The Program in Biochemistry & Molecular Pharmacology is an academic program of the Graduate School of Biomedical Sciences (GSBS) at the University of Massachusetts Medical School. The program offers graduate study and research focused in the areas of molecular, cellular and regulatory biochemistry; molecular biophysics; chemical biology; and structural biology. This collection showcases publications and presentations authored by students in this program.

Attention GSBS Biochemistry & Molecular Pharmacology students: To submit your publications, go to GSBS Student Publications and click on Submit Research in the left sidebar. You’ll need to log in or create a free account. If you have the article's PubMed ID, submission is very easy. Enter the PubMed ID and information from PubMed will be used to populate the submission form. Questions? Contact Lisa Palmer.

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Publications from 2007

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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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Long-range side-chain-main-chain interactions play crucial roles in stabilizing the (betaalpha)8 barrel motif of the alpha subunit of tryptophan synthase, Xiaoyan Yang, Ramakrishna Vadrevu, Ying Wu, and C. Robert Matthews

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Dissociation of halted T7 RNA polymerase elongation complexes proceeds via a forward-translocation mechanism, Yi Zhou, Deanna M. Navaroli, Metewo Selase Enuameh, and Craig T. Martin

Publications from 2006

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The Tec family tyrosine kinases Itk and Rlk regulate the development of conventional CD8+ T cells, Luana O. Atherly, Julie Ann Lucas, Martin Felices, Catherine C. Yin, Steven L. Reiner, and Leslie J. Berg

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Reconstitution of Runx2/Cbfa1-null cells identifies a requirement for BMP2 signaling through a Runx2 functional domain during osteoblast differentiation, Jong-Sup Bae, Soraya E. Gutierrez, Radhika Narla, Jitesh Pratap, Rajitha Devados, Andre J. Van Wijnen, Janet L. Stein, Gary S. Stein, Jane B. Lian, and Amjad Javed

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IFN-induced attrition of CD8 T cells in the presence or absence of cognate antigen during the early stages of viral infections, Kapil Bahl, Sung-Kwon Kim, Claudia Calcagno, Dario Ghersi, Roberto Puzone, Franco Celada, Liisa K. Selin, and Raymond M. Welsh

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Self-renewal of human embryonic stem cells is supported by a shortened G1 cell cycle phase, Klaus A. Becker, Prachi N. Ghule, Jaclyn A. Therrien, Jane B. Lian, Janet L. Stein, Andre J. Van Wijnen, and Gary S. Stein

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Establishment of histone gene regulation and cell cycle checkpoint control in human embryonic stem cells, Klaus A. Becker, Janet L. Stein, Jane B. Lian, Andre J. Van Wijnen, and Gary S. Stein

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H2AX chromatin structures and their response to DNA damage revealed by 4Pi microscopy, Jorg Bewersdorf, Brian Thomas Bennett, and Kendall L. Knight

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The classic receptor for 1alpha,25-dihydroxy vitamin D3 is required for non-genomic actions of 1alpha,25-dihydroxy vitamin D3 in osteosarcoma cells, Soraya Bravo, Roberto Paredes, Pamela Izaurieta, Jane B. Lian, Janet L. Stein, Gary S. Stein, Maria Victoria Hinrichs, Juan Olate, Luis G. Aguayo, and Martin A. Montecino

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Enterohaemorrhagic Escherichia coli Tir requires a C-terminal 12-residue peptide to initiate EspF-mediated actin assembly and harbours N-terminal sequences that influence pedestal length, Kenneth Geno Campellone, Michael John Brady, Judith G. Alamares, Daniel C. Rowe, Brian M. Skehan, Donald J. Tipper, and John M. Leong

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KCNE1 subunits require co-assembly with K+ channels for efficient trafficking and cell surface expression, Kshama D. Chandrasekhar, Tuba Bas, and William R. Kobertz

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S. pombe FEAR protein orthologs are not required for release of Clp1/Flp1 phosphatase from the nucleolus during mitosis, Chun-Ti Chen, Marie-Pierre Peli-Gulli, Viesturs Simanis, and Dannel McCollum

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Slow translocon gating causes cytosolic exposure of transmembrane and lumenal domains during membrane protein integration, Zhiliang Cheng and Reid Gilmore

