J Craig Venter Institute Inc

Programs: Department of health and human servicesduring 2016, jcvi had 40 active research grants and five active contracts from agencies within dhhs. Among these was jcvi's largest funded program, a grant from the national institute of allergy and infectious diseases (niaid/nih) to serve as a genome center for infectious diseases (gcid). The gcid program scope includes analysis of viral, bacterial, and parasite pathogens. The bacterial and parasite programs have a particular emphases on antimicrobial resistance. The bacterial program is focused on the evolution and transmission of carbapenem-resistant enterobacteriaceae and other gram-negative bacteria. All genome sequence data produced with gcid funding is rapidly deposited in public repositories to promote the widest possible use among research scientists. Of the 45 funded awards, 29 involve formal collaborative agreements with 27 different universities, research institutes, and companies, reflecting a highly interactive research portfolio. Jcvi, in collaboration with northrup grumman, serves as the main developer of the viral pathogen resource (www. Viprbrc. Org) and the influenza research database (www. Fludb. Org). These resources serve as free public portals to a wide range of information, data, and analytical tools for interpreting viral genomes in the context of disease. Over 3000 researchers throughout the world use these resources every week. Several additional dhhs grants are human microbiome studies. The microbiome is the collection of microbes that live in and on the human body; these have received considerable attention in recent years because a new appreciation of the complex roles that they play in health and disease. Some of these studies are aimed at basic characterization of the composition and activity of the microbiome, while others seek to understand the contribution of the microbiome to the development of various diseases including alcoholic hepatitis, type 1 diabetes, dental caries, diarrhea, and esophageal cancer, among others. The institute also participates in the h3africa program via a collaboration with addis ababa university to study the spread and pathogenesis of tuberculosis and a collaboration with the university of cape town to train collaborators in human microbiome analysis. The program is sponsored by the nih common fund to bring technological resources and training in a capital investment-intensive field (genomics) to the african content via collaborations with u. S. Scientists with expertise in this field. Jcvi has numerous grants that are designed to understand the human genetic contribution to disease based on analysis of genetic variation in families and in case/control studies, particularly in the context of psychiatric disorders, the systems biology of infectious diseases and antimicrobial resistance/new antibiotics discovery.

national science foundationduring 2016, jcvi had 14 active research grants from the national science foundation (nsf). These encompassed diverse areas of research in environmental microbiology, bioremediation, computational biology, and education. Jcvi, along with other collaborators, is the developer and host of the arabidopsis information portal a public resource of information about this important model plant species. In addition to providing data and analysis tools, the portal offers users the ability to design their own analytical "apps" that can be run within the system on all of the data accessible through the portal, providing considerable latitude for new and innovative uses of the information. One large program is devoted to development of a vaccine to prevent bovine pleuropneumonia, an infectious disease of cattle in sub-saharan africa. Several grants pertain to environmental microbiology, analyzing the roles of microbes in important ecosystems throughout the world.

department of defenseduring 2016, jcvi had 5 active research awards from the department of defense (dod). These awards focus on the understanding of polymicrobial infections in wounds, the development of synthetic genomic technologies for manipulation of chromosomes and genomes and for the development of safe methods for dna isolation and analysis from biothreat agents. Funded by the defense threat reduction agency (dtra), the jcvi is investigating an aspect of the wellrecognized public health threat of antibiotic drug resistance in pathogenic bacteria. In addition to standard bacterial resistance to antibiotics, infection causing bacteria are able to assume a metabolic state that makes the bacteria highly tolerant of massive doses of antibiotics. This state is termed the persister state and accounts for antibiotic failure in patients being treated for infections and for the reemergence of an infection after an apparent clearing of the disease by antibiotic treatment. Jcvi is investigating the genetic/genomic infrastructure of the persister state in the public health and biothreat bacterial pathogen burkholderia pseudomallei using both genome based technologies and traditional microbiology approaches with the ultimate goal of finding ways to eliminate even bacteria in the persister state from patients with bacterial infections. Jcvi, funded through the defense advanced research projects agency (darpa) biological control program is applying the lessons learned from minimizing and reorganizing a bacterial genome to remodel the genome of an industrially useful, vastly more complicated eukaryotic yeast, called kluyveromyces marxianus. In using a single k. Marxianus chromosome as a platform, jcvi is developing a generalized set of algorithms for minimization and defragmenting the genes into functional modules that could be applied to all small genome eukaryotes, such as yeasts, eukaryotic algae, and parasites.

other program servicesthe jcvi grant portfolio also included support from several other federal agencies and foundations including:u. S. Department of justice jcvi is developing a forensic microbiome database that will allow for human trafficking. As part of this award we will work with 5 international cohorts at diverse global locations. The richard lounsbery foundation the jcvi team is working in collaboration with a group in europe to decipher the genome of leonardo da vinci and his relatives, and also using the microbiome as an approach to improve art conservation. Human vaccines project jcvi, in collaboration with the san diego supercomputer center, serves as the main developer of the central data management and bioinformatics hub for the human vaccines project (hvp), with direct support from the hvp general fund. The mission of the hvp is to accelerate the development of vaccines and immunotherapies against major global infectious diseases and cancers by decoding the human immune system. The goal of the hvp bioinformatics hub is to provide high-availability, standardized data and advanced analytical capabilities to the human vaccine project. Jcvi is also contributing single cell genomics assays and analysis examining cellular responses to hepatitis b vaccination. California institute for regenerative medicine (cirm) jcvi, in collaboration with the university of california, santa cruz, the university of california, san diego, and stanford university, is involved in the development of the main data management portal for the cirm center of excellence in stem cell genomics (cescg). Jcvi's role has been to develop a series of data standards to support the integration and dissemination of cescg experimental genomics data, and to develop novel statistical methods for single cell genomics data analysis. The roddenberry foundation for development of sustainable wastewater treatment solutions for the developing world. The gates foundation for understanding and optimizing the efficacy of pneumococcal vaccination nasa for understanding the impact of space travel on the human microbiome.