Publications from the Department of Cell and Molecular Biology faculty at the University of Rhode Island.

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Submissions from 2011

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An Integrated Genomic and Immunoinformatic Approach to H. pylori Vaccine Design, Matthew Ardito, Joanna Fueyo, Ryan Tassone, Frances Terry, Kristin DaSilva, Songhua Zhang, William Martin, Anne S. De Groot, Steven F. Moss, and Leonard Moise

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FANCP/SLX4: A Swiss army knife of DNA interstrand crosslink repair, Kelly E. Cybulski and Niall G. Howlett

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Immunogenic Consensus Sequence T Helper Epitopes for a Pan-Burkholderia Biodefense Vaccine, Anne S. De Groot, Matthew Ardito, Leonard Moise, Eric A. Gustafson, Denice Spero, Gloria Tejada, and William Martin

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Genotype and Phenotypes of an Intestine-Adapted Escherichia coli K-12 Mutant Selected by Animal Passage for Superior Colonization, Andrew J. Fabich, Mary P. Leatham, Joe E. Grissom, Graham Wiley, Hongshing Lai, Fares Najar, Bruce A. Roe, Paul S. Cohen, and Tyrrell Conway

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Characterization of Putative Iron Responsive Genes as Species-specific Indicators of Iron Stress in Thalassiosiroid Diatoms, Bethany D. Jenkins, LeAnn P. Whitney, Jeremy J. Lins, Margaret P. Hughes, Mark L. Wells, and P. Dreux Chappell

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Anaerobic Respiration of Escherichia coli in the Mouse Intestine, Shari A. Jones, Terri Gibson, Rosalie C. Maltby, Fatema Z. Chowdhury, Valley Stewart, Paul S. Cohen, and Tyrrell Conway

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Bioassays of Analogs of Pleurocidin-Amide Indicate that Change at N-Terminus is Key to Improved Efficacy, Roxanne LaCroix, Krishna Tamminedi, David E. Ryder, Jay F. Sperry, and Lenore M. Martin

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HlyU Is a Positive Regulator of Hemolysin Expression in Vibrio anguillarum, Ling Li, Xiangyu Mou, and David R. Nelson

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A Comparison of Two Methods for T Cell Epitope Mapping: “Cell Free” In Vitro Versus Immunoinformatics, Timothy J. Messitt, Frances Terry, Leonard Moise, William Martin, and Anne S. De Groot

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Immunoinformatic discovery of potential cross-reactive T cell epitopes in the measles genome, Lenny Moise, Eric Gustafson, Matthew Ardito, Alan Rothman, William Martin, and Anne S. De Groot

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Harnessing the power of genomics and immunoinformatics to produce improved vaccines, Leonard Moise, Leslie Cousens, Joanna Fueyo, and Anne S. De Groot

Immunity to dengue virus: a tale of original antigenic sin and tropical cytokine storms, Alan L. Rothman

Dengue - How Best to Classify It, Anon Srikiatkhachorn, Alan L. Rothman, Robert V. Gibbons, Nopporn Sittisombut, Prida Malasit, Francis A. Ennis, Suchitra Nimmannitya, and Siripen Kalayanarooj

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The deficient cleavage of M protein-bound IgG by IdeS: Insight into the escape of Streptococcus pyogenes from antibody-mediated immunity, Yu Fang Su, Woei Jer Chuang, Shih Min Wang, Wen Yi Chen, Chuan Chiang-Ni, Yee Shin Lin, Jiunn Jong Wu, and Ching Chuan Liu

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An echovirus 18-associated outbreak of aseptic meningitis in Taiwan: Epidemiology and diagnostic and genetic aspects, Huey Pin Tsai, Sheng Wen Huang, Feng Ling Wu, Pin Hwa Kuo, Shih Min Wang, Ching Chuan Liu, Ih Jen Su, and Jen Ren Wang

Submissions from 2010

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Differential roles for DNA polymerases eta, zeta, and REV1 in lesion bypass of intrastrand versus interstrand DNA cross-links, J. Kevin Hicks, Colleen L. Chute, Michelle T. Paulsen, Ryan L. Ragland, Niall G. Howlett, Quentin Guéranger, Thomas W. Glover, and Christine E. Canman

