The second draft is ready for public comment through January 29th. Please be sure to take some time to review.
J. Craig Venter Institute Science Blog
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.
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.
Some of the intern projects were:
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/
The JCVI La Jolla construction site has been busy since earthwork began in 2011. After grading the site to specified levels, a detailed excavation began to make room for the structural concrete footings, supporting slabs, and underground utilities. With all of the holes in just the right place, crews began installing steel rebar to provide reinforcement for the large structural footings which will eventually carry the building’s weight. Once the steel had been placed, it was inspected and filled with concrete. The largest structural footing was so large that it took 45 concrete trucks to fill the hole!
Concrete wasn’t the only thing being placed under the building. Of the many sustainable strategies included in the building’s design, two of these systems require large underground water tanks to operate. The first is a rainwater harvesting system which will collect precipitation from the building roof and site. Three tanks, totaling 90,000 gallons, collect the water so that it can be treated and then reused for toilets and irrigation. This system will reduce the building’s potable water demand by 70% annually. Pictured here is a 5,000 gallon fiberglass tank being lowered into position.
To become a net-zero building it is critical that electrical demands are minimized. The new JCVI La Jolla building is being designed with an ultra-efficient mechanical system to help reduce the building’s energy profile. At the core of this design are two 25,000 gallon thermal energy storage (TES) tanks. These tanks will store both warm and cool water which will be used to either heat or cool the building depending on the building’s internal temperatures. Using water to move heat in and out of the building uses 87% less energy than using air and allows the mechanical systems to operate at much higher energy efficiencies than standard building systems.
Most of the building structure is made with concrete and, after the underground work was complete, McCarthy wasted no time in constructing the vertical support walls. The walls are architectural concrete because they are designed to complement the other materials such as wood that will make up the building’s exterior. Using information from the concrete mock-ups (See Moving Dirt at JCVI La Jolla) the team selected a 30% fly-ash concrete mix. Fly ash is a waste material from coal-fired power plants that lowers the amount of cement needed to make concrete, thus both lowers the energy and carbon dioxide emissions of manufacture and increases the overall volume of recycled content used in building.
Constructing architectural concrete is akin to making art. Huge forms are built with meticulous detail using special materials, fastening methodologies, and custom routed grooves to create the desired finish. Those forms are filled with steel rebar, filled with concrete at lightning speed, and then stripped (formwork is removed) at just the right time to produce the final product. The work is even more challenging given the complex geometries of the building and the performance characteristics of using a 30% fly-ash concrete mix.
As of September 2012, the team has almost completed the parking garage and podium deck upon which the building structure will sit. Concrete work will continue through the fall and is expected to complete in early 2013.
There is a new “Biowalk of Fame” in Maryland, and our own Craig Venter was one of the first honorees receiving a plaque, which is there for all to see as you stroll through lovely Silver Spring.
Other honorees include Dr. Martin Rodbell and Ben Carson. The event to honor the awardees was on April 22, which also it happens to be Earth Day. Although it rained heavily throughout the event, there were a large number of people in attendance including several local government officials including Council member Valerie Ervin and Chairman Ike Leggett. Dr Martine Rothblatt, CEO of United Therapeutics, emceed the event.
The idea behind the BioWall and the Biowalk is very innovative. The Wall is a live movie like screen that allows videos from students and the public that relate to science to be continuously aired. A student observing a paramecium under the microscope for example can mail the clip in to United Therapeutics, and it will be available for all to see. The Biowalk also has plaques dedicated to those who have made the most outstanding contributions to the State of Maryland in the sciences – hence Craig.
The take home message is, if you are wondering through Silver Spring do not be surprised if you see Craig’s name on a plaque on 1040 Spring Street. Congratulations!
After celebrating the ground breaking of JCVI La Jolla, McCarthy Building Companies immediately got to work preparing the land for construction. First the crew set up a work area to house the staff and equipment needed for the project. The site was cleared and stabilized for construction trailers and a temporary road was built for construction vehicles and equipment. Water trucks were used to control dust and special shaker plates were installed at the entrance of the site to minimize loose dirt and stones on nearby roads.
With basic infrastructure in place, the team moved next to save three large Torrey Pines growing within the construction zone. The trees had been identified during the design process and were flagged for relocation to protected areas on the site where they will remain as part of the natural landscape. Big Trees of California, a firm specializing in relocation of large tree species, began the process of “boxing” these trees in custom built structures 14’ wide by 14’ long and 5’ deep. Wooden lifting beams were installed underneath to provide connection points for the vertical lift. A large crane was used to “fly” full grown Torrey Pine trees to their new homes.
With the Torrey Pines now safe, preparations for the building pad began. Several pieces of heavy earth working equipment arrived to begin the dig for the building’s foundation. However, the crew soon discovered a local soil condition, known as “Lindavista formation,” which proved to be a challenge for even some of the largest machinery. Fortunately, the team was prepared, and with a few equipment modifications, they reached the designed grading levels required for the excavation in just slightly more time than expected. The earthen building pad was moisture conditioned, compacted, and surveyed by geotechnical engineers. The first major construction milestone was met! The team is now focused on installing the concrete foundation and underground utilities.
