Posts by JCVI Staff

Genomic Workshop for Native American College students

A Genomic Science Workshop was held  last week (May 24-26, 2016) at the J Craig Venter Institute Rockville campus for a group of ten Native American college students.  The students participated in two full-day intensive training activities learning how to study the “microbiome” of natural water sources. Each student had the chance to perform hands-on lab work including DNA isolation from an environmental water source, PCR of the 16S ribosomal RNA gene, and gel electrophoresis. Individual computer workstations were provided for the computer lab sessions for students to follow along.  The group was introduced to basic Linux command-line analysis and the popular 16S analysis package QIIME. Overall, the workshop provided the students a foundation of knowledge and tools to identify and classify microbial populations in environmental water sources, and enabled the students to participate in water quality analysis and monitoring efforts of their homeland reservations.

Collage from Maize Cell Genomics Workshop for Undergraduates

Collage from Genomic Workshop for Native American College students

The workshop students were welcomed by JCVI President Karen Nelson and Rockville Campus Director Rembert Pieper. Informal discussion panels were also held to provide networking and research career development opportunities with invited guest speakers including Science Education Directors from the Howard Hughes Medical Institute (HHMI), and Native research scholars from the National Institute of Health (NIH). The students were also presented with a preview of the astronaut microbiomes as an application of human microbiome study. Workshop students also had the opportunity to visit the US Capitol and the National Museum of the American Indian.

The workshop was funded by the National Science Foundation through a Maize Cell Genomics grant and was organized by Agnes Chan (JCVI; co-PI), in collaboration with the Cold Spring Harbor Laboratory (CSHL; PI Dave Jackson, Outreach Educator Joslynn Lee), the University of Wyoming (UW; co-PI Ann Sylvester), Montana State University (Mari Eggers), and the Little Big Horn College (LBHC; John Doyle).  LBHC is a tribal college located in the Crow Reservation, MT. The NSF Maize project has established a long-term outreach relationship with LBHC, and has organized a number of training workshops for Native students previously at LBHC, UW, and CSHL. Participants for the 2016 workshop included Native students recruited from the LBHC, Montana State University, Fort Lewis College, and Northern Arizona State University.

The PIs of the Maize Genomics Project would like to express sincere thanks to instructors from JCVI including Hernan Lorenzi, Yongwook Choi, Vivek Krishnakumar, Stephanie Mounaud,  the JCVI Information Technology team, the Administrative Assistant team, and all colleagues for their generous assistance, support, and patience for a successful outreach educational workshop.

To find out more information on workshop schedule, notes, and manuals, please visit the Maize Cell Genomics project web site at http://maize.jcvi.org/cellgenomics/2016_pcr.php.

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.

Unlocking the Mysteries of the Microbiome

In the early 2000s, JCVI researchers pioneered in the exploration of the human microbiome, the community of microbes that live in and on the human body. Originally while at The Institute for Genomic Research (TIGR, now part of JCVI) Drs. Craig Venter and Hamilton Smith were awarded a grant from DARPA to examine the microbes found in the human gut.  This work was carried out by researchers at JCVI and published in 2006 in Science.  While this team had previously published 16S surveys of the human body, this paper in which the researchers found more than 60,000 microbial genes was the first metagenomic description of microbes resided anywhere on the human body.  Ten years since this seminal publication, our scientists continue to pave the way for a broader understanding of these vast microbial populations.

fragment recruitment plot

Visualization of ocean microbial data collected on JCVI’s Global Ocean Sampling Expedition (GOS). The Sorcerer II circumnavigated the globe for more than two years, covering a staggering 32,000 nautical miles, visiting 23 different countries and island groups on four continents.

On May 13, 2016, Drs. Craig Venter and Karen Nelson were present at the White House for the launch of the National Microbiome Initiative (NMI).  The NMI will invest $121 million in new microbiome studies in fiscal years 2016 and 2017.  The goals of the project are to supplement fundamental research, develop new technologies and engage more people in this area of research.

