Posts by JCVI Staff

Scientist Spotlight: Sinem Beyhan, Ph.D.

Sinem Beyhan, Ph.D. recently joined the JCVI team as an Assistant Professor in the Department of Infectious Diseases and is working closely with Dr. Bill Nierman, Director of JCVI’s Infectious Diseases Program to expand our studies on fungal pathogens. Sinem is interested in understanding how pathogenic fungi can sense and respond to their environment and cause disease. Her current focus is investigating how the fungal pathogen Histoplasma capsulatum uses mammalian host temperature as a signal to alter cell morphology and virulence traits to infect human and mammalian hosts.

Dr. Sinem Beyhan

Dr. Sinem Beyhan

Sinem was born in Turkey. At a young age, she was infinitely curious about the world around her, asking how and why at every opportunity. She was a successful student and was supported by her parents and teachers. Sinem’s early exposure to science was limited. Growing up she did not have access to science camps or scientific experimentation in the classroom. Although culturally girls were pushed away from science and engineering studies, Sinem never heard “no” or “you can’t.”   During high school biology she began her exploration of how organisms work. Even though the class was all memorization, Sinem’s teacher encouraged her to ask questions and to study. Sinem attended the Middle East Technical University in Ankara, Turkey to study genetics and molecular biology. She decided to focus on microbiology and left Turkey for the University of California, Santa Cruz (UCSC) in 2003.

At UCSC, Sinem would begin her investigation of pathogens. During this time she focused on Vibrio cholerae, the etiologic agent of the disease cholera. Another significant event occurred during her time at UCSC, Sinem met her advisor Dr. Fitnat Yildiz. Dr. Yildiz also happened to be a Turkish woman, and the two researchers clicked immediately. They published 14 papers together. After receiving her Ph.D. in Microbiology and Environmental Toxicology, Sinem decided to stay in the United States. She moved to the University of California, San Francisco for her postdoctoral research. Here, Sinem would be mentored by Dr. Anital Sil, and she would shift her focus to fungal pathogens.

After being mentored by scientists like Drs. Yildiz and Sil, two intelligent women who inspired Sinem and showed her that it is possible to balance research and a family, it is not surprising that Sinem also thrives in the role of adviser. She has mentored students throughout her graduate and postdoctoral posts. In addition to establishing her lab at JCVI, Sinem’s is excited to be part of the training programs at JCVI. She also wants to inspire students and interns to pursue a career in science. Although Sinem jokes that her mother now wishes she had told Sinem “no” when she wanted to leave Turkey (it is challenging being so far from her family), it is clear that our new scientist will continue to encourage her team and interns that they “can.”

In addition to uncovering the mechanisms of fungal pathogens, Sinem is also passionate about running, scuba diving, and playing games with her 1-year-old daughter.

2015: JCVI Marks Another Banner Year

jcvi-timeline-2015

JCVI Promotes Science Literacy in the U.S.

Welcomes New Education Manager Amani Rushing

The issue of our society’s science literacy continues to circulate through the media. Recently, reporters focused on results of the Pew Research Center’s Science Knowledge Quiz, which indicates that most Americans would score a grade of C on a basic science test. The gender and racial gaps revealed by the study were equally discouraging.

“Our planet is in crisis, and we need to mobilize all our intellectual forces to save it. One solution could lie in building a scientifically literate society in order to survive.”-  J. Craig Venter, 2015.

This latest examination of what we know about science literacy follows a report by the National Science Foundation (NSF) in 2014 that 26 percent of its respondents were unaware the Earth revolves around the sun. Results from that report on the more controversial topics of climate change and evolution also left scientists and science educators cringing.

San Diego High Tech Fair

On board JCVI’s DiscoverGenomics Mobile Lab at the San Diego High Tech Fair 2015

San Diego High Tech Fair

JCVI’s Dr. Orianna Bretschger greet the public at the San Diego High Tech Fair 2015

Rapid developments in science and technology continually raise new questions for the public debate.  JCVI believes that it is critical that today’s students have an understanding of the basic facts and concepts of science. It is equally important that these students have an understanding of how ideas are investigated and analyzed so that they can develop a perspective on any issue up for discussion. We need to cultivate the next generation of scientists, and we need to ensure that these same generations who may not pursue the sciences formally remain informed and knowledgeable voters.

