Building the World’s First Net-Zero Energy Lab
And see the construction in time-lapes.
J. Craig Venter Institute Science Blog
Building the World’s First Net-Zero Energy Lab
And see the construction in time-lapes.
Yesterday, JCVI expedition scientist Jeff Hoffman embarked from Manaus on a sampling expedition of the Amazon River and its tributaries, which contains 1/5th of the Earth’s river flow. In collaboration with scientists Dr. Guilherme Oliviera and Dr. Sara Cuadros from the Centro de Excelencia em Bioinformatica (CEBIO) of Belo Horizonte, Jeff is taking samples to characterize the genomes of microbes found along 2/3rds of the entire Amazon watershed, including inflowing rivers from Manaus to Macapa. Our collaborators at CEBIO will be sequencing the samples with a joint Brazil-USA effort on analysis. Long recognized for the biodiversity of visible organisms, the Amazon is understudied with regards to the diversity of microscopic organisms and this expedition will substantially increase our understanding of the biological diversity on Earth. This work continues, leverages, and complements previous and ongoing JCVI work characterizing the unexplored microbiomes of marine, estuarine, freshwater, and terrestrial environments around the world.
See a gallery of the expedition on Facebook. More pictures will be added throughout the trip.
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.
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.
I’m off again on an ocean sampling voyage but this time instead of being onboard the JCVI’s Sorcerer II, I am onboard the R/V Endeavor as part of a multi-institution, international scientific sampling team that is headed from the US to the Azores.
On Thursday August 22 we left Morehead City, North Carolina for Ponta Delgada on Sao Miguel Island in the Azores. The research vessel will take multiple samples along the 23 day transect. Here is a rundown of the teams and the science we are conducting.
I will be filtering large volumes of seawater on 293mm filters for DNA sequencing, as well as smaller volumes onto smaller Sterivex filters for RNA sequencing and associated studies of gene expression within various microbial communities. This research expedition is funded by a grant from the National Science Foundation program in Dimensions of Biodiversity to Bess Ward at Princeton University and Andrew Allen at JCVI. The goal of our JCVI group is to extend findings from the Sorcerer II Global Ocean Sampling program, which documented massive genomic diversity and unusual physiological and biochemical capabilities within and between many lineages of marine microorganism. With samples collected on this research cruise, we will have the opportunity to document large-scale patterns in gene expression, and generate key hypotheses related to the most biochemically-active microbes across a major section of the upper 1000m of the North Atlantic. Data obtained from this study will be combined with similar data we collected last February and August on cruises out of Bermuda to the Bermuda Atlantic Time Series (BATS) stations in the in the sub-tropical Atlantic.
The Princeton team headed up by Bess Ward includes Sarah Fawcett, Nicolas Van Oostende, Jess Lueders-Dumont, Dario Marconi, and Keiran Swart. Their primary research involves using flow cytometry to physically capture, size fractionate and identify microbes living in the sunlit layer of the ocean. These microbes are directly responsible for assimilation of dissolved nitrate, which accumulates in the dark interior of the ocean. Specific identification of these microbes is an important research goal for microbial oceanography because the regulation and magnitude of global oceanic CO2 assimilation is driven explicitly by nitrate assimilation by photosynthetic microbes. Such microorganisms also produce a large fraction of the oxygen in the atmosphere. The Princeton group will perform nitrification experiments and measure levels of dissolved nitrate, ammonia and carbon by using stable and natural isotope tracers. The team will investigate the origins of dissolved inorganic nitrogen by measuring the natural abundance of the nitrogen isotopes. Net tows will also be performed to collect the “bigger” planktonic organisms, such as zooplankton, within the ocean food chain.
Real time nutrient data down to nanomolar levels will be determined by Malcolm Woodward of Plymouth Marine Laboratory (PML) and Amandine Sabadel from the University of Otago in New Zealand.
As we motor to our first station, which we should reach on Monday September 2nd, we stop every morning at 5 am to perform a CTD cast to 1000 meters. Based on biological and physical features, observable in real time via CTD sensors cabled to the shipboard computer,12 bottles, each containing 30 liters of sea water, are sealed at varied depths and the 360 liters is brought to the boats deck. Once the CTD is on the deck, the different scientists scurry to gather their allocated amount of water from the CTD rosette and hurry back to their labs to do the appropriate work.
As of Wednesday August 28, 2013, we have done 7 transect CTD casts, all but one to 1000 meters. Today we sampled on the Grand Banks and the water column depth was only 57 meters. For every cast I have collected RNA samples at 1000 meters, 250 meters, within the Deep Chlorophyll Max (DCM) (if no DCM is apparent, then just below the Chlorophyll max), a sample from within the Chlorophyll max and in the mixed layer (normally at 20 meters).
The weather has been great except for one 24 hour period when the swells grew to about 7 feet and the boat was really rolling back and forth. The crew is great, the food is awesome, good thing they have a small gym or I don’t think most of us would fit in our clothes after a few weeks out here! The scientists are working well as a team and this should be a very exciting and beneficial science expedition.
Once we get to the our first station we will stay there for two days………….it will be a very intense two days, then a day motor to the second station followed by another crazy two days of sampling………….more on that next blog!
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!
‘Twas the night before Christmas, when all through the building
All our creatures were stirring, even our mold;
The dishes were placed in the incubator with prayer,
In hopes that pure growth soon would be there;
The scientists were nestled all close to their screens instead
While swirls of DNA danced in their heads;
My coworker in her labcoat, and I with my pipettor,
Had just settled down for a long overnighter,
When out in the lab there arose such a clatter,
I sprang from my microscope to see what was the matter.
Away to the incubator I flew like a flash,
Tore open the doors then saw what was trash.
When, what to my tired red eyes should appear,
But a bunch of contaminated plates, there goes my career.
Last year, still in an isolated fungal room placed far away from others, I made an attempt at this one, but my stocks were contaminated. Something all fungal folks know something about. (Aspergillus is just EVERYWHERE). So with a little luck (let’s face it, with complete luck) I was able to clean things up and told the fungus to be on its best behavior. However, N. fischeri still did not want to play nice with the P. marneffei…so they remained slightly separated.
I hope everyone enjoys my creation, although the credit goes to my jolly ole fungus for being so wonderfully diverse and satisfying my slightly nerdy creative side.
Let us all show the world the true side of fungus and all its amazing potential. Because we all know they can do more than just sit there and look pretty.