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Narrowed TCR repertoire and viral escape as a consequence of heterologous immunity, Markus Cornberg, Alex T. Chen, Lee A. Wilkinson, Michael A. Brehm, Sung-Kwon Kim, Claudia Calcagno, Dario Ghersi, Roberto Puzone, Franco Celada, Raymond M. Welsh, and Liisa K. Selin

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Regulation of the MDM2-p53 pathway by ribosomal protein L11 involves a post-ubiquitination mechanism, Mu-Shui Dai, Dingding Shi, Yetao Jin, Xiao-Xin Sun, Yanping Zhang, Steven R. Grossman, and Hua Lu

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Noble metals strip peptides from class II MHC proteins, Stephen J. De Wall, Corrie A. Painter, Jennifer D. Stone, Rajintha M. Bandaranayake, Don C. Wiley, Timothy J. Mitchison, Lawrence J. Stern, and Brian S. DeDecker

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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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Non-enzymatic interactions of glyoxylate with lysine, arginine, and glucosamine: a study of advanced non-enzymatic glycation like compounds, Udayan Dutta, Menashi A. Cohenford, Madhumita Guha, and Joel A. Dain

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E2F1 induces MRN foci formation and a cell cycle checkpoint response in human fibroblasts, Fiona M. Frame, Harry A. Rogoff, Mary Theresa Pickering, W. Douglas Cress, and Timothy F. Kowalik

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Asymmetric ERM activation at the Schwann cell process tip is required in axon-associated motility, Cheryl L. Gatto, Barbara J. Walker, and Stephen Lambert

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Asymmetric ERM activation at the Schwann cell process tip is required in axon-associated motility, Cheryl Lynn Gatto, Barbara J. Walker, and Stephen Lambert

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Ultrastructure of human erythrocyte GLUT1, Christopher A. Graybill, Alfred N. van Hoek, D. Desai, Andrew M. Carruthers, and Anthony Carruthers

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BMP2 commitment to the osteogenic lineage involves activation of Runx2 by DLX3 and a homeodomain transcriptional network, Mohammad Q. Hassan, Rahul S. Tare, Suk Hee Lee, Matthew Mandeville, Maria I. Morasso, Amjad Javed, Andre J. Van Wijnen, Janet L. Stein, Gary S. Stein, and Jane B. Lian

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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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Exploiting pathogenic Escherichia coli to model transmembrane receptor signalling, Richard D. Hayward, John M. Leong, Vassilis Koronakis, and Kenneth Geno Campellone

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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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Thiol/disulfide exchange is required for membrane fusion directed by the Newcastle disease virus fusion protein, Surbhi Jain, Lori McGinnes, and Trudy G. Morrison

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Dynamics and magnitude of virus-induced polyclonal B cell activation mediated by BCR-independent presentation of viral antigen, Evan Robert Jellison, Heath M. Guay, Eva Szomolanyi-Tsuda, and Raymond M. Welsh

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Co-evolution of nelfinavir-resistant HIV-1 protease and the p1-p6 substrate, Madhavi Kolli, Stephane Lastere, and Celia A. Schiffer

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Cdc2 tyrosine phosphorylation is not required for the S-phase DNA damage checkpoint in fission yeast, Naveen Kommajosyula and Nicholas R. Rhind

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Itk and Th2 responses: action but no reaction, Yoko Kosaka, Martin Felices, and Leslie J. Berg

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Cbf beta-SMMHC induces distinct abnormal myeloid progenitors able to develop acute myeloid leukemia, Ya-Huei Kuo, Sean F. Landrette, Susan Ann Heilman, Paola N. Perrat, Lisa Garrett, Pu P. Liu, Michelle M. Le Beau, Scott C. Kogan, and Lucio H. Castilla

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Deregulation of DNA damage signal transduction by herpesvirus latency-associated M2, Xiaozhen Liang, Mary Theresa Pickering, Nam-Hyuk Cho, Heesoon Chang, Michael R. Volkert, Timothy F. Kowalik, and Jae U. Jung

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Mechanism of substrate recognition by drug-resistant human immunodeficiency virus type 1 protease variants revealed by a novel structural intermediate, Moses Prabu-Jeyabalan, Ellen A. Nalivaika, Keith Romano, and Celia A. Schiffer

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Designing siRNA that distinguish between genes that differ by a single nucleotide, Dianne S. Schwarz, Hongliu Ding, Lori A. Kennington, Jessica T. Moore, Janell M. Schelter, Julja Burchard, Peter S. Linsley, Neil Aronin, Zuoshang Xu, and Phillip D. Zamore

