Research Topics
| B PalenikSummaryAffiliation: University of California Country: USA Publications
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Detail Information
Publications
Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteriaAlexis Dufresne
Université Paris 6 and CNRS, UMR 7144, Station Biologique, 29682 Roscoff, France
Genome Biol 9:R90. 2008..Yet, the genetic basis of niche partitioning is still poorly understood in this ecologically important group...- Computational prediction of the osmoregulation network in Synechococcus sp. WH8102Xizeng Mao
Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
BMC Genomics 11:291. 2010..Very little is known about the detailed response mechanism to osmotic stress in marine Synechococcus, one of the major oxygenic phototrophic cyanobacterial genera that contribute greatly to the global CO2 fixation... 
The genome of a motile marine SynechococcusB Palenik
Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093 0202, USA
Nature 424:1037-42. 2003..On the basis of its genome, WH8102 is more of a generalist than two related marine cyanobacteria...- Chromatic adaptation in marine Synechococcus strainsB Palenik
Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093 0202, USA
Appl Environ Microbiol 67:991-4. 2001..This ability of at least some marine Synechococcus strains to chromatically adapt may help explain their greater abundance in particular ocean environments than cyanobacteria of the genus Prochlorococcus... - The genomics of symbiosis: hosts keep the baby and the bath waterBrian Palenik
Marine Biology Research Division, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093-0202, USA
Proc Natl Acad Sci U S A 99:11996-7. 2002 - The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciationBrian Palenik
Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093 0202, USA
Proc Natl Acad Sci U S A 104:7705-10. 2007..As reported here, selenoenzymes, novel fusion proteins, and loss of some major protein families including ones associated with chromatin are likely important adaptations for achieving a small cell size... 
Coastal Synechococcus metagenome reveals major roles for horizontal gene transfer and plasmids in population diversityB Palenik
Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
Environ Microbiol 11:349-59. 2009....- Swimming marine Synechococcus strains with widely different photosynthetic pigment ratios form a monophyletic groupG Toledo
Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093 0202, USA
Appl Environ Microbiol 65:5247-51. 1999..These findings indicate that the PUB/PEB pigment ratio is not a useful characteristic for defining phylogenetic groups of marine Synechococcus strains... - Genetic identification of a high-affinity Ni transporter and the transcriptional response to Ni deprivation in Synechococcus sp. strain WH8102C L Dupont
Scripps Institution of Oceanography, University of California, San Diego, San Diego, California, USA
Appl Environ Microbiol 78:7822-32. 2012..Both sodT::sodB and sodN::sodB lines exhibited an impaired ability to grow at low Fe concentrations. We propose a posttranslational allosteric SodT regulation involving the binding of Ni to a histidine-rich intracellular protein loop... - The marine cyanobacterium Synechococcus sp. WH7805 requires urease (urea amidohydrolase, EC 3.5.1.5) to utilize urea as a nitrogen source: molecular-genetic and biochemical analysis of the enzymeJ L Collier
Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla 92093 0202, USA
Microbiology 145:447-59. 1999.... - Gene expression induced by copper stress in the diatom Thalassiosira pseudonanaAubrey K Davis
Marine Biology Research Division, Scripps Institution of Oceanography, University of California--San Diego, La Jolla, California 92093-0202, USA
Eukaryot Cell 5:1157-68. 2006..Additionally, some of the inverted repeat genes demonstrated a dose-dependent response to Cu, but not Cd, and appear to belong to a multigene family. This multigene family may be the diatom functional homolog of metallothioneins... - Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environmentBrian Palenik
Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093, USA
Proc Natl Acad Sci U S A 103:13555-9. 2006..In addition, the types of potentially horizontally transferred genes are markedly different between the coastal and open ocean genomes and suggest a more prominent role for phages in horizontal gene transfer in oligotrophic environments... - Modern proteomes contain putative imprints of ancient shifts in trace metal geochemistryChristopher L Dupont
Department of Chemistry and Biochemistry, The Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093, USA
Proc Natl Acad Sci U S A 103:17822-7. 2006..We hypothesize that these conserved trends are proteomic imprints of changes in trace metal bioavailability in the ancient ocean that highlight a major evolutionary shift in biological trace metal usage... - Characterization of a modular, cell-surface protein and identification of a new gene family in the diatom Thalassiosira pseudonanaAubrey K Davis
Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093 0202, USA
Protist 159:195-207. 2008..The response of the gene encoding p100 at the mRNA level during synchronized progression through the normal cell cycle is similar to previously characterized genes in T. pseudonana encoding cell wall proteins called silaffins... - Dynamics of marine bacterial and phytoplankton populations using multiplex liquid bead array technologyXavier Mayali
Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0202, USA
Environ Microbiol 12:975-89. 2010..Bacterial taxa belonging to the same broad taxonomic groups did not necessarily correlate with one another, confirming recent results suggesting that inferring ecological role from broad taxonomic identity may not always be accurate... - Computational inference and experimental validation of the nitrogen assimilation regulatory network in cyanobacterium Synechococcus sp. WH 8102Zhengchang Su
Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
Nucleic Acids Res 34:1050-65. 2006..Moreover, for some of these genes, this coordination is probably mediated by NtcA through the canonical NtcA promoters in their regulatory regions... - The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolismE Virginia Armbrust
School of Oceanography, University of Washington, Seattle, WA 98195, USA
Science 306:79-86. 2004.... - Ni uptake and limitation in marine Synechococcus strainsChristopher L Dupont
Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, USA
Appl Environ Microbiol 74:23-31. 2008..These results, combined with an analysis of fully sequenced marine cyanobacterial genomes, suggest that the growth of many marine Synechococcus and all Prochlorococcus strains is dependent upon Ni... - Carbon sequestration in Synechococcus Sp.: from molecular machines to hierarchical modelingGrant S Heffelfinger
Sandia National Laboratories, Building 701 2101, MS 0885, 1515 Eubank SE, Albuquerque, NM 87123, USA
OMICS 6:305-30. 2002.... - Computational inference of regulatory pathways in microbes: an application to phosphorus assimilation pathways in Synechococcus sp. WH8102Zhengchang Su
Department of Biochemistry and Molecular Biology, University of Georgia at Athens, and Computational Biology Institute, Oak Ridge National Laboratory
Genome Inform 14:3-13. 2003..To demonstrate the effectiveness of this procedure, we have applied it to the construction of the phosphorus assimilation pathways in cyanobacterium sp. WH8102. We present, in this paper, a model of the core components of this pathway...