Arrived at Thule, Greenland after a 5 hr flight from Copenhagen. It was pretty interesting seeing a long line of people all getting on a flight that was headed to a part of the world that usually has less than 600 people there at any given time. Arrival was pretty straightforward, no jetway, no customs, no LCD screens telling you where to pick up your bag. Just a few military personnel checking your documents to ensure that you have the approval from the Danish government and USAF to be on base. First impression getting off the plane…it’s cold. Not as cold as I expected it to be but it was just 90 degrees F when I left home a few days ago. Today’s high was 39 degrees F. Standing in the sun it’s not so bad but when the wind starts blowing it turns into a recipe for chapped lips and windburn. Oh and did I mention the massive mosquitos here? Not much wildlife in this part of the world but the mosquitos outnumbers the vertebrates probably a million to one. They are also VERY aggressive; they even swarmed the trucks while we were driving around the base. We were shown our living quarters, which were very nice, kind of reminded me of living in the dorms during undergrad. There are individual rooms and a shared bathroom on each floor. We toured the various sites that our collaborator Slava Epstein already pointed out as good sampling sites that vary in vegetation and proximity to water. The land here is quite desolate, not much green, mostly moss and small shrubs growing. Traditional trees are nonexistent but “ground trees” are actually common. They are trees that grow outward on the grass and not upward. The rest resembles pictures taken by the mars rover. As the day goes by I noticed the sun was circling and I came to the realization that the typical artic summer was happening right in front of me. The sun literally circles and will not go down until around September. It was quite odd, getting in bed at midnight and seeing the sun still in the sky. Tomorrow will be more interesting since we will be going further away from base to sample additional areas.
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.
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 second draft is ready for public comment through January 29th. Please be sure to take some time to review.
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!
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 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/
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!
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
- 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
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 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
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
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
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
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 SchoolThe Hill School
The Hill School
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!