Posts in category Education

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Thule, Greenland – Day Three

Day three started with me missing breakfast. It seems that folks around here only eat breakfast between 5am and 8am. Today was a very rough day for sampling.  About an hour drive to the area near the site, about a three-mile hike to one spot another half-mile hike to another spot followed by the three and a half mile hike back to the truck. We sampled “rich” soil and “rich” soil from a lake. These two sites were sampled and categorized as “rich” due to the abundance of vegetation around and near the sites. The area surrounding Thule is very desolate so I can imagine the plants have a hard enough time growing.  It would be very interesting to see what microbes are present in these two sites to allow such vegetation to grow; even more interesting to see how water affects the microbial population. Samples were frozen once we got back to the on site lab. A small portion was saturated with AllProtect to ensure preservation of RNA for transcriptomics analysis.

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The day ended with a lecture from another NSF grant recipient to install a telescope on the Greenlandic ice cap. It was an interesting idea to coordinate radio imaging from other telescopes around the world to look at quantum singularities that were very far away. After speaking to some of the other scientists here I found out that our group, which includes myself and our collaborators Slava Epstein and Dawoon Jung, were the ONLY Microbiologists on the base. Everyone else was either a Geologist, Environmental Scientist, Astronomer, or Meteorologist. It was great to hear about everyone else’s projects.

The Next Generation Science Standards are Ready for Review

The second draft is ready for public comment through January 29th. Please be sure to take some time to review.

http://www.nextgenscience.org/next-generation-science-standards

Plant Bioinformatics Workshop

JCVI recently held its 3rd Annual Plant Bioinformatics Workshop from July 15-19th. During the week-long workshop, 20 scientists from the Plant Research community visited JCVI and learned many aspects of Bioinformatics from the members of Chris Town’s Plant Genome group. Attendees included undergraduate and graduate students, post-doctoral fellows, research scientists and faculty at various Universities throughout the United States as well as a biotech company. In addition to the on-site participants, we had 5 additional participants attend the workshop via WebEx. The virtual participants had the opportunity to sit in on the lectures and complete the hands on exercises by logging into an Amazon Cloud instance, which was set up specifically for this purpose. The topics covered during the workshop included UNIX tools for Bioinformatics, Genome Assembly, Structural and Functional Annotation, RNA-seq assembly and analysis and SNPs. In addition to JCVI’s instructors, we had additional sections covered by external instructors. Eric Lyons (University of Arizona and iPlant) presented on Comparative Genomics and the iPlant Infrastructure and Ann Loraine (UNC Charlotte) presented on Integrated Genome Browser. All sessions contained a hands-on component so the students would have the opportunity to use the tools that we discussed during the lecture portion.  Watch our website for future offerings!

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JCVI Internship Information for 2013 Is Ready

We are now accepting applications for the 2013 Summer Internship Program.  We are excited to be able to continue to inspire young scientists!  Last year, we received 546 applications.  Of which, thirty-one interns were selected to work in diverse areas.

 

2012 San Diego Summer Interns

2012 San Diego Summer Interns

 

2012 Rockville Summer Interns

2012 Rockville Summer Interns

 

Some of the intern projects were:

  • Isolation and Characterization of Electricity Generating Bacteria
  • Characterizing the Microbial Population of Rabbit GI Tract
  • Cloning Ureaplasma urealyticum: An Odyssey
  • Comparative Genomics of three isolate strains in the actively serpentinizing Cedars Springs
  • Coronavirus: Amplification of the HE and Spike genes in human coronavirus genomes

The 2013 JCVI Internship Program is open to accept spring and summer applications. The application process includes the submission of a resume, essay and transcripts as one PDF file via our online application site. We do not require letters of recommendation.

Information about the 2013 program can be found at http://www.jcvi.org/cms/education/internship-program/

2012 JCVI Internship Program Is Now Accepting New Applications

Wow! Another year has gone by.  Its hard to think it is November – almost December with the warm weather we have been enjoying.  However it did not start that way.

Halloween Snow in Maryland!

The 2012 JCVI Internship Program is open to accept spring and summer applications. The application process includes the submission of a resume, essay and transcripts as one PDF file via our online application site. We no longer require letters of recommendation.