Publications from 2005

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Monoclonal antibody routinely used to identify avirulent strains of Newcastle disease virus binds to an epitope at the carboxy terminus of the hemagglutinin-neuraminidase protein and recognizes individual mesogenic and velogenic strains, Judith G. Alamares, Jianrong Li, and Ronald M. Iorio

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Aberrant termination triggers nonsense-mediated mRNA decay, Nadia Amrani, Shuyun Dong, Feng He, Robin Ganesan, Shubhendu Ghosh, Stephanie Kervestin, Chunfang Li, David A. Mangus, Phyllis Spatrick, and Allan Jacobson

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Cellular localization of human Rad51C and regulation of ubiquitin-mediated proteolysis of Rad51, Brian Thomas Bennett and Kendall L. Knight

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Tec family kinases in T lymphocyte development and function, Leslie J. Berg, Lisa D. Finkelstein, Julie Ann Lucas, and Pamela L. Schwartzberg

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Biaxial failure properties of planar living tissue equivalents, Kristen L. Billiar, Angela M. Throm, and Margo Tilley Frey

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Quench-flow analysis reveals multiple phases of GluT1-mediated sugar transport, David M. Blodgett and Anthony Carruthers

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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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Target accessibility dictates the potency of human RISC, Kirk M. Brown, Chia-ying Chu, and Tariq M. Rana

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Differential effects of cisplatin and MNNG on dna mutants of Escherichia coli, Melissa A. Calmann 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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Nck-independent actin assembly is mediated by two phosphorylated tyrosines within enteropathogenic Escherichia coli Tir, Kenneth Geno Campellone and John M. Leong

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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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Human cytomegalovirus IE1-72 activates ataxia telangiectasia mutated kinase and a p53/p21-mediated growth arrest response, Jonathan Patrick Castillo, Fiona M. Frame, Harry A. Rogoff, Mary T. Pickering, Andrew D. Yurochko, and Timothy F. Kowalik

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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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Identification of cytoplasmic residues of Sec61p involved in ribosome binding and cotranslational translocation, Zhiliang Cheng, Ying Jiang, Elisabet C. Mandon, and Reid Gilmore

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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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Dissecting RNA-interference pathway with small molecules, Ya-Lin Chiu, Chimmanamada U. Dinesh, Chia-ying Chu, Akbar Ali, Kirk M. Brown, Hong Cao, and Tariq M. Rana

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

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microPrimer: the biogenesis and function of microRNA, Tingting Du and Phillip D. Zamore

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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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The bone-specific expression of Runx2 oscillates during the cell cycle to support a G1-related antiproliferative function in osteoblasts, Mario Galindo, Jitesh Pratap, Daniel W. Young, Hayk Hovhannisyan, Hee-Jeong Im, Je-Yong Choi, Jane B. Lian, Janet L. Stein, Gary S. Stein, and Andre J. Van Wijnen

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Bloom syndrome ortholog HIM-6 maintains genomic stability in C. elegans, Melissa M. Grabowski, Nenad Svrzikapa, and Heidi A. Tissenbaum

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Coordinate control and selective expression of the full complement of replication-dependent histone H4 genes in normal and cancer cells, William F. Holmes, Corey D. Braastad, Partha Mitra, Cornelia Hampe, Detlef Doenecke, Werner Albig, Janet L. Stein, Andre J. Van Wijnen, and Gary S. Stein

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Myosin X is a high duty ratio motor, Kazuaki Homma and Mitsuo Ikebe

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Spatial regulation of beta-actin translation by Src-dependent phosphorylation of ZBP1, Stefan Huttelmaier, Daniel Zenklusen, Marcell Lederer, Jason B. Dictenberg, Mike Lorenz, Xiuhua Meng, Gary J. Bassell, John S. Condeelis, and Robert H. Singer

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Impaired intranuclear trafficking of Runx2 (AML3/CBFA1) transcription factors in breast cancer cells inhibits osteolysis in vivo, Amjad Javed, George L. Barnes, Jitesh Pratap, Tomasz Antkowiak, Louis C. Gerstenfeld, Andre J. Van Wijnen, Janet L. Stein, Jane B. Lian, and Gary S. Stein

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Cutting edge: MHC class II-restricted killing in vivo during viral infection, Evan Robert Jellison, Sung-Kwon Kim, and Raymond M. Welsh

