Posts in category JCVI

Summer 2016 Intern Program

Interns in both Rockville, MD and La Jolla, CA participated in our summer 2016 internship program at the J. Craig Venter Institute (JCVI). A total of 19 interns were hired for the summer 2016 program, selected from 578 applicants. Of the 19 interns, six interns were part of the Genomic Scholar Program (GSP) that 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. The interns were mentored by JCVI faculty and research scientists. Mentors design a research project for each intern depending on their education and prior research experience.

GSP interns Emily Samuels, Rolande Tra Lou, Erica Ngouajio, Raja Venkatappa (mentor), Claudia Najera, Kat Rocha, Tayah Bolt (from La Jolla) and Kenya Platero gather at JCVI Rockville's poster session.

GSP interns Emily Samuels, Rolande Tra Lou, Erica Ngouajio, Raja Venkatappa (mentor), Claudia Najera, Kat Rocha, Tayah Bolt (from La Jolla) and Kenya Platero gather at JCVI Rockville’s poster session.

The involvement of fellows in individually focused research projects was designed to stimulate interest in biomedical research as well as to develop independent critical thinking and communication skills with other team members. In addition to research activities, throughout the summer interns participated in professional development activities that included:  education on the importance of documenting research activities and maintaining accurate laboratory records,  responsible conduct of research, the art of reading scientific literature (interns participated in weekly science journal clubs that aimed to teach how to dissect and interpret scientific literature), and scientific presentations. All the interns participated in JCVI internal presentations and presented their summer research as a poster.

Summer 2016 Interns gather for a picture in the courtyard at JCVI La Jolla.

Summer 2016 Interns gather for a picture in the courtyard at JCVI La Jolla.

A brief summary of 2016 interns summer research projects and their mentors are listed below.

Intern Name(s) Research Project Mentor(s)
Roshni Bhattachara Structural implications of unique substitutions found in a paralysis-associated enterovirus D68 clade Richard Scheuermann
Christopher Henderson Assessment of the Contribution of Ascertainment Cohort to the Genetic Architecture of Alzheimer’s Disease Nicholas Schork
Nathan Lian and Anthony Kang Experimental Validation of ChIP-Seq Identified Centremeres Philip Weyman
Rohith Kodukula The Oral Microbiome of Caries in Children: A Study on Twins Andres Gomez
Ian Lamb Identifying Bacterial Antibiotic Resistance Markers in gut microbes Manolito Torralba
Stephanie Mountain Hydrogen peroxide tolerance variation among different isolates of Acinetobacter baumannli Mark Adams and Meredith Wright
Kathryn O’Nell Cell-Type Clustering in Cortical Brain Cells via differential Expression Analysis of Single Nuclei Richard Scheuermann
Josefa Rivera Identifying new promoter elements in Phaeodactylum tricornutum Vincent Bielinski, Philip Weyman, and Chris Dupont
Jennifer Tuman Pan-Cancer Analysis of Somatic Mutations in DNA Damage Repair Genes Alexandra Buckley  and Nicholas Schork
Ben Grimes Using Synthetic Biology Methods to Engineer Herpes Simples Virus-1 and Mycoplasma mycoides subspecies capri Genomes Suchismita Chandran and Sanjay Vashee
Nicolette Maragh Technical Improvements of Sample Preparation for Proteome Analysis Yanbao Yu
Claudia Najera (GSP fellow) Using Synthetic Biology to Engineer Herpes Simplex Virus Type 1 Lauren Oldfield and Sanjay Vashee
Erica Ngouajio (GSP fellow) Developing a method to optimize sequencing of the Zika virus genomic termini Kari Dilley and Reed Shabman
Tayah Bolt (GSP fellow) Reduction of GUS Activity in Phaeodactylum via Episomal hpRNA Expression Philip Weyman
Alexandra Rocha (GSP fellow) Fibronectin and LRG1 protein interactions in T1D patients Rajagopala Venkatappa
Emily Samuels (GSP fellow) Cloning and Expression of proteins in Zika Virus and Legionella pneumophila in E. coli Keehwan Kwon
Rolande Tra Lou (GSP fellow) Filovirus-human protein-protein interaction Reed Shabman and Rajagopala Venkatappa
Carolina Hatanpaa Constructing a Novel Hidden Markov Model for a tRNA Binding Domain Architecture in the Minimal Cell Granger Sutton and David Haft

Scientist Spotlight: Anna Edlund, Ph.D.

Although Sweden is synonymous with Ikea, Volvo, meatballs and ABBA, the country has had a significant impact on science and discovery as far back as the 17th Century. Scientist Anna Edlund, Ph.D. who recently joined JCVI is another Swede pushing the boundaries of discovery in her new role as Assistant Professor, Department of Genomic Medicine.

Anna Edlund, Ph.D.

Anna Edlund, Ph.D.

Anna grew up in the middle of nature on a horse farm in the northern part of Sweden. Inspired by her country’s natural beauty and wilderness, she grew to care a great deal about the environment. During her first years at Södertörn University College she studied ‘green ecology’ and population genetics while she kept her job as a ranger for the Swedish Environmental Protection Agency working in a National park. Dr. Janet K. Jansson first introduced Anna to microbiology during an undergraduate course, and she immediately became fascinated with the unexplored world of microbes – she could not resist becoming a microbiologist. Anna finished her studies at the Karolinska Institute with a Master’s in microbiology and molecular biology. Under the guidance of Dr. Jansson, she pursued her Ph.D. studies in microbiology at the Swedish University of Agricultural Science in Uppsala. Between 2002 and 2007, she studied marine biology specifically exploring the microbial life in sediments of the Baltic Sea. She continued her education in marine microbial ecology as a Postdoctoral Scholar at Scripps Institute of Oceanography at the Center for Marine Biotechnology and Biomedicine, and ultimately returned to Sweden as an Assistant Professor at the Department of Systems Ecology at Stockholm University.

Anna’s trajectory changed in March 2012 when she returned to California at the invitation of Dr. Jeff McLean, a former JCVI scientist and pioneer in the human oral microbiome. As a Project Scientist and Postdoctoral Fellow at UCLA’s School of Dentistry and JCVI, Anna turned her focus from studying bacterial ecological functions in the marine environment towards understanding the role of the oral microbiome in human health.

As a scientist at JCVI, Anna’s research focuses on the complex human oral microbiome and how bacterial gene expression and signaling molecules orchestrate the development of both health and disease associated communities. Anna joined the team at JCVI to work with world-leading experts in microbiology in an environment where most of her time can be spent doing research.

Recently, Anna received a three-year award of $750,000 from the National Institute of Dental and Craniofacial Research (NIDCR) to investigate oral pathogen virulence within complex oral biofilm communities. Her goal is to deepen our knowledge of the molecular processes of oral biofilms during stress and disease-like conditions (e.g. pathogen invasion, low pH). She hopes her findings will lead to improvements in treating and preventing oral diseases.

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 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.

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.

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

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.