Information about the 2012 program can be found at http://www.jcvi.org/cms/education/internship-program/

For summer 2011, we received 544 applicants.  Of these applicants, 30 Interns were selected (10 in San Diego and 20 in Rockville):

  • 7 high school students
  • 9 undergraduate students
  • 13 graduate students
  • 1 secondary teacher

The intern projects ranged across the Institute:

  • A lethal set of virulence factors in uropathogenic E. coli ?
  • Expanding genome transplantation: Streptococcus thermophilus
  • Random Assembly for Use in Swapping as a Tool for Genome Minimization
  • Assembling terminators and promoters
  • Developing Galaxy Tools for the Ordination Analysis of Meta-genomic samples

Good luck to all the applicants this year!

The Mobile Lab Is Going to Sunny San Diego

Late one evening in January 2006, the mobile lab pulled into the parking lot at 9704 Medical Center Drive.  It was such an exciting evening!!  Within a few days, we had all the lab supplies on it and began visiting students.  The first school in the Washington Area was Patapsco Middle School in Howard County.  In addition the other inaugural participating schools were Ron Brown Middle School, Hines Junior High School, and Eliot Junior High School in Washington, DC.  Since then, we had the opportunity to bring the mobile lab to thousands of students in the past 5 years.
First Class on the DG! Mobile Lab, January 2006

First Class on the DG! Mobile Lab, January 2006

Today, the mobile lab began its journey across the US to San Diego.  Let us know if you see it on the highway!
 As you may have seen in September, we just broke ground on our new facility in San Diego.  We began offering education programming in San Diego at our temporary facility in 2007 – we have worked with over 30 teachers.  From these relationships, we look forward to bringing the same opportunities to San Diego students we have in the Washington Area.
Students on the DG! Mobile Lab

Students on the DG! Mobile Lab

 With the current economic environment, keeping this program rolling is challenging.  Yet, it is needed more and more in the classroom.  We need your help!  To find out how you can help keep this science program rolling, visit our Giving Page.

The Hill School: Day 2

The day started early Tuesday with first period.  Thirty eager students arrived on the bus to determine the results of the amplification of the DNA they extracted the day before.  The PCR ran overnight, copying part of a conserved gene in plants, RuBisCo, that can be used to identify the species of land plants.

Loading Gels at the Hill School

Loading Gels at the Hill School

 Using gel electrophoresis, we were able to load gels and run them quickly to see the results.  Most students successfully had amplicons – this was a great since they had not ever done DNA extraction or electrophoresis. The samples have been brought back to Rockville for sequencing and will be available for the students to analyze in about two-weeks.
Loading Gels like a Professional at the Hill School

Loading Gels like a Professional at the Hill School

We had a great visit with the students and are curious to see what plants they brought from around campus.

We look forward to working with them again in the future!

To support our Education program visit http://www.jcvi.org/cms/giving/overview

The Hill School: Day 1

DiscoverGenomics! Mobile Laboratory at the Hill School

DiscoverGenomics! Mobile Laboratory at the Hill School

The day started early with reagent and lab preparation before we even left for school OR had coffee.  We expected to do over 100 DNA Extractions as the first step in the DNA Barcoding. We arrived on campus as the first period was starting –we didn’t have class until after 9:00.

Grinding samples at the Hill School

Grinding samples at the Hill School

 It was a full house (bus) most of the day and busy getting through the DNA extraction.  Various specimens were brought in from around campus to determine their species.  It will be interesting to see the diversity of plants on campus.

Moving through the protocol at The Hill School

Moving through the protocol at The Hill SchoolThe Hill School

 

The Hill School

The Hill School

The Mobile Laboratory Hits the Road

After a hiatus this summer, the Mobile Laboratory hit the road again today for a trip to Pottstown, Pennsylvania.  Driving through the rolling hills of northern Maryland into southeastern Pennsylvania, it passed small towns and beautiful foliage.  Tomorrow and Tuesday, we will be working with students from the Hill School. 

The students will be exploring their campus by determining the species of plants they collect.  This process is often called “DNA Barcoding.”  DNA Barcoding is a standardized procedure using PCR, sequencing and bioinformatic analysis to determine the various species of plants, bacteria, etc. based on conserved genes.

Stay posted for more updates tomorrow!

A Look Back at 2010 at the JCVI…

As the J. Craig Venter Institute (JCVI) soars into its 19th year, we reflect on the past year of highlights and accomplishments to mark the close 2010 and look forward to more significant scientific advances in 2011.

