Posts by JCVI Staff

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

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 kcollins@jcvi.org.

Impact: Ebola Research Efforts at JCVI

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.

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

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.

JCVI Ebola Research Efforts

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 virus (both are filoviruses) infections result in such severe human disease.

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.

JCVI Scientists Join NASA-Funded Astrobiology Research Teams

Scientists from J. Craig Venter Institute are part of teams awarded grants from NASA to “study the origins, evolution, distribution, and future life in the universe.” Dr. Christopher Dupont is part of a team led by the University of California, Riverside and will study chemical energy stored in rocks as a potential power source, while Dr. Shino Ishii will work with a team from NASA’s Jet Propulsion Laboratory looking at the habitability of extraterrestrial icy worlds.

Artist concept of an early Earth

Artist concept of an early Earth. Image Credit: NASA

From NASA’s Press Release:

NASA’s Jet Propulsion Laboratory, Pasadena, California. Team lead is Isik Kanik. Research will conduct laboratory experiments and field research in environments on Earth, such as The Cedars in Northern California, to understand the habitability of extraterrestrial icy worlds such as Europa, Ganymede and Enceladus.

University of California, Riverside. Team lead is Timothy Lyons. Research will examine the history of oxygen in Earth’s atmosphere and ocean between 3.2 and 0.7 billion years ago. This is a time range in which the amount of oxygen present is thought to have increased from almost nothing to the amounts present today. This work will address the question of how Earth has remained persistently inhabited through most of its dynamic history and would provide NASA exploration scientists a template to investigate the presence of habitable conditions on Mars and other planetary bodies.

See the complete release.

Study Signals Bat Flu Unlikely to Jump to Humans

Bats species harbor a large number of viruses that cause human disease.  So, when the first influenza sequences from Guatemalan little yellow-shouldered bats were uncovered in 2009, the question arose of whether bat influenza viruses pose a threat to human health.  A collaborative project between JCVI and Kansas State University was recently published in PLoS Pathogens to address this question.

batsignal

The approach employed cutting-edge synthetic biology approaches and demonstrated that, while the sequences of the bat influenza virus of the subtype H17N10 are viable, they are unable to infect human cells. Additional experiments clearly indicated that these bat virus sequences are not able to reassort with other influenza A and B viruses known to infect humans. Therefore, the potential for a pandemic bat influenza entering the human population is extremely unlikely.

David Wentworth, the former Director of Viral Programs at JCVI, was the lead investigator for this study.  Additional authors from JCVI include Tim Stockwell, Wei Wang, Xudong Lin, Bin Zhou (now at NYU), and Reed Shabman.

For additional information see the press release.

H3Africa Update

The National Institutes of Health (NIH) and the UK-based Wellcome Trust, in partnership with the African Society of Human Genetics, developed a program to foster genomic and epidemiological research in African scientific institutions. The laboratory and computational infrastructure available to most scientists on the African continent is currently insufficient to keep up with the rapid developments in DNA sequencing technologies and the need to use advanced computationally intensive methods to analyze this data.

Through the H3Africa Consortium, a partnership between NIH and Wellcome Trust, funding has become available to support knowledge development and implementation of genomics-centered research in several African academic institutions. The first scientific paper to come from this effort, Enabeling the Genomic Revolution in Africa, was published in the journal Science in June 2014.

H3Africa Efforts at J. Craig Venter Institute (JCVI)

One of the main initiatives of H3Africa is to foster scientific exchange between US-based partners and their African-based consortium members. JCVI is involved in a number of such partnerships through training and research collaborations.

Tuberculosis Research with Addis Ababa University

Addis Ababa University is the only Ethiopian institution to receive a primary award from NIH under H3Africa. It is based on a collaboration with JCVI. Professor Gobena Ameni of Addis Ababa University and Dr. Rembert Pieper of JCVI developed a proposal on Systems Biology for Molecular Analysis of Tuberculosis in Ethiopia which was initiated earlier this year. The research focuses on genomic variability in M. tuberculosis strains in Ethiopian pastoralist societies and also has an oral microbiome and proteomic biomarker discovery component.

