Institution
J. Craig Venter Institute
Nonprofit•La Jolla, California, United States•
About: J. Craig Venter Institute is a nonprofit organization based out in La Jolla, California, United States. It is known for research contribution in the topics: Genome & Gene. The organization has 1268 authors who have published 2300 publications receiving 304083 citations. The organization is also known as: JCVI & The Institute for Genomic Research.
Topics: Genome, Gene, Genomics, Population, Microbiome
Papers published on a yearly basis
Papers
More filters
••
TL;DR: It is found that lateral gene transfer has played a fundamental role in the evolution of S. aureus, demonstrating that methicillin-resistant strains have evolved multiple independent times, rather than from a single ancestral strain.
Abstract: An emerging theme in medical microbiology is that extensive variation exists in gene content among strains of many pathogenic bacterial species. However, this topic has not been investigated on a genome scale with strains recovered from patients with well-defined clinical conditions. Staphylococcus aureus is a major human pathogen and also causes economically important infections in cows and sheep. A DNA microarray representing >90% of the S. aureus genome was used to characterize genomic diversity, evolutionary relationships, and virulence gene distribution among 36 strains of divergent clonal lineages, including methicillin-resistant strains and organisms causing toxic shock syndrome. Genetic variation in S. aureus is very extensive, with ≈22% of the genome comprised of dispensable genetic material. Eighteen large regions of difference were identified, and 10 of these regions have genes that encode putative virulence factors or proteins mediating antibiotic resistance. We find that lateral gene transfer has played a fundamental role in the evolution of S. aureus. The mec gene has been horizontally transferred into distinct S. aureus chromosomal backgrounds at least five times, demonstrating that methicillin-resistant strains have evolved multiple independent times, rather than from a single ancestral strain. This finding resolves a long-standing controversy in S. aureus research. The epidemic of toxic shock syndrome that occurred in the 1970s was caused by a change in the host environment, rather than rapid geographic dissemination of a new hypervirulent strain. DNA microarray analysis of large samples of clinically characterized strains provides broad insights into evolution, pathogenesis, and disease emergence.
463 citations
••
TL;DR: Comparison of B. suis with Brucella melitensis has defined a finite set of differences that could be responsible for the differences in virulence and host preference between these organisms, and indicates that phage have played a significant role in their divergence.
Abstract: The 3.31-Mb genome sequence of the intracellular pathogen and potential bioterrorism agent, Brucella suis, was determined. Comparison of B. suis with Brucella melitensis has defined a finite set of differences that could be responsible for the differences in virulence and host preference between these organisms, and indicates that phage have played a significant role in their divergence. Analysis of the B. suis genome reveals transport and metabolic capabilities akin to soil/plant-associated bacteria. Extensive gene synteny between B. suis chromosome 1 and the genome of the plant symbiont Mesorhizobium loti emphasizes the similarity between this animal pathogen and plant pathogens and symbionts. A limited repertoire of genes homologous to known bacterial virulence factors were identified.
460 citations
••
TL;DR: Genes predicted to encode transporters were strongly overrepresented among the genes transcriptionally upregulated under conditions that stimulate penicillinG production, illustrating potential for future genomics-driven metabolic engineering.
Abstract: Industrial penicillin production with the filamentous fungus Penicillium chrysogenum is based on an unprecedented effort in microbial strain improvement. To gain more insight into penicillin synthesis, we sequenced the 32.19 Mb genome of P. chrysogenum Wisconsin54-1255 and identified numerous genes responsible for key steps in penicillin production. DNA microarrays were used to compare the transcriptomes of the sequenced strain and a penicillinG high-producing strain, grown in the presence and absence of the side-chain precursor phenylacetic acid. Transcription of genes involved in biosynthesis of valine, cysteine and alpha-aminoadipic acid-precursors for penicillin biosynthesis-as well as of genes encoding microbody proteins, was increased in the high-producing strain. Some gene products were shown to be directly controlling beta-lactam output. Many key cellular transport processes involving penicillins and intermediates remain to be characterized at the molecular level. Genes predicted to encode transporters were strongly overrepresented among the genes transcriptionally upregulated under conditions that stimulate penicillinG production, illustrating potential for future genomics-driven metabolic engineering.
457 citations
••
TL;DR: A new, large-scale sequencing effort to provide a more comprehensive picture of the evolution of influenza viruses and of their pattern of transmission through human and animal populations is reported, encompassing a total of 2,821,103 nucleotides.