JCVI Top 10 of 2010 …

1. First Synthetic Cell: Fifteen years in the making, 2010 brought to bear with huge anticipation the successful construction of the first self-replicating, synthetic bacterial cell. The work was published in Science in May. The synthetic cell called Mycoplasma mycoides JCVI-syn1.0 is the proof of principle that genomes can be designed in the computer, chemically made in the laboratory and transplanted into a recipient cell to produce a new self-replicating cell controlled only by an artificial genome. Although the first synthetic cell was not designed to produce a specific bioproduct, the team has shown that this can be done and the potential benefits are numerous. The research team, lead by JCVI President Craig Venter, Hamilton Smith, Clyde Hutchison, and Daniel Gibson, envision a future where the rapid design and production of biological products using synthetic biology techniques will be used to produce clean fuels, medicines, and other bioproducts. Throughout the course of this work, the JCVI Policy group has extensively engaged in outside review of the ethical and societal implications of this work, including advising the new Presidential Commission on Bioethics on their recommendations for oversight.

M. mycoides JCVI-syn1

M. mycoides JCVI-syn1

2. Synthetic Vaccines: Following on the heels of the announcement of the first synthetic cell, the company Synthetic Genomics Inc. and JCVI announced in October the formation of a new company, Synthetic Genomics Vaccines Inc. (SGVI). The privately held company is focused on developing next generation vaccines that can be rapidly produced and tested, which is especially important for outbreaks of new infectious diseases. SGVI also announced a three-year collaboration with Novartis to apply synthetic genomics technologies to accelerate the production of the influenza (flu) seed strains required for vaccine manufacturing. The seed strain is the starter culture of a virus, and is the base from which larger quantities of the vaccine virus can be grown. Under this collaboration, Novartis and SGVI will work to develop a “bank” of synthetically constructed seed viruses ready to go into production as soon as WHO makes recommendations on the flu strains. The technology could reduce vaccine production time by up to two months, which is particularly critical in the event of a pandemic.

3. Hydra Genome – one of the animal kingdom’s earliest common ancestors: JCVI scientists along with more than 70 other researchers from around the world, have sequenced and analyzed the genome of Hydra magnipapillata, a fresh water member of the cnidaria– stinging animals that include jellyfish, sea anemones and corals. The research, published in the March 14 edition of Nature, was co-led by Ewen F. Kirkness, JCVI, Jarrod A. Chapman, Department of Energy Joint Genome Institute, and Oleg Simakov, University of California, Berkeley. This is the second sequenced cnidarian genome, following that of a sea anemone, Nematostella vectensis, in 2007. The ancestors of these two species diverged more than 500 million years ago, and comparison of their genomes has revealed common features of the earliest animals that gave rise to the diversity of animals on Earth today. The team found clear evidence for conserved genome structure between the Hydra and other animals, like humans. Unexpectedly, the sequencing also revealed a novel bacterium that lives in close association with the Hydra.

4. Uncovering the Human Microbiome: Microbes are living within and on the human body and this collective community is called the human microbiome. JCVI Scientists, as one component of the large scale NIH Roadmap Human Microbiome Project, and along with colleagues at three other genome centers sequenced the genomes of ~180 microbes from the human body, published in the May 21 edition of Science. At the JCVI we anticipate sequencing an additional 400 species over the next few months. Colleagues at the JCVI are also using single cell approaches to isolate new strains that have not been cultured – isolates whose genomes will also be completely sequenced. The role these microbes play in human health and disease is still relatively unknown and these approaches are allowing us to gain a greater understanding of these enigmatic species.

5. Body Louse Genome: A global research team led by Ewen Kirkness and colleagues from JCVI published a study in the Proceedings of the National Academy of Sciences in June describing the sequencing and analysis of the human body louse, Pediculus humanus humanus, a human parasite responsible for the transmission of bacteria that cause epidemic typhus, relapsing fever and trench fever. Detailed analysis of the genome was then conducted by a large international group of 71 scientists, coordinated by Barry Pittendrigh, University of Illinois, and Professor Evgeny Zdobnov, University of Geneva Medical School. Comparative studies of the body louse genome with other species revealed features that will enhance our understanding of the relationships between disease-vector insects, the pathogens they transmit, and the human hosts. In addition to the targeted louse genome, the project unexpectedly yielded the complete genome sequence of a bacterial species, Riesia, that lives in close association with lice, and which is essential for survival of the insects. The researchers believe that the genome will be a valuable reference for evolutionary studies of insect species, especially in the areas related to insect growth and development.

