Posts in category Bioinformatics

Research Impact: Accelerating Efforts to Contain and Prevent the Zika Virus (ZIKV)

Published by JCVI Staff on 18 October 2016 in Bioinformatics, Genomic Medicine and Infectious Disease.

The rapidly developing Zika virus (ZIKV) outbreak has research groups, government agencies, and industry is all striving to develop a response plan to contain and ultimately prevent ZIKV spread. Currently JCVI is working with both private and public sector funders to sequence and analyze historical and current ZIKV strains. Work at JCVI is geared toward developing sensitive ZIKV diagnostics, significantly increasing the number of ZIKV genomic sequences available, and performing cutting-edge analysis on current and future sequence data. We expect these efforts to guide the rational design of ZIKV antivirals and vaccines to treat and prevent ZIKV-induced disease. Here we highlight areas of ongoing ZIKV related work at JCVI. In each area, additional funding would accelerate our efforts to understand and ultimately control ZIKV infection in the human population.

ZIKV

As of October 12, 2016 the Centers for Disease Control and Prevention reported 3,936 cases of ZIKV infection, with two Florida cities identified as the Ground Zero for local transmission.

ZIKV sequencing efforts at JCVI:

  • JCVI, through an existing NIH funded grant, is working with the Biodefense and Emerging Infections Research Resources Repository (BEI Resources) to provide high quality sequence data for publically available ZIKV strains. These strains represent a collection of ZIKV isolates, ranging from the initial 1947 isolate from Uganda to 2015 isolates from Puerto Rico, Colombia, and Panama, Mexico, and Honduras. JCVI is providing the gold standard annotated reference sequence for all strains available from BEI and will continue this effort as BEI obtains additional ZIKV isolates.
  • Shortly after the recent Zika virus outbreak emerged in eastern Brazil, Dr. Richard Scheuermann and his bioinformatics team at JCVI collaborated with software engineers at Northrop Grumman to develop a custom Zika website portal to provide genomic sequence and other data about Zika virus through the public Virus Pathogen Resource (ViPR). As of September 2016, the ViPR Zika portal contains 389 genomic and 2399 protein sequences representing the three major Zika lineages – East African, West African and Asian. To support comparative genomics analysis to investigate the evolution of virulence in the newly emerging outbreak isolates, Scheuermann’s group developed an algorithm for predicting the proteolytic cleavage sites that generate Zika mature peptides, and applied this method to produce a comprehensive record of all predicted mature peptides for all Zika genomic sequence in the ViPR database.
  • JCVI is currently working with collaborators in Colombia and Nicaragua to collect sera from patients suspected to harbor ZIKV and to sequence the viral genome from these patients.
  • JCVI was recently awarded NIH supplemental funding to work with Sanofi-Pasteur to screen and sequence human samples suspected to be positive for ZIKV. The majority of samples, provided by Sanofi, are from children and adolescents from the Americas and the South Pacific where mosquito transmitted viruses are common. Over the upcoming year, JCVI anticipates screening both retrospective and prospective human serum samples for ZIKV, with the assumption that many of these samples are from individuals infected with other viral diseases (e.g. Dengue Virus).

Toward the development of a rapid ZIKV diagnostic:

  • Brett Pickett recently received funding from the US Agency for International Development (USAID) to develop a method for detecting antibodies against Zika virus in human patients. A bioinformatics analysis performed previously at JCVI uncovered regions of Flavivirus proteins that differentiate between 10 species of viruses—including Zika. Custom peptide arrays will be constructed to identify immunodominant epitopes in human serum, which we will then optimize as an ELISA-based diagnostic for use in developing countries.
  • To distinguish between ZIKV and other viral diseases, we are developing a highly sensitive and specific ZIKV diagnostic PCR assay.
  • Our assay is sensitive, and we have demonstrated the ability for the assay to identify ZIKV from diverse geographical regions. Future work seeks to move this technology from the laboratory to the field.

Next generation vaccine technology at JCVI can be applied to ZIKV:

  • JCVI has previously coupled synthetic biology for the rapid generation of an Influenza vaccine.
  • Currently, JCVI is using both synthetic biology and vaccinology to develop a universal vaccine for the common cold in partnership with Synthetic Genomics (A company founded by Dr. Venter) and private funders
  • The established vaccine technology at JCVI and our ability to rapidly identify and sequence ZIKV would allow the institute to pursue novel ZIKV vaccine platforms.

Mosquito genomic sequencing:

  • JCVI is currently sequencing the genome of a mosquito that is known to harbor ZIKV and is present in the Americas.
  • Determining the genomic sequence of this mosquito will help research groups identify develop targeted approaches to impair ZIKV replication in the mosquito host.

Current efforts to combat Zika virus involve CLIA-approved methods to detect viral genetic material. In addition, there are multiple players currently developing a vaccine including GlaxoSmithKline, Sanofi, and Onovio Pharmaceuticals. Ensuring that any vaccine doesn’t cause any neurodevelopmental problems further complicates these efforts. Vector control departments around the United States are currently spraying to eradicate adult and larval mosquitoes. While these endeavors serve to prevent virus infection and spread through mosquitoes, they have negatively affected bee populations and organic crops—potentially increasing public acceptance of sterile GMO mosquitoes.

