San Diego, CA, United States

J. Craig Venter Institute

jcvi.org
San Diego, CA, United States

The J. Craig Venter Institute is a non-profit genomics research institute founded by J. Craig Venter, Ph.D. in October 2006. The Institute was the result of consolidating four organizations: the Center for the Advancement of Genomics, The Institute for Genomic Research , the Institute for Biological Energy Alternatives, and the J. Craig Venter Science Foundation Joint Technology Center. It has facilities in Rockville, Maryland and La Jolla, California.The Institute studies the societal implications of genomics in addition to genomics itself. The Institute's research involves genomic medicine; environmental genomic analysis; clean energy; synthetic biology; and ethics, law, and economics. The Institute employs over 400 people, including Nobel laureate Hamilton Smith. Wikipedia.

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Patent
Novartis and J. Craig Venter Institute | Date: 2015-07-22

The invention provides proteins from group B streptococcus (Streptococcus agalactiae) and group A streptococcus (Streptococcus pyogenes), including amino acid sequences and the corresponding nucleotide sequences. Data are given to show that the proteins are useful antigens for vaccines, immunogenic compositions, and/or diagnostics. The proteins are also targets for antibiotics.


Patent
Novartis and J. Craig Venter Institute | Date: 2015-06-26

The invention provides proteins from group B streptococcus (Streptococcus agalactiae) and group A streptococcus (Streptococcus pyogenes), including amino acid sequences and the corresponding nucleotide sequences. Data are given to show that the proteins are useful antigens for vaccines, immunogenic compositions, and/or diagnostics. The proteins are also targets for antibiotics.


Patent
Novartis and J. Craig Venter Institute | Date: 2016-05-26

The invention provides proteins from group B streptococcus (Streptococcus agalactiae) and group A streptococcus (Streptococcus pyogenes), including amino acid sequences and the corresponding nucleotide sequences. Data are given to show that the proteins are useful antigens for vaccines, immunogenic compositions, and/or diagnostics. The proteins are also targets for antibiotics.


Lasken R.S.,J. Craig Venter Institute | McLean J.S.,University of Washington
Nature Reviews Genetics | Year: 2014

The vast majority of microbial species remain uncultivated and, until recently, about half of all known bacterial phyla were identified only from their 16S ribosomal RNA gene sequence. With the advent of single-cell sequencing, genomes of uncultivated species are rapidly filling in unsequenced branches of the microbial phylogenetic tree. The wealth of new insights gained from these previously inaccessible groups is providing a deeper understanding of their basic biology, taxonomy and evolution, as well as their diverse roles in environmental ecosystems and human health. © 2014 Macmillan Publishers Limited. All rights reserved.


Haft D.H.,J. Craig Venter Institute
Current Opinion in Microbiology | Year: 2015

Bioinformatics looks to many microbiologists like a service industry. In this view, annotation starts with what is known from experiments in the lab, makes reasonable inferences of which genes match other genes in function, builds databases to make all that we know accessible, but creates nothing truly new. Experiments lead, then biocuration and computational biology follow. But the astounding success of genome sequencing is changing the annotation paradigm. Every genome sequenced is an intercepted coded message from the microbial world, and as all cryptographers know, it is easier to decode a thousand messages than a single message. Some biology is best discovered not by phenomenology, but by decoding genome content, forming hypotheses, and doing the first few rounds of validation computationally. Through such reasoning, a role and function may be assigned to a protein with no sequence similarity to any protein yet studied. Experimentation can follow after the discovery to cement and to extend the findings. Unfortunately, this approach remains so unfamiliar to most bench scientists that lab work and comparative genomics typically segregate to different teams working on unconnected projects. This review will discuss several themes in comparative genomics as a discovery method, including highly derived data, use of patterns of design to reason by analogy, and in silico testing of computationally generated hypotheses. © 2014 Elsevier Ltd.


Patent
J. Craig Venter Institute | Date: 2015-03-17

A modular device that is optimized for preliminary water treatment and energy generation and methods for operating the same are described.


Patent
Glaxosmithkline and J. Craig Venter Institute | Date: 2016-05-09

Disclosed herein are various open reading frames from a strain of E. coli responsible for neonatal meningitis (MNEC), and a subset of these that is of particular interest for preparing compositions for immunising against MNEC infections.


Grant
Agency: NSF | Branch: Standard Grant | Program: | Phase: CHEMICAL OCEANOGRAPHY | Award Amount: 301.71K | Year: 2016

The importance of iron (Fe) as a limiting micronutrient in the ocean is a relatively new discovery. And while critical advances have been made in understanding the marine iron cycle, a full description remains elusive due to its biogeochemical complexity and the low concentrations of iron in the ocean. The research funded in this project seeks to advance our understanding of the chemical forms of Fe in seawater. This will be done by first refining a novel, selective electrochemical analytical method for looking at Fe at natural concentrations in seawater and then relating the resulting data to the genetic composition of the microbial communities responsible for creating the organic molecules that control the fate and chemical form of Fe in the ocean. We now know that iron is an incredibly important micronutrient to biological communities, and this new approach of linked genomic and analytical data has the potential to provide important insights that will significantly advance the study of iron composition in the ocean. This project will also support two graduate students at Scripps Institute of Oceanography, both participating in a new outreach program with 6th graders initiated by the Birch Aquarium at Scripps.