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Using the molecular toolbox to compare harmful algal blooms in upwelling systems, R. M. Kudela, M. D.A. Howard, B. D. Jenkins, P. E. Miller, and G. J. Smith

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KV4.2 channels tagged in the S1-S2 loop for alpha-bungarotoxin binding provide a new tool for studies of channel expression and localization, Leonard Moise, Jing Liu, Evgeny Pryazhnikov, Leonard Khiroug, Andreas Jeromin, and Edward Hawrot

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The Chitobiose Transporter, chbC, is Required for Chitin Utilization in Borrelia Burgdorferi, Ryan G. Rhodes, Janet A. Atoyan, and David R. Nelson

Synthesis and evaluation of conformationally constrained peptide analogues as the Src SH3 domain binding ligands, Rakesh Tiwari, Alex Brown, Seetha Narramaneni, Gongqin Sun, and Keykavous Parang

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Empirical Bayes Analysis of Sequencing-Based Transcriptional Profiling Without Replicates, Zhijin Wu, Bethany D. Jenkins, Tatiana A. Rynearson, Sonya T. Dyhrman, Mak A. Saito, Melissa Mercier, and LeAnn P. Whitney

Submissions from 2009

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tasselseed1 is a lipoxygenase affecting jasmonic acid signaling in sex determination of maize, Iván F. Acosta, Hélène Laparra, Sandra P. Romero, Eric Schmelz, Mats Hamberg, John P. Mottinger, Maria A. Moreno, and Stephen L. Dellaporta

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Synthesis of Nucleoside Mono-, Di-, and Triphosphoramidates from Solid-Phase cycloSaligenyl Phosphitylating Reagents, Yousef Ahmadibeni, Rakesh K. Tiwari, Gongqin Sun, and Keykavous Parang

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A Method for Individualizing the Prediction of Immunogenicity of Protein Vaccines and Biologic Therapeutics: Individualized T Cell Epitope Measure (iTEM), Tobias Cohen, Leonard Moise, Matthew Ardito, William Martin, and Anne S. De Groot

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P17-26. Effective Design of T-Cell Driven Vaccines Applied to the GAIA HIV Vaccine: Advances in Vaccine Design Based on Current Preclinical Success, Anne S. De Groot, Leonard Moise, J. Desrosiers, C. Weber, and W. Martin

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The Pic Protease of Enteroaggregative Escherichia coli Promotes Intestinal Colonization and Growth in the Presence of Mucin, Susan M. Harrington, Jalaluddin Sheikh, Ian R. Henderson, Fernando Ruiz-Perez, Paul S. Cohen, and James P. Nataro

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Functional Interaction between the Fanconi Anemia D2 Protein and Proliferating Cell Nuclear Antigen (PCNA) via a Conserved Putative PCNA Interaction Motif, Niall G. Howlett, Julie A. Harney, Meghan A. Rego, Frederick W. Kolling IV, and Thomas W. Glover

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Identification of N-Terminal Lobe Motifs that Determine the Kinase Activity of the Catalytic Domains and Regulatory Strategies of Src and Csk Protein Tyrosine Kinases, Kezhen Huang, Yue-Hao Wang, Alex Brown, and Gongqin Sun

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Direct and specific inactivation of protein tyrosine kinases in the Src and FGFR families by reversible cysteine oxidation, David J. Kemble and Gongqin Sun

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Precolonized Human Commensal Escherichia coli Strains Serve as a Barrier to E. coli O157:H7 Growth in the Streptomycin-Treated Mouse Intestine, Mary P. Leatham, Swati Banerjee, Steven M. Autieri, Regino Mercado-Lubo, Tyrrell Conway, and Paul S. Cohen

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Novel Features of the Polysaccharide-Digesting Gliding Bacterium Flavobacterium johnsoniae as Revealed by Genome Sequence Analysis, Mark J. McBride, Gary Xie, Eric C. Martens, Alla Lapidus, Bernard Henrissat, Ryan G. Rhodes, Eugene Goltsman, Wei Wang, Jian Xu, David W. Hunnicutt, Andrew M. Staroscik, Timothy R. Hoover, Yi-Qiang Cheng, and Jennifer L. Stein