One of the key questions that arose as a result of the Zika outbreak in the western hemisphere is if the virus has mutated to become more virulent, causing more severe neurological pathology than previously circulating strains. Comparative genomics analysis using sequences and analysis tools in ViPR has identified both nucleotide and amino acid substitutions in the outbreak lineage that warrant further investigation to determine if they are responsible for the apparent increased virulence of the new outbreak strain. With the detection of mosquito-borne transmission in Puerto Rica and the continental US, there is now a critical need for more funding for further research into the genomic determinants of virulence and for accelerated development of targeted diagnostics, therapeutics and vaccines. Donate today!

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Genomic Workshop for Native American College students

Published by JCVI Staff on 17 June 2016 in Bioinformatics, Education and Plant Genomics.

A Genomic Science Workshop was held last week (May 24-26, 2016) at the J Craig Venter Institute Rockville campus for a group of ten Native American college students. The students participated in two full-day intensive training activities learning how to study the “microbiome” of natural water sources. Each student had the chance to perform hands-on lab work including DNA isolation from an environmental water source, PCR of the 16S ribosomal RNA gene, and gel electrophoresis. Individual computer workstations were provided for the computer lab sessions for students to follow along. The group was introduced to basic Linux command-line analysis and the popular 16S analysis package QIIME. Overall, the workshop provided the students a foundation of knowledge and tools to identify and classify microbial populations in environmental water sources, and enabled the students to participate in water quality analysis and monitoring efforts of their homeland reservations.

Collage from Maize Cell Genomics Workshop for Undergraduates

Collage from Genomic Workshop for Native American College students

The workshop students were welcomed by JCVI President Karen Nelson and Rockville Campus Director Rembert Pieper. Informal discussion panels were also held to provide networking and research career development opportunities with invited guest speakers including Science Education Directors from the Howard Hughes Medical Institute (HHMI), and Native research scholars from the National Institute of Health (NIH). The students were also presented with a preview of the astronaut microbiomes as an application of human microbiome study. Workshop students also had the opportunity to visit the US Capitol and the National Museum of the American Indian.

The workshop was funded by the National Science Foundation through a Maize Cell Genomics grant and was organized by Agnes Chan (JCVI; co-PI), in collaboration with the Cold Spring Harbor Laboratory (CSHL; PI Dave Jackson, Outreach Educator Joslynn Lee), the University of Wyoming (UW; co-PI Ann Sylvester), Montana State University (Mari Eggers), and the Little Big Horn College (LBHC; John Doyle). LBHC is a tribal college located in the Crow Reservation, MT. The NSF Maize project has established a long-term outreach relationship with LBHC, and has organized a number of training workshops for Native students previously at LBHC, UW, and CSHL. Participants for the 2016 workshop included Native students recruited from the LBHC, Montana State University, Fort Lewis College, and Northern Arizona State University.

The PIs of the Maize Genomics Project would like to express sincere thanks to instructors from JCVI including Hernan Lorenzi, Yongwook Choi, Vivek Krishnakumar, Stephanie Mounaud, the JCVI Information Technology team, the Administrative Assistant team, and all colleagues for their generous assistance, support, and patience for a successful outreach educational workshop.

To find out more information on workshop schedule, notes, and manuals, please visit the Maize Cell Genomics project web site at http://www.weizhongli-lab.org/cellgenomics/2016_pcr.php.

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Ongoing Zika virus work at JCVI

Published by JCVI Staff on 31 May 2016 in Bioinformatics and Infectious Disease.

The rapidly developing Zika virus (ZIKV) outbreak has research groups, government agencies, and industry all striving to develop a response plan to contain and ultimately prevent ZIKV spread. Currently JCVI is working with both private and public sector funders to sequence and analyze historical and current ZIKV strains. Work at JCVI is geared toward developing sensitive ZIKV diagnostics, significantly increasing the number of ZIKV genomic sequences available, and performing cutting-edge analysis on current and future sequence data. We expect these efforts to guide the rational design of ZIKV antivirals and vaccines to treat and prevent ZIKV-induced disease. Here we highlight two areas of ongoing ZIKV related work at JCVI.

