Posts in category Education

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

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.

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.

Animal Forensics and Molecular Biology Techniques

A one-day high school workshop for New Hampton School’s Project Week

Hosted by the J. Craig Venter Institute, Rockville, Maryland – March 11, 2015

Every March, the New Hampton School, an independent high school in New Hampshire, holds Project Week, an experiential learning program that allows students to choose from a wide array of unique activities, both on and off campus.  This year, one project group traveled to Washington D.C. to complete a program on forensic biology, which included activities at both the Crime Museum and the J. Craig Venter Institute (JCVI).

On Wednesday, March 11, 2015, ten high school students and two teachers visited JCVI to learn about molecular biology techniques and animal forensics.  Their activities were coordinated by Dr. Karla Stucker, a Postdoctoral Fellow in the Virology Group at JCVI, and included a review of DNA structure and replication, a tour of the Institute, lessons about PCR and gel electrophoresis techniques, hands-on laboratory exercises, and a discussion about animal forensics with case examples.  Dr. Suchismita Chandran, a Postdoctoral Fellow in the Synthetic Biology Group at JCVI, assisted with the laboratory exercises.

Animal Forensics Discussion with Dr. Karla Stucker. Photo courtesy New Hampton School.

Animal Forensics Discussion with Dr. Karla Stucker. Photo courtesy of New Hampton School.

Upon arrival, each participant “adopted” a dog for the day by picking from various photos of different pure-bred and mixed breed dogs. They thus became dog owners living in an upscale apartment complex in Bethesda, where they were required to submit cheek swab samples from their pets to be entered into a DNA database. Our gel electrophoresis experiment was designed to reveal which dog owner(s) failed to pick up after their pet(s) by checking for a match between cheek swab samples and a stool sample.  The test made use of size differences in PCR amplicons from a hypothetical microsatellite marker that helps distinguish dog breeds.  We also discussed more serious animal forensic cases, including those involving wildlife trafficking and the recent case of a poisoned show dog at Crufts, a large dog show in the UK.

Dr. Suchi Chandran assists students with a hand-on gel electrophoresis activity. Photo courtesy of New Hampton School.

Dr. Suchi Chandran assists students with a hand-on gel electrophoresis activity. Photo courtesy of New Hampton School.

Each day, the students blog about their experiences.  One student, Amy, wrote, “We saw many young and passionate researchers working hard in their labs, which made us feel excited and got us looking forward to being scientists. The lab room was clean, organized and bright. We were not allowed to touch anything without gloves due to personal protection. After visiting, we have a better understanding of how scientists’ workplaces should look like, and their rigorous attitudes towards science.”

2015 Advanced Genomics, Metagenomics, and Bioinformatics Workshop Wrap-up

I was lucky enough to help set up and plan a workshop covering genomics, metagenomics, proteomics and bioinformatics at the University of the West Indies campus in St. Augustine, Trinidad & Tobago on February 19th and 20th. The workshop was sponsored by the National Institute of Allergy and Infectious Diseases through the Genomic Center for Infectious Diseases cooperative agreement. UWI was a co-sponsor and a gracious host. Participants included 60 individuals from Trinidad, England, Guyana and Barbados. On-line participants were from all over the world including Gambia, Ethiopia, Kenya, India, USA, and the Caribbean.

file-pdf Workshop Slides (PDF – 29MB)

The team of presenters from the JCVI included Karen Nelson, Bill Nierman, Andrey Tovchigrechko, Rembert Pieper, and Shibu Yooseph.  Presenters from UWI included Drs. Christine Carrington and Adesh Ramsubhag.

Karen opened the workshop with a welcome message and overview. She has been a driving force behind the growing relationship between UWI and JCVI. Bill delivered very interesting talks on the history of research on the human microbiome and currently emerging infectious diseases. Rembert handled a presentation and tutorial on proteomic analysis strategies, which was a big hit. If time was not a factor, the question and answer period could have lasted longer than his talk. Finally, Andrey and Shibu presented and gave lessons on statistics, UNIX, and bioinformatics analyses for genomics, metagenomics, and microbiome work.

Dr. Carrington’s presentation on infectious diseases in Trinidad focused on Dengue Fever and Chickungunya, and dovetailed quite nicely with Bill’s presentation on emerging infectious diseases.

