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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Zoo in You Exhibit Now Open

Published by JCVI Staff on 9 April 2015 in Education, Genomic Medicine, Infectious Disease and Microbial & Environmental Genomics.

Did you know trillions of microbes make their homes inside your body? In fact, these microorganisms outnumber our human cells 10 to 1, “colonize” us right from birth, and are so interwoven into our existence that without each other, none of us would survive! Thanks to new sophisticated technology and the cutting-edge research of the Human Microbiome Project, we are just starting to discover what these microbes are up to and how they affect us. And now in Zoo in You: The Human Microbiome, a new 2,000 square foot bilingual traveling exhibit created in partnership between JCVI and the Oregon Museum of Science and Industry (OMSI), and funded by a SEPA grant from the NIH, visitors can now explore this fascinating and complex world inside us that is our microbiome—a dynamic, adaptable, and delicately balanced ecosystem like any other found in nature.

A few of the Zoo in You components including “Weather Reports” and “Microbes in the Family”

A few of the Zoo in You components including “Weather Reports” and “Microbes in the Family”

The exhibition features 15 interactive, free floating hands on components that are designed to focus on three overarching topic areas to educate and inform visitors on the concept that our bodies are complex ecosystems that we are just starting to understand and explore. Through these exhibit components museum goers will “meet the microbes” to learn about the organisms which live on and inside us from the moment we are born, to understanding the importance of the dynamic and delicately balanced human microbiome in “balanced ecosystems”, and lastly visitors will “explore the microbiome” to learn the importance of scientific research to increase our understanding of human health.

Zoo In You introduction component “Meet the Microbes”

Zoo In You introduction component “Meet the Microbes”

There are numerous interactive, hands on activities for visitors. Such activities include “Weather Reports” where guests will have the opportunity to interact with green screen technology to give a weather report on the climate conditions of your nose, gut or skin. They also will be able to build a DNA Puzzle where they race against the clock to assemble a DNA strand and participate in a hand washing contest. Participants can challenge each other in exhibit components such as “Microbes in Balance”, a large touch screen video game to see if they can keep their “health-o-meter” in balance and in “Microbe Mirror” a motion sensing activity where visitors come face to face with their full body reflection and control the changes in their microbiome as they react to everyday occurrences. Throughout the exhibit components feature contributions by JCVI Scientists Dr. Karen E. Nelson, Dr. Hernan A. Lorenzi, and Dr. Ramana Madupu including “Stories & Choices” an activity where visitors listen to the scientist interviews and make choices based on various fun questions which relate to microbiome research.

The Zoo in You exhibit is now on display at the Oregon Museum of Science and Industry (OMSI) in Portland, OR through July 2015, it will then travel to Science Works Hands-On Museum in Ashland, OR October through December 2015. It will begin its national tour at the Reuben H. Fleet Science Center in San Diego, CA in partnership with JCVI.

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In Memory of Dr. J. Robert Beyster

Published by JCVI Staff on 30 March 2015 in JCVI.

The JCVI family mourns the loss of a true friend and generous supporter, Dr. J. Robert Beyster. Dr. Beyster was a World War II Veteran, a nuclear engineer whose research propelled the Department of Defense’s weapons systems and submarines into the future of war fighting, but most notably, he founded Science Applications International Corporation (SAIC), an employee-owned multi-billion dollar corporation.

Bob and Betty Beyster

Bob and Betty Beyster

The Beyster Family have been generous supporters of science programs at the JCVI since 2009 when they, along with matching funds from Life Technologies Foundation, sponsored a two year leg of the Sorcerer II Global Ocean Sampling Expedition. This substantial support from the Beyster Family enabled sampling research of microbial life in the waters of the Baltic, Mediterranean, and Black Seas. These are scientifically important because they are among the world’s largest seas isolated from the major oceans. To date more than 80 million new genes and protein families have been discovered as part of the Sorcerer II Expedition.

The Beysters have also supported JCVI scientist Andy Allen, Ph.D. and his Southern California Upwelling Sampling Project. Dr. Allen has conducted sampling expeditions along the Southern California coast to better understand the microbes living in these waters. Dr. Beyster participated in 8 of the 11 sampling excursions that were conducted from his own boat, Solutions. He blogged about a major regional dinoflagellate bloom that was sampled as part of this project.

