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Potential Breakthroughs in Treating Oral Disease Through Better Understanding of the Oral Microbiome
Most people think of bacteria as the enemy, but scientists at the J. Craig Venter Institute (JCVI) are exploring ways to harness bacteria and phages (the viruses that infect bacteria) as a new way to fight infection. JCVI scientist, Anna Edlund, PhD, is leading one of our efforts to understand the human oral microbiome and learn what role bacteria play in both oral health and disease. Inflammatory gum disease (gingivitis/periodontal disease) and tooth decay are not only the two biggest...
Development of a high throughput sequencing and analysis pipeline for West Nile virus
Emmi Mueller1, Rebecca A. Halpin1, Nadia Fedorova1, Timothy B. Stockwell2, Danny Katzel2, Laura Kramer3, Suman R. Das1 1Virology Group and 2Informatics Department, J. Craig Venter Institute, Rockville, MD; and 3 Wadsworth Center, New York State Department of Health, Slingerlands, NY West Nile virus (WNV) is a member of the Flaviviridae family of enveloped, single-stranded RNA viruses with a linear, non-segmented, positive-sense ~11,000bp genome. WNV is an enzootic virus...
Identifying Bacterial Antibiotic Resistance Markers in gut microbes
Ian Lamb, Manolito Torralba J. Craig Venter Institute, La Jolla, CA The gut microbiome plays a critical role in our health and well-being, but it also facilitates sharing of antibiotic resistance genes. However, antibiotic resistance genes can be identified by distinct markers which we screen in this study. Plasmids pTRACA18, pTRACA20, and pTRACA22 were chosen since they have demonstrated to be present in many gut microbes. This in turn allows the bacteria to spread antibiotic...
Genomic Data Analysis and Visualization for identification and characterization of WGS
Enrique Garcia-Assad, Indresh Singh, Pratap Venepally, Jason Inman J. Craig Venter Institute, Rockville, MD Whole-genome sequencing (WGS) is becoming available as a common place tool for clinical microbiology. If applied directly on clinical samples, this could further reduce diagnostic times and thereby improve control and treatment especially in outbreak events. A major bottleneck is the availability of fast and reliable bioinformatic tools to identify and characterize large...
Everybody is Kung-Flu Fighting: Deep Sequencing of Clinical Influenza A Virus Reveals Patterns of Emerging/ Re-emerging Amino Acid Substitutions
Emma Roth, Brian Aevermann, Vinita Puri, Nadia Fedorova, Susmita Shrivastava, Lihui Wu, Paolo Amedeo, Rafael Medina, Gene Tan, Brett E. Pickett J. Craig Venter Institute, La Jolla, CA Infection by influenza A virus (IAV) can occur in birds or swine, and results in approximately 700,000 hospitalizations and 56,000 human deaths each year. Although vaccines exist and are reformulated each year, the rapid mutation rates (antigenic drift) and reassortment (antigenic shift) across...
Optimizing Phagehunting Methods to Isolate and Amplify Bacteriophages
Shriya Singh, Enrique Assad-Garcia, Nacyra Assad-Garcia, Lauren Oldfield, Sanjay Vashee, and Derrick E. Fouts J. Craig Venter Institute, Rockville, MD 20872 There are an estimated 1031 bacteriophages (phage), viruses that infect bacteria, in the biosphere, thus comprising a significant portion of the biosphere on Earth. Of these, a mere 10,733 phages have been isolated and 2,061 phages have sequenced, complete genomes, with even fewer, only 1,073,...
Genomic and Antigenic Analysis of Seasonal H3N2 Influenza a Virus From 2012-2013
Haley Hochstein1, Karla M. Stucker1, Seth Schobel2, Xudong Lin1, Randall J. Olsen3, Anju Subba1, Rebecca A. Halpin1, Asmik Akopov1, Nadia Fedorova1, Timothy B. Stockwell2, James M. Musser3, Suman R. Das1, David E. Wentworth1 1Virology Group and 2Informatics Department, J. Craig Venter Institute, Rockville, MD 20850 3Center for Molecular and Translational Human Infectious Diseases Research, The Methodist Hospital Research Institute, Houston, TX 77030 Influenza is an acute viral...
Generating a Library of Influenza a Virus Hemagglutanin and Neuraminidase Genes
Titas Bera, Anthony Bennici, Haley Hochstein, Karla M. Stucker, Suman R. Das, David E. Wentworth Virology Group, J. Craig Venter Institute, Rockville, MD 20850 Every year, five to twenty percent of the United States population is infected with seasonal influenza, making the construction of a seasonal vaccine of high importance. However, due to antigenic drift among seasonal influenza viruses, the vaccine strains need frequent updating. Antigenic drift occurs as the genes encoding...
Sequence-independent Amplification of Rotaviruses for High-throughput Next-generation Sequencing
Anthony K. Bennici1, Karla M. Stucker1, Asmik Akopov1, Nadia Fedorova1, Rebecca A. Halpin1, Timothy B. Stockwell2, David E. Wentworth 1Virology Group and 2Informatics Department, J. Craig Venter Institute, Rockville, MD 20850 Rotavirus is a segmented dsRNA virus that causes gastroenteritis and is the primary cause of severe pediatric diarrhea, which results in over half a million deaths per year globally. There are eight known species of rotaviruses (A-H) that infect humans and...
Translational Health Science and Technology Institute (THSTI) Training
In September 6-8, 2017, Translational Health Science and Technology Institute (THSTI), NIAID Division of Microbiology and Infectious Diseases (DMID) , NIAID PATRIC Bioinformatics Resource Center/University of Chicago and NIAID Genomic Center for Infectious Diseases at J. Craig Venter Institute participated in three days training in Delhi, India for Indo-US Workshop on Genomics and Bioinformatics to Explore Human Microbiome Ecology in Health and Diseases. The Translational Health Science and...