Zika virus

This is a digitally-colorized transmission electron micrograph (TEM) of Zika virus, which is a member of the family Flaviviridae. Virus particles, here colored red, are 40 nm in diameter, with an outer envelope, and an inner dense core. Image credit: CDC/ Cynthia Goldsmith

JCVI/BEI Resources/NIAID: JCVI, through an existing NIH funded grant, is working with the Biodefense and Emerging Infections Research Resources Repository (BEI Resources) to provide high quality sequence data for publically available ZIKV strains. These strains represent a collection of ZIKV isolates, ranging from the initial 1947 isolate from Uganda to 2015 isolates from Puerto Rico, Colombia, and Panama. JCVI is providing the gold-standard annotated reference sequence for all strains available from BEI and will continue this effort as BEI obtains additional ZIKV isolates. A list of the ZIKV isolates sequenced by JCVI are found here: https://www.beiresources.org/Organism/118/Zika-virus.aspx

JCVI/Sanofi-Pasteur/NIAID: JCVI was recently awarded NIH supplemental funding to work with Sanofi-Pasteur to screen and sequence human samples suspected to be positive for ZIKV. The majority of samples, provided by Sanofi, are from children and adolescents from the Americas and the South Pacific where mosquito transmitted viruses are common. Over the upcoming year, JCVI anticipates screening both retrospective and prospective human serum samples for ZIKV, with the assumption that many of these samples are from individuals infected with other viral diseases (e.g. Dengue Virus). To distinguish between ZIKV and other viral diseases, we are developing a highly sensitive and specific ZIKV diagnostic assay. After confirming ZIKV positive samples, JCVI will perform whole genome sequencing and sequence analysis to understand the evolution of the virus over time and geographical location. We hope that results from this collaborative work will significantly increase our understanding of the origins of the ZIKV outbreak in the Americas and lay the groundwork for future collaborations with NIAID and Sanofi.

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Unlocking the Mysteries of the Microbiome

Published by JCVI Staff on 31 May 2016 in Bioinformatics and Microbial & Environmental Genomics.

In the early 2000s, JCVI researchers pioneered in the exploration of the human microbiome, the community of microbes that live in and on the human body. Originally while at The Institute for Genomic Research (TIGR, now part of JCVI) Drs. Craig Venter and Hamilton Smith were awarded a grant from DARPA to examine the microbes found in the human gut. This work was carried out by researchers at JCVI and published in 2006 in Science. While this team had previously published 16S surveys of the human body, this paper in which the researchers found more than 60,000 microbial genes was the first metagenomic description of microbes resided anywhere on the human body. Ten years since this seminal publication, our scientists continue to pave the way for a broader understanding of these vast microbial populations.

fragment recruitment plot

Visualization of ocean microbial data collected on JCVI’s Global Ocean Sampling Expedition (GOS). The Sorcerer II circumnavigated the globe for more than two years, covering a staggering 32,000 nautical miles, visiting 23 different countries and island groups on four continents.

On May 13, 2016, Drs. Craig Venter and Karen Nelson were present at the White House for the launch of the National Microbiome Initiative (NMI). The NMI will invest $121 million in new microbiome studies in fiscal years 2016 and 2017. The goals of the project are to supplement fundamental research, develop new technologies and engage more people in this area of research.

Today we know that the human body is host to more than 1 trillion microbes. Thanks to continued advances in genome sequencing technologies and metagenomic analysis JCVI scientists are providing a deeper understanding of these microbes across a variety of fields. JCVI researchers know that translating the role of the microbiome in the development of health and disease in humans is essential. We believe that eventually the screening of the human microbiome will be a routine part of medical care, leading to prescribed diets and preventive measures personalized to an individual.

JCVI currently has several dozen microbiome studies underway. In this issue of Amplifier, we are highlighting some of our most exciting and cutting edge work unlocking the mysteries of the human microbiome.

The Effects of Long-Term Space Travel on the Microbiome of Astronauts

On March 1, the world celebrated the safe return of NASA astronaut Scott Kelly after 340 days in space. Researchers are fascinated to learn more about the impact of long-term space travel on the human body, and JCVI scientists are excited to be a part of the process. During a mission to space, astronauts are subject to many stressful conditions (g-forces, radiation, microgravity, anxiety, etc.) that can have a negative impact on their health. For example, astronauts lose muscle mass, bone density, and experience a wide range of health problems with everything from their vision to their gastrointestinal tract. Several studies have demonstrated that space travel also affects the astronauts’ immune systems (for example the reactivation of latent viruses like Herpes Simplex Virus 1 and Epstein Bar virus) and have shown some evidence suggesting that stool microbes change after space flight.

JCVI researchers want to determine how the composition of the astronauts’ microbiome changes during long-term space missions (six or more months), and to evaluate potential risks to astronaut health from changes in the microbiome. We are also interested in how the microbiome of astronauts interacts with other factors such as the microbial communities that inhabit the International Space Station (ISS). To accomplish this, we will monitor the astronauts’ health status, environmental stress, and exposure to space conditions. The skin, tongue, nose and gut of each astronaut will be sampled at multiple time points before, during, and after the mission to the ISS. By sampling the microbiome of astronauts on earth while in peak physical health and during subsequent space flight, we will be able to define signatures of human response to a variety of relevant aspects of space travel. Astronauts will also sample different surfaces and the water supply during their stay at the ISS to correlate crew microbiomes with the microbes living at the ISS. We will also assess changes in the astronauts’ immune function and stress levels throughout the mission by analyzing their saliva and blood for metabolic markers. Finally, we will correlate the microbiome and immune function data collected with other measured metadata including astronaut health and hygiene as well as environmental factors such as temperature, humidity and environmental factors.