Importantly, this work has led to an exciting new San Diego-based collaboration between JCVI, NOAA and the Scripps Institution of Oceanography (SIO) to integrate genome-enabled techniques and technologies (i.e., ‘omics) into the California Cooperative Oceanic Fisherines Investigations (CalCOFI). CalCOFI is a multi-partner, long-term ecosystem and fisheries study off the coast of California in it’s 7th decade.

The most recent $2.5 Million gift in 2012 for the completion of the new J. Craig Venter Institute sustainable laboratory was recognized by naming the third floor ocean view conference room and terrace the “Bob and Betty Beyster Conference Room” and the “Bob and Betty Beyster Terrace”.

Beyster Conference Room and Terrace

Left: Looking up at the Beyster Conference Room and Terrace from the ground floor. Right: Sunset on the Beyster Terrace.

Dr. Beyster will be greatly missed by his family, friends and colleagues. We are fortunate to have a constant a reminder of his generosity and support. A link to his obituary can be found here.

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Science on the Sea Ice Edge

Published by JCVI Staff on 30 March 2015 in Microbial & Environmental Genomics.

On Sunday, December 14th JCVI scientists Andy Allen, Erin Bertrand, and Jeff Hoffman flew to New Zealand to begin the arduous journey to the sea ice edge of Antarctica. The JCVI team was joined by three members of the University of Southern California, led by David Hutchins, and three members of the Virginia Institute of Marine Science (VIMS), led by Deborah Bronk. This is the second field season of the second three-year NSF funded collaborative project for the Allen team. The first field season for the current project was in December 2012/January 2013; the second year was postponed due to the government shutdown in late 2013 delaying our trip until December 2014. The major objectives of this collective fieldwork are to understand how changes in micronutrient availability, temperature, and pCO2 will impact growth, community composition, and nutrient utilization in Southern Ocean phytoplankton.

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JCVI Antarctic Expedition
JCVI Antarctic ExpeditionPictures from Antarctic Expedition

Antarctica and the Southern Ocean remain one of the most untouched regions on the planet making this area extremely valuable for research related to the impacts of climate change on biota. The Southern Ocean is a system of currents linking all of the Earth’s ocean. It is the most prolific of our oceans, and by conducting genome-enabled investigations targeting phytoplankton, plant like organisms consisting mostly of algae and bacteria that are the base of oceanic food webs, JCVI scientists glean insight into key biological underpinnings. A key research challenge is identification of basic characteristics, features and genomic fingerprints that are sensitive to environmental shifts that impact surface waters and result in nutrient cascading effects. JCVI scientists are establishing valuable baselines to identify impacts of climate change on ocean ecosystems. This research is used in turn to create models of ocean circulation and phytoplankton distribution patterns that will help scientists, policy makers and politicians identify and address the worldwide effects of climate change.

This research can be especially challenging because of the geographic isolation of the Southern Ocean. Upon arrival in New Zealand, the JCVI team spends a day securing extreme cold weather gear and viewing safety videos. We then wait patiently to depart on a military plane: LC-130 Hercules. While the LC-130 is known for its reliability to reach austere locations, the flight is often at the mercy of mechanical failure and weather changes. After a nine hour, extremely loud and rumbling flight, the team disembarks onto a sheet of ice. Despite this being a repeat trip for many of us, it is still amazing to find yourself traversing a remote sheet of ice. From here, we board the transport vehicle Ivan the Terra Bus for the 45-minute ride to McMurdo Station on Ross Island.

Orientation to station life can be challenging. There are acronyms for everything. Despite the presence of approximately 1000 residents, one is aware of the lack of “home like” sounds from pets and children, and the feelings of isolation are real and enduring. Interestingly less than 10% of the Station population is scientists. We work with military and station support staff daily, and despite the isolation, a sense of camaraderie and a bond based on shared experience develops immediately. Another note of interest is that the weather at times is not that bad at McMurdo despite what you may have seen in the movies. In fact, our friends and family in Boston had it much worse!

