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Browsing MIT Open Access Articles by Author "Chisholm, Sallie (Penny)"

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Browsing MIT Open Access Articles by Author "Chisholm, Sallie (Penny)"

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  • Analysis of High-Throughput Sequencing and Annotation Strategies for Phage Genomes 
    Chisholm, Sallie (Penny); Sullivan, Matthew B.; Birren, Bruce W.; Nusbaum, Chad; Young, Sarah K.; Giannoukos, Georgia; Saif, akina; Sparrow, Todd; Weiand, Michael; Zeng, Qiandong; Kodira, Chinnappa; Yandava, Chandri; Kelly, Libusha; Berlin, Aaron M.; Osburne, Marcia; Stange-Thomann, Nicole; Henn, Matthew R. (Public Library of Science, 2010-02)
    Background: Bacterial viruses (phages) play a critical role in shaping microbial populations as they influence both host mortality and horizontal gene transfer. As such, they have a significant impact on local and global ...
  • Catalytic Promiscuity in the Biosynthesis of Cyclic Peptide Secondary Metabolites in Planktonic Marine Cyanobacteria 
    Li, Bo; Sher, Daniel; Kelly, Libusha; Shi, Yanxiang; Huang, Katherine; Knerr, Patrick J.; Joewono, Ike; Rusch, Doug; Chisholm, Sallie (Penny); van der Donk, Wilfred A. (National Academy of Sciences (U.S.), 2010-05)
    Our understanding of secondary metabolite production in bacteria has been shaped primarily by studies of attached varieties such as symbionts, pathogens, and soil bacteria. Here we show that a strain of the single-celled, ...
  • Choreography of the transcriptome, photophysiology, and cell cycle of a minimal photoautotroph, prochlorococcus 
    Zinser, Erik R.; Lindell, Debbie; Johnson, Zackary I.; Futschik, Matthias E.; Steglich, Claudia; Coleman, Maureen L.; Wright, Matthew A.; Rector, Trent; Steen, Robert; McNulty, Nathan; Thompson, Luke Richard; Chisholm, Sallie (Penny) (Public Library of Science, 2009-04)
    The marine cyanobacterium Prochlorococcus MED4 has the smallest genome and cell size of all known photosynthetic organisms. Like all phototrophs at temperate latitudes, it experiences predictable daily variation in available ...
  • Ecosystem-specific selection pressures revealed through comparative population genomics 
    Coleman, Maureen L.; Chisholm, Sallie (Penny) (National Academy of Sciences (U.S.), 2010-10)
    Bacterial populations harbor vast genetic diversity that is continually shaped by abiotic and biotic selective pressures, as well as by neutral processes. Individuals coexisting in the same geographically defined population ...
  • The genome and structural proteome of an ocean siphovirus: a new window into the cyanobacterial 'mobilome' 
    Sullivan, Matthew B.; Krastins, Bryan; Hughes, Jennifer L.; Hughes, Jennifer L.; Kelly, Libusha; Chase, Michael; Sarracino, David; Chisholm, Sallie (Penny) (2009-10)
    Prochlorococcus, an abundant phototroph in the oceans, are infected by members of three families of viruses: myo-, podo- and siphoviruses. Genomes of myo- and podoviruses isolated on Prochlorococcus contain DNA replication ...
  • Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments 
    Sullivan, Matthew B.; Huang, Katherine H.; Ignacio-Espinoza, Julio C.; Berlin, Aaron M.; Kelly, Libusha; Weigele, Peter; DeFrancesco, Alicia S.; Kern, Suzanne Elizabeth; Thompson, Luke Richard; Young, Sarah; Yandava, Chandri; Fu, Ross; Krastins, Bryan; Chase, Michael; Sarracino, David; Osburne, Marcia; Henn, Matthew R.; Chisholm, Sallie (Penny) (Society for Applied Microbiology and Blackwell Publishing Ltd, 2010-11)
    T4-like myoviruses are ubiquitous, and their genes are among the most abundant documented in ocean systems. Here we compare 26 T4-like genomes, including 10 from non-cyanobacterial myoviruses, and 16 from marine ...
  • Identification and Structural Analysis of a Novel Carboxysome Shell Protein with Implications for Metabolite Transport 
    Klein, Michael G.; Zwart, Peter; Bagby, Sarah C.; Cai, Fei; Chisholm, Sallie (Penny); Heinhorst, Sabine; Cannon, Gordon C.; Kerfeld, Cheryl A. (Elsevier, 2009-09)
    Bacterial microcompartments (BMCs) are polyhedral bodies, composed entirely of proteins, that function as organelles in bacteria; they promote subcellular processes by encapsulating and co-localizing targeted enzymes with ...
  • Marine Viruses Exploit Their Host's Two-Component Regulatory System in Response to Resource Limitation 
    Zeng, Qinglu; Chisholm, Sallie (Penny) (Elsevier, 2012-01)
    Phosphorus (P) availability, which often limits productivity in marine ecosystems, shapes the P-acquisition gene content of the marine cyanobacteria Prochlorococcus [ [1], [2], [3] and [4]] and its viruses (cyanophages) [ ...
  • Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea 
    McCarren, Jay; Becker, Jamie William; Repeta, Daniel J.; Shi, Yanmei; Young, Curtis Robert, III; Malmstrom, Rex R.; Chisholm, Sallie (Penny); DeLong, Edward (National Academy of Sciences, 2010-08)
    Marine dissolved organic matter (DOM) contains as much carbon as the Earth's atmosphere, and represents a critical component of the global carbon cycle. To better define microbial processes and activities associated with ...