This research program is being led by Dr. Hernan Lorenzi.

The Gut Microbiome and Human Evolution

Who we are, where we come from and how we came to be as we are, are questions that have always fascinated biologists. The reasons to answer these questions are multiple, but one critical aspect centers on understanding what makes us human. To start addressing these issues JCVI scientists are exploring the gut microbiome of non-human primates, our closest living relatives, and of populations that most faithfully reflect the lifestyles of early hominids: hunter-gatherers. The goal of this project is to establish an evolutionary baseline to shed light on the host-microbe factors that impacted health and disease in modern and western human populations.

Our scientists have shown, in several recent publications, that the gut microbiome of wild gorillas, is strongly shaped by the external environment, namely by diet. Specifically, we showed that gut microbes adapt to different dietary stimuli, probably providing gorillas with energetic plasticity when preferred feeding resources are seasonally and temporally absent. Interestingly, we also suggested that, in conditions in which gorillas exploit high-energy diets, their gut microbiomes resembles those of humans. This fact has critical implications to understanding the evolutionary origins of obesity and inflammation in modern human populations from a microbe perspective. Along these lines, our most recent publication on the gut microbiome of central African hunter-gatherers, traditional agriculturalists and western humans shows evidence that transitions to agriculture and industrialization, and giving up hunting and gathering could have radically changed our gut microbiomes for good. This observation is vital considering that traditional hunter-gatherers, whose microbiomes resemble those of wild gorillas, do not show symptoms of modern inflammatory disease. These observations highlight the potential impact of gut microbes in human evolution.

The research team consists of Drs. Andres Gomez and Karen Nelson.

Solving Crimes with Your Microbial Signature

In January 2016, JCVI received a two-year, $962,500 award from the United States Department of Justice to design and build an open-access microbiome database for the forensic science community. The Forensic Microbiome Database (FMD), the first of its kind will be populated with several thousand microbiome datasets and associated metadata available from the public domain. The database will be based on established procedures for database development designed at the JCVI, incorporating expansive sets of data and metadata that relate to forensic evidence.

The goals of this project are to: provide a host location and continuous monitoring of the database; define well-structured standard operating procedures for data generation and searching against and uploading data into the FMD; and test the utility of the FMD by sequencing a range of samples obtained geographically for querying and proof of concept against the database. The foundation of this project will serve for future enhancements of the FMD and utility for forensic casework. The research team expects this will become the community resource for analysis of microbiome data and for attributing weight to microbial forensic evidence.

The research team consists of Rhonda Roby, Lauren Brinkac, Toby Clarke, Andres Gomez, Karen Nelson, Harinder Singh, and Shibu Yooseph,

Using the Microbiome to Advance Wound Therapies

Chronic wounds are wounds that fail to heal after 4 months of proper wound care and management. It is a major public healthcare burden that affects an estimated 1% of the US population and costs $25 billion per year. Common chronic wounds are leg, foot, and pressure ulcers occur in adults especially the elderly with diabetes, vascular diseases, or specific body locations under prolonged pressure. According to the Centers for Disease Control and Prevention, approximately 12% of U.S. adults with diabetes had a history of foot ulcer and 11% of U.S. nursing home residents had pressure ulcers. In addition to the economic burden, from the perspective of patients chronic wounds can also lead to loss of function (e.g. amputation), decreased quality of life, and increased rate of mortality.

At JCVI we are interested in deciphering not only the microbial communities present in chronic wounds but also their potential impacts and relationship with the wound healing outcome, for working towards more effective clinical strategies of wound healing. In collaboration with George Washington University, we are conducting a study to analyze chronic wounds. Samples are selected from patients enrolled in the Wound Etiology and Healing biospecimen and data repository (WE-HEAL). We will analyze the chronic wound microbiome at the molecular level, and attempt to identify biological indicators that can be used to predict the healing outcome to further advance wound therapies and management.

This project is being led by Dr. Agnes Chan.

Metagenomic Epidemiology of Antibiotic Resistance in Infectious Diarrhea

Genes that encode antimicrobial resistance (AMR) to antibiotics have been detected in environmental, insect, human and animal metagenomes and the sum of these are known as “resistomes.” While metagenomic datasets have been mined to characterize the healthy human gut resistome, directed metagenomic sequencing has not been used to examine the spread of AMR. Especially in developing countries where sanitation is poor, diarrhea and enteric pathogens likely serve to disseminate AMR elements of clinical significance. Unregulated use of antibiotics further exacerbates the problem by selection for acquisition of resistance. This is exemplified by recent reports of multiple AMR in Shigella strains in India, in Escherichia coli in India and Pakistan, and in nontyphoidal Salmonella (NTS) in South-East Asia.

Sarah Highlander, Ph.D. and her team are characterizing the microbial composition and its component AMR transfer elements (such as plasmids and transposons) by metagenomic sequencing of stool samples from pediatric patients from Colombia who are suffering from diarrhea. Our goal is to assess whether groups of species/strains associate with specific mobile genetic elements and whether their presence is enhanced or amplified in diarrheal microbiomes. This work could potentially identify clonal complexes with enhanced resistance and potential pathogenesis.