Today we know that the human body is host to more than 1 trillion microbes. Thanks to continued advances in genome sequencing technologies and metagenomic analysis JCVI scientists are providing a deeper understanding of these microbes across a variety of fields. JCVI researchers know that translating the role of the microbiome in the development of health and disease in humans is essential.  We believe that eventually the screening of the human microbiome will be a routine part of medical care, leading to prescribed diets and preventive measures personalized to an individual.

JCVI currently has several dozen microbiome studies underway.  In this issue of Amplifier, we are highlighting some of our most exciting and cutting edge work unlocking the mysteries of the human microbiome.

The Effects of Long-Term Space Travel on the Microbiome of Astronauts

On March 1, the world celebrated the safe return of NASA astronaut Scott Kelly after 340 days in space.  Researchers are fascinated to learn more about the impact of long-term space travel on the human body, and JCVI scientists are excited to be a part of the process.  During a mission to space, astronauts are subject to many stressful conditions (g-forces, radiation, microgravity, anxiety, etc.) that can have a negative impact on their health. For example, astronauts lose muscle mass, bone density, and experience a wide range of health problems with everything from their vision to their gastrointestinal tract. Several studies have demonstrated that space travel also affects the astronauts’ immune systems (for example the reactivation of latent viruses like Herpes Simplex Virus 1 and Epstein Bar virus) and have shown some evidence suggesting that stool microbes change after space flight.

JCVI researchers want to determine how the composition of the astronauts’ microbiome changes during long-term space missions (six or more months), and to evaluate potential risks to astronaut health from changes in the microbiome. We are also interested in how the microbiome of astronauts interacts with other factors such as the microbial communities that inhabit the International Space Station (ISS). To accomplish this, we will monitor the astronauts’ health status, environmental stress, and exposure to space conditions. The skin, tongue, nose and gut of each astronaut will be sampled at multiple time points before, during, and after the mission to the ISS. By sampling the microbiome of astronauts on earth while in peak physical health and during subsequent space flight, we will be able to define signatures of human response to a variety of relevant aspects of space travel. Astronauts will also sample different surfaces and the water supply during their stay at the ISS to correlate crew microbiomes with the microbes living at the ISS. We will also assess changes in the astronauts’ immune function and stress levels throughout the mission by analyzing their saliva and blood for metabolic markers. Finally, we will correlate the microbiome and immune function data collected with other measured metadata including astronaut health and hygiene as well as environmental factors such as temperature, humidity and environmental factors.

This research program is being led by Dr. Hernan Lorenzi.

The Gut Microbiome and Human Evolution

Who we are, where we come from and how we came to be as we are, are questions that have always fascinated biologists. The reasons to answer these questions are multiple, but one critical aspect centers on understanding what makes us human. To start addressing these issues JCVI scientists are exploring the gut microbiome of non-human primates, our closest living relatives, and of populations that most faithfully reflect the lifestyles of early hominids: hunter-gatherers. The goal of this project is to establish an evolutionary baseline to shed light on the host-microbe factors that impacted health and disease in modern and western human populations.

Our scientists have shown, in several recent publications, that the gut microbiome of wild gorillas, is strongly shaped by the external environment, namely by diet. Specifically, we showed that gut microbes adapt to different dietary stimuli, probably providing gorillas with energetic plasticity when preferred feeding resources are seasonally and temporally absent. Interestingly, we also suggested that, in conditions in which gorillas exploit high-energy diets, their gut microbiomes resembles those of humans. This fact has critical implications to understanding the evolutionary origins of obesity and inflammation in modern human populations from a microbe perspective. Along these lines, our most recent publication on the gut microbiome of central African hunter-gatherers, traditional agriculturalists and western humans shows evidence that transitions to agriculture and industrialization, and giving up hunting and gathering could have radically changed our gut microbiomes for good. This observation is vital considering that traditional hunter-gatherers, whose microbiomes resemble those of wild gorillas, do not show symptoms of modern inflammatory disease. These observations highlight the potential impact of gut microbes in human evolution.