JCVI has been committed to K-12 and teacher science education since 1999 and is expanding its role in addressing the science literacy challenge. We recently hired Amani Rushing as our Education Manager.  Amani, a graduate of Stanford University, comes to JCVI from the National Center for Missing & Exploited Children (NCMEC). Prior to NCMEC, Amani worked as a Project Coordinator in the Education and Human Resources Division of the American Association for the Advancement of Science (AAAS).  Amani brings ten years of experience of developing and delivering education and training programs for educators and families. She will continue to expand JCVI’s reputation in the STEM education field and will manage and expand the following JCVI education initiatives:

  • DiscoverGenomics! Mobile Lab (DG!). Established in 2006, DG! is a self-sufficient laboratory/learning center on wheels that provides middle school students and teachers the opportunity to learn current bioscience concepts and to master the use of laboratory equipment.  JCVI is committed to getting DG! back on the road again in San Diego.  We are actively seeking funding for DG! for the 2016/2017 school year.  Your name or corporate logo could be on display as DG! travels to San Diego area schools.
  • Internship Program. The Internship Program provides opportunities to inspire young scientists and other science professionals to work in all areas of the Institute. Interns are assigned to a mentor who is a member of the Institute’s faculty or senior staff. This past summer, JCVI welcomed 24 high school students, college students, and high school science educators to our Rockville and La Jolla campuses. Interns on both coasts worked on fascinating projects on everything from helping to develop a high throughput sequencing and analysis pipeline to establishing a CRISPR/Cas9 gene editing system in M. mycoides.
  • Genomics Scholars Program. The Genomics Scholars Program (GSP) is a transition program focusing on the leap from a community college to a four-year college using a combination of activities including undergraduate research experience with mentoring and professional development. Our program incorporates multiple avenues of support for students through a multi-year research experience with the Principal Investigators as mentors, and supplemental professional development provided by the JCVI. Selected students can also participate in undergraduate research conferences.
  • Zoo in You. Zoo in You is a new 2,000 square foot bilingual (English and Spanish) traveling exhibition that will engage visitors in the cutting edge research of the NIH Human Microbiome Project and explore the impact of the microbiome on human health. The first stop on the tour will be the Reuben H. Fleet Science Center in San Diego, CA in 2016. JCVI will work with Fleet to introduce the exhibit to the San Diego community and raise public understanding of the science behind the microbiome.

For more information about our efforts and opportunities to partner with JCVI, please contact Amani Rushing at arushing@jcvi.org.

JCVI’s Global Voyage of Discovery Continues

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, kcollins@jcvi.org.

JCVI Gala “2015: A Genome Odyssey” Celebrates Discovery

On October 24th, JCVI welcomed 200 guests to our third annual gala “2015: A Genome Odyssey.”  Our annual gala has become a signature La Jolla event, and this year’s guests were not disappointed.  Guests experienced an evening odyssey through land, sea and space interacting with JCVI scientists to learn first-hand what explorations are happening today.  Proceeds from the gala will support JCVI’s Innovation Fund.

As in past galas, our research was the focus. Guests learned how scientists Chris Dupont, Ph.D. and Jeff Hoffman collect, filter and analyze the organisms we find as part of our Global Ocean Sampling Expedition. They also saw a demonstration by Orianna Bretschger, Ph.D. on how microbial fuel cells can be used to clean wastewater streams.

JCVI Global Ocean Sampling scientist Jeff Hoffman demonstrates the filtration process used on board Sorcerer II.

JCVI Global Ocean Sampling scientist Jeff Hoffman demonstrates the filtration process used on board Sorcerer II.

Orianna Bretschger, PhD, explains how microbial fuel cell technology hef lab developed works.

Orianna Bretschger, PhD, explains how microbial fuel cell technology her lab developed works.

