B Palenik

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Selection in coastal Synechococcus (cyanobacteria) populations evaluated from environmental metagenomes
    Vera Tai
    Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
    PLoS ONE 6:e24249. 2011
  2. pmc Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria
    Alexis Dufresne
    Université Paris 6 and CNRS, UMR 7144, Station Biologique, 29682 Roscoff, France
    Genome Biol 9:R90. 2008
  3. pmc Computational prediction of the osmoregulation network in Synechococcus sp. WH8102
    Xizeng Mao
    Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
    BMC Genomics 11:291. 2010
  4. pmc The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation
    Brian 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
  5. doi request reprint Coastal Synechococcus metagenome reveals major roles for horizontal gene transfer and plasmids in population diversity
    B Palenik
    Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
    Environ Microbiol 11:349-59. 2009
  6. ncbi request reprint The genome of a motile marine Synechococcus
    B 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
  7. pmc The genomics of symbiosis: hosts keep the baby and the bath water
    Brian 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
  8. pmc Chromatic adaptation in marine Synechococcus strains
    B Palenik
    Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093 0202, USA
    Appl Environ Microbiol 67:991-4. 2001
  9. pmc Swimming marine Synechococcus strains with widely different photosynthetic pigment ratios form a monophyletic group
    G 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
  10. pmc Genetic identification of a high-affinity Ni transporter and the transcriptional response to Ni deprivation in Synechococcus sp. strain WH8102
    C L Dupont
    Scripps Institution of Oceanography, University of California, San Diego, San Diego, California, USA
    Appl Environ Microbiol 78:7822-32. 2012

Collaborators

Detail Information

Publications21

  1. pmc Selection in coastal Synechococcus (cyanobacteria) populations evaluated from environmental metagenomes
    Vera Tai
    Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
    PLoS ONE 6:e24249. 2011
    ..By developing a means to analyze population diversity data from these environmental metagenomes, we have provided the first insight into the role of selection in the evolution of Synechococcus, a globally significant primary producer...
  2. pmc Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria
    Alexis 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...
  3. pmc Computational prediction of the osmoregulation network in Synechococcus sp. WH8102
    Xizeng 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...
  4. pmc The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation
    Brian 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...
  5. doi request reprint Coastal Synechococcus metagenome reveals major roles for horizontal gene transfer and plasmids in population diversity
    B Palenik
    Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
    Environ Microbiol 11:349-59. 2009
    ....
  6. ncbi request reprint The genome of a motile marine Synechococcus
    B 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...
  7. pmc The genomics of symbiosis: hosts keep the baby and the bath water
    Brian 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
  8. pmc Chromatic adaptation in marine Synechococcus strains
    B 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...
  9. pmc Swimming marine Synechococcus strains with widely different photosynthetic pigment ratios form a monophyletic group
    G 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...
  10. pmc Genetic identification of a high-affinity Ni transporter and the transcriptional response to Ni deprivation in Synechococcus sp. strain WH8102
    C 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...
  11. ncbi request reprint 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 enzyme
    J 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
    ....
  12. pmc Modern proteomes contain putative imprints of ancient shifts in trace metal geochemistry
    Christopher 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...
  13. pmc Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment
    Brian 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...
  14. pmc Gene expression induced by copper stress in the diatom Thalassiosira pseudonana
    Aubrey 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...
  15. ncbi request reprint Characterization of a modular, cell-surface protein and identification of a new gene family in the diatom Thalassiosira pseudonana
    Aubrey 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...
  16. doi request reprint Dynamics of marine bacterial and phytoplankton populations using multiplex liquid bead array technology
    Xavier 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...
  17. pmc Computational inference and experimental validation of the nitrogen assimilation regulatory network in cyanobacterium Synechococcus sp. WH 8102
    Zhengchang 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...
  18. ncbi request reprint The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism
    E Virginia Armbrust
    School of Oceanography, University of Washington, Seattle, WA 98195, USA
    Science 306:79-86. 2004
    ....
  19. pmc Ni uptake and limitation in marine Synechococcus strains
    Christopher 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...
  20. ncbi request reprint Carbon sequestration in Synechococcus Sp.: from molecular machines to hierarchical modeling
    Grant S Heffelfinger
    Sandia National Laboratories, Building 701 2101, MS 0885, 1515 Eubank SE, Albuquerque, NM 87123, USA
    OMICS 6:305-30. 2002
    ....
  21. ncbi request reprint Computational inference of regulatory pathways in microbes: an application to phosphorus assimilation pathways in Synechococcus sp. WH8102
    Zhengchang 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...