This collection showcases the books, journal articles, book reviews, and other publications and presentations written by faculty and researchers of the Department of Biochemistry and Molecular Pharmacology.

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Publications from 2007

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Tec kinases in T cell and mast cell signaling, Martin Felices, Markus Falk, Yoko Kosaka, and Leslie J. Berg

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Endoplasmic reticulum stress signaling in pancreatic beta-cells, Sonya G. Fonseca, Kathryn L. Lipson, and Fumihiko Urano

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The human Rad51 K133A mutant is functional for DNA double-strand break repair in human cells, Anthony L. Forget, Matthew S. Loftus, Dharia A. McGrew, Brian Thomas Bennett, and Kendall L. Knight

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Drosophila microRNAs are sorted into functionally distinct argonaute complexes after production by dicer-1, Klaus Forstemann, Michael D. Horwich, LiangMeng Wee, Yukihide Tomari, and Phillip D. Zamore

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Topology and sequence in the folding of a TIM barrel protein: global analysis highlights partitioning between transient off-pathway and stable on-pathway folding intermediates in the complex folding mechanism of a (betaalpha)8 barrel of unknown function from B. subtilis, William R. Forsyth, Osman Bilsel, Zhenyu Gu, and C. Robert Matthews

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Hydrophobic sliding: a possible mechanism for drug resistance in human immunodeficiency virus type 1 protease, Jennifer E. Foulkes-Murzycki, Walter Robert Peter Scott, and Celia A. Schiffer

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Microscopic methods for measuring the elasticity of gel substrates for cell culture: microspheres, microindenters, and atomic force microscopy, Margo Tilley Frey, Adam Engler, Dennis E. Discher, Juliet Lee, and Yu-Li Wang

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ubiquilin antagonizes presenilin and promotes neurodegeneration in Drosophila, Atish Ganguly, R. M. Renny Feldman, and Ming Guo

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Cell cycle dependent phosphorylation and subnuclear organization of the histone gene regulator p220(NPAT) in human embryonic stem cells, Prachi N. Ghule, Klaus A. Becker, J. Wade Harper, Jane B. Lian, Janet L. Stein, Andre J. Van Wijnen, and Gary S. Stein

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Danger-free autoimmune disease in Aire-deficient mice, Daniel H. D. Gray, Irina Catrinel Gavanescu, Christophe Benoist, and Diane Mathis

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Differential effects of EGF and TGF-beta1 on fibroblast activity in fibrin-based tissue equivalents, Jaime L. Grouf, Angela M. Throm, Jenna L. Balestrini, Katie A. Bush, and Kristen L. Billiar

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A chromatin landmark and transcription initiation at most promoters in human cells, Matthew G. Guenther, Stuart S. Levine, Laurie A. Boyer, Rudolf Jaenisch, and Richard A. Young

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Chromatin remodeling by SWI/SNF results in nucleosome mobilization to preferential positions in the rat osteocalcin gene promoter, Jose L. Gutierrez, Roberto Paredes, Fernando Cruzat, David A. Hill, Andre J. Van Wijnen, Jane B. Lian, Gary S. Stein, Janet L. Stein, Anthony N. Imbalzano, and Martin A. Montecino

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Structural analysis of kinetic folding intermediates for a TIM barrel protein, indole-3-glycerol phosphate synthase, by hydrogen exchange mass spectrometry and Go model simulation, Zhenyu Gu, Maithreyi K. Rao, William R. Forsyth, John M. Finke, and C. Robert Matthews

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HOXA10 controls osteoblastogenesis by directly activating bone regulatory and phenotypic genes, Mohammad Q. Hassan, Rahul S. Tare, Suk Hee Lee, Matthew Mandeville, Brian Weiner, Martin A. Montecino, Andre J. Van Wijnen, Janet L. Stein, Gary S. Stein, and Jane B. Lian

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Evolutionarily conserved structural and functional roles of the FYVE domain, Akira Hayakawa, Susan J. Hayes, Deborah Marie Leonard, David G. Lambright, and Silvia Corvera