Bioinformatics Training for African Scientists

As part of H3Africa, JCVI is leveraging its recent GCID award, where appropriate, for training of African Scientists. As part of this effort Dr. Andrey Tovchigrechko  taught microbiome analysis to graduate students in Ibadan, Nigeria. The workshop was organized by the local H3Africa Bioinformatics Network node. The workshop took place in July, 2014 and comprised of students from Nigeria and other West and Central African countries.

Symposium presenters.

Symposium presenters.

Workshop student participants.

Workshop participants.

The workshop was held at IITA.

The workshop was held at IITA.

During the three day workshop, Dr. Tovchigrechko taught the students launching and controlling computing instances on Amazon cloud, the basics of Python and R programming, MG-RAST Web interface, MG-RAST R package matR and JCVI-developed R code MGSAT. MG-RAST tutorials were provided by one of its developers Andreas Wilke (ANL).

Dr. Tovchigrechko also gave a talk, along with a dozen other speakers, at a one-day symposium at the University of Ibadan that preceded the workshop and included approximately 200 participants. Special thanks go to Nash Oyekanmi, the organizer and manager of the whole event, for his relentless efforts.

Collaborations with University of Cape Town

Also as part of the H3Africa Consortium, Dr. William Nierman from JCVI and Dr. Mark Nicol from the University of Cape Town, South Africa are in collaboration to study the nasopharyngeal microbiome and respiratory disease in African children. Dr. Nierman’s group has conducted a month long in house microbiome training workshop with students from Dr. Nicol’s group.

The focus of the training was to teach students JCVI’s complete microbiome pipeline (including sample preparation, sequencing generation, and final association analysis). The aim of the training collaboration is to ensure that this complete pipeline can be performed at the University of Cape Town, to help build independent and sustainable capacity in this field within South Africa.

 

J. Craig Venter at Recent Google Zeitgeist Conference [VIDEO]

Dr. J. Craig Venter recently spoke at a Google Zeitgeist conference in Arizona where he spoke on advances in genomics, synthetic biology, and DNA as the software of life.

La Jolla Community Celebrates Art and Science at Venter Institute Event

On Friday, September 12, the J. Craig Venter Institute (JCVI) hosted a reception at its La Jolla campus to celebrate the installation of “LIFE FORCE,” an original painting by San Diego-based artist and architect Fred Gemmell. This spectacular piece now hangs prominently in the entry of JCVI’s sustainable laboratory. Nearly 100 community leaders attended this beautiful evening which featured live music, award-winning wine courtesy of Coomber Family Ranch Wines, and delicious sushi from executive chef James Holder of James’ Place, the new restaurant at the La Jolla Playhouse.

JCVI is extremely grateful to Mr. Gemmell for his generous donation to the Institute. His work will serve as a daily inspiration not only to JCVI researchers but also to our community and the many visitors to our building. When asked about his inspiration for the work Mr. Gemmell said, “I try to capture, with complex detail and bold gestures, the amazing diversity and adaptability of life in all its interaction and beauty.” Gemmell employs a unique method of acrylic painting in reverse on museum quality, low-reflective plexiglass.

Fred Gemmell and Craig Venter

Fred Gemmell and Craig Venter looking at “LIFE FORCE.”

Reena Horowitz, Helene Gould, Jessie Knight, Eve Benton, George Gould

Reena Horowitz, Helene Gould, Jessie Knight, Eve Benton, George Gould

Peter Farrell, Betty Beyster and Craig Venter

Peter Farrell, Betty Beyster and Craig Venter

Ramin Pourteymour, Tara Tarrant, Linda Chester and Ken Rind

Ramin Pourteymour, Tara Tarrant, Linda Chester and Ken Rind

Bob Friedman, Jessie Knight, Peter Ellsworth

Bob Friedman, Jessie Knight, Peter Ellsworth

Katie Collins, Jack McGrory, Maureen and Skip Coomber

Katie Collins, Jack McGrory, Maureen and Skip Coomber

J. Craig Venter, Ph.D., JCVI Founder and CEO recognized this generous donation in remarks at the event saying, “Fred is a true visionary, and his art reminds me of how I think about science — abstract yet with bold and intended purpose. His incredible contribution is a testament to Fred’s passion for science and his fascination with the natural world. We couldn’t be more grateful for this addition to our new building.”