During the dinner program, Craig Venter, Ph.D. and Board Vice Chairman Erling Norrby, M.D., Ph.D. led guests through our timeline of discovery over the past 20 years. Craig also celebrated the career of Hamilton O. Smith. M.D., JCVI Distinguished Professor and Scientific Director, and presented him with JCVI’s inaugural Innovation Award.  Throughout his career, Ham has been at the forefront of discoveries that have advanced the field of molecular biology.  Ham received the 1978 Nobel Prize in Physiology or Medicine for “discoveries with far reaching consequences for genetics.”  His methods have indeed led to innumerable breakthroughs by scientists around the globe, and his own work has led to some of the most profound discoveries in modern science.

Dr. J. Craig Venter presents JCVI's Innovation Award to Dr. Hamilton Smith.

Dr. J. Craig Venter presents JCVI’s Innovation Award to Dr. Hamilton Smith.

All attendees agreed it was another beautiful and inspiring evening. Thank you to event sponsors BioMed Realty, CapitalOne, Human Longevity, Inc., Synthetic Genomics, NuVasive, CBRE, JLL, Rady Children’s Hospital Foundation, Celgene, Reena Horowitz, Iris and Matt Strauss and the Beyster Family Foundation Fund.  Guests also delighted in our gift bags again this year.  Sponsored by Kowalski Communications, the Esperos backpack was filled with donations from Tata Harper, Blue Lizard, Health Warrior, La Fresh, Thrive Market, Moon Cheese, Aromaflage, Estancia La Jolla Hotel & Spa, The Lodge Torrey Pines, Rite in the Rain and Waters Fine Foods & Catering.

Thank you to our Gift Bag Sponsors!

Thank you to our Gift Bag Sponsors!

For more information on JCVI’s 2016 gala, please contact Katie Collins at kcollins@jcvi.org.

June Grant Update

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.

Q&A with Jessie J. Knight, Jr.

The JCVI CEO Council is a small group of distinguished men and women who are thought leaders in business, medicine, law, the arts and humanities, and community affairs. JCVI is fortunate to have individuals willing to serve as knowledgeable and enthusiastic ambassadors for our scientists and their research, and we are excited to introduce you to our inaugural member, Jessie J. Knight, Jr., Executive Vice President for External Relations at Sempra Energy. Knight is a board member of the Seattle-based Alaska Air Group and Alaska Airline, life member of the Council on Foreign Relations in New York and member of the corporate council of the Hoover Institution of Stanford University. Knight is a well-respected businessman and philanthropist in San Diego. He is also a frustrated musician and has been playing jazz guitar for 30 years. For the past 5 years Knight has been playing the Chinese instrument called Erhu. The entire JCVI team is thrilled to have access to all of Knight’s talents and resources.

Jessie J. Knight, Jr.

Jessie J. Knight, Jr.

You are a native of Missouri. How did you end up in San Diego?

I moved to San Diego in 1999 from San Francisco after serving for six (6) years as the commissioner for the California Public Utilities Commission (CPUC), after being appointed by then-Gov. Pete Wilson. I was recruited to be the president and chief executive officer of the San Diego Regional Chamber of Commerce.

You and your wife, Joye Blount, are respected philanthropists in San Diego. How important is giving back to your community?

As the executive vice president of external affairs for Sempra Energy and with Joye being a Wealth Advisor at US Bank of the Private Client Reserve, we have a professional duty to be present and active in the community and it serves our personal philanthropic interests as well. We have a special interest for organizations that cater to military families, education, improving health and the support of women.

How did you become interested in the J. Craig Venter Institute?

Joye and I have a special interest in JCVI as we have been following the impact of the discovery of the human genome. We believe it’s not only going to have an economic impact in San Diego but also on health worldwide. We believe gaining a better understanding of genetic diseases will allow for improved health and the opportunity to change the course of medicine.

We are excited to have you join the JCVI CEO Council. What do you hope to accomplish in this new role?

Joye and I have had the opportunity to build many great relationships with many individuals and organizations. We’d like to expose JCVI to those we know and increase the reach of JCVI and drive community involvement and philanthropic support to the great work of JCVI.

What environmental/health goals do you personally hope to see JCVI tackle?

I have a personal interest in learning more about the possibilities for gene therapy. My family has been dealing with a genetic disorder for many years, and I’m hoping with my involvement with JCVI that I can understand the opportunities that genomics has for new possible treatments for rare genetic disorders.

