Posts in category Education

JCVI Launches New Internship Partnership with Smithsonian Science Education Center

Are you passionate about science education? If so, we have a unique hands-on opportunity for you to be a part of real teams of scientists and educators. This opportunity doesn’t require any previous lab experience, and is open to undergraduate and graduate students in the United States.

The internship will be split between the J. Craig Venter Institute (JCVI) and the Smithsonian Science Education Center (SSEC). At JCVI you will participate in cutting-edge research. This will dovetail into curriculum enhancement previously developed at the SSEC, which aligns with the U.N.’s Global Sustainability Development Goals (SDGs).

This is an excellent opportunity for both science majors who may be interested in pursuing a path in education, and for education majors looking to gain valuable experience in a professional laboratory.

Space-fill drawing of the outside of one Zika virus particle, and a cross-section through another as it interacts with a cell. Image courtesy David Goodsell.

What will do you?

At the JCVI, you will work on a part of a larger project geared towards the development of rapid tests for virus genes that suppress host antiviral defenses. The project, which will focus on the mosquito-borne Zika Virus Disease, will use synthetic biology techniques to help scientists identify virulent strains.

At the SSEC, you will work with curriculum developers and experts in the field of global science education to support the development and rollout of the SSEC’s curriculum module “Zika!,” which helps students understand mosquito-borne diseases through inquiry-based science education methods.

The outcomes of this internship will lead to not only a better understanding of current research being done in the field, but will also result in the development of effective ways to communicate scientific research to the public.

Apply on our website today!

The 2017 JCVI Summer Internship Program

JCVI’s long-running internship program just concluded its summer 2017 session with a well-attended poster symposium held in both its Rockville and La Jolla locations. Eighteen of our interns presented their research in a session open to all JCVI faculty and staff. Montgomery College professors and staff attended, as well to support our Genomic Scholar Program (GSP) Interns in Rockville.

2017 Rockville Interns

2017 Rockville Interns

This past session was one of our most competitive yet, with over 1700 unique candidates applying to the program. A total of 20 interns took part in the program, 10 at each campus. Of the entire intern cohort, eight were part of our Genomic Scholar Internship Program (GSP), which is a 15-month long internship focused on helping community college students transition successfully into a four-year university. This year, the GSP was excited to include a bioinformatics intern into the program for the first time. Four of our GSP interns successfully completed their internship and are continuing their undergraduate careers at various universities, including Georgetown University, University of Maryland and UC Davis. Our remaining GSP cohort will be staying on throughout the academic year as they continue their studies at local universities.

2017 La Jolla Interns

2017 La Jolla Interns

JCVI strives to prepare future scientists by exposing them to multiple facets of scientific research as well as the professional working environment. During our summer internship program, interns not only conduct their own research project and present their findings to the JCVI community, but also are involved in a variety of professional development activities. Our interns participate in a weekly journal club, which exposes them to current scientific literature. There they present and discuss a scientific journal article selected by JCVI mentors. JCVI also holds a weekly intern-only seminar series, where our cohort has the opportunity to learn more about JCVI research, talk with graduate students and learn about different career options in the field of science.

Hands-on informatics training with Rockville interns

Hands-on informatics training with Rockville interns

If you are interested in JCVI’s internship program, please check our website for additional information and updates about our upcoming 2018 summer session.

Summer 2016 Intern Program

Interns in both Rockville, MD and La Jolla, CA participated in our summer 2016 internship program at the J. Craig Venter Institute (JCVI). A total of 19 interns were hired for the summer 2016 program, selected from 578 applicants. Of the 19 interns, six interns were part of the Genomic Scholar Program (GSP) that is a transition program focusing on the leap from a community college to a four-year college using a combination of activities including undergraduate research experience with mentoring and professional development. The interns were mentored by JCVI faculty and research scientists. Mentors design a research project for each intern depending on their education and prior research experience.

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

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

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

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

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

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

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

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.

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.

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.

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.