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Complete genome sequence of a virulent isolate of Streptococcus pneumoniae.
The 2,160,837-base pair genome sequence of an isolate of Streptococcus pneumoniae, a Gram-positive pathogen that causes pneumonia, bacteremia, meningitis, and otitis media, contains 2236 predicted coding regions; of these, 1440 (64%) were assigned a biological role. Approximately 5% of the genome is composed of insertion sequences that may contribute to genome rearrangements through uptake of foreign DNA. Extracellular enzyme systems for the metabolism of polysaccharides and hexosamines...
Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis.
Shewanella oneidensis is an important model organism for bioremediation studies because of its diverse respiratory capabilities, conferred in part by multicomponent, branched electron transport systems. Here we report the sequencing of the S. oneidensis genome, which consists of a 4,969,803-base pair circular chromosome with 4,758 predicted protein-encoding open reading frames (CDS) and a 161,613-base pair plasmid with 173 CDSs. We identified the first Shewanella lambda-like phage,...
Coastal upwelling regions threatened by increased ocean acidification
La Jolla, CA—November 10, 2023—Scientists at the J. Craig Venter Institute (JCVI) and Scripps Institution of Oceanography at the University of California San Diego have for the first time shown that increased acidification of ocean water in an upwelling region reduces the availability of iron for phytoplankton, thereby threatening to reduce overall phytoplankton productivity. Given that phytoplankton sit at the base of the oceanic food web, acidification is a concern to all life in...
Scientists Identify Genome-Wide Traits Associated with Microbial Growth Strategy and Ecosystem Nutrient Status
(La Jolla, California)—February 18, 2020—Scientists from the J. Craig Venter Institute (JCVI), Arizona State University (ASU), Flathead Lake Biological Station, United States Department of Agriculture (USDA), and Universidad Nacional Autónoma de México, Mexico published results in the journal eLife, identifying key genomic traits indicative of an ecosystem’s nutrient status with respect to nitrogen and phosphorus, key ingredients in fertilizer. The study, focused on a...
Whole-genome shotgun assembly and comparison of human genome assemblies.
We report a whole-genome shotgun assembly (called WGSA) of the human genome generated at Celera in 2001. The Celera-generated shotgun data set consisted of 27 million sequencing reads organized in pairs by virtue of end-sequencing 2-kbp, 10-kbp, and 50-kbp inserts from shotgun clone libraries. The quality-trimmed reads covered the genome 5.3 times, and the inserts from which pairs of reads were obtained covered the genome 39 times. With the nearly complete human DNA sequence [National...
Novel insight into the genetic basis of high-altitude pulmonary hypertension in Kyrgyz highlanders.
The Central Asian Kyrgyz highland population provides a unique opportunity to address genetic diversity and understand the genetic mechanisms underlying high-altitude pulmonary hypertension (HAPH). Although a significant fraction of the population is unaffected, there are susceptible individuals who display HAPH in the absence of any lung, cardiac or hematologic disease. We report herein the analysis of the whole-genome sequencing of healthy individuals compared with HAPH patients and other...
The complete genome sequence of the gastric pathogen Helicobacter pylori.
Helicobacter pylori, strain 26695, has a circular genome of 1,667,867 base pairs and 1,590 predicted coding sequences. Sequence analysis indicates that H. pylori has well-developed systems for motility, for scavenging iron, and for DNA restriction and modification. Many putative adhesins, lipoproteins and other outer membrane proteins were identified, underscoring the potential complexity of host-pathogen interaction. Based on the large number of sequence-related genes encoding outer...
Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi.
The genome of the bacterium Borrelia burgdorferi B31, the aetiologic agent of Lyme disease, contains a linear chromosome of 910,725 base pairs and at least 17 linear and circular plasmids with a combined size of more than 533,000 base pairs. The chromosome contains 853 genes encoding a basic set of proteins for DNA replication, transcription, translation, solute transport and energy metabolism, but, like Mycoplasma genitalium, it contains no genes for cellular biosynthetic reactions....
NSF announces new awards for Understanding the Rules of Life
The National Science Foundation (NSF) announced 29 awards in support of Understanding the Rules of Life, one of the agency’s “10 Big Ideas for Future NSF Investments.” The awards, totaling $15 million, demonstrate NSF’s commitment to address some of the greatest challenges in understanding the living world, in all of its complex levels of organization, from the molecular scale through to the biosphere. "These awards get to the heart of fundamental questions about biological...
The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus.
Archaeoglobus fulgidus is the first sulphur-metabolizing organism to have its genome sequence determined. Its genome of 2,178,400 base pairs contains 2,436 open reading frames (ORFs). The information processing systems and the biosynthetic pathways for essential components (nucleotides, amino acids and cofactors) have extensive correlation with their counterparts in the archaeon Methanococcus jannaschii. The genomes of these two Archaea indicate dramatic differences in the way these...