Christopher L Dupont
Affiliation: J. Craig Venter Institute
- History of biological metal utilization inferred through phylogenomic analysis of protein structuresChristopher L Dupont
Microbial and Environmental Genomics Group, J Craig Venter Institute, La Jolla, CA 92121, USA
Proc Natl Acad Sci U S A 107:10567-72. 2010..The results presented here provide an evolutionary timeline based on genomic characteristics, and key hypotheses can be tested by alternative geochemical methods...
- Genomes of uncultured eukaryotes: sorting FACS from fictionAlexandra Z Worden
Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, CA 95039, USA
Genome Biol 12:117. 2011..A recent study explores the genome content of uncultured unicellular marine eukaryotes and provides insights about interactions between uncultured eukaryotes and other biological entities...
- Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineageChris L Dupont
Microbial and Environmental Genomics, J Craig Venter Institute, San Diego, CA 92121, USA
ISME J 6:1186-99. 2012..Like the abundant planktonic marine bacterial clade SAR11, SAR86 exhibits metabolic streamlining, but also a distinct carbon compound specialization, possibly avoiding competition...
- Genomic and functional adaptation in surface ocean planktonic prokaryotesShibu Yooseph
J Craig Venter Institute, Rockville, Maryland 20850, USA
Nature 468:60-6. 2010..Their genomic features also lead us to propose that one method used to avoid predation by viruses and/or bacterivores is by means of slow growth and the maintenance of low biomass...
- 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 Prochlorococcus clades from iron-depleted oceanic regionsDouglas B Rusch
J Craig Venter Institute, Rockville, MD 20855, USA
Proc Natl Acad Sci U S A 107:16184-9. 2010....
- Evolution and metabolic significance of the urea cycle in photosynthetic diatomsAndrew E Allen
J Craig Venter Institute, San Diego, California 92121, USA
Nature 473:203-7. 2011..The diatom ornithine-urea cycle therefore represents a key pathway for anaplerotic carbon fixation into nitrogenous compounds that are essential for diatom growth and for the contribution of diatoms to marine productivity...
- Transcriptomic analysis of metabolic function in the giant kelp, Macrocystis pyrifera, across depth and seasonTalina Konotchick
J Craig Venter Institute, 10355 Science Center Drive, San Diego, CA, USA
New Phytol 198:398-407. 2013..g. nitrite reductase) were upregulated at depth compared with the surface, supporting a conceptual biological model of depth-dependent physiology...
- Efficient de novo assembly of single-cell bacterial genomes from short-read data setsHamidreza Chitsaz
Department of Computer Science, University of California, La Jolla, CA, USA
Nat Biotechnol 29:915-21. 2011..Our approach enables acquisition of genome assemblies for individual uncultivated bacteria using only short reads, providing cell-specific genetic information absent from metagenomic studies...
- 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...
- Sequence analysis of a complete 1.66 Mb Prochlorococcus marinus MED4 genome cloned in yeastChristian Tagwerker
Department of Synthetic Biology and Bioenergy, J Craig Venter Institute, 10355 Science Center Drive, San Diego, CA 92121, USA
Nucleic Acids Res 40:10375-83. 2012..We thus provide evidence of transformation, replication and maintenance of this 1.66 Mb intact bacterial genome in S. cerevisiae...
- Copper toxicity and the origin of bacterial resistance--new insights and applicationsChristopher L Dupont
Microbial and Environmental Genomics, J Craig Venter Institute, San Diego, CA, USA
Metallomics 3:1109-18. 2011..In an "arms race," some pathogenic bacteria have evolved new mechanisms for copper resistance, which is relevant given renewed interest in the use of copper surfaces due to their antimicrobial properties...