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In and out of the ER: protein folding, quality control, degradation, and related human diseases, Daniel N. Hebert and Maurizio Molinari

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Multispectral quantification of tissue types in a RIF-1 tumor model with histological validation. Part I, Erica C. Henning, Chieko Azuma, Christopher H. Sotak, and Karl G. Helmer

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Multispectral tissue characterization in a RIF-1 tumor model: monitoring the ADC and T2 responses to single-dose radiotherapy. Part II, Erica C. Henning, Chieko Azuma, Christopher H. Sotak, and Karl G. Helmer

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Verification of enhancement of the CSF space, not parenchyma, in acute stroke patients with early blood-brain barrier disruption, Erica C. Henning, Lawrence L. Latour, and Steven Warach

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The Drosophila RNA methyltransferase, DmHen1, modifies germline piRNAs and single-stranded siRNAs in RISC, Michael D. Horwich, Chengjian Li, Christian B. Matranga, Vasily V. Vagin, Gwen Farley, Peng Wang, and Phillip D. Zamore

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The transcription factor XBP-1 is essential for the development and survival of dendritic cells, Neal N. Iwakoshi, Marc Pypaert, and Laurie H. Glimcher

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A novel alloantigen-specific CD8+PD1+ regulatory T cell induced by ICOS-B7h blockade in vivo, Atsushi Izawa, Kazuhiro Yamaura, Monica J. Albin, Mollie Jurewicz, Katsunori Tanaka, Michael R. Clarkson, Takuya Ueno, Antje Habicht, Gordon J. Freeman, Hideo Yagita, Reza Abdi, Todd Pearson, Dale L. Greiner, Mohamed H. Sayegh, and Nader Najafian

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The nucleolar Net1/Cfi1-related protein Dnt1 antagonizes the septation initiation network in fission yeast, Quan-Wen Jin, Samriddha Ray, Sung Hugh Choi, and Dannel McCollum

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Drosophila rasiRNA pathway mutations disrupt embryonic axis specification through activation of an ATR/Chk2 DNA damage response, Carla Andrea Klattenhoff, Diana P. Bratu, Nadine Schultz, Birgit S. Koppetsch, Heather A. Cook, and William E. Theurkauf

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SWI/SNF is required for transcriptional memory at the yeast GAL gene cluster, Sharmistha Kundu, Peter J. Horn, and Craig L. Peterson

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ATP-Dependent Sugar Transport Complexity in Human Erythrocytes, Jeffry M. Leitch and Anthony Carruthers

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Programmed death-1 (PD-1) defines a transient and dysfunctional oligoclonal T cell population in acute homeostatic proliferation, Sue-Jane Lin, Craig D. Peacock, Kapil Bahl, and Raymond M. Welsh

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The interactome of the histone gene regulatory factor HiNF-P suggests novel cell cycle related roles in transcriptional control and RNA processing, Angela Miele, Ricardo F. Medina, Andre J. Van Wijnen, Gary S. Stein, and Janet L. Stein

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N88D facilitates the co-occurrence of D30N and L90M and the development of multidrug resistance in HIV type 1 protease following nelfinavir treatment failure, Yumi Mitsuya, Mark A. Winters, W. Jeffrey Fessel, Soo-Yon Rhee, Leo Hurley, Michael Horberg, Celia A. Schiffer, Andrew R. Zolopa, and Robert W. Shafer

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Nucleosome organization and targeting of SWI/SNF chromatin-remodeling complexes: contributions of the DNA sequence, Martin A. Montecino, Janet L. Stein, Gary S. Stein, Jane B. Lian, Andre J. Van Wijnen, Fernando Cruzat, Soraya E. Gutierrez, Juan Olate, Sylvain Marcellini, and Jose L. Gutierrez

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A derivatized scorpion toxin reveals the functional output of heteromeric KCNQ1-KCNE K+ channel complexes, Trevor J. Morin and William R. Kobertz