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Salmonella enterica Serovar Typhimurium Mutants Unable To Convert Malate to Pyruvate and Oxaloacetate Are Avirulent and Immunogenic in BALB/c Mice, Regino Mercado-Lubo, Mary P. Leatham, Tyrrell Conway, and Paul S. Cohen

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Chitobiose Utilization in Borrelia burgdorferi is Dually Regulated by RpoD and RpoS, Ryan G. Rhodes, Wendy M. Coy, and David R. Nelson

To C or not to C: Direct and indirect redox regulation of Src protein tyrosine kinase, Gongqin Sun and David J. Kemble

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T cell epitope: Friend or Foe? Immunogenicity of biologics in context, Constanze A. Weber, Preema J. Mehta, Matthew Ardito, Leonard Moise, William Martin, and Anne S. De Groot

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P19-43. Regulatory T Cell Epitopes in a Dendritic Cell-Targeted HIV Vaccine Delivery Platform, C. Weber, C. Weber, Leonard Moise, H. Veelken, and W. Martin

Manuscripts from 2008

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The Phaeodactylum genome reveals the evolutionary history of diatom genomes, Chris Bowler, Bethany D. Jenkins, Tatiana A. Rynearson, and et al

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Severity of alcohol withdrawal symptoms depends on developmental stage of Long–Evans rats, Chun-Shiang Chung, Jian Wang, Monh Wehman, and Dennis E. Rhoads

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Activation of natural regulatory T cells by IgG Fc-derived peptide "Tregitopes", Anne S. De Groot, Leonard Moise, Julie A. McMurry, Erik Wambre, Laurence Van Overtvelt, Philippe Moingeon, David W. Scott, and William Martin

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Comparison of Carbon Nutrition for Pathogenic and Commensal ,Escherichia coli Strains in the Mouse Intestine, Andrew J. Fabich, Shari A. Jones, Fatema Z. Chowdhury, Amanda Cernosek, April Anderson, Darren Smalley, J. Wesley McHargue, G. Aaron Hightower, Joel T. Smith, Steven M. Autieri, Mary P. Leatham, Jeremy J. Lins, Regina L. Allen, David C. Laux, Paul S. Cohen, and Tyrrell Conway

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A randomized, placebo-controlled trial of repeated IV antibiotic therapy for Lyme encephalopathy, B. A. Fallon, J. G. Keilp, K. M. Corbera, E. Petkova, C. B. Britton, E. Dwyer, I. Slavov, J. Cheng, David R. Nelson, and H. A. Sackeim

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FLP recombinase-mediated site-specific recombination in rice, Qian Hu, Halina Kononowicz-Hodges, Kimberly Nelson-Vasilchik, David Viola, Peiyu Zeng, Haibo Liu, Albert P. Kausch, Joel M. Chandlee, Thomas K. Hodges, and Hong Luo

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Molecular Approaches to the Nitrogen Cycle, Bethany D. Jenkins and Jonathan P. Zehr

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Glycogen and Maltose Utilization by Escherichia coli O157:H7 in the Mouse Intestine, Shari A. Jones, Mathias Jorgensen, Fatema Z. Chowdhury, Rosalie Rodgers, James Hartline, Mary P. Leatham, Carsten Struve, Karen A. Krogfelt, Paul S. Cohen, and Tyrrell Conway

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Identification and Characterization of a Repeat-in-Toxin Gene Cluster in Vibrio anguillarum, Ling Li, Jessica L. Rock, and David R. Nelson

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A Salmonella enterica Serovar Typhimurium Succinate Dehydrogenase/Fumarate Reductase Double Mutant Is Avirulent and Immunogenic in BALB/c Mice, Regino Mercado-Lubo, Eric J. Gauger, Mary P. Leatham, Tyrrell Conway, and Paul S. Cohen

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Phylogenetic diversity of cyanobacterial narB genes from various marine habitats, Ryan W. Paerl, Rachel A. Foster, Bethany D. Jenkins, Joseph P. Montoya, and Jonathan P. Zehr

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The influence of salmon surface mucus on the growth of Flavobacterium columnare, A. M. Staroscik and D. R. Nelson

