Search Results - "Serres, Margrethe H."

Genomic Analysis of Carbon Source Metabolism of Shewanella oneidensis MR-1: Predictions versus Experiments by SERRES, Margrethe H, RILEY, Monica

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Comparative Systems Biology across an Evolutionary Gradient within the Shewanella Genus by Konstantinidis, Konstantinos T., Serres, Margrethe H., Romine, Margaret F., Rodrigues, Jorge L M., Auchtung, Jennifer, McCue, Lee-Ann, Lipton, Mary S., Obraztsova, Anna, Giometti, Carol S., Nealson, Kenneth H., Fredrickson, James K., Tiedje, James M., Gordon, Jeffrey I.

“…To what extent genotypic differences translate to phenotypic variation remains a poorly understood issue of paramount importance for several cornerstone…”
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Large-Scale Comparative Phenotypic and Genomic Analyses Reveal Ecological Preferences of Shewanella Species and Identify Metabolic Pathways Conserved at the Genus Level by RODRIGUES, Jorge L. M, SERRES, Margrethe H, TIEDJE, James M

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Live Cell Chemical Profiling of Temporal Redox Dynamics in a Photoautotrophic Cyanobacterium by Sadler, Natalie C, Melnicki, Matthew R, Serres, Margrethe H, Merkley, Eric D, Chrisler, William B, Hill, Eric A, Romine, Margaret F, Kim, Sangtae, Zink, Erika M, Datta, Suchitra, Smith, Richard D, Beliaev, Alexander S, Konopka, Allan, Wright, Aaron T

“…Protein reduction–oxidation (redox) modification is an important mechanism that allows microorganisms to sense environmental changes and initiate cellular…”
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Evolution by leaps: gene duplication in bacteria by Serres, Margrethe H, Kerr, Alastair R W, McCormack, Thomas J, Riley, Monica

“…Sequence related families of genes and proteins are common in bacterial genomes. In Escherichia coli they constitute over half of the genome. The presence of…”
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Towards environmental systems biology of Shewanella by Fredrickson, James K, Tiedje, James M, Romine, Margaret F, Beliaev, Alexander S, Auchtung, Jennifer M, Driscoll, Michael E, Gardner, Timothy S, Nealson, Kenneth H, Osterman, Andrei L, Pinchuk, Grigoriy, Reed, Jennifer L, Rodionov, Dmitry A, Rodrigues, Jorge L. M, Saffarini, Daad A, Serres, Margrethe H, Spormann, Alfred M, Zhulin, Igor B

“…Key Points Shewanella species couple the decomposition of organic matter to the reduction of various terminal electron acceptors that are present in the…”
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Microbial eukaryotic predation pressure and biomass at deep-sea hydrothermal vents by Hu, Sarah K, Anderson, Rika E, Pachiadaki, Maria G, Edgcomb, Virginia P, Serres, Margrethe H, Sylva, Sean P, German, Christopher R, Seewald, Jeffrey S, Lang, Susan Q, Huber, Julie A

“…Deep-sea hydrothermal vent geochemistry shapes the foundation of the microbial food web by fueling chemolithoautotrophic microbial activity. Microbial…”
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Draft genome sequence of Methanocalculus natronophilus sp. strain Z-7105T, an alkaliphilic, methanogenic archaeon isolated from a soda lake by Elkassas, Sabrina M., Serres, Margrethe H., Richardson, Derrick, Zhilina, Tatyana N., Huber, Julie A.

“…A methanogenic archaeon was isolated from bottom sediments in the vicinity of Lake Tanatar II (Altai, Russia), an alkaline soda lake. Here we present the draft…”
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Draft genome sequence of Methanocalculus natronophilus sp. strain Z-7105 T , an alkaliphilic, methanogenic archaeon isolated from a soda lake by Elkassas, Sabrina M, Serres, Margrethe H, Richardson, Derrick, Zhilina, Tatyana N, Huber, Julie A

“…A methanogenic archaeon was isolated from bottom sediments in the vicinity of Lake Tanatar II (Altai, Russia), an alkaline soda lake. Here we present the draft…”
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Escherichia coli K-12: a cooperatively developed annotation snapshot—2005 by Riley, Monica, Abe, Takashi, Arnaud, Martha B., Berlyn, Mary K.B., Blattner, Frederick R., Chaudhuri, Roy R., Glasner, Jeremy D., Horiuchi, Takashi, Keseler, Ingrid M., Kosuge, Takehide, Mori, Hirotada, Perna, Nicole T., Plunkett, Guy, Rudd, Kenneth E., Serres, Margrethe H., Thomas, Gavin H., Thomson, Nicholas R., Wishart, David, Wanner, Barry L.

