Posts in category Infectious Disease

Scientist Spotlight: Brett Pickett, Ph.D.

The son of a dentist, Brett Pickett grew up in Salt Lake City, Utah focused initially on a career in the family business (his siblings are hygienists and an oral surgeon). Brett believed from an early age that he would follow in his father’s footsteps. He enrolled in Brigham Young University committed to dental school. It was not until Brett’s zoology major was canceled that he became a student of microbiology, where he began researching antibiotic resistance genes in gut microbiota. Dental school was out. Brett received his B.S. in microbiology and continued his studies at the University of Alabama at Birmingham (UAB).

Brett Pickett, Ph.D.

While working in UAB’s bacteria pathogenesis labs, Brett’s path would take another detour as he encountered West Nile, Hepatitis C, and Dengue viruses in his work. He also began to cultivate an interest in computers, technology, and statistics as it related to biological data. These experiences have led to him to his current field of research: viral bioinformatics.

In 2010, Brett moved to the University of Texas Southwestern Medical Center at Dallas to begin his postdoctoral research with Dr. Richard Scheuermann (presently the Director of JCVI La Jolla). Working with Richard, Brett began to shift his focus on how a virus behaves to examining how the human host is responding to being infected. While at UT Southwestern, Brett worked with Richard and his team to identify and develop new statistical, analysis, and visualization tools for the National Institutes of Health (NIH)-funded Viral Pathogen Resource Bioinformatics Database (ViPR). In 2012, Brett moved his family to La Jolla to be a part of JCVI’s informatics team. During this time, his work focused on enhancing the Virus Pathogen Resource and Influenza Research Database bioinformatics resource centers.

Brett stepped away from JCVI for a brief period to work at Thomson Reuters. There he analyzed “-omics” data with pathway analysis and network-building tools, together with drugs and protein target information to better understand viral infection, differences between pathogenic and commensal bacteria, oncology, and other therapeutic areas. This experience allowed him to gain a better understanding of human genetics, disease profiling, and biomarker identification before returning to research at JCVI in 2016.

At JCVI, Brett continues to work on cutting-edge science. He appreciates “the access to collaborators to solve big problems,” and Brett’s efforts are addressing the world’s biggest health challenges. He recently received funding from the US Agency for International Development (USAID) to develop a method for differentiating antibodies against Zika and other closely-related viruses in human patients.

Brett lives in San Diego with his wife and five children. When he is not in the lab, Brett enjoys golf, waterskiing, playing the piano, and visiting the beach with his family. His children, ranging in ages from 1-11, want to be scientists or doctors when they grow up. While there may be no dentists in this generation either, it is clear Brett’s children will have inspirational and accomplished footsteps in which to follow.

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.

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

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

ZIKV

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

ZIKV sequencing efforts at JCVI: 

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

Toward the development of a rapid ZIKV diagnostic:

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

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

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

Mosquito genomic sequencing:

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

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

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

Ongoing Zika virus work at JCVI

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

Zika virus

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

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

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

Zoo in You: The Human Microbiome Exhibit Opens in San Diego

On January 28, over 250 scientists, philanthropists and other STEM community notables, including JCVI CEO Council Member Reena Horowitz, came out to support the San Diego premier of the Zoo in You: The Human Microbiome exhibit at the Reuben H. Fleet Science Center. The Zoo in You is a new 2,000 sq. ft. exhibit funded by a SEPA grant from NIH in partnership with JCVI. Through May 8, 2016 visitors to the display can learn about our constant microbial companions, where they live, how diverse they are, and in what ways scientists are realizing just how important they are to our personal health.

Dr. Karen Nelson

JCVI’s President, Karen Nelson, Ph.D., spoke about JCVI’s passion for STEM education and dedication to encouraging STEM growth in San Diego.

JCVI at Zoo in You Opening

JCVI staff and friends came out to support the event (from left to right): Hernan Lorenzi, Katie Collins, Karen Beeri, Amani Rushing, CEO Council Member Reena Horowitz, Nicole Deberg, Mark Adams.

Thanks to new, sophisticated technology and the cutting-edge research of the National Institutes of Health’s Human Microbiome Project, the world is just starting to discover what the microbes in each of us are up to and how they affect us.

JCVI is taking other steps to help the San Diego community learn about the importance of their microbiomes. In addition to the exhibit, JCVI scientist Karen Beeri led a class of 23 girls in activities about microbes and DNA sequencing at Fleet’s Saturday Science Club for Girls on February 13. The girls toured the Zoo in You exhibit, made DNA bracelets, and used RNA decoders to decode the secret messages found in our amino acids.

Zoo in You: The Human Microbiome will be on display at Fleet until May 8, 2016. Check it out!

For more information about JCVI’s education initiatives, please contact Education Manager Amani Rushing at arushing@jcvi.org.

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.

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.

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.

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.

Zoo in You Exhibit Now Open

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.