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

As you may have heard, Carl Woese died of pancreatic cancer yesterday at the age of 84. I had the honor of working with Carl in grad school at the University of Illinois where my advisor, Gary Olsen, ran a joint lab with Carl.

Carl Woese. Photo courtesy IGB.

As the originator of the use of ribosomal RNA to distinguish and classify organisms (including obviously the Archaea), Carl both revolutionized evolutionary biology and created a method that is still very much in use today. Even in the latest metagenomic study of the oceans or of the human gut, a 16S rRNA diversity study is required as a control in addition to whatever additional markers or random sequencing is used.

One of the things that fascinated me about Carl is how he constantly reinvented himself and explored new fields of biology — his early work in the 1960s dealt with classical molecular biology and the genetic code (the origins of which continued to fascinate him for the rest of his life). He then transfered to the study of the ribosome and its structure, which in turn led to his study of 16S and its evolutionary implications. In the 1990s, when I worked with him, he was a pioneeering microbial genomicist and collaborated with TIGR to sequence the first two Archaeal genomes. And in his final years he focused on early evolution and the last common ancestor of life in the light of what genomics has taught us.

Carl also had his humorous and counter-cultural side. I remember him telling me how his lab in the 1960s heard about the rumor that compounds in banana peels were a legal narcotic and how they launched an unofficial research project to isolate these. His verdict was that there was nothing there and neither the peels nor anything in them could get you high — but he wanted to empirically test that. Also, when reading about a supposed “Qi master” who claimed to be able to influence mutation rates with his mind, he invited him to the lab to give a demonstation — which naturally failed to show any effect under controlled conditions — but he wanted to see if the guy could really do it.

Genomics, metagenomics, and evolutionary biology has lost one of its greats — but his legacy lives on.

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.

Brim and ball: Neosartorya fischeri; Hat: Penicillium marneffei; Ho,Ho,Ho: Aspergillus flavus. Image Credit: Stephanie Mounaud / J. Craig Venter Institute.

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.

Star: Talaromyces stipitatus; Tree: Aspergillus nidulans Ornaments: Penicillium marneffei; Trunk: Aspergillus terreus. Image Credit: Stephanie Mounaud / J. Craig Venter Institute.

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.

Hat, Eyes, Mouth, Buttons: Aspergillus niger; Arms: Aspergillus nidulans; Nose: Aspergillus terreus with Penicillium marneffei; Body: Neosartorya fischeri. Image Credit: Stephanie Mounaud / J. Craig Venter Institute.

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.

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/

Our NextGen pipeline, which utilizes SISPA-generated libraries with Roche/454 and Illumina sequencing, enables us to complete a wide variety of viral genomes including challenging samples. Automated assembly pipeline employs CLCbio command-line tools and JCVI cas2consed, a cas to ace assembly format conversion tool. Our complimentary Sanger pipeline software is currently being integrated with the NextGen pipeline. This will improve our data processing and will allow us