joel D. Richter

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Networking at the second Interactome Meeting, Albertha J. M. Walhout

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Biochemistry and Molecular Biology, Albertha J. M. Walhout and Simon J. Boulton

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C. elegans 14-3-3 proteins regulate life span and interact with SIR-2.1 and DAF-16/FOXO, Yamei Wang, Seung Wook Oh, Bart Deplancke, Jianyuan Luo, Albertha J. M. Walhout, and Heidi A. Tissenbaum

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Drosophila myosin VIIA is a high duty ratio motor with a unique kinetic mechanism, Shinya Watanabe, Reiko Ikebe, and Mitsuo Ikebe

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Regulation of Smad activities, Lan Xu

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Radial spoke proteins of Chlamydomonas flagella, Pinfen Yang, Dennis R. Diener, Chun Yang, Takahiro Kohno, Gregory J. Pazour, Jennifer M. Dienes, Nathan S. Agrin, Stephen M. King, Winfield S. Sale, Ritsu Kamiya, Joel L. Rosenbaum, and George B. Witman (Journal of cell science)

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Analysis of the C. elegans Argonaute family reveals that distinct Argonautes act sequentially during RNAi, Erbay Yigit, Pedro J. Batista, Yanxia Bei, Ka Ming Pang, Chun-Chieh G. Chen, Niraj H. Tolia, Leemor Joshua-Tor, Shohei Mitani, Martin J. Simard, and Craig C. Mello

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DNA translocation and loop formation mechanism of chromatin remodeling by SWI/SNF and RSC, Yongli Zhang, Corey Lewis Smith, Anjanabha Saha, Stephan W. Grill, Shirley Mihardja, Steven B. Smith, Bradley R. Cairns, Craig L. Peterson, and Carlos Bustamante

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Modest but reproducible inhibition of human immunodeficiency virus type 1 infection in macrophages following LEDGFp75 silencing, Steven P. Zielske and Mario Stevenson

Publications from 2005

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Differential phosphorylation controls Maskin association with eukaryotic translation initiation factor 4E and localization on the mitotic apparatus, Daron C. Barnard, Quiping Cao, and Joel D. Richter

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Egr-2 and PD-1 Are Required for Induction and Maintenance of T Cell Anergy: A Dissertation, Kenneth D. Bishop

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The v-SNARE Vti1a regulates insulin-stimulated glucose transport and Acrp30 secretion in 3T3-L1 adipocytes, Avirup Bose, Adilson L. Guilherme, Shaohui Huang, Andrea C. Hubbard, Charles R. Lane, Neil A. Soriano, and Michael P. Czech

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Regulation and Function of Stress-Activated Protein Kinase Signal Transduction Pathways: A Dissertation, Deborah Marie Brancho

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Role of MLK3 in the regulation of mitogen-activated protein kinase signaling cascades, Deborah Marie Brancho, Juan-Jose Ventura, Anja Jaeschke, Beth Doran, Richard A. Flavell, and Roger J. Davis

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Separation of mutation avoidance and antirecombination functions in an Escherichia coli mutS mutant, Melissa A. Calmann, Anetta Nowosielska, and Martin G. Marinus

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The MutS C terminus is essential for mismatch repair activity in vivo, Melissa A. Calmann, Anetta Nowosielska, and Martin G. Marinus

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Amyloid precursor proteins anchor CPEB to membranes and promote polyadenylation-induced translation, Quiping Cao, Yi-Shuian Huang, Ming-Chung Kan, and Joel D. Richter

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A member of the polymerase beta nucleotidyltransferase superfamily is required for RNA interference in C. elegans, Chun-Chieh G. Chen, Martin J. Simard, Hiroaki Tabara, Daniel R. Brownell, Jennifer A. McCollough, and Craig C. Mello

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Nuclear targeting of transforming growth factor-beta-activated Smad complexes, Hong B. Chen, Jonathan G. Rud, Kai Lin, and Lan Xu

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Phosphorylation of histone H4 serine 1 during DNA damage requires casein kinase II in S. cerevisiae, Wang L. Cheung, Fiona B. Turner, Thanuja Krishnamoorthy, Branden Wolner, Sung-Hee Ahn, Melissa Anne Foley, Jean A. Dorsey, Craig L. Peterson, Shelley L. Berger, and C. David Allis

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Cross-reactive influenza virus-specific CD8+ T cells contribute to lymphoproliferation in Epstein-Barr virus-associated infectious mononucleosis, Shalyn Catherine Clute, Levi B. Watkin, Markus Cornberg, Yuri N. Naumov, John L. Sullivan, Katherine Luzuriaga, Raymond M. Welsh, and Liisa K. Selin