For more information on how you can support or human microbiome research program at JCVI, please contact [email protected].

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Durban Microbiome Workshop

Published by JCVI Staff on 28 April 2016 in Bioinformatics, Education and Sequencing.

As part of our continued effort to bring genomics to other communities, Alex Voorhies, Derek Harkins and Andres Gomez traveled to Durban, South Africa to lead a series of workshops on microbiome data analyses. The two days of presentations were made to students, postdocs and faculty at the Durban University of Technology, and was co-sponsored by the NIAID funded JCVI Genomic Center for Infectious Disease. On day one, the JCVI team provided an introductory lecture on microbiomes and technical considerations to plan and conduct microbiome related projects. The lecture followed up with an introduction to sequencing technologies and bioinformatics tools to analyze 16S rRNA next generation sequencing data. The day one session ended up with a lecture on the differences between metagenomics and 16S rRNA sequencing and analyses pipelines and one on one advising with students and faculty on how to analyze and plan their own projects.

On day two the JCVI team provided a hands-on tutorial where students analyzed a time series of mouse microbiome data. Students learned each step of working with a 16S rRNA dataset, from processing raw reads to statistical analysis and figure generation. The morning started with a practical exercise processing 16S reads using mothur to assign taxonomic classification. In the afternoon students used the output from the mothur workshop to learn about analyzing data in R. Students explored alpha and beta diversity as well as indicator species analysis and statistical significance of their findings. The hands-on workshop concluded with various ways to display 16S microbiome data in publication quality figures.

The students were very enthusiastic and active participants in the lectures and hands on units. It is our sincere hope that the workshop helps them to expand their research and data analysis capabilities in the future.

Our hosts, Drs. Suren Singh and Nokuthula Mchunu, sent along nice messages in appreciation for the event:

Have no words to pass the amount of appreciation the student and the supervisors had for the workshop. Andres, Derek and Alex were fantastic in the delivery of the material and having time to address every question we were asking. We hope that we can have another sometime in the future and if we had choice we would pick them. Thank you again.
- Dr. Nokuthula Mchunu

Thank you for sending out a wonderful, and extremely knowledgeable team to ignite one of many workshops at DUT. It was truly a great exposure for many of my students and staff. They enjoyed the theoretical and hands on sessions alike. Let’s continue this association for many more years ahead.

- Dr. Suren Singh

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JCVI’s Global Voyage of Discovery Continues

Published by JCVI Staff on 9 November 2015 in Bioinformatics and Microbial & Environmental Genomics.

Global Ocean Sampling Expedition Planned for 2016

Over the past 12 years, JCVI’s Global Ocean Sampling (GOS) Expedition has continued to explore all of the world’s oceans, along with major inland seas such as the Baltic and Mediterranean. The research team maintains ongoing sampling in the waters off of California and in extreme conditions such as Antarctica and the Amazon River. JCVI’s effort is the largest marine microbial study to date, quantifying both the taxonomic and functional diversity of microbes within these environments, and examining how both the natural environment and humans shape these communities.

Planned 2016 route for the Sorcerer II Global Ocean Sampling Expedition

Planned 2016 route for the Sorcerer II Global Ocean Sampling Expedition

The scientific goals and ideas on the first Sorcerer II Expedition sprung from the sequencing and analysis of Methanococcus jannaschii by Dr. Craig Venter and his research team after the organism was isolated from a hot, deep-sea vent in the Pacific. M. jannaschii is from the Archeal branch of life and is also known as an autotroph, in that it makes all it needs for survival from carbon dioxide, nitrogen, and hydrogen in water. Dr. Venter and the team continue to believe that the unknown and unseen world in the oceans is vital to understanding diversity on the planet and potentially holds the key to solving growing environmental issues.

The deck of the Sorcerer II is equipped with scientific tools including advanced water filtration and communications systems.

The deck of the Sorcerer II is equipped with scientific tools including advanced water filtration and communications systems.

Past GOS efforts have been funded by The Gordon and Betty Moore Foundation, the Beyster Family Foundation Fund, Life Technologies, and additional anonymous donors. To date, the GOS team has analyzed billions of DNA sequences and discovered over a billion new genes, 1700 unique protein families, and assembled dozens of whole genomes for uncultivated microbes. The GOS data are freely available to the public and have resulted in follow-on research across several fields by scientists worldwide. The GOS team utilizes a shotgun metagenomics technique to examine the presence and possible role of microbes in open ocean ecosystems. JCVI has ongoing research internally and with international collaborators to characterize the unexplored microbiomes of marine, estuarine, freshwater, and terrestrial environments around the world.

