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Leading Department of Energy Genome Scientist to Direct Joint Marine Microbial Metagenomics Cyberinfrastructure Initiative
San Diego, CA — APRIL 27, 2006 — An experienced genomics science program administrator has been recruited to direct a $24.5-million effort to develop an innovative cyberinfrastructure that will allow scientists to organize and analyze a vast amount of data on the genomes and community ecologies of ocean-dwelling microbes. Paul Gilna will become the executive director of the Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA)...
DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae.
Here we determine the complete genomic sequence of the gram negative, gamma-Proteobacterium Vibrio cholerae El Tor N16961 to be 4,033,460 base pairs (bp). The genome consists of two circular chromosomes of 2,961,146 bp and 1,072,314 bp that together encode 3,885 open reading frames. The vast majority of recognizable genes for essential cell functions (such as DNA replication, transcription, translation and cell-wall biosynthesis) and pathogenicity (for example, toxins, surface antigens and...
Sequence analysis of a complete 1.66 Mb Prochlorococcus marinus MED4 genome cloned in yeast.
Marine cyanobacteria of the genus Prochlorococcus represent numerically dominant photoautotrophs residing throughout the euphotic zones in the open oceans and are major contributors to the global carbon cycle. Prochlorococcus has remained a genetically intractable bacterium due to slow growth rates and low transformation efficiencies using standard techniques. Our recent successes in cloning and genetically engineering the AT-rich, 1.1 Mb Mycoplasma mycoides genome in yeast encouraged us to...
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Synthetic generation of influenza vaccine viruses for rapid response to pandemics.
During the 2009 H1N1 influenza pandemic, vaccines for the virus became available in large quantities only after human infections peaked. To accelerate vaccine availability for future pandemics, we developed a synthetic approach that very rapidly generated vaccine viruses from sequence data. Beginning with hemagglutinin (HA) and neuraminidase (NA) gene sequences, we combined an enzymatic, cell-free gene assembly technique with enzymatic error correction to allow rapid, accurate gene...
Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage.
Bacteria in the 16S rRNA clade SAR86 are among the most abundant uncultivated constituents of microbial assemblages in the surface ocean for which little genomic information is currently available. Bioinformatic techniques were used to assemble two nearly complete genomes from marine metagenomes and single-cell sequencing provided two more partial genomes. Recruitment of metagenomic data shows that these SAR86 genomes substantially increase our knowledge of non-photosynthetic bacteria in...
Genetic variation in an individual human exome.
There is much interest in characterizing the variation in a human individual, because this may elucidate what contributes significantly to a person's phenotype, thereby enabling personalized genomics. We focus here on the variants in a person's 'exome,' which is the set of exons in a genome, because the exome is believed to harbor much of the functional variation. We provide an analysis of the approximately 12,500 variants that affect the protein coding portion of an individual's genome. We...
Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides.
We have improved upon the methodology and dramatically shortened the time required for accurate assembly of 5- to 6-kb segments of DNA from synthetic oligonucleotides. As a test of this methodology, we have established conditions for the rapid (14-day) assembly of the complete infectious genome of bacteriophage X174 (5386 bp) from a single pool of chemically synthesized oligonucleotides. The procedure involves three key steps: (i). gel purification of pooled oligonucleotides to reduce...
Global Ocean Sampling Expedition (GOS)
Overview In 2004, after a successful pilot project of shotgun metagenomics sequencing at the Bermuda Atlantic Time Series site, J. Craig Venter, PhD, and a Venter Institute team launched the Sorcerer II Global Ocean Sampling (GOS) Expedition. Inspired by 19th Century sea voyages like Darwin's on the H.M.S. Beagle and Captain George Nares on the H.M.S. Challenger, The Sorcerer II circumnavigated the globe for more than two years, covering a staggering 32,000 nautical miles, visiting 23...
Building Bridges through Science.
Science is ideally suited to connect people from different cultures and thereby foster mutual understanding. To promote international life science collaboration, we have launched "The Science Bridge" initiative. Our current project focuses on partnership between Western and Middle Eastern neuroscience communities.