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Development of Methods for the Genetic Manipulation of Flavobacterium columnare, Andrew M. Staroscik, David W. Hunnicutt, Kate E. Archibald, and David R. Nelson

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Identification and Characterization of Epp, the Secreted Processing Protease for the Vibrio anguillarum EmpA Metalloprotease, Maureen Varina, Steven M. Denkin, Andrew M. Staroscik, and David R. Nelson

Submissions from 2007

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Metal-binding properties of a dicysteine-containing motif in protein tyrosine kinases, Yousef Ahmadibeni, Michael Hanley, Millie White, Marina Ayrapetov, Xiaofeng Lin, Gongqin Sun, and Keykavous Parang

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l-Fucose Stimulates Utilization of d-Ribose by Escherichia coli MG1655 ΔfucAO and E. coli Nissle 1917 ΔfucAO Mutants in the Mouse Intestine and in M9 Minimal Medium, Steven M. Autieri, Jeremy J. Lins, Mary P. Leatham, David C. Laux, Tyrrell Conway, and Paul S. Cohen

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Computer-vision determination of 3-D geometric parameters of LDL particles via cryogenic transmission electron microscopy, W. Lewis Collier, Lenore M. Martin, and Rik Van Antwerpen

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Role of Motility and the flhDC Operon in Escherichia coli MG1655 Colonization of the Mouse Intestine, Eric J. Gauger, Mary P. Leatham, Regino Mercado-Lubo, David C. Laux, Tyrrell Conway, and Paul S. Cohen

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Characteristics of diazotrophs in surface to abyssopelagic waters of the Sargasso Sea, Ian Hewson, Pia H. Moisander, Katherine M. Achilles, Craig A. Carlson, Bethany D. Jenkins, Elizabeth A. Mondragon, Amanda E. Morrison, and Jonathan P. Zehr

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Respiration of Escherichia coli in the Mouse Intestine, Shari A. Jones, Fatema Z. Chowdhury, Andrew J. Fabich, April Anderson, Darrel M. Schreiner, Anetra L. House, Steven M. Autieri, Mary P. Leatham, Jeremy J. Lins, Mathias Jorgensen, Paul S. Cohen, and Tyrrell Conway

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Cell cycle arrest of stamen initials in maize sex determination, Cheol Kim Jong, Hélène Laparra, Alejandro Calderón-Urrea, John P. Mottinger, Maria A. Moreno, and Stephen L. Dellaporta

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Clinical validation of the "in silico" prediction of immunogenicity of a human recombinant therapeutic protein, E. Koren, Anne S. De Groot, V. Jawa, K. D. Beck, T. Boone, D. Rivera, L. Li, D. Mytych, M. Koscec, D. Weeraratne, S. Swanson, and W. Martin

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Synthesis and evaluation of 3-phenylpyrazolo[3,4-d]pyrimidine-peptide conjugates as Src kinase inhibitors, Anil Kumar, Yuehao Wang, Xiaofeng Lin, Gongqin Sun, and Keykavous Parang

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Accuracy limits for efficiently determining shape and size of low-density lipoprotein macromolecules from cryogenic transmission electron microscope images, W. Lewis Collier, Lenore M. Martin, and Rik Van Antwerpen

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Spatial-temporal variability in diazotroph assemblages in Chesapeake Bay using an oligonucleotide nifH microarray, Pia H. Moisander, Amanda E. Morrison, Bess B. Ward, Bethany D. Jenkins, and Jonathan P. Zehr

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Subdomain switching reveals regions that harbor substrate specificity and regulatory properties of protein tyrosine kinases, Yue Hao Wang, Kezhen Huang, Xiaofeng Lin, and Gongqin Sun

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Experiments linking nitrogenase gene expression to nitrogen fixation in the North Pacific subtropical gyre, Jonathan P. Zehr, Joseph P. Montoya, Bethany D. Jenkins, Ian Hewson, Elizabeth Mondragon, Cindy M. Short, Matthew J. Church, Andrew Hansen, and David M. Karl

Submissions from 2006

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Conformational basis for SH2-Tyr(P)527 binding in Src inactivation, Marina K. Ayrapetov, Yue Hao Wang, Xiaofeng Lin, Xianfeng Gu, Keykavous Parang, and Gongqin Sun