Highlights of past and present expeditions:

  • The Gordon and Betty Moore Foundation was a significant funder of the first phase of the GOS Expedition from 2004-2006. To date, there are 41 publications from this phase, and an evaluation of the scientific impact of their support shows that these publications have been cited over 2700 times.
  • During the J. Robert Beyster and Life Technologies Foundation 2009-2010 Research Voyage of the Sorcerer II Expedition, aquatic samples were collected by filtration from over 300 aquatic environments in 12 nations and international waters, resulting in over 1100 possible metagenomic samples. The data generated has fostered collaborative projects between JCVI and institutions in eight nations and formed the focus of nine postdoctoral projects and five graduate student theses. The expedition extensively cataloged the microbial diversity and function of nearly all global oceans and marginal seas, and has further developed a mechanistic understanding for the distribution of microbes and function that can be applied to all aquatic environments.
  • In 2014, JCVI embarked on a sampling expedition of the Amazon River and its tributaries, which contains 1/5th of the Earth’s river flow. Long recognized for the biodiversity of visible organisms, the Amazon is understudied with regards to the diversity of microorganisms and the goal of this effort is to continue to increase our understanding of the biological diversity of Earth.
  • Since 2008, JCVI scientists have traveled to the continent of Antarctica. As one of the most untouched regions on the planet and home to the world’s largest marine ecosystem, Antarctica and the Southern Ocean are invaluable to JCVI research involving climate change. Major objectives of the fieldwork are to understand how changes in micronutrient availability, temperature, and pCO2 impact growth, community composition, and nutrient utilization in Southern Ocean phytoplankton. Recently JCVI researchers in collaboration with Scripps Institute of Oceanography uncovered a series of complicated relationships among marine microbes in their fight for important resources, like vitamin B12, that has critical consequences for coastal Southern Ocean food webs. Scientists at J. Craig Venter Institute, Scripps Institution of Oceanography and Other Collaborators, Publish Paper Outlining New View of Microbial Relationships in Southern Ocean Phytoplankton Blooms.

2016 Global Sampling Expedition Addresses Plastic Pollution & Environmental Policy

The planned 2016 GOS Expedition, led by Chris Dupont, Ph.D., Assistant Professor, combines the basic science approaches of previous expeditions with applied science. The team plans to study the wide variety of marine protected areas (MPAs) found throughout the Caribbean Sea, the Florida Straits, the Gulf of Mexico, and the Sea of Cortez. The goal is to profile the ecosystem health of the MPAs and the impact to them by fishing, pollution, habitat degradation and climate change. With dramatic differences in the levels of protection of various MPAs, JCVI researchers will assess the conservation strategy of each MPA then evaluate the outcomes of those strategies on a microbial level, with the goal of making policy recommendations for better ocean preservation.

Chris also proposes to examine the microbes found on plastic pollution in the ocean. Plastic is the most common type of marine litter in the world, and it is wreaking untold havoc on marine ecosystems. This pollution, currently 50 million metric tons per year, has been examined by JCVI researchers and collaborators in preliminary studies, and they have found that these plastics harbor microbes that are not normally found to be abundant in the ocean. With 100 million tons of plastic in the “Great Pacific Garbage Patch”—visualize Texas covered with plastic and floating in the Pacific Ocean, —there is a real and timely need to address the declining health of our oceans. Chris hopes that this research will not only further characterize what microbes are found on plastic pollution, but will also provide the genomic information necessary for building designer microorganisms for the biological degradation and recovery of plastic waste

Exploring the microbes of the oceans is even more exciting and promising than it was when JCVI launched the Sorcerer II Expedition from Halifax, Nova Scotia in August 2003. Each JCVI expedition has led to new discoveries that have deepened our understanding of the world’s waters. What else will we discover in the coming months and years? Whatever it may be, count on JCVI being at the forefront of the discovery. There are many ways that you can support the next phase of discovery and help JCVI scientists find solutions to these environmental challenges. For more information about our GOS expeditions, as well as details on partner opportunities for our 2016/2017 voyages, please contact Katie Collins, [email protected].

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June Grant Update

Published by JCVI Staff on 13 July 2015 in Bioinformatics, Genomic Medicine, Infectious Disease, JCVI, Microbial & Environmental Genomics, Plant Genomics and Synthetic Biology & Bioenergy.

Congratulations to our JCVI Principal Investigators for the several successful grants that were awarded or that we received notification of in the month of June. All of the following PIs received official confirmation of awards to be made to them. Christopher Dupont, John Glass, Granger Sutton, Daniel Gibson, Charles Merryman, Rembert Pieper, Richard Scheuermann, Christopher Town, Reed Shabman, Orianna Bretschger, Sanjay Vashee and Sarah Highlander to the sum of $6,365,099. The topics of these awards ranged from synthetic approaches to studying the human microbiome, vaccine development, protein modeling, studies on tuberculosis strain diversity, and immune profiling.

Of notable mention are the awards to be made to Sanjay Vashee $1,879,282 from the NSF (BREAD supplement that will allow for an extension of the current program focused on developing a synthetic vaccine for Bovine pleuropneumonia), Reed Shabman from DHS ($1,135,654; The development and validation of sequence subtraction databases to improve virus discovery through next generation sequencing – special acknowledgement to Tim Stockwell and Derek Harkins for their contributions to this proposal), and to Chris Town from NSF ($883,704; Federated Plant Data Base Initiative for Legumes).