  • Modeling Selective Pressures on Phytoplankton in the Global Ocean 
    Chisholm, Sallie (Penny); Follows, Michael J.; Jahn, Oliver; Dutkiewicz, Stephanie; Bragg, Jason G. (Public Library of Science, 2010-03)
    Our view of marine microbes is transforming, as culture-independent methods facilitate rapid characterization of microbial diversity. It is difficult to assimilate this information into our understanding of marine microbe ...
  • Modeling the Fitness Consequences of a Cyanophage-Encoded Photosynthesis Gene 
    Chisholm, Sallie (Penny); Bragg, Jason G. (Public Library of Science, 2008-10)
    Background: Phages infecting marine picocyanobacteria often carry a psbA gene, which encodes a homolog to the photosynthetic reaction center protein, D1. Host encoded D1 decays during phage infection in the light. Phage ...
  • Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism 
    Thompson, Luke Richard; Zeng, Qinglu; Kelly, Libusha; Huang, Katherine H.; Singer, Alexander U.; Stubbe, JoAnne; Chisholm, Sallie (Penny) (National Academy of Sciences (U.S.), 2011-09)
    Cyanophages infecting the marine cyanobacteria Prochlorococcus and Synechococcus encode and express genes for the photosynthetic light reactions. Sequenced cyanophage genomes lack Calvin cycle genes, however, suggesting ...
  • ProPortal: a resource for integrated systems biology of Prochlorococcus and its phage 
    Kelly, Libusha; Huang, Katherine H.; Ding, Huiming; Chisholm, Sallie (Penny) (Oxford University Press, 2011-11)
    ProPortal (http://proportal.mit.edu/) is a database containing genomic, metagenomic, transcriptomic and field data for the marine cyanobacterium Prochlorococcus. Our goal is to provide a source of cross-referenced data ...
  • Report of a review of the NSF ocean research section 
    Duce, Robert; Chisholm, Sallie (Penny); Kinder, Thomas; Liss, Peter; Moore, Ted; Moore, Ted (The Oceanography Society, 1996)
    EVERY THREE YEARS a Committee of Visitors is formed by the National Science Foundation (NSF) Advisory Committee on Geosciences to review the various aspects of NSF funding in the Directorate for Geosciences. This year ...
  • Response of Prochlorococcus ecotypes to co-culture with diverse marine bacteria 
    Sher, Daniel; Thompson, Jessie W.; Kashtan, Nadav; Croal, Laura; Chisholm, Sallie (Penny) (Nature Publishing Group, 2011-02)
    Interactions between microorganisms shape microbial ecosystems. Systematic studies of mixed microbes in co-culture have revealed widespread potential for growth inhibition among marine heterotrophic bacteria, but similar ...
  • Response to Luo & Konstantinidis: Phosphorus-related genes are enriched in Prochlorococcus populations from the North Atlantic 
    Coleman, Maureen L.; Chisholm, Sallie (Penny) (National Academy of Sciences, 2011-04)
    Luo and Konstantinidis (1) assert that there is no difference in phosphorus (P)-related gene content between surface Prochlorococcus populations in the North Atlantic [Bermuda Atlantic Time Series (BATS)] and North Pacific ...
  • Short RNA half-lives in the slow-growing marine cyanobacterium Prochlorococcus 
    Steglich, Claudia; Lindell, Debbie; Futschik, Matthias; Rector, Trent; Steen, Robert; Chisholm, Sallie (Penny) (BioMed Central Ltd, 2010-05)
    Background: RNA turnover plays an important role in the gene regulation of microorganisms and influences their speed of acclimation to environmental changes. We investigated whole-genome RNA stability of Prochlorococcus, ...
  • Short RNA half-lives in the slow-growing marine cyanobacterium Prochlorococcus 
    Steglich, Claudia; Lindell, Debbie; Futschik, Matthias; Rector, Trent; Steen, Robert; Chisholm, Sallie (Penny) (BioMed Central Ltd, 2010-05)
    Background RNA turnover plays an important role in the gene regulation of microorganisms and influences their speed of acclimation to environmental changes. We investigated whole-genome RNA stability of Prochlorococcus, a ...
  • The spontaneous mutation frequencies of Prochlorococcus strains are commensurate with those of other bacteria 
    Osburne, Marcia; Holmbeck, Brianne M.; Coe, Allison; Chisholm, Sallie (Penny) (Wiley-Blackwell, 2011-09)
    The marine cyanobacterium Prochlorococcus, the smallest and most abundant oxygenic phototroph, has an extremely streamlined genome and a high rate of protein evolution. High-light adapted strains of Prochlorococcus in ...
  • Structural changes in a marine podovirus associated with release of its genome into Prochlorococcus 
    Liu, Xiangan; Zhang, Qinfen; Murata, Kazuyoshi; Baker, Matthew L.; Sullivan, Matthew B.; Fu, Caroline; Dougherty, Matthew; Schmid, Michael F.; Osburne, Marcia; Chisholm, Sallie (Penny); Chiu, Wah (Nature Publishing Group, 2010-06)
    Podovirus P-SSP7 infects Prochlorococcus marinus, the most abundant oceanic photosynthetic microorganism. Single particle cryo-electron microscopy (cryo-EM) yields icosahedral and asymmetrical structures of infectious ...
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