Abstract: Influenza viruses are remarkably adept at surviving in the human population over a long timescale. The human influenza A virus continues to thrive even among populations with widespread access to vaccines, and continues to be a major cause of morbidity and mortality. The virus mutates from year to year, making the existing vaccines ineffective on a regular basis, and requiring that new strains be chosen for a new vaccine. Less-frequent major changes, known as antigenic shift, create new strains against which the human population has little protective immunity, thereby causing worldwide pandemics. The most recent pandemics include the 1918 'Spanish' flu, one of the most deadly outbreaks in recorded history, which killed 30-50 million people worldwide, the 1957 'Asian' flu, and the 1968 'Hong Kong' flu. Motivated by the need for a better understanding of influenza evolution, we have developed flexible protocols that make it possible to apply large-scale sequencing techniques to the highly variable influenza genome. Here we report the results of sequencing 209 complete genomes of the human influenza A virus, encompassing a total of 2,821,103 nucleotides. In addition to increasing markedly the number of publicly available, complete influenza virus genomes, we have discovered several anomalies in these first 209 genomes that demonstrate the dynamic nature of influenza transmission and evolution. This new, large-scale sequencing effort promises to provide a more comprehensive picture of the evolution of influenza viruses and of their pattern of transmission through human and animal populations. All data from this project are being deposited, without delay, in public archives.
457 citations
••
University of California, Riverside1, Swiss Institute of Bioinformatics2, University of Geneva3, University of Notre Dame4, J. Craig Venter Institute5, University of Santiago de Compostela6, Iowa State University7, Colorado State University8, Harvard University9, Indiana University10, University of Barcelona11, Broad Institute12, University of Texas at Arlington13, University of Maryland, Baltimore14, Max Planck Society15, Liverpool School of Tropical Medicine16, Swedish University of Agricultural Sciences17, Hoffmann-La Roche18, Virginia Tech19, University of Wisconsin-Madison20, Kansas State University21, Auburn University22, University of A Coruña23, International Livestock Research Institute24, University of Maryland, College Park25, National Institutes of Health26, University of Illinois at Urbana–Champaign27, University of Göttingen28, Imperial College London29, University of Texas Medical Branch30, Johns Hopkins University31, University of California, Davis32, George Washington University33, Boston College34
TL;DR: The genomic sequence of C. quinquefasciatus is described, which reveals distinctions related to vector capacities and habitat preferences, and confirmed that inoculation with unfamiliar bacteria prompted strong immune responses in Culex.
Abstract: Culex quinquefasciatus (the southern house mosquito) is an important mosquito vector of viruses such as West Nile virus and St. Louis encephalitis virus, as well as of nematodes that cause lymphatic filariasis. C. quinquefasciatus is one species within the Culex pipiens species complex and can be found throughout tropical and temperate climates of the world. The ability of C. quinquefasciatus to take blood meals from birds, livestock, and humans contributes to its ability to vector pathogens between species. Here, we describe the genomic sequence of C. quinquefasciatus: Its repertoire of 18,883 protein-coding genes is 22% larger than that of Aedes aegypti and 52% larger than that of Anopheles gambiae with multiple gene-family expansions, including olfactory and gustatory receptors, salivary gland genes, and genes associated with xenobiotic detoxification.
452 citations
Authors
Showing all 1274 results
Name | H-index | Papers | Citations |
---|---|---|---|
John R. Yates | 177 | 1036 | 129029 |
Anders M. Dale | 156 | 823 | 133891 |
Ronald W. Davis | 155 | 644 | 151276 |
Steven L. Salzberg | 147 | 407 | 231756 |
Mark Raymond Adams | 147 | 1187 | 135038 |
Nicholas J. Schork | 125 | 587 | 62131 |
William R. Jacobs | 118 | 490 | 48638 |
Ian T. Paulsen | 112 | 354 | 69460 |
Michael B. Brenner | 111 | 393 | 44771 |
Kenneth H. Nealson | 108 | 483 | 51100 |
Claire M. Fraser | 108 | 352 | 76292 |
Stephen L. Hoffman | 104 | 458 | 38597 |
Michael J. Brownstein | 102 | 274 | 47929 |
Amalio Telenti | 102 | 421 | 40509 |
John Quackenbush | 99 | 427 | 67029 |