6. Castor Bean Genome Sequencing: A research team co-led by Agnes P. Chan and colleagues from JCVI and Jonathan Crabtree and others at the Institute for Genome Sciences, University of Maryland School of Medicine, published the sequence and analysis of the castor bean (Ricinus communis) genome in Nature Biotechnology in August. Because of the potential use of castor bean as a biofuel and its production of the potent toxin ricin, the team focused efforts on analysis of genes related to oil and ricin production. The analyses could be important for comparative studies with other oilseed crops, and could also allow for genetic engineering of castor bean to produce oil without ricin. Identifying and understanding the ricin–producing gene family in castor bean will be important in preventing and dealing with potential bioterrorism events. Genomics enables enhanced diagnostic and forensic methods for the detection of ricin and precise identification of strains and geographical origins. As a next step, the group suggests further comparative genomic studies with the close relative cassava, a major crop in the developing world, to further elucidate their disease resistance aspects.

7. Science Education: JCVI was an Official Partner of the inaugural USA Science and Engineering Festival held on the National Mall in Washington, DC in October. The Festival, which was the country’s first national science festival, included over 500 of the country’s leading science and engineering organizations with the aim to reignite the interest of our nation’s youth in the sciences. The JCVI ‘Discover Genomes’ Bus was showcased during a two-day expo and some of the research being done at JCVI was presented to around 1700 visitors by our scientists and staff.

There were lines all day!

8. Viral Genomics– In 2010 the JCVI has published over 1600 influenza genomes and over 75% of all published flu genomes to date have been sequenced by the JCVI, totaling over 6000 genomes. This year the diversity of viral genomes we have sequenced has significantly expanded under the NIH Genomic Sequencing Center for Infectious Diseases contract. Some of the projects include viruses causing diseases such as measles, mumps, rubella, encephalitis, SARS, and the common cold, just to name a few. The viral group has annotated and published 79 Rotavirus (stomach flu) and 33 Coronavirus genomes (includes SARS and common cold) this year and many more will be published in 2011. The pace of sequencing and finishing genomes has also increased this year as a result of adoption of nextgen platforms (e.g. Illumina/454 and Illumina/Solexa) and the development of more efficient methodologies to increase productivity while reducing costs.

9. Marine Microbial Genome Sequencing Project: JCVI scientists have continued their quest to isolate and sequencing microbes living in global ocean waters to discover new genes and enzymes, and to help understand the role microbes play in the ocean ecosystem. Shibu Yooseph, Kenneth Nealson and colleagues at JCVI published an analysis of 137 known marine microbial genomes living in the global ocean surface in Nature in November. These genomes were compared to metagenomic samples of ocean waters of 10.97 million sequences of JCVI’s Sorcerer II Global Ocean Sampling (GOS) metagenomic data and thousands of 16S rRNA sequences. The marine genomes were collected as part of the Gordon and Betty Moore Foundation-funded Marine Microbial Genome Sequencing Project, a project coordinated by JCVI that has a primary goal of obtaining whole genome sequences of ecologically important microbes from a variety of diverse, global marine environments. The work provides a good example of combining metagenomic data with sequenced genomes data to study microbial communities and to generate testable hypotheses in microbial ecology.

10. Sorcerer II Global Ocean Sampling Expedition: On December 17th 2010 Sorcerer II arrived in Florida after spending the last two years with her crew collecting samples in The Baltic, Mediterranean and Black Seas. Funded generously by the Beyster Family Foundation Fund, The San Diego Foundation, and Life Technologies Foundation, Sorcerer II has sailed ~28,000 nautical miles since departing San Diego in March 2009. During this time 212 samples were collected and over 5,100 liters of sea water was filtered and sent to JCVI for analysis of the microbial life contained within these samples. The JCVI established strong collaborations with scientists in all 16 countries in which samples were collected, which will lead to joint publications and future collaborative studies in the new year. Read more.

Sunrise in the Ligurian Sea

Looking Forward to 2011…

Ten-year anniversary of the Human Genome Project: To commemorate the anniversary of the publications of the first human genome sequences in 2001, JCVI and Nature are hosting a conference and celebration in February 2011 titled – Human Genomics: The Next 10 Years. The conference will look forward to the promises of human genomics for the next 10 years, with sessions on medical advances related to genomics; the technological and ethical challenges of human genomics; personalized and familial genomics; the human microbiome project; variation in the human genome; and making sense of the genetic code. This conference will be a great way to jump into the new year and inspire the grandiose ideas and achievements that genomic scientists will accomplish over the years to come.