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Dam methyltransferase is required for stable lysogeny of the Shiga toxin (Stx2)-encoding bacteriophage 933W of enterohemorrhagic Escherichia coli O157:H7, Kenan C. Murphy, Jennifer M. Ritchie, Matthew K. Waldor, Anders Lobner-Olesen, and Martin G. Marinus

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Crystal structure of lysine sulfonamide inhibitor reveals the displacement of the conserved flap water molecule in human immunodeficiency virus type 1 protease, Madhavi N. L. Nalam, Anik Peeters, Tim H. M. Jonckers, Inge Dierynck, and Celia A. Schiffer

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DNA mismatch repair-induced double-strand breaks, Anetta Nowosielska and Martin G. Marinus

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Molecular basis of RNA recognition by the embryonic polarity determinant MEX-5, John M. Pagano Jr., Brian M. Farley, Lisa M. McCoig, and Sean P. Ryder

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The alternative reading frame tumor suppressor antagonizes hypoxia-induced cancer cell migration via interaction with the COOH-terminal binding protein corepressor, Seema Paliwal, Ramesh C. Kovi, Bharath D. Nath, Ya-Wen Chen, Brian C. Lewis, and Steven R. Grossman

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Development of Ad-mda7/IL-24-resistant lung cancer cell lines, Abujiang Pataer, Sunil Chada, Jack A. Roth, Kelly K. Hunt, and Stephen G. Swisher

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Progress, paradox, and potential: parathyroid hormone research over five decades, John T. Potts and Thomas James Gardella

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Design and synthesis of HIV-1 protease inhibitors incorporating oxazolidinones as P2/P2' ligands in pseudosymmetric dipeptide isosteres, G. S. Kiran Kumar Reddy, Akbar Ali, Madhavi N. L. Nalam, Saima G. Anjum, Hong Cao, Robin S. Nathans, Celia A. Schiffer, and Tariq M. Rana

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Effects of vpu start-codon mutations on human immunodeficiency virus type 1 replication in macrophages, Kathryn H. Richards and Paul R. Clapham

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Nitrite does not provide additional protection to thrombolysis in a rat model of stroke with delayed reperfusion, Bawarjan Schatlo, Erica C. Henning, Ryszard M. Pluta, Lawrence L. Latour, Nahal Golpayegani, Marsha J. Merrill, Naomi Lewin, Yong Chen, and Edward H. Oldfield

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Zebrafish ae2.2 encodes a second slc4a2 anion exchanger, Boris E. Shmukler, Jeffrey S. Clark, Ann Hsu, David H. Vandorpe, Andrew K. Stewart, Christine E. Kurschat, Seong-Kyu Choe, Yi Zhou, Julio D. Amigo, Barry H. Paw, and Seth L. Alper

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Single-molecule tracking in eukaryotic cell nuclei, Jan Peter Siebrasse, David Grunwald, and Ulrich Kubitscheck

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Measuring the rates of transcriptional elongation in the female Drosophila melanogaster germ line by nuclear run-on, Alla A. Sigova, Vasily V. Vagin, and Phillip D. Zamore

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Supply and Demand in Cerebral Energy Metabolism: the Role of Nutrient Transporters, Ian A. Simpson, Anthony Carruthers, and Susan J. Vannucci

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Distinct Roles for Two G{alpha} G Interfaces in Cell Polarity Control by a Yeast Heterotrimeric G Protein, Shelly Catherine Strickfaden and Peter M. Pryciak

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grp (chk1) replication-checkpoint mutations and DNA damage trigger a Chk2-dependent block at the Drosophila midblastula transition, Saeko Takada, Seongae Kwak, Birgit S. Koppetsch, and William E. Theurkauf

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Type 1 IFN mediates cross-talk between innate and adaptive immunity that abrogates transplantation tolerance, Thomas B. Thornley, Nancy E. Phillips, Britte C. Beaudette-Zlatanova, Thomas G. Markees, Kapil Bahl, Michael A. Brehm, Leonard D. Shultz, Evelyn A. Kurt-Jones, John P. Mordes, Raymond M. Welsh, Aldo A. Rossini, and Dale L. Greiner