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Detecting invisible bacillus spores on surfaces using a portable surface-enhanced Raman analyzer, Stuart Farquharson, Frank Inscore, and Jay F. Sperry

Design and evaluation of hydroxamate derivatives as metal-mediated inhibitors of a protein tyrosine kinase, Xianfeng Gu, Yuehao Wang, Anil Kumar, Guofeng Ye, Keykavous Parang, and Gongqin Sun

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Cyanobacterial assimilatory nitrate reductase gene diversity in coastal and oligotrophic marine environments, Bethany D. Jenkins, Jonathan P. Zehr, Angela Gibson, and Lisa Campbell

Bacterial expression and characterization of catalytic loop mutants of Src protein tyrosine kinase, David J. Kemble, Yue Hao Wang, and Gongqin Sun

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Synthesis and structure-activity relationships of linear and conformationally constrained peptide analogues of CIYKYY as Src tyrosine kinase inhibitors, Anil Kumar, Guofeng Ye, Yuehao Wang, Xiaofeng Lin, Gongqin Sun, and Keykavous Parang

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Docking-based Substrate Recognition by the Catalytic Domain of a Protein Tyrosine Kinase, C-terminal Src Kinase (Csk), Sungsoo Lee, Marina K. Ayrapetov, David J. Kemble, Keykavous Parang, and Gongqin Sun

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Structural basis for domain-domain communication in a protein tyrosine kinase, the C-terminal Src kinase, Xiaofeng Lin, Yuehao Wang, Yousef Ahmadibeni, Keykavous Parang, and Gongqin Sun

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RTS, a rice anther-specific gene is required for male fertility and its promoter sequence directs tissue-specific gene expression in different plant species, Hong Luo, Jang Yong Lee, Qian Hu, Kimberly Nelson-Vasilchik, Timothy K. Eitas, Colin Lickwar, Albert P. Kausch, Joel M. Chandlee, and Thomas K. Hodges

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Application of a nifH oligonucleotide microarray for profiling diversity of N2-fixing microorganisms in marine microbial mats, Pia H. Moisander, Lily Shiue, Grieg F. Steward, Bethany D. Jenkins, Brad M. Bebout, and Jonathan P. Zehr

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Identification and Characterization of a Hemolysin Gene Cluster in Vibrio anguillarum, Jessica L. Rock and David R. Nelson

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Role of Gluconeogenesis and the Tricarboxylic Acid Cycle in the Virulence of Salmonella enterica Serovar Typhimurium in BALB/c Mice, Merlin Tchawa Yimga, Mary P. Leatham, James H. Allen, David C. Laux, Tyrrell Conway, and Paul S. Cohen

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A new strategy to produce active human Src from bacteria for biochemical study of its regulation, Yue Hao Wang, Marina K. Ayrapetov, Xiaofeng Lin, and Gongqin Sun

Submissions from 2005

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Functional diversity of Csk, Chk, and Src SH2 domains due to a single residue variation, Marina K. Ayrapetov, Nguyen Hai Nam, Guofeng Ye, Anil Kumar, Keykavous Parang, and Gongqin Sun

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Mouse Intestine Selects Nonmotile flhDC Mutants of Escherichia coli MG1655 with Increased Colonizing Ability and Better Utilization of Carbon Sources, Mary P. Leatham, Sarah J. Stevenson, Eric J. Gauger, Karen A. Krogfelt, Jeremy J. Lins, Traci L. Haddock, Steven M. Audtieri, Tyrrell Conway, and Paul S. Cohen

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Phosphoryl Transfer Step in the C-terminal Src Kinase Controls Src Recognition, Scot A. Lieser, Caitlin Shindler, Brandon E. Aubol, Sungsoo Lee, Gongqin Sun, and Joseph A. Adams

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Probing the communication between the regulatory and catalytic domains of a protein tyrosine kinase, Csk, Xiaofeng Lin, Marina K. Ayrapetov, Sungsoo Lee, Keykavous Parang, and Gongqin Sun