“…The goal of this group project has been to coordinate and bring up-to-date information on all genes of Escherichia coli K-12. Annotation of the genome of an…”
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Gene fusions and gene duplications: relevance to genomic annotation and functional analysis by Serres, Margrethe H, Riley, Monica

“…Escherichia coli a model organism provides information for annotation of other genomes. Our analysis of its genome has shown that proteins encoded by fused…”
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Shewanella knowledgebase: integration of the experimental data and computational predictions suggests a biological role for transcription of intergenic regions by Karpinets, Tatiana V, Romine, Margaret F, Schmoyer, Denise D, Kora, Guruprasad H, Syed, Mustafa H, Leuze, Michael R, Serres, Margrethe H, Park, Byung H, Samatova, Nagiza F, Uberbacher, Edward C

“…Shewanellae are facultative gamma-proteobacteria whose remarkable respiratory versatility has resulted in interest in their utility for bioremediation of heavy…”
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Draft Genome Sequence of Desulfurobacterium sp. Strain AV08, a Thermophilic Chemolithoautotroph Isolated from a Deep-Sea Hydrothermal Vent by Skoog, Emilie J, Huber, Julie A, Serres, Margrethe H, Levesque, Alice, Zeigler Allen, Lisa

“…A thermophilic chemolithoautotrophic bacterium was isolated from vent fluids at Axial Seamount, an active deep-sea volcano in the northeast Pacific Ocean. We…”
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Detection of transcriptional triggers in the dynamics of microbial growth: application to the respiratorily versatile bacterium Shewanella oneidensis by Beg, Qasim K, Zampieri, Mattia, Klitgord, Niels, Collins, Sara B, Altafini, Claudio, Serres, Margrethe H, Segrè, Daniel

“…The capacity of microorganisms to respond to variable external conditions requires a coordination of environment-sensing mechanisms and decision-making…”
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Comparisons of Shewanella strains based on genome annotations, modeling, and experiments by Ong, Wai Kit, Vu, Trang T, Lovendahl, Klaus N, Llull, Jenna M, Serres, Margrethe H, Romine, Margaret F, Reed, Jennifer L

“…Shewanella is a genus of facultatively anaerobic, Gram-negative bacteria that have highly adaptable metabolism which allows them to thrive in diverse…”
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GenProtEC: an updated and improved analysis of functions of Escherichia coli K‐12 proteins by Serres, Margrethe H., Goswami, Sulip, Riley, Monica

“…Using more than one approach to characterizing functions of unknown proteins, we now present in GenProtEC (http://genprotec.mbl.edu/) some level of function…”
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A functional update of the Escherichia coliK-12 genome by Serres, Margrethe H, Gopal, Shuba, Nahum, Laila A, Liang, Ping, Gaasterland, Terry, Riley, Monica

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Changes in translational efficiency is a dominant regulatory mechanism in the environmental response of bacteria by Taylor, Ronald C, Webb Robertson, Bobbie-Jo M, Markillie, Lye Meng, Serres, Margrethe H, Linggi, Bryan E, Aldrich, Joshua T, Hill, Eric A, Romine, Margaret F, Lipton, Mary S, Wiley, H Steven

“…To understand how cell physiological state affects mRNA translation, we used Shewanella oneidensis MR-1 grown under steady state conditions at either 20% or…”
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Protein families reflect the metabolic diversity of organisms and provide support for functional prediction by Nahum, Laila A, Goswami, Sulip, Serres, MargreH

“…1 The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts 2 Centro de Pesquisas…”
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Conserved synteny at the protein family level reveals genes underlying Shewanella species’ cold tolerance and predicts their novel phenotypes by Karpinets, Tatiana V., Obraztsova, Anna Y., Wang, Yanbing, Schmoyer, Denise D., Kora, Guruprasad H., Park, Byung H., Serres, Margrethe H., Romine, Margaret F., Land, Miriam L., Kothe, Terence B., Fredrickson, Jim K., Nealson, Kenneth H., Uberbacher, Edward C.

“…Bacteria of the genus Shewanella can thrive in different environments and demonstrate significant variability in their metabolic and ecophysiological…”
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