Dr. Ramsubhag described the results of his work examining the bacterial diversity of the Nariva Swamp in Trinidad, which uncovered many unique bacterial strains. Perhaps the most important portion of his talk described how important this type of workshop/collaboration is for UWI. Lessons from subject matter experts are invaluable to the undergraduate, graduate and faculty members that attended the workshop as students. In addition, Dr. Ramsuhbag described how a relationship that started through a workshop has given UWI access to cutting edge technologies and data analysis strategies that would be otherwise unavailable without the collaboration with the JCVI.

The students that attended the workshop were all very enthusiastic and eager to learn. They seemingly hung on every word from the presenters, and paid very close attention during the presentations and hands on informatics sessions. A few attendees even asked us to make the lunch break shorter so that the workshop time could be lengthened…but we needed that time to break down the video equipment, haul it to another building and set it up for the afternoon classes. It was a pleasure to help make this learning experience possible for the workshop students!

The workshop was the second time that staff from the JCVI have presented at the St. Augustine Campus of UWI. Tim Stockwell held an 8 hour workshop focused on viruses in 2013.  We look forward to working together in the future.

Special thanks to Tim Stayeas for handling all of the technology associated with on-line broadcasts of the meeting.

Watch all four training sessions below:

Day 1, AM Session

Day 1, PM Session

Day 2, AM Session

Day 2, PM Session

International Bioinformatics Workshop

20th International Bioinformatics Workshop on Virus Evolution & Molecular Epidemiology (VEME) on behalf of the International Centre for Genetic Engineering and Biotechnology

The International Bioinformatics Workshop on VEME workshop is recognized as one of the best virus bioinformatics courses in the world and has so far been organized in Belgium, Brazil, Finland, Greece, Portugal, the USA, South Africa, The Netherlands, Serbia and Italy. The 20th edition will be held 9 – 14 August 2015 at the University of the West Indies (UWI) in Trinidad and Tobago. The workshop is co-organized by the UWI, J. Craig Venter Institute (JCVI) and the University of Leuven.

The workshop will provide intensive training in the mathematical principles and computer applications used in the study virus evolution and for conducting detailed molecular epidemiological investigations. The workshop will include lectures and computer practical session where students will have the opportunity to analyze their own research data. Teachers will include 24 world-renowned researchers (including Richard Scheuermann, Tim Stockwell and Karen E. Nelson from JCVI).

Note: the application deadline has been extended to March 29, 2015.

Detailed information and online applications may be accessed at:


H3Africa Update

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

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

H3Africa Efforts at J. Craig Venter Institute (JCVI)

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

Tuberculosis Research with Addis Ababa University

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

Bioinformatics Training for African Scientists

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

Symposium presenters.

Symposium presenters.

Workshop student participants.

Workshop participants.

The workshop was held at IITA.

The workshop was held at IITA.

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

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

Collaborations with University of Cape Town

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

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


Professional Development Opportunities this Summer

This summer we are offering two professional development workshops: GenomeSolver and Bioinformatics: Unlocking Life through Computation.  Both explore bioinformatics, microbial diversity and the implementation in the undergradauate or high school classrooms. 

The GenomeSolver workshop trains faculty on genome analysis. Workshop attendees will learn about general methodologies, standards, and processes used to annotate and analyze microbial genomes. The workshop contents will be available to aid the faculty in developing teaching modules. In addition, extensive documentation on methodologies and tools will be available via the online environment created for this project. On online web portal Genome Solver ( will be a virtual space for development and sustaining of community. Genome Solver will assist faculty with technical issues and curricular design, as well as an online environment for the ongoing sharing of information including publication of student work.

Bioinformatics: Unlocking Life through Computation is a new opportunity for high school teachers. Genomics and biotechnology are valuable tools in our quest to understand life and nature. However, introducing the science classroom to the computational and mathematical underpinnings of biology can be challenging. The goal of this workshop is to introduce a curriculum for mathematics and science education in the area of genomics (with a focus on the fascinating world of microbes). Educators will be introduced to the various analysis and computational challenges that arise in this discipline. Workflow examples illustrating comparative genomic analysis will be made available through the JCVI Metagenomics Report (METAREP) software infrastructure. The eventual aim is for the educational material to be integrated with local high school curricula requirements to expose students to both hypothesis-driven and discovery-based science.