The research team consists of  Drs. Andres Gomez and Karen Nelson.

Solving Crimes with Your Microbial Signature

In January 2016, JCVI received a two-year, $962,500 award from the United States Department of Justice to design and build an open-access microbiome database for the forensic science community. The Forensic Microbiome Database (FMD), the first of its kind will be populated with several thousand microbiome datasets and associated metadata available from the public domain. The database will be based on established procedures for database development designed at the JCVI, incorporating expansive sets of data and metadata that relate to forensic evidence.

The goals of this project are to: provide a host location and continuous monitoring of the database; define well-structured standard operating procedures for data generation and searching against and uploading data into the FMD; and test the utility of the FMD by sequencing a range of samples obtained geographically for querying and proof of concept against the database. The foundation of this project will serve for future enhancements of the FMD and utility for forensic casework. The research team expects this will become the community resource for analysis of microbiome data and for attributing weight to microbial forensic evidence.

The research team consists of Rhonda Roby, Lauren Brinkac, Toby Clarke, Andres Gomez, Karen Nelson, Harinder Singh, and Shibu Yooseph,

Using the Microbiome to Advance Wound Therapies

Chronic wounds are wounds that fail to heal after 4 months of proper wound care and management.  It is a major public healthcare burden that affects an estimated 1% of the US population and costs $25 billion per year. Common chronic wounds are leg, foot, and pressure ulcers occur in adults especially the elderly with diabetes, vascular diseases, or specific body locations under prolonged pressure. According to the Centers for Disease Control and Prevention, approximately 12% of U.S. adults with diabetes had a history of foot ulcer and 11% of U.S. nursing home residents had pressure ulcers. In addition to the economic burden, from the perspective of patients chronic wounds can also lead to loss of function (e.g. amputation), decreased quality of life, and increased rate of mortality.

At JCVI we are interested in deciphering not only the microbial communities present in chronic wounds but also their potential impacts and relationship with the wound healing outcome, for working towards more effective clinical strategies of wound healing. In collaboration with George Washington University, we are conducting a study to analyze chronic wounds. Samples are selected from patients enrolled in the Wound Etiology and Healing biospecimen and data repository (WE-HEAL). We will analyze the chronic wound microbiome at the molecular level, and attempt to identify biological indicators that can be used to predict the healing outcome to further advance wound therapies and management.

This project is being led by Dr. Agnes Chan.

Metagenomic Epidemiology of Antibiotic Resistance in Infectious Diarrhea

Genes that encode antimicrobial resistance (AMR) to antibiotics have been detected in environmental, insect, human and animal metagenomes and the sum of these are known as “resistomes.” While metagenomic datasets have been mined to characterize the healthy human gut resistome, directed metagenomic sequencing has not been used to examine the spread of AMR. Especially in developing countries where sanitation is poor, diarrhea and enteric pathogens likely serve to disseminate AMR elements of clinical significance. Unregulated use of antibiotics further exacerbates the problem by selection for acquisition of resistance. This is exemplified by recent reports of multiple AMR in Shigella strains in India, in Escherichia coli in India and Pakistan, and in nontyphoidal Salmonella (NTS) in South-East Asia.

Sarah Highlander, Ph.D. and her team are characterizing the microbial composition and its component AMR transfer elements (such as plasmids and transposons) by metagenomic sequencing of stool samples from pediatric patients from Colombia who are suffering from diarrhea. Our goal is to assess whether groups of species/strains associate with specific mobile genetic elements and whether their presence is enhanced or amplified in diarrheal microbiomes. This work could potentially identify clonal complexes with enhanced resistance and potential pathogenesis.

For more information on how you can support or human microbiome research program at JCVI, please contact development@jcvi.org.