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Fluorogenic probes for monitoring peptide binding to class II MHC proteins in living cells, Prasanna Venkatraman, Tina T. Nguyen, Matthieu Sainlos, Osman Bilsel, Sriram Chitta, Barbara Imperiali, and Lawrence J. Stern

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TRAIL is a novel antiviral protein against dengue virus, Rajas V. Warke, Katherine J. Martin, Krisanthi Giaya, Sunil K. Shaw, Alan L. Rothman, and Irene Bosch

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A tightly packed hydrophobic cluster directs the formation of an off-pathway sub-millisecond folding intermediate in the alpha subunit of tryptophan synthase, a TIM barrel protein, Ying Wu, Ramakrishna Vadrevu, Sagar V. Kathuria, Xiaoyan Yang, and C. Robert Matthews

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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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Discovery of HIV-1 protease inhibitors with picomolar affinities incorporating N-aryl-oxazolidinone-5-carboxamides as novel P2 ligands, Akbar Ali, G. S. Kiran Kumar Reddy, Hong Cao, Saima G. Anjum, Madhavi N. L. Nalam, Celia A. Schiffer, and Tariq M. Rana

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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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RecA dimers serve as a functional unit for assembly of active nucleoprotein filaments, Anthony L. Forget, Michelle M. Kudron, Dharia A. McGrew, Melissa A. Calmann, Celia A. Schiffer, and Kendall L. Knight

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Role of invariant Thr80 in human immunodeficiency virus type 1 protease structure, function, and viral infectivity, Jennifer E. Foulkes-Murzycki, Moses Prabu-Jeyabalan, Deyna Cooper, Gavin J. Henderson, Janera Harris, Ronald I. Swanstrom, and Celia A. Schiffer

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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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Direct observation of single protein molecules in aqueous solution, David Grunwald, Andreas Hoekstra, Thomas Dange, Volker Buschmann, and Ulrich Kubitscheck

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Intranuclear binding kinetics and mobility of single native U1 snRNP particles in living cells, David Grunwald, Beatrice Spottke, Volker Buschmann, and Ulrich Kubitscheck

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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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The beta sliding clamp binds to multiple sites within MutL and MutS, Francisco J. Lopez de Saro, Martin G. Marinus, Paul Modrich, and Mike O'Donnell

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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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Substrate specificity in HIV-1 protease by a biased sequence search method, Nevra Ozer, Turkan Haliloglu, and Celia A. Schiffer

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Substrate envelope and drug resistance: crystal structure of RO1 in complex with wild-type human immunodeficiency virus type 1 protease, Moses Prabu-Jeyabalan, Nancy M. King, Ellen A. Nalivaika, Gabrielle Heilek-Snyder, Nick Cammack, and Celia A. Schiffer

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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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Hda-mediated inactivation of the DnaA protein and dnaA gene autoregulation act in concert to ensure homeostatic maintenance of the Escherichia coli chromosome, Leise Riber, Jan A. Olsson, Rasmus B. Jensen, Ole Skovgaard, Santanu Dasgupta, Martin G. Marinus, and Anders Lobner-Olesen

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Introduction on the use of the Drosophila embryonic/larval neuromuscular junction as a model system to study synapse development and function, and a brief summary of pathfinding and target recognition, Catalina Ruiz-Canada and Vivian Budnik

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Synaptic cytoskeleton at the neuromuscular junction, Catalina Ruiz-Canada and Vivian Budnik

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S-nitrosothiol depletion in amyotrophic lateral sclerosis, Christopher M. Schonhoff, Masaaki Matsuoka, Hemachand Tummala, Michael A. Johnson, Alvaro G. Estevez, Rui Wu, Andres Kamaid, Karina C. Ricart, Yuichi Hashimoto, Benjamin M. Gaston, Timothy L. Macdonald, Zuoshang Xu, and Joan B. Mannick