After arriving at McMurdo, the team spent 9 days completing required safety training, securing logistical support and preparing the lab. Our research activities consisted of weekly helicopter expeditions to the sea ice edge where large volumes of water were filtered for analyses of DNA, RNA and proteins. Live phytoplankton samples were also collected in a manner specifically designed to prevent contamination by iron and other trace metals. There are inherent dangers traveling to the sea ice edge. In the company of penguins and whales, the team must be aware of potential ice shifts, developing cracks and breakouts. We travel with a mountaineer who works to maintain our safety. When working close to the ice edge, we are each secured via ropes and pulleys—it can be intense. We also have to watch the weather. Many times in order to keep samples from freezing, you could see us breaking out the hairdryers and camping stoves. Whatever it takes!

Our “live water” samples were transported back to the laboratory at McMurdo and used to conduct various manipulative experiments aimed at investigating the synergistic impact of change in Iron (Fe) and Vitamin B12 availability as well as increases in temperature and pCO2 levels. One of the major challenges the team faced was keeping these experiments free of dust in order to avoid iron contamination. This was a particular challenge because McMurdo Station is built on a pile of extremely dry, dusty, volcanic soil. The team persevered, of course, and completed numerous trace metal clean experiments.

To date, these manipulative experiments have yielded preliminary results suggesting that changing micronutrient availability and increasing temperature will have major impacts on the base of the Antarctic food web. These include changes in mutualistic relationships between phytoplankton and bacteria and changes in the rate of consumption in major nutrients, both of which are likely to have important downstream effects throughout the global ocean. Analyses of gene and protein expression changes in the field and in these experiments are just beginning to yield further insight into how the Southern Ocean will respond to a changing earth.

On January 27th, exhausted, but with a very successful expedition completed, the team returned to New Zealand. It is challenging to be away from your friends and family for 2 months at time. As we return to the real world though, we arrive feeling lucky and privileged. JCVI scientists see a region of the world and experience amazing days of wildlife that few people will ever know first-hand. Studying phytoplankton and ocean ecosystems is in fact a privilege and the research JCVI scientists and other teams are doing in Antarctica will have a lasting impact on the future of our planet.

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Animal Forensics and Molecular Biology Techniques

Published by JCVI Staff on 16 March 2015 in Education.

A one-day high school workshop for New Hampton School’s Project Week

Hosted by the J. Craig Venter Institute, Rockville, Maryland – March 11, 2015

Every March, the New Hampton School, an independent high school in New Hampshire, holds Project Week, an experiential learning program that allows students to choose from a wide array of unique activities, both on and off campus. This year, one project group traveled to Washington D.C. to complete a program on forensic biology, which included activities at both the Crime Museum and the J. Craig Venter Institute (JCVI).

On Wednesday, March 11, 2015, ten high school students and two teachers visited JCVI to learn about molecular biology techniques and animal forensics. Their activities were coordinated by Dr. Karla Stucker, a Postdoctoral Fellow in the Virology Group at JCVI, and included a review of DNA structure and replication, a tour of the Institute, lessons about PCR and gel electrophoresis techniques, hands-on laboratory exercises, and a discussion about animal forensics with case examples. Dr. Suchismita Chandran, a Postdoctoral Fellow in the Synthetic Biology Group at JCVI, assisted with the laboratory exercises.

Animal Forensics Discussion with Dr. Karla Stucker. Photo courtesy New Hampton School.

Animal Forensics Discussion with Dr. Karla Stucker. Photo courtesy of New Hampton School.

Upon arrival, each participant “adopted” a dog for the day by picking from various photos of different pure-bred and mixed breed dogs. They thus became dog owners living in an upscale apartment complex in Bethesda, where they were required to submit cheek swab samples from their pets to be entered into a DNA database. Our gel electrophoresis experiment was designed to reveal which dog owner(s) failed to pick up after their pet(s) by checking for a match between cheek swab samples and a stool sample. The test made use of size differences in PCR amplicons from a hypothetical microsatellite marker that helps distinguish dog breeds. We also discussed more serious animal forensic cases, including those involving wildlife trafficking and the recent case of a poisoned show dog at Crufts, a large dog show in the UK.

