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Cell-free cloning using phi29 DNA polymerase.
We describe conditions for rolling-circle amplification (RCA) of individual DNA molecules 5-7 kb in size by >10(9)-fold, using phi29 DNA polymerase. The principal difficulty with amplification of small amounts of template by RCA using phi29 DNA polymerase is "background" DNA synthesis that usually occurs when template is omitted, or at low template concentrations. Reducing the reaction volume while keeping the amount of template fixed increases the template concentration, resulting in a...
Genome sequence of the human malaria parasite Plasmodium falciparum.
The parasite Plasmodium falciparum is responsible for hundreds of millions of cases of malaria, and kills more than one million African children annually. Here we report an analysis of the genome sequence of P. falciparum clone 3D7. The 23-megabase nuclear genome consists of 14 chromosomes, encodes about 5,300 genes, and is the most (A + T)-rich genome sequenced to date. Genes involved in antigenic variation are concentrated in the subtelomeric regions of the chromosomes. Compared to the...
Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii.
Species of malaria parasite that infect rodents have long been used as models for malaria disease research. Here we report the whole-genome shotgun sequence of one species, Plasmodium yoelii yoelii, and comparative studies with the genome of the human malaria parasite Plasmodium falciparum clone 3D7. A synteny map of 2,212 P. y. yoelii contiguous DNA sequences (contigs) aligned to 14 P. falciparum chromosomes reveals marked conservation of gene synteny within the body of each chromosome. Of...
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...
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....