JCVI Hosts South African Scientists to Share Microbiome Research Techniques

Two scientists from the University of Cape Town, South Africa have joined Dr. Bill Nierman’s lab for the next month as part of NIH’s Human Heredity and Health in Africa (H3Africa) Initiative, a training program designed to build out technical biological skills in the African research community. This training relates specifically to developing techniques around the area of microbiome analysis, a relatively new field in the biological sciences.

Microbiome analysis for the collaborative study is looking at entire community of microorganisms in the respiratory tract of South African infants to better understand how the microbiome is associated with infant pneumonia and wheezing episodes. The expectation is that the organisms that reside in the infant respiratory tract will provide protection from or a predisposition to the pneumonia or wheezing episodes.


The Nierman Group

The Nierman group left to right Sarah Lucas, Bill Nierman, Shantelle Claassen, Mamadou Kaba and Stephanie Mounaud (unpictured Jyoti Shanker and Lilliana Losada) welcomes visiting scientists Ms. Classeen and Dr. Kaba from University of Cape Town for a month long training in microbiome sequencing and analysis.

Mamado Kaba, MD, PhD and colleague Shantelle Claassen from the University of Cape Town will be working closely under the guidance of JCVI’s Stephanie Mounaud who is functioning as the project manager and coordinating the laboratory components of a similar project at JCVI studying the microbiomes of inafnts in the Philippines and also in South Africa. These studies are sponsored by the Bill and Melinda Gates Foundation. The training will focus initially on preparing samples for DNA sequencing on a modern DNA sequencing platform, the Illumina MiSeq instrument. Once the sequence reads are off the sequencer, the instructional focus will shift to analysis of the reads by means of an informatics pipeline that develop phylogenies, or family trees, of the microbes that are obtained from the infant respiratory tract so that the abundance and relatedness of the microbes can be established. The bioinformatics training will be provided by Jyoti Shankar, the statistical analyst working on the Gates Foundation Project.

Mamadou Kaba is a Wellcome Trust Fellow working in the Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town. Mamadou’s research interests include the molecular epidemiology of infectious diseases and the study of human microbiome in healthy and disease conditions. He has contributed in establishing a new research group conducting studies on how the composition of the upper respiratory tract, gastrointestinal, and the house dust microbial communities influences the development of respiratory diseases.

Prior to joining the University of Cape Town, Mamadou worked as Research Associate at the Laboratory of Medical Microbiology, Timone University Hospital, Marseille, France, where he studied the epidemiological characteristics of infection with hepatitis E virus in South-eastern France.

Shantelle Claassen is pursuing a Masters degree in the Division of Medical Microbiology at the University of Cape Town. She has completed a BSc (Med) Honours degree in Infectious Diseases and Immunology at the University of Cape Town, during which she examined the relative efficacy of extracting bacterial genomic DNA from human faecal samples using five commercial DNA extraction kits. The DNA extraction kits were evaluated based on their ability to efficiently lyse bacterial cells, cause minimal DNA shearing, produce reproducible results and ensure broad-range representation of bacterial diversity.

Mamadou and Shantelle are currently involved in an additional prospective, longitudinal study of which the primary objective is to investigate the association between fecal bacterial communities and recurrent wheezing during the first two years of life.

The 2014 Summer Internship Application is Open and Announcing the Genomics Scholar Program

The 2014 Summer Internship Application is now open.   Last summer, we hosted 49 interns from a pool of 424 applicants. They presented their research in the First Annual Summer Internship Poster Sessions held in San Diego and Rockville. The posters were judged by a team of volunteer JCVI scientists and the poster sessions were open to all employees, interns and their guests to share what great work they all participated in this summer.



2013 Intern Poster Session

2013 Intern Poster Session

We are also excited to announce the new Genomics Scholar Program beginning this summer and also accepting applications.  The Genomic Scholar Program (GSP) is a targeted research experience program to community college students in Rockville. Our program incorporates multiple avenues of support for students through the research experience with the Principal Investigators as mentors, and supplemental professional development provided by the JCVI.  Additionally, selected students will have the opportunity to participate in undergraduate research conferences.

The GSP is supported by the National Institute of Diabetes and Digestive and Kidney Diseases of the National Institutes of Health under award number R25DK098111.