Durban Microbiome Workshop

As part of our continued effort to bring genomics to other communities, Alex Voorhies, Derek Harkins and Andres Gomez traveled to Durban, South Africa to lead a series of workshops on microbiome data analyses.  The two days of presentations were made to students, postdocs and faculty at the Durban University of Technology, and was co-sponsored by the NIAID funded JCVI Genomic Center for Infectious Disease.  On day one, the JCVI team provided an introductory lecture on microbiomes and technical considerations to plan and conduct microbiome related projects. The lecture followed up with an introduction to sequencing technologies and bioinformatics tools to analyze 16S rRNA next generation sequencing data.  The day one session ended up with a lecture on the differences between metagenomics and 16S rRNA sequencing and analyses pipelines and one on one advising with students and faculty on how to analyze and plan their own projects.

On day two the JCVI team provided a hands-on tutorial where students analyzed a time series of mouse microbiome data.  Students learned each step of working with a 16S rRNA dataset, from processing raw reads to statistical analysis and figure generation.  The morning started with a practical exercise processing 16S reads using mothur to assign taxonomic classification.  In the afternoon students used the output from the mothur workshop to learn about analyzing data in R.  Students explored alpha and beta diversity as well as indicator species analysis and statistical significance of their findings.  The hands-on workshop concluded with various ways to display 16S microbiome data in publication quality figures.

The students were very enthusiastic and active participants in the lectures and hands on units. It is our sincere hope that the workshop helps them to expand their research and data analysis capabilities in the future.

Our hosts, Drs. Suren Singh and Nokuthula Mchunu, sent along nice messages in appreciation for the event:

Have no words to pass the amount of appreciation the student and the supervisors had for the workshop. Andres, Derek and Alex were fantastic in the delivery of the material and having time to address every question we were asking. We hope that we can have another sometime in the future and if we had choice we would pick them. Thank you again.
– Dr. Nokuthula Mchunu

Thank you for sending out a wonderful, and extremely knowledgeable team to ignite one of many workshops at DUT. It was truly a great exposure for many of my students and staff. They enjoyed the theoretical and hands on sessions alike. Let’s continue this association for many more years ahead.

– Dr. Suren Singh

What Does It Really Mean to Be a Scientist?

In the spring of 2016, JCVI partnered with Del Lago Academy to provide internships for some of its students.

Junior Stephanie Mountain shares about her experience and what her time at JCVI taught her:

Being an intern at JCVI was an amazing experience I will never forget. I learned so much through this internship that I would have been unable to learn in school. I learned a lot about coding and the importance of using computers to analyze data that is generated in the lab. Through my classes at Del Lago I had a good amount of hands on lab experience, but this internship was completely different than anything else I had done previously. It exposed me to the opposite side of scientific research, the kind that isn’t in the lab. I had very minimal computer skills at the start, but now I know how to run command prompt, a little bit on two coding languages, R and Perl, and how to use the Mothur program to run data analysis.

Stephanie with her JCVI mentors, Drs. Zhong and Zhu, and her Del Lago teacher Marc Kibler.

Stephanie with her JCVI mentors, Drs. Zhong and Zhu, and her Del Lago teacher Marc Kibler.

It was really fun to work with my mentors and “help” them analyze their data. Granted, they probably could have done everything much faster and with less problems than me, but it helped me see what happens in a day of the life of a researcher. Before this internship, I wanted to be a scientific researcher, but in my mind that meant doing strictly wet lab stuff. Now, I know that being a scientific researcher means a lot more than I had previously though. All of the computer stuff I did was really fun and cool, and it kind of surprised me how much math was involved in all of the computer things. I’m definitely going to take some computer science classes in college if I get the opportunity to. The math associated with computers seems really challenging and fun, and a lot less like a black box where I press buttons and the computer gives me stuff I want.

Overall, this internship has been eye opening to a new side of scientific research I didn’t know existed. All of the things I learned were really interesting and new. I now know that I really would love to be a scientific researcher in the future.

Junior Janine Vasquez worked with Dr. Orianna Bretschger, Dr. Sofia Babanova, and Jason Jones to research the development of microbial fuel cells for wastewater treatment. One big part of that research…pig poop!