A sincere Congratulations to the team.

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Meet Richard Scheuermann, Ph.D., JCVI’s Director of Bioinformatics

Published by JCVI Staff on 18 May 2015 in Bioinformatics, Infectious Disease and JCVI.

Richard H. Scheuermann, Ph.D., who joined JCVI in 2012 from the University of Texas Southwestern as the Director of Bioinformatics, is an accomplished researcher and educator. He and his team apply their deep knowledge in molecular immunology and infectious disease to develop novel computational data mining methods and knowledge representation approaches.

Richard Scheuermann

Richard Scheuermann, Ph.D., JCVI’s Director of Bioinformatics

From an early age, Richard was very interested in science and the living world around him. He was a curious child who loved to explore the ponds and fields in his hometown of Warwick, New York. This rural community in upstate New York is covered with dairy farms and apple orchards. He demonstrated an early aptitude for math and science and was fortunate to have talented high school teachers who recognized his potential. Although neither of Richard’s parents were college educated, they encouraged his academic pursuits. When Richard and his father met the high school guidance counselor, Richard told of his intention to attend the Massachusetts Institute of Technology (MIT). The response from the counselor was a resounding, “There is no way you’ll ever get in.” Richard applied to MIT (and only MIT) anyway, and was accepted by early decision.

At MIT Richard intended to pursue a career in chemical engineering (CE) but to his surprise, he found that he loathed the CE classes. While trying to identify a new study path, Richard took a biochemistry class to fulfill a CE requirement. This class would change Richard’s career path. While at MIT, Richard worked in the lab of Annamaria Torrianni-Gorini, Ph.D. and received first hand experience in conducting scientific research. He was inspired by his peers and professors and had found his calling. During this time he also had the privilege to study with Salvador Luria, Ph.D., David Baltimore, Ph.D., David Botstein, Ph.D., and Phil Sharp, Ph.D., all luminaries in their fields. Richard received a B.S. in Life Sciences from MIT in 1981.

Richard went on to complete his Ph.D. in Molecular Biology at the University of California, Berkeley. After completing his doctoral research on bacterial replication fidelity at U.C. Berkeley with Hatch Echols, Ph.D., Richard was offered his own research lab in Europe. He accepted an independent research position at the Basel Institute for Immunology in Switzerland, where he identified the CDP protein as a critical regulator of immunoglobin gene expression and the role of nuclear matrix attachment in transcription regulation.

Although Richard had trained as a molecular biologist, in 1992 he was recruited into the Department of Pathology at the University of Texas Southwestern Medical Center (U.T. Southwestern) in Dallas. Apprehensive at the beginning to find himself in a clinical department, as he had at every previous crossroads, Richard quickly embraced the opportunity before him. He changed his research focus to disease and disease pathogenesis, and he rose to the rank of Professor with tenure. Richard established a robust research program at U.T. Southwestern investigating signal transduction pathways that regulate normal lymphocyte development and function and that induce cell cycle arrest, apoptosis and dormancy in lymphomas. This important work was supported through numerous research grants from the National Institutes of Health, the American Cancer Society, the Texas Higher Education Coordinating Board, and other granting agencies. In the Pathology Department, he also worked on the development and validation of novel diagnostic methods for viruses that mediate chronic infectious disease and for chromosomal translocations that drive leukemia and lymphoma development.

Half way through his U.T. Southwestern career, Richard had found life in the wet lab less and less fulfilling. Through his involvement in several high-throughput research projects Richard realized that it was becoming relatively easy to generate lots of data but more difficult to analyze the information. And so he decided to take a sabbatical year at the San Diego Supercomputer Center to immerse himself into the emerging field of bioinformatics. After his time in San Diego, Richard was drawn into the bioinformatics discipline, and he redirected his career with three research and development proposals funded in rapid succession.

Richard established a very successful bioinformatics program at U.T. Southwestern; however, he was searching for new opportunities to expand on his success. In 2012, the invitation to join JCVI, a “bleeding-edge research institution that valued informatics” could not be ignored.

As the Director of Bioinformatics at JCVI, Richard leads a multi-disciplinary team of computational biologists. Richard and his team continue to develop novel computational methods to accelerate data mining and statistical analysis. These methods have been made available to the research community through several public database and analysis resources, including the Influenza Research Database (IRD; www.fludb.org), the Virus Pathogen Resource (ViPR; www.viprbrc.org) and the Immunology Database and Analysis Portal (ImmPort; www.immport.org) supported by the National Institutes of Health. His current research is focused on human pathogenic viruses—how they spread and cause disease. He is a part of the elite community that responds to virus outbreaks, such as the recent Ebola and Enterovirus D68 occurrences. This “real time sorting out” of emerging infectious diseases keeps his still curious New York state of mind engaged and excited about his work.