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Characterization of the Interactions Between the Active Site of a Protein Tyrosine Kinase and a Divalent Metal Activator, Xiaofeng Lin, Marina K. Ayrapetov, and Gongqin Sun

Protein Kinase Inhibitors Drug Discovery, Keykavous Parang and Gongqin Sun

Recent advances in the discovery of Src kinase inhibitors, Keykavous Parang and Gongqin Sun

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Regulation of the Vibrio anguillarum Metalloprotease EmpA by Posttranslational Modification, Andrew M. Staroscik, Steven M. Denkin, and David R. Nelson

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Solid-phase binding assays of peptides using EGFP-Src SH2 domain fusion protein and biotinylated Src SH2 domain, Guofeng Ye, Marina Ayrapetov, Nguyen Hai Nam, Gongqin Sun, and Keykavous Parang

Submissions from 2004

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Use of β-glucuronidase reporter gene for gene expression analysis in turfgrasses, Chhandak Basu, Albert P. Kausch, and Joel M. Chandlee

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Carbon nutrition of Escherichia coli in the mouse intestine, Dong-Eun Chang, Darren J. Smalley, Don L. Tucker, Mary P. Leatham, Wendy E. Norris, Sarah J. Stevenson, April B. Anderson, Joe E. Grissom, David C. Laux, Paul S. Cohen, and Tyrrell Conway

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Regulation of Vibrio anguillarum empA Metalloprotease Expression and Its Role in Virulence, Steven M. Denkin and David R. Nelson

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Gel Shift Analysis of the empA Promoter Region in Vibrio Anguillarum, Steven M. Denkin, Pedja Sekaric, and David R. Nelson

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Detecting Bacillus cereus spores on a mail sorting system using Raman spectroscopy, Stuart Farquharson, Lawrence Grigely, Victor Khitrov, Wayne Smith, Jay F. Sperry, and Gerard Fenerty

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Agrobacterium tumefaciens-mediated creeping bentgrass (Agrostis stolonifera L.) transformation using phosphinothricin selection results in a high frequency of single-copy transgene integration, H. Luo, Q. Hu, K. Nelson, C. Longo, A. P. Kausch, J. M. Chandlee, J. K. Wipff, and C. R. Fricker

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Glycolytic and Gluconeogenic Growth of Escherichia coli O157:H7 (EDL933) and E. coli K-12 (MG1655) in the Mouse Intestine, Regina L. Miranda, Tyrrell Conway, Mary P. Leatham, Dong Eun Chang, Wendy E. Norris, James H. Allen, Sarah J. Stevenson, David C. Laux, and Paul S. Cohen

ATP-phosphopeptide conjugates as inhibitors of Src tyrosine kinases, Nguyen Hai Nam, Sungsoo Lee, Guofeng Ye, Gongqin Sun, and Keykavous Parang

Design of tetrapeptide ligands as inhibitors of the Src SH2 domain, Nguyen Hai Nam, Rebecca L. Pitts, Gongqin Sun, Soroush Sardari, Amie Tiemo, Mingxing Xie, Bingfang Yan, and Keykavous Parang

Conformationally constrained peptide analogues of pTyr-Glu-Glu-Ile as inhibitors of the Src SH2 domain binding, Nguyen Hai Nam, Guofeng Ye, Gongqin Sun, and Keykavous Parang

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Intensities of calcium dipicolinate and Bacillus subtilis spore Raman spectra excited with 244 nm light, W. H. Nelson, R. Dasari, M. Feld, and J. F. Sperry

Design strategies for protein kinase inhibitors, Keykavous Parang and Gongqin Sun

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Jittery, a Mutator distant relative with a paradoxical mobile behavior: Excision without reinsertion, Zhennan Xu, Xianghe Yan, Steve Maurais, Huihua Fu, David G. O'Brien, John Mottinger, and Hugo K. Dooner

Submissions from 2003

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Expression, purification, and biochemical characterization of Chk, a soluble protein tyrosine kinase, Marina K. Ayrapetov, Sungsoo Lee, and Gongqin Sun

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Promoter analysis in transient assays using a GUS reporter gene construct in creeping bentgrass (Agrostis palustris), Chhandak Basu, Albert P. Kausch, Hong Luo, and Joel M. Chandlee