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lin-8, which antagonizes Caenorhabditis elegans Ras-mediated vulval induction, encodes a novel nuclear protein that interacts with the LIN-35 Rb protein, Ewa M. Davison, Melissa M. Harrison, Albertha J. M. Walhout, Marc Vidal, and H. Robert Horvitz

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A cell-surface receptor for lipocalin 24p3 selectively mediates apoptosis and iron uptake, Laxminarayana R. Devireddy, Claude Gazin, Xiaochun Zhu, and Michael R. Green

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Differential light chain assembly influences outer arm dynein motor function, Linda M. DiBella, Oksana Gorbatyuk, Miho Sakato, Ken-ichi Wakabayashi, Ramila S. Patel-King, Gregory J. Pazour, George B. Witman, and Stephen M. King (Molecular biology of the cell)

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Centrosome control of the cell cycle, Stephen J. Doxsey, Wendy Cherie Zimmerman, and Keith Mikule

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Activity-dependent polyadenylation in neurons, Ling Du and Joel D. Richter

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Nuclear localization of HIV type 1 Vif isolated from a long-term asymptomatic individual and potential role in virus attenuation, Melissa Ann Farrow, Mohan Somasundaran, Chengsheng Zhang, Dana Gabuzda, John L. Sullivan, and Thomas C. Greenough

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WFS1 is a novel component of the unfolded protein response and maintains homeostasis of the endoplasmic reticulum in pancreatic beta-cells, Sonya G. Fonseca, Mariko Fukuma, Kathryn L. Lipson, Linh X. Nguyen, Jenny R. Allen, Yoshitomo Oka, and Fumihiko Urano

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Normal microRNA maturation and germ-line stem cell maintenance requires Loquacious, a double-stranded RNA-binding domain protein, Klaus Forstemann, Yukihide Tomari, Tingting Du, Vasily V. Vagin, Ahmet M. Denli, Diana P. Bratu, Carla Andrea Klattenhoff, William E. Theurkauf, and Phillip D. Zamore

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Drosophila WntD is a target and an inhibitor of the Dorsal/Twist/Snail network in the gastrulating embryo, Atish Ganguly, Jin Jiang, and Y. Tony Ip

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ZPR1 is essential for survival and is required for localization of the survival motor neurons (SMN) protein to Cajal bodies, Laxman Gangwani, Richard A. Flavell, and Roger J. Davis

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Development and characterization of a severe acute respiratory syndrome-associated coronavirus-neutralizing human monoclonal antibody that provides effective immunoprophylaxis in mice, Thomas C. Greenough, Gregory J. Babcock, Anjeanette Roberts, Hector J. Hernandez, William D. Thomas, Jennifer A. Coccia, Robert F. Graziano, Mohan Srinivasan, Israel Lowy, Robert W. Finberg, Kanta Subbarao, Leatrice Vogel, Mohan Somasundaran, Katherine Luzuriaga, John L. Sullivan, and Donna M. Ambrosino

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Centriolin anchoring of exocyst and SNARE complexes at the midbody is required for secretory-vesicle-mediated abscission, Adam Scott Gromley, Charles Yeaman, Jack Rosa, Sambra D. Redick, Chun-Ting Chen, Stephanie Mirabelle, Minakshi Guha, James Sillibourne, and Stephen J. Doxsey

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The anaphase promoting complex: a critical target for viral proteins and anti-cancer drugs, Destin W. Heilman, Michael R. Green, and Jose G. Teodoro

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Effects of HMGN1 on chromatin structure and SWI/SNF-mediated chromatin remodeling, David A. Hill, Craig L. Peterson, and Anthony N. Imbalzano

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A Rik1-associated, cullin-dependent E3 ubiquitin ligase is essential for heterochromatin formation, Peter J. Horn, Jean-Noel M. Bastie, and Craig L. Peterson

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Disruption of the Jnk2 (Mapk9) gene reduces destructive insulitis and diabetes in a mouse model of type I diabetes, Anja Jaeschke, Mercedes Rincon, Beth Doran, Judith Reilly, Donna S. Neuberg, Dale L. Greiner, Leonard D. Shultz, Aldo A. Rossini, Richard A. Flavell, and Roger J. Davis

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Identification of WNK1 as a substrate of Akt/protein kinase B and a negative regulator of insulin-stimulated mitogenesis in 3T3-L1 cells, Zhen Y. Jiang, Qiong L. Zhou, John Holik, Shraddha Patel, John D. Leszyk, Kerri Coleman, My T. Chouinard, and Michael P. Czech

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XBP1 activates the transcription of its target genes via an ACGT core sequence under ER stress, Soshi Kanemoto, Shinichi Kondo, Maiko Ogata, Tomohiko Murakami, Fumihiko Urano, and Kazunori Imaizumi