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Lymphocyte enhancer-binding factor 1 (Lef1) inhibits terminal differentiation of osteoblasts, Rachel A. Kahler, Mario Galindo, Jane B. Lian, Gary S. Stein, Andre J. Van Wijnen, and Jennifer J. Westendorf

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Four novel RUNX2 mutations including a splice donor site result in the cleidocranial dysplasia phenotype, Hyo-Jin Kim, Soon-Hyeun Nam, Hyun-Jung Kim, Hyo-Sang Park, Hyun-Mo Ryoo, Shin-Yoon Kim, Tae-Joon Cho, Seung-Gon Kim, Suk-Chul Bae, In-San Kim, Janet L. Stein, Andre J. Van Wijnen, Gary S. Stein, Jane B. Lian, and Je-Yong Choi

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Private specificities of CD8 T cell responses control patterns of heterologous immunity, Sung-Kwon Kim, Markus Cornberg, Xiaoting Z. Wang, Hong D. Chen, Liisa K. Selin, and Raymond M. Welsh

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The bone-related Zn finger transcription factor Osterix promotes proliferation of mesenchymal cells, Yeon-Ju Kim, Hyun-Nam Kim, Eui-Kyun Park, Byung-Heon Lee, Hyun-Mo Ryoo, Shin-Yoon Kim, In-San Kim, Janet L. Stein, Jane B. Lian, Gary S. Stein, Andre J. Van Wijnen, and Je-Yong Choi

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Haem repression of the housekeeping 5-aminolaevulinic acid synthase gene in the hepatoma cell line LMH, Sridevi Kolluri, Timothy J. Sadlon, Brian K. May, and Herbert L. Bonkovsky

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Bone marrow microenvironmental changes in aged mice compromise V(D)J recombinase activity and B cell generation, Joseph E. Labrie, Lisa A. Borghesi, and Rachel M. Gerstein

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Properties of the human erythrocyte glucose transport protein are determined by cellular context, Kara B. Levine, Trista K. Robichaud, Stephanie Hamill, Lisa A. Sultzman, and Anthony Carruthers

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Variable Meis-dependence among paralog group-1 Hox proteins, Choe Seong-Kyu and Charles G. Sagerstrom

Publications from 2004

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Smad function and intranuclear targeting share a Runx2 motif required for osteogenic lineage induction and BMP2 responsive transcription, Faiza Afzal, Jitesh Pratap, Kosei Ito, Yoshiaki Ito, Janet L. Stein, Andre J. Van Wijnen, Gary S. Stein, Jane B. Lian, and Amjad Javed

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Unconstrained steps of myosin VI appear longest among known molecular motors, M. Yusuf Ali, Kazuaki Homma, Atsuko Hikikoshi Iwane, Kengo Adachi, Hiroyasu Itoh, Kazuhiko Kinosita, Toshio Yanagida, and Mitsuo Ikebe

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High ER stress in beta-cells stimulates intracellular degradation of misfolded insulin, Jenny R. Allen, Linh X. Nguyen, Karen E.G. Sargent, Kathryn L. Lipson, Anthony Hackett, and Fumihiko Urano

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A faux 3'-UTR promotes aberrant termination and triggers nonsense-mediated mRNA decay, Nadia Amrani, Robin Ganesan, Stephanie Kervestin, David A. Mangus, Shubhendu Ghosh, and Allan Jacobson

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Worniu, a Snail family zinc-finger protein, is required for brain development in Drosophila, Shovon Imtiaz Ashraf, Atish Ganguly, John Roote, and Y. Tony Ip

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Conventional transport assays underestimate sugar transport rates in human red cells, David M. Blodgett and Anthony Carruthers

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The SANT domain: a unique histone-tail-binding module, Laurie A. Boyer, Robert R. Latek, and Craig L. Peterson

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Functional characterization of a human histone gene cluster duplication, Corey D. Braastad, Hayk Hovhannisyan, Andre J. Van Wijnen, Janet L. Stein, and Gary S. Stein

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Clustering of Nck by a 12-residue Tir phosphopeptide is sufficient to trigger localized actin assembly, Kenneth Geno Campellone, Susannah Rankin, Tony Pawson, Marc W. Kirschner, Donald J. Tipper, and John M. Leong

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EspFU is a translocated EHEC effector that interacts with Tir and N-WASP and promotes Nck-independent actin assembly, Kenneth Geno Campellone, Douglas Robbins, and John M. Leong