JCVI, a global leader in genomic research, has nearly 250 scientists engaged in a variety of important science programs including those focused on better understanding and improving human health and the environment. For more information about our research and how you can support us, please contact Katie Collins, Director of Development at kcollins@jcvi.org or 858-200-1847.

Understanding Complex Data through Better Visualization

Recently, researchers at JCVI reported on the Rhizoctonia solani mitochondrial genome which was the largest fungal mitochondrion to be sequenced to date. We showed that its unusually large size was probably due to the expansion of multiple genetic elements that populated the genome in somewhat of a ‘parasitic’ relationship. The visualization was meant to impress the number and variety of these repetitive genetic elements, and was selected in a commentary in  FEMS Microbiology Letters as an example of how to summarize molecular data in order to obtain an overall view of the results.

The outermost circle represents the chromosome and repetitive elements. Other important features such as genes, endonucleases, exons, RNAseq coverage are represented in the concentric circles respectively. Grey links represent short repeats (< 35bp) found up to 100 times in the genome; colored links show the location of repeats and follow the coloration in Track 1.

The outermost circle represents the chromosome and repetitive elements. Other important features such as genes, endonucleases, exons, RNAseq coverage are represented in the concentric circles respectively. Grey links represent short repeats (< 35bp) found up to 100 times in the genome; colored links show the location of repeats and follow the coloration in Track 1.

JCVI Research Impact

JCVI ranks in the top 1% of research institutions worldwide for research impact based on an analysis of Elsevier and Thompson Reuters data. The ranking was done by looking at institutional publication reach as seen through the number of citations referencing them.

Institution Excellence Rate
Broad Institute of MIT and Harvard 49.53
Whitehead Institute for Biomedical Research 47.92
Cold Spring Harbor Laboratory 41.64
Howard Hughes Medical Institute 41.62
Institute for Systems Biology 40.10
J. Craig Venter Institute 37.49
Wellcome Trust Sanger Institute 37.16
Harvard-MIT Division of Health Sciences and Technology 36.73
Salk Institute for Biological Studies 34.68
Institute of Electrical and Electronics Engineers, USA 34.14
Novartis Institutes for Biomedical Research 33.98
National Bureau of Economic Research 33.67
The Rockefeller University 33.40
European Molecular Biology Laboratory Heidelberg 33.28
Flanders Interuniversity Institute for Biotechnology 33.23
Novartis Pharma SA, East Hanover 33.20
Dana Farber Cancer Institute 32.95
F. Hoffmann-La Roche, Ltd 32.47
Group Health Cooperative 32.37
Microsoft Research Cambridge 32.08
International Agency for Research on Cancer 31.21
Nathan S. Kline Institute for Psychiatric Research 31.10
American Cancer Society 31.01
FOM Institute for Atomic and Molecular Physics 31.00
Medical Research Council 30.73
Scripps Research Institute 30.57
London Business School 30.51
World Health Organization Switzerland 30.38
Perimeter Institute for Theoretical Physics 30.32
Cancer Research UK 30.20

In a separate report Thompson Reuters published the “World’s Most Influential Scientific Minds 2014.” Seven JCVI scientists made the list, including: Daniel Haft, Lauren Brinkac, Scott Durkin, Ramana Madupu, Karen Nelson, Chris Town, and Weizhong Li.

Scientist Spotlight: Meet Sarah Highlander

Sarah Highlander Ph.D. is an esteemed scientist and professor who joined JCVI in La Jolla this year. She comes from a long line of academically successful Professors, including a great uncle who was a University Dean. As a young child, Sarah was influenced by her parents: her mother was a musician and her father was a Ph.D. chemical engineer. Sarah too was a musician and she still enjoys jazz and the opera. But it was her father’s scientific career that influenced her own decision to pursue scientific research as her career.

Dr. Sarah Highlander

Dr. Sarah Highlander

As a chemical engineer and early IT specialist, he shared his interests with her at the kitchen table by doing mathematical puzzles and simple experiments. They explored the impact light had on grass growth by placing plants in the closet. Then in high school, she had the opportunity to work on a microbiology project with the help of her father. Using agar slants from his colleague’s lab, she looked for antimicrobial features of bacteria in the soil. Even with these opportunities, her focus in the sciences wasn’t fully set until she began working as a technician in a fermentation research lab where she had the opportunity to work with plasmids after completing her bachelor’s degree. At this point, plasmids and restriction enzymes were not readily available and researchers had to isolate them in their labs. She was extremely successful as a technician and even published several papers and secured several patents.