Dr. Suchi Chandran assists students with a hand-on gel electrophoresis activity. Photo courtesy of New Hampton School.

Dr. Suchi Chandran assists students with a hand-on gel electrophoresis activity. Photo courtesy of New Hampton School.

Each day, the students blog about their experiences. One student, Amy, wrote, “We saw many young and passionate researchers working hard in their labs, which made us feel excited and got us looking forward to being scientists. The lab room was clean, organized and bright. We were not allowed to touch anything without gloves due to personal protection. After visiting, we have a better understanding of how scientists’ workplaces should look like, and their rigorous attitudes towards science.”

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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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Warm Wishes

Published by Stephanie Mounaud on 22 December 2014 in JCVI.

It has been another year and with that more fungus in my life (and another more human bundle of joy). I tried my best to get these fungus to behave (and my children) but we can’t always control them. So below is my newest artwork. It says Warm Wishes and is as cozy and warm (and fuzzy) of a cabin I could get with fungus. Enjoy and happy holidays to you.

Warm Wishes

Snow and smoke: Neosartorya fischeri 181; Wreath and ‘Warm wishes’: Aspergillus nidulans A4; Cabin: Aspergillus terreus 20843. Image: Stephanie Mounaud / JCVI

Inoculating loops roasting in an open fire
The negative 80 nipping at your fingers
The incubators beeping like a choir
And the aroma of bacteria just seems to linger

Everybody knows resistance and recombination
Help to give us such a fright
Teeny Tiny Bacteria with their constant mutations
Will make it hard for us to sleep at night

But they all know that scientists will find a way
We’re using sequencing and synthetic life
And every single strand of DNA
To see if we can really end the lifelong strife

And so really think before you join the craze,
You will be in the lab every day.
Although it’s rewarding, many times we’re in a daze
But we do take a break for the happy holidays!

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Guest Speakers Marlo Gottfurcht Longstreet and Dean Ornish Inspire Guests at JCVI‘s “Life at the Speed of Light” Gala

Published by JCVI Staff on 23 October 2014 in Genomic Medicine, JCVI, Microbial & Environmental Genomics and Sequencing.

On October 18, J. Craig Venter Institute (JCVI) hosted our “Life at the Speed of Light” black tie gala featuring special guests Dean Ornish, MD, and Marlo Gottfurcht Longstreet. JCVI welcomed 200 community leaders, sponsors and supporters including Representative Scott Peters, Susan Taylor, Reena Horowitz, Linda Chester, Jack McGrory, Jessie Knight, Jr., Joye Blount, Wendy Walker, Randy Woods, Andrew and Erna Viterbi, Mary Ann Beyster, and JCVI Board Member Bill Walton and wife Lori.

Guests experienced our science first hand through various displays and had the opportunity to interact with many JCVI scientists to learn how advances in genomics are impacting our health and environment.

microbiome station

JCVI Scientists Manny Torralba and Stephanie Mounaud welcomed guests with a brief introduction to the palm microbiome by taking swabs and sharing aggregate population results midevening.

Following welcome remarks by J. Craig Venter, Ph.D., Founder & CEO of JCVI, Marlo Gottfurcht Longstreet shared her son Tanner’s battle with a Giloblastoma Brain Tumor. It is understood that the tumor developed as a result of a mutation in the TP53 tumor suppressor gene. Sadly, Tanner Jay Longstreet passed away in 2013 at the age of 11.

Marlo Gottfurcht Longstreet sharing her personal story about her son Tanner and ongoing work at the Tanner Project.

Marlo Gottfurcht Longstreet sharing her personal story about her son Tanner and ongoing work at the Tanner Project.

Personal tragedy turned mission for Marlo as she set out to do everything she could to better understand what afflicted Tanner, which gave rise to the Tanner Project at JCVI. Led by Nicholas Schork, Ph.D., the Tanner Project is what is referred to as an “N of 1” project – a single patient case study. Rather than go in for yearly checkups, the patient in the study is monitored daily so that any evidence of cancer can be detected at onset. The goal is to keep the study patient at what is referred to as stage 0. By closely monitoring the condition in this “N of 1” study, its application can be applied more broadly in personalized medicine – “N of 1 for everyone.”