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Identification of genes that synergize with Cbfb-MYH11 in the pathogenesis of acute myeloid leukemia, Lucio H. Castilla, Paola N. Perrat, Natalia Julia Martinez, Sean F. Landrette, R. Keys, Sarah R. Oikemus, J. Flanegan, Susan Ann Heilman, Lisa Garrett, A. Dutra, S. Anderson, German A. Pihan, L. Wolff, and Pu P. Liu

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Structural basis of heteromeric smad protein assembly in TGF-beta signaling, Benoy Maramparambil Chacko, Bin Y. Qin, Ashutosh Tiwari, Genbin Shi, Suvana S. Lam, Lawrence J. Hayward, Mark De Caestecker, and Kai Lin

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Visualizing a correlation between siRNA localization, cellular uptake, and RNAi in living cells, Ya-Lin Chiu, Akbar Ali, Chia-ying Chu, Hong Cao, and Tariq M. Rana

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Inhibition of human immunodeficiency virus type 1 replication by RNA interference directed against human transcription elongation factor P-TEFb (CDK9/CyclinT1), Ya-Lin Chiu, Hong Cao, Jean-Marc Jacque, Mario Stevenson, and Tariq M. Rana

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Structural determinants of phosphoinositide selectivity in splice variants of Grp1 family PH domains, Thomas Charles Cronin, Jonathan P. DiNitto, Michael P. Czech, and David G. Lambright

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A peptidyl transferase ribozyme capable of combinatorial peptide synthesis, Zhiyong Cui, Lele Sun, and Biliang Zhang

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Structure, exchange determinants, and family-wide rab specificity of the tandem helical bundle and Vps9 domains of Rabex-5, Anna M. Delprato, Eric Lee Merithew, and David G. Lambright

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Stress induction and mitochondrial localization of Oxr1 proteins in yeast and humans, Nathan Andrew Elliott and Michael R. Volkert

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Regulation of cerebellar neuronal migration and neurite outgrowth by thyroxine and 3,3',5'-triiodothyronine, Alan P. Farwell, Susan A. Dubord-Tomasetti, Andrzej Z. Pietrzykowski, Stanley J. Stachelek, and Jack L. Leonard

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Imaging cocaine-induced changes in the mesocorticolimbic dopaminergic system of conscious rats, Marcelo Febo, Annabell C. Segarra, Jeffrey R. Tenney, Mathew E. Brevard, Timothy Q. Duong, and Craig F. Ferris

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Xrcc3 is recruited to DNA double strand breaks early and independent of Rad51, Anthony L. Forget, Brian Thomas Bennett, and Kendall L. Knight

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KCNE3 truncation mutants reveal a bipartite modulation of KCNQ1 K+ channels, Steven D. Gage and William R. Kobertz

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Effect of substrate mechanics on chondrocyte adhesion to modified alginate surfaces, Nicholas G. Genes, Jon A. Rowley, David J. Mooney, and Lawrence J. Bonassar

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The vitamin D response element in the distal osteocalcin promoter contributes to chromatin organization of the proximal regulatory domain, Soraya E. Gutierrez, Jilin Liu, Amjad Javed, Martin A. Montecino, Gary S. Stein, Jane B. Lian, and Janet L. Stein

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Kinetic analysis of the RNAi enzyme complex, Benjamin Haley and Phillip D. Zamore

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Dlx3 transcriptional regulation of osteoblast differentiation: temporal recruitment of Msx2, Dlx3, and Dlx5 homeodomain proteins to chromatin of the osteocalcin gene, Mohammad Q. Hassan, Amjad Javed, Maria I. Morasso, Jeremy Karlin, Martin A. Montecino, Andre J. Van Wijnen, Gary S. Stein, Janet L. Stein, and Jane B. Lian

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The repressor function of snail is required for Drosophila gastrulation and is not replaceable by Escargot or Worniu, Kirugaval Hemavathy, Xiaodi Hu, Shovon Imtiaz Ashraf, Stephen J. Small, and Y. Tony Ip

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Fabrication of tissue engineered tympanic membrane patches using computer-aided design and injection molding, Morgan E. Hott, Cliff A. Megerian, Rich Beane, and Lawrence J. Bonassar

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Initiation of cytokinesis is controlled through multiple modes of regulation of the Sid2p-Mob1p kinase complex, Ming-Chin Hou, David A. Guertin, and Dannel McCollum