JCVI Scientist Tackles Global Sanitation Challenges

Orianna Bretschger received her B.S. in Physics and Astronomy at the University of Northern Arizona. After a five- year career in aerospace and consulting, she completed a Ph.D. in Materials Science at the University of Southern California. Eager to focus her efforts on alternative energy and sustainability, she joined the J. Craig Venter Institute in 2008. Over the course of her research tenure, Dr. Bretschger has established a productive team of researchers dedicated to understanding the fundamental mechanisms associated with extracellular electron transfer (a process that enables microbes to respire solid surfaces, i.e., “breathe rocks”) and applying that understanding to technology development for bioremediation, bioenergy, and water recycling.

Dr. Bretschger and team at White Labs with JCVI constructed reactor.

Dr. Bretschger and team at White Labs with JCVI constructed reactor.

Bretschger’s research group has secured over $11M of external funding from diverse resources including NASA, The State of California, The San Diego Foundation – Blasker Science and Technology Award, the National Science Foundation, the Office of Naval Research, Synthetic Genomics Inc. and the Roddenberry Foundation. Her publications have drawn over 800 citations and most recently includes an article in Nature Communications, which describes a novel metatranscriptomic method for understanding metabolic relationships in highly diverse (over 400 species) microbial communities and new findings related to how microbes share electrons. The approach developed by her team can now be applied to many different environmental samples and begins to unravel the complex interactions that exist in our sediments, soils, oceans and fresh water resources. These studies will shed new light on how our changing environment will impact ecosystem function.

Reacter installation at San Pasqual High School

Reacter installation at San Pasqual High School

Her applied projects include the development and integration of microbial fuel cell systems that can remove contaminants from wastewater and transform the waste into direct electrical energy. Bretschger’s most recent awards include a $5M grant from the Roddenberry Foundation to demonstrate her microbial fuel cell technology as a sustainable sanitation approach to address the sanitation and related public health impacts in Latin America.  Further, a recent award from SPAWAR Pacific will test her technology at an S.E.R.E training base outside of San Diego and demonstrate its effectiveness for providing cost-effective water recycling and wastewater treatment to our militaries forward operating bases.

UABC and JCVI teams showing local elementary student how to do titrations while testing water quality in Baja MX.

UABC and JCVI teams showing local elementary student how to do titrations while testing water quality in Baja MX.

Bretschger has developed methods for how to apply her technology for the removal of medications and other toxic personal care products from wastewater; and is developing new methods for addressing the removal of nitrogen and phosphorous from agricultural waste streams (two big factors in creating ‘dead zones’ in our coastal waters).

Growing up in the Southwest, access to water has always been paramount in Bretschger’s life.  She lived through periods without access to plumbing and running water, and therefore knows first hand some of the basic challenges families face.  One third of the world’s population has no access to sanitation, resulting in high child mortality rates and a critical lack of public health and safety. Today, Bretschger directs a lab of nine researchers and five interns (high school through master’s level students) and conducts collaborative work throughout San Diego and across the International boarder. Her installations can be seen at the San Pasqual High School Agricultural center and previously at White Labs. Bretschger believes her team is poised to have a real impact on the global sanitation crisis, she just needs more funding “ to go faster and to go bigger.” Her Roddenberry funded efforts will lead to the installation of improved sanitation systems at a school in San Quintin, Mexico over the next two years, and she hopes to expand these efforts globally to begin addressing the critical sanitation needs for nearly 2.6 billion people world-wide.

Dr. Venter Delivers UCSD 2015 School of Medicine Commencement


Continue reading ‘Dr. Venter Delivers UCSD 2015 School of Medicine Commencement’

Johns Hopkins Announces Inaugural Recipient of Hamilton Smith Award for Innovative Research

JCVI’s Hamilton O. Smith, MD has been recognized by Johns Hopkins University with a research award in his honor. The inaugural recipient of the award is Jie Xiao, an associate professor of biophysics and biophysical chemistry at the Johns Hopkins University School of Medicine. Dr. Smith was awarded the Nobel Prize in 1978 for his discovery of restriction enzymes, work he conducted while he was a young faculty member at Johns Hopkins.