This experience launched Highlander into Medical Microbiology. She went to the Sackler Institute of Biomedical Sciences at the New York University School of Medicine, where she earned her Ph.D. in 1985. With her curious nature and the bourgeoning field of biotechnology, she began to research the replication of DNA plasmids in Staphylococcus. She asked basic but as yet unanswered questions such as, “How are these molecules controlled in the cell?” and “How can they best be manipulated in the laboratory?” Her thesis involved characterizing small RNA molecules that control plasmid copy number.

During her Post-doctoral fellowship, she shifted her focus to infectious diseases and worked on vaccine development for a cattle disease called “shipping fever” at the University of Texas Health Science Center. Shipping fever is the most common and costly problem affecting calves. It accounts for major economic losses to the cattle producer by reducing average daily weight gain, impairs feed efficiency, and diminishes overall performance and health of beef calves. Vaccination is key to reduce the disease and Highlander’s research culminated in the development of a subunit vaccine that is still in use.

After her fellowship, she began her professorship at Baylor’s College of Medicine (BCM), where she continued her research into shipping fever. The primary bacterial agent in this disease is Mannheimia haemolytica, which is the same family as the human respiratory pathogen, Haemophilus influenzae. JCVI scientists were the first to sequence and publish the H flu genome in 1995. Dr. Highlander’s group performed extensive characterization of the M. haemolytica leukotoxin and developed numerous genetic tools for manipulation and tagging of the organism. She holds patents for subunit and live-attenuated vaccines to prevent shipping fever.

In 2002, Highlander founded Prokaryon Technologies, a for-profit company focused on animal health to prevent and control diseases associated with food animals. One of Prokaryon’s lead products was a genomics-derived vaccine to prevent shipping fever in cattle.

While leading and growing her company, Highlander stayed committed to her academic research interests and joined the Human Genome Sequencing Center at Baylor. At BCM, she participated in genome sequencing of several pathogens (including M. haemolytica) and she moved to focus more on human pathogens. From 2006 to 2013, Highlander was a principal investigator for the Human Microbiome Project (HMP), a National Institutes of Health-funded program in which JCVI researchers were also key leaders.

In addition to her research, Highlander was involved in graduate and medical education at BCM. She was the co-director of the departmental graduate program for 15 years and directed and taught courses focused on bacterial physiology and molecular laboratory methods. Preparation for lectures and interactions with students helped her stay on top of new techniques and research, which in turn helped her further her own research. Sarah had the opportunity to mentor many graduate students both formally and informally.

At JCVI, Highlander is continuing her work on the microbes that live in and on the human body. Specifically she and her team are looking at the complex microbial communities that live in the human gut. While many microbes are associated with disease, most in the human body are associated with health. Highlander and her team are working to develop specific healthy bacterial mixtures that could be used treat conditions such recurrent Clostridium difficile diarrhea, inflammatory bowel disease and others. She is also using bioinformatics tools to look for new causes of diarrhea. “I am delighted to be a part of the collaborative environment here at JCVI and to be surrounded by colleagues who share common interests in bacterial genetics, genomics, microbial physiology and pathogenesis. The microbiome group at JCVI is strong and I hope to be able to make significant contributions to ongoing and future projects here”.

Even in her personal life, Sarah researches, through her hobby of tracing her genealogy. She has been able to find family roots dating back to the 1500s. This detective work is challenging but it keeps her mind sharp and detailed oriented. She points out that learning family naming patterns can be critical to genealogy research just as algorithm development is to genomic research.

Never having lost that early scientific curiosity and excitement of discovery that her father instilled in her as a young girl, Sarah loves working in the laboratory at JCVI and asking questions. Her analytical and inquisitive nature is one of her greatest professional strengths. She is fascinated by the complexity of the microbial ecosystem in our bodies and the impact these microbes have on our health. As she says, “Microbes are going to continue to win through evolution. We need to figure out the next step to keep ahead!” Let’s hope Highlander and her team can win this battle.