Dr. Ornish discussed advances in personalized medicine and how simple behavioral changes can greatly affect patient outcomes. He addressed ideas presented in his most recent book, The Spectrum, suggesting diet and exercise are not all or nothing propositions. If today wasn’t a great food day, there is no reason tomorrow can’t be. This kind of thinking can greatly improve longevity and quality of life.

Dean Ornish speaking to gala attendees on advances in medicine.

Nobel Laureate Hamilton Smith (right) walks gala attendees through JCVI advances.

Rangers and the Re-Arrangers

The evening was rounded out with a delectable dinner, dancing, and gypsy jazz music by Seattle’s Rangers and the Re-Arrangers.

JCVI is grateful to its event sponsors – CapitalOne Bank, BioMed Realty, Synthetic Genomics, Inc., Human Longevity, Inc., Thermo Fisher Scientific, Gunderson Dettmer, ZGF, and Egon Zehnder – for their support. Thank you as well to our DNA gift bag sponsors: Way Better Snacks, GoodBelly, Kowalski Communications, La Jolla Playhouse, Lean & Green Café, and Travel Set Go.

JCVI remains committed to tackling today’s pressing medical and environmental concerns, and we continue to rely on your generosity to achieve our goals. For more information on funding needs and opportunities, please contact Katie Collins as [email protected].

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Impact: Ebola Research Efforts at JCVI

Published by JCVI Staff on 10 October 2014 in Infectious Disease.

We have all read the stories with concern about the rapid spread of Ebola virus disease (EVD) in Africa. Now, with the first diagnosis of the virus in the United States, it is clear this virus is not under control. If not contained, Ebola poses a significant threat to the African continent and beyond. JCVI is on the front lines of working to better understand this infectious agent. Dr. Reed Shabman, a member of JCVI’s infectious disease team, is seeking to understand why Ebola and Marburg viruses (both are filoviruses) infections result in such severe human disease.

Ebola virus

Produced by the National Institute of Allergy and Infectious Diseases (NIAID), under a magnification of 25,000X, this digitally-colorized scanning electron micrograph (SEM) depicts numerous filamentous Ebola virus particles (red) budding from a chronically-infected VERO E6 cell (blue). Image credit: NIAID

During his time as a postdoc at the Icahn School of Medicine at Mount Sinai in New York, Reed helped to develop research platforms designed to understand how Ebola virus mediates its replication, gene expression and evades the immune system. The innovative approaches used at JCVI do not require high level containment facilities and through established collaborations with Biosafety level-4 (BSL-4) labs his group is able to confirm their results in the context of actual Ebola infection.

Some of the ongoing collaborative projects in the group include:

  • Determining how Ebola virus evades the host immune system, specifically the innate immune response.
  • Employing sequencing platforms to identify previously undescribed aspects of Ebola and Marburg virus RNAs.
  • Developing reporter systems to understand how the untranslated regions (UTRs) of Ebola and Marburg virus control their protein production.

This important research seeks to enhance the scientific community’s understanding of Ebola and Marburg virus biology which will aid in our ability to rationally design ways to combat these deadly viruses.

Ebola Background

Ebola has entered the human population before, with the first documented cases occurring in 1976 in areas that are now South Sudan and the Democratic Republic of Congo. Since 1976, there have been approximately 20 outbreaks in central Africa resulting in just over 2300 confirmed cases of Ebola virus disease (EVD).

One unusual aspect of the current Ebola outbreak is that instead of central Africa, this outbreak is occurring in west Africa. Initial cases were reported in February in Guinea. Shortly after these initial reports, EVD spread into Liberia followed by cases in Sierra Leeone and Nigeria. While efforts to control the virus in Nigeria appear to be successful, the number of cases since the first reported case now totals approximately 8000 with almost 4000 fatalities. The numbers from this single outbreak are larger than all other previous outbreaks combined.

Ebola virus was identified almost 40 years ago; however, there are still no approved vaccines or antiviral approaches beyond supportive care. There are promising therapies and vaccines on the horizon, but a fundamental understanding of how the virus interacts with human host is critical to advance the progress of treating the deadly disease.

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