In his spare time Richard enjoys swimming, soccer and skiing and spending time with his wife, Nancy, and sons, Alex and Derek. Over the past thirteen years, he has studied martial arts, earning his first-degree black belt. As it was in the outskirts of Warwick, Richard continues to explore his new San Diego environment, and is rapidly becoming an avid sailor.

Richard’s commitment and determination to a path, whether on the high seas or in the lab, are unrivaled. Like him, his peers at JCVI are excited to see where his research will take us next.

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2015 Advanced Genomics, Metagenomics, and Bioinformatics Workshop Wrap-up

Published by JCVI Staff on 13 March 2015 in Bioinformatics, Education, Infectious Disease, Microbial & Environmental Genomics and Sequencing.

I was lucky enough to help set up and plan a workshop covering genomics, metagenomics, proteomics and bioinformatics at the University of the West Indies campus in St. Augustine, Trinidad & Tobago on February 19th and 20th. The workshop was sponsored by the National Institute of Allergy and Infectious Diseases through the Genomic Center for Infectious Diseases cooperative agreement. UWI was a co-sponsor and a gracious host. Participants included 60 individuals from Trinidad, England, Guyana and Barbados. On-line participants were from all over the world including Gambia, Ethiopia, Kenya, India, USA, and the Caribbean.

file-pdf Workshop Slides (PDF - 29MB)

The team of presenters from the JCVI included Karen Nelson, Bill Nierman, Andrey Tovchigrechko, Rembert Pieper, and Shibu Yooseph. Presenters from UWI included Drs. Christine Carrington and Adesh Ramsubhag.

Karen opened the workshop with a welcome message and overview. She has been a driving force behind the growing relationship between UWI and JCVI. Bill delivered very interesting talks on the history of research on the human microbiome and currently emerging infectious diseases. Rembert handled a presentation and tutorial on proteomic analysis strategies, which was a big hit. If time was not a factor, the question and answer period could have lasted longer than his talk. Finally, Andrey and Shibu presented and gave lessons on statistics, UNIX, and bioinformatics analyses for genomics, metagenomics, and microbiome work.

Dr. Carrington’s presentation on infectious diseases in Trinidad focused on Dengue Fever and Chickungunya, and dovetailed quite nicely with Bill’s presentation on emerging infectious diseases.

Dr. Ramsubhag described the results of his work examining the bacterial diversity of the Nariva Swamp in Trinidad, which uncovered many unique bacterial strains. Perhaps the most important portion of his talk described how important this type of workshop/collaboration is for UWI. Lessons from subject matter experts are invaluable to the undergraduate, graduate and faculty members that attended the workshop as students. In addition, Dr. Ramsuhbag described how a relationship that started through a workshop has given UWI access to cutting edge technologies and data analysis strategies that would be otherwise unavailable without the collaboration with the JCVI.

The students that attended the workshop were all very enthusiastic and eager to learn. They seemingly hung on every word from the presenters, and paid very close attention during the presentations and hands on informatics sessions. A few attendees even asked us to make the lunch break shorter so that the workshop time could be lengthened…but we needed that time to break down the video equipment, haul it to another building and set it up for the afternoon classes. It was a pleasure to help make this learning experience possible for the workshop students!

The workshop was the second time that staff from the JCVI have presented at the St. Augustine Campus of UWI. Tim Stockwell held an 8 hour workshop focused on viruses in 2013. We look forward to working together in the future.

Special thanks to Tim Stayeas for handling all of the technology associated with on-line broadcasts of the meeting.

Watch all four training sessions below:

Day 1, AM Session

Day 1, PM Session

Day 2, AM Session

Day 2, PM Session

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International Bioinformatics Workshop

Published by JCVI Staff on 4 March 2015 in Bioinformatics, Education and Microbial & Environmental Genomics.

20th International Bioinformatics Workshop on Virus Evolution & Molecular Epidemiology (VEME) on behalf of the International Centre for Genetic Engineering and Biotechnology

The International Bioinformatics Workshop on VEME workshop is recognized as one of the best virus bioinformatics courses in the world and has so far been organized in Belgium, Brazil, Finland, Greece, Portugal, the USA, South Africa, The Netherlands, Serbia and Italy. The 20th edition will be held 9 - 14 August 2015 at the University of the West Indies (UWI) in Trinidad and Tobago. The workshop is co-organized by the UWI, J. Craig Venter Institute (JCVI) and the University of Leuven.

The workshop will provide intensive training in the mathematical principles and computer applications used in the study virus evolution and for conducting detailed molecular epidemiological investigations. The workshop will include lectures and computer practical session where students will have the opportunity to analyze their own research data. Teachers will include 24 world-renowned researchers (including Richard Scheuermann, Tim Stockwell and Karen E. Nelson from JCVI).

Note: the application deadline has been extended to March 29, 2015.

Detailed information and online applications may be accessed at:

http://rega.kuleuven.be/cev/veme-workshop/2015

OR

http://www.icgeb.org/trinidad-and-tobago-veme-bioinformatics-2015.html

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