While most of the team was focused on moving dirt, McCarthy’s concrete team began assembling 4’x8’ mock-ups of the architectural concrete that will be used for building’s exterior. The mock-ups are done to determine the best method for constructing future concrete forms, while simultaneously giving the architects a glimpse at the final appearance of the finished product. In this first series of concrete mock-ups the team is particularly focused on two important decisions:
1) How much recycled fly-ash material can be added to the concrete while still maintaining the desired look and strength characteristics? Adding fly-ash to a concrete mix design increases the amount of recycled building material used and can count towards LEED credits. The JCVI building is intended to be one of the few LEED Certified Platinum lab building in the US so every step counts.
2) How will the concrete forms be constructed to produce the desired finish and house the necessary structural steel elements?
Stay tuned for updates on progress of the concrete mock-ups and other design elements of the building. Also, if you haven’t seen it already, check out the web-cam image here which provides hourly updates from the job site.
During the height of the H1N1 Flu pandemic, David Wentworth was running a microbial genetics laboratory at the Wadsworth Center, New York State Department of Health (NYSDOH) where he was instrumental in developing a method to amplify influenza genomes regardless of strain using “universal primers” or short strands of DNA that recognize conserved segments across the genomes of many different flu strains. This amplification process was developed to generate recombinant influenza A viruses (the most common flu type affecting humans and animals) that could be used for the production of new vaccines. From a clinical swab it took his team 9-12 days to develop vaccine seed stocks. It was this work that first brought Dave to JCVI’s attention.
Several years ago Dave began collaborations with JCVI scientists to sequence human and avian influenza viruses. The collaborations intensified two years ago when all pandemic flu samples (or suspected flu samples) were first sent to Dave’s lab so the virus could be amplified in sufficient quantities for sequencing using his new amplification pipeline. The amplification took only a day and then isolated, non-infectious, DNA was sent to JCVI for sequencing. JCVI was the natural choice for this work since we are host to the government-funded “Influenza Genome Sequencing Project,” with the goal of sequencing large numbers of viral genomes to help scientists worldwide to understand how flu viruses evolve and cause disease. JCVI researchers then deposited influenza sequences into GenBank within two days of receiving DNA from Dave’s lab, enabling researchers worldwide to track what strains are circulating and how they are evolving. JCVI has sequenced over 75% of the influenza genomes in GenBank, the NIH public repository for sharing genetic sequencing data.
Dave was soon invited for a talk at JCVI. “The opportunities at JCVI were to help build the [viral genomics] program. And already good, quality people are here studying viruses with a focus on viral evolution and sequencing analysis,” Dave remarked. “Being part of generating that information, I think makes you have a better feel for the biology.” The capabilities for viral sequencing combined with IFX strengths and the interest in viral evolution at JCVI was a draw for Dave and he soon joined the team. Moreover, there are opportunities at JCVI to work with collaborators who send specimens from various regions of the world for sequencing so that we can “more deeply understand the mutations that contribute to virulence,” he said. He is particularly interested in antigenic drift (how viruses escape immunity) that contributes to the “annual influenza escape,” which is critical in developing vaccine strains.
The need for new and improved methods to develop vaccines, coupled with the advances in synthetic genomics developed at JCVI led to the formation last year by JCVI and the company Synthetic Genomics Inc. of a new company, Synthetic Genomics Vaccines Inc. (SGVI). JCVI scientists, through SGVI, are working on a three-year collaboration agreement with Novartis to apply synthetic genomics tools and technologies to accelerate the production of the influenza seed strains required for vaccine manufacturing. The agreement, supported by an award from the U.S. Biomedical Advanced Research and Development Authority (BARDA), could ultimately lead to a more timely and effective response to seasonal and pandemic influenza outbreaks. The idea is to create viruses de novo or synthesize genes critical for its antigenicity and put these in normal vaccine strains for production. The goal of the work at SGVI is to synthesize a virus in one week, or rather a seed stock, which still needs to be amplified in big fermenters. New seed stocks take 3-4 weeks to produce which is currently a rate liming step.
You don’t hear too many people singing its praises and saying “I love the flu!” as Dave has remarked, but put in context, his enthusiasm for his work shines through best when talking about his love of teaching. He gets excited teaching young scientists about virology, especially helping them to understand the important areas to study, and where the research will lead to solve a major problem. “The rewarding part of being a mentor is to see all of the people who have found their niche – it might not be bench research but they are still carrying knowledge with them.”
Aside from spending time with his family, Dave enjoys a hobby started by his dad – to cultivate honey bees. A community gardens group at a middle school in Albany, NY was looking for bees to pollinate their plants. Dave spearheaded the effort and used it as a learning tool for kids, who helped feed honey to caterpillars and moths. He also used to give lectures on bee cultivation and has taught college courses in animal science. Dave’s enthusiasm for science among his students and peers could be considered infectious, just like the subject of his research!