I first want to thank everyone for allowing us to have the privilege to work with JCVI. I learned so much throughout this internship and I was able to get a lot of hands-on experience. During this internship, I learned the process of collecting data, running tests and analyzing the results. Our project was to run COD tests to see how different amounts of NaCL would affect the COD readings.

When we first arrived at the farm at San Pasqual, I did not know what I would be doing. When I found out that one of my tasks was to blend pig feces, I was really surprised. At first it was hard because I was still getting used to the smell but after a while, I surprisingly was not bothered by the fact that I was blending pig feces in a blender. I really enjoyed getting the experience of working in the farm and the lab. Some of my friends who also worked in a lab setting only got one side of the experience. Anabel and I were able to experience more than one working setting and I found that interesting.

One thing that I felt was kind of challenging was actually meeting new people. I am not really a social person but I tried to get out of my comfort zone; in the end, I got to meet great people. This internship really made me think about my future. I’ve always had this mindset that people in this industry only work in labs all day and I realized that is not true. I was actually relieved to find out that projects like these have you working in all kinds of places because I like trying different things and working in different work settings. This experience made me realize that this is something that I may want to do in the future.

JCVI is committed to helping youth pursue careers in science. To join our efforts, please contact Education Manager Amani Rushing at arushing@jcvi.org.

JCVI’s Scientists Inspire the Next Generation!

JCVI’s Education Program has been working to bring science to life (sometimes literally!) for San Diego’s students.

It started off March 4 with our participation in President Obama’s recently announced science education initiative “Take Your Child to the Lab” week. Nine children of JCVI’s staff visited the Institute for a tour and hands-on science experiment.

The morning started with a talk from JCVI’s La Jolla Campus Director, Mark Adams. Dr. Adams began by asking the kids, “What are you curious about?” This prompted a flurry of enthusiastic responses. “At JCVI,” he continued, “That’s what we – and your parents – do. We’re curious. We ask questions that no one has answered and then we try to figure out answers.”

JCVI scientists Phil Weyman and Nicole Yee talk about synthetic biology and bacteria cultures.

JCVI scientists Phil Weyman and Nicole Yee talk about synthetic biology and bacteria cultures.

Next, the children heard about some of the specific questions we’re asking and answering at JCVI from synthetic biology with Dr. Phillip Weyman to waste water treatment with Kayla Carpenter to bacteria growth and antibiotic testing with Nicole Yee and Manny Torralba. They also went on a tour of JCVI’s sustainable lab led by Dr. Robert Friedman. He helped the children think not only about doing science, but the impact of doing science. “It’s really cool that the building is made out of recycled materials,” said eleven-year old Charlie Myers. “I’ve never seen anything like that!”

Before leaving, our young guests tried their own hands at culturing bacteria by gathering samples from the environment around them. Over the next week they’ll be monitoring their samples to see what happens next!

The children take bacteria samples and show off their experiments.

The children take bacteria samples and show off their experiments.

The San Diego Festival of Science & Engineering

The very next day, JCVI was once again sharing our passion for science with the San Diego community. The JCVI Mobile Lab was one of 143 exhibitors participating in the 2016 San Diego Festival of Science & Engineering’s free Expo Day. Approximately 500 visitors boarded the mobile lab and learned about sequencing, marine microbes, using DNA in forensics, and the human microbiome. Volunteers Andres Gomez, Marcus Jones, Drishti Kaul, Ebony Miller, Aubrie O’Rourke, Joey Steward, Michelle Tull and Angela Zoumpliswowed group after group by sharing about JCVI’s research.

Drishti Kaul and Aubrie O’Rourke guide festival attendees through JCVI’s Mobile Laboratory.

Drishti Kaul and Aubrie O’Rourke guide festival attendees through JCVI’s Mobile Laboratory.

“Can this mobile lab come to my child’s school?” more than one parent wanted to know. The JCVI Education Program would love to make that a reality. Contact Education Manager Amani Rushing at arushing@jcvi.org to talk about supporting the mobile lab your community!

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.

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.