The importance of iron as a limiting micronutrient in the ocean has become a topic of avid research, and there have been many advances in the field. However, characterizations of iron speciation in seawater are still broad by nature due to the lack of precision in the electrochemical analytical techniques. Competitive ligand exchange - adsorptive cathodic stripping voltammetry (CLE-ACSV) has been a commonly used technique to study iron speciation in seawater. This research seeks to improve this method by applying CLE-ACSV at multiple analytical windows (MAW) to increase resolution at the strong and weak ends of the iron-binding ligand spectrum. Additionally, by relating data from this technique to data on the metagenomic composition of the resident microbial community, the work should be able to make meaningful connections between the microbial communities that produce the organic ligands that we now know dominate iron speciation, solubility, and uptake in the ocean. This research has the potential to make a significant contribution to the current understanding of iron cycling in seawater, and it will help us to better understand the larger global ocean biogeochemical processes that control the distribution and availability of iron and its controls on global productivity.


Patent
Glaxosmithkline and J. Craig Venter Institute | Date: 2015-10-06

Polypeptides comprising various amino acid sequences derived from Haemophilus influenzae type b, including a number of lipoproteins. These can be used in the development of vaccines for preventing and/or treating bacterial meningitis. They may also be useful for diagnostic purposes, and as targets for antibiotics. Antibodies against the polypeptides are also disclosed, as are the coding nucleic acids.


Grant
Agency: NSF | Branch: Standard Grant | Program: | Phase: Dimensions of Biodiversity | Award Amount: 402.15K | Year: 2016

All cells require energy. This fact is somewhat taken for granted in biodiversity studies of plants and animals, but is at the forefront of discovering novel microbial biodiversity. As an electrical charge flows through energy transfer molecules in a cell, it is coupled to the production of ATP molecules (akin to charging the battery that powers the cell) or the production of other compounds that are critical for life function. Until recently, it was thought that all cells require electron energy transfer molecules that are soluble in water, so that they can be brought into the cell. However, scientists discovered that some bacteria are able to use solid metals such as rust (iron oxides) located outside the cell as an energy source. They do so by shuttling electrons from the inside of the cell to the outside of the cell, via energy transfer molecules that deliver electrical charge to metal deposits in the environment. In other words, part of these microbes energy production pathways have evolved to be outside of the cell. This process, termed extracellular electron transfer (EET), transformed how we think about cellular life and in particular how microbes may impact the global elemental cycles that sustain life on Earth. This research team will conduct the first wide-ranging assessment of the diversity of EET across all three domains of life (Bacteria, Archaea and Eukarya). The project will also broaden public understanding about microbial life through developing interactive museum exhibits that present microbial EET to the public. Project investigators will work with the Encyclopedia of Life to broaden the representation of microbes in their databases and in school curricula. The project is also uniquely poised to strengthen industry and academic pipelines through educational curriculum that engages middle school students in interdisciplinary EET research, and a pedagogical training and lab exchange program that affords students and postdoctoral scholars an opportunity to conduct interdisciplinary research.

Consistent with the objectives of the DIMENSIONS program, this proposal aims to establish the degree to which ribotypes and genotypes relate to function and activity. This is also a grand challenge in environmental microbiology, and our ability to use bioelectrochemical systems to selectively target electroactive communities affords a unique opportunity to selectively isolate and characterize microbes capable of extracellular electron transfer (EET). To these ends, the overarching goal of this proposal is to comprehensively assess and relate the phylogenetic diversity, genetic/genomic diversity, and functional diversity of microorganisms engaged in EET across all three domains of life. The work plan includes: 1) conducting the first broad, systematic assessment of the phylogenetic diversity of EET-enabled microbes in natural habitats; 2) using the results of these data to identify 20 representative communities for co-registered metagenomic, metatranscriptomic, and biogeochemical characterization to target differentially expressed transcripts associated with EET and the biogeochemical processes that are mediated by these communities; 3) characterizing the genetic, biochemical and biophysical attributes of cultivated but uncharacterized microbes commonly found on electroactive surfaces; 4) integrating these results to develop a better capacity to predict the physiologies and biogeochemical impacts of electroactive communities in nature; and 5) archiving these data in robust databases to allow others to relate the projects findings to their data. These efforts will provide, for the first time, a comprehensive dataset linking phylogenetic data (16S, 18S) with functional potential (genomics), physiological poise (transcriptomics) and metabolic activity (geochemical measurements) that will have many applications to beyond biodiversity science. For example, the combined omics and rate measurements will allow the investigators to constrain the extent to which EET contributes to biogeochemical cycles in nature. The transposon mutagenesis and biophysical studies, in turn, will help researchers understand the means by which common but poorly characterized microbes carry out EET. While the value of each of the proposed efforts is significant, the coordination of these activities enables true integration of these findings to provide a comprehensive perspective on the relationships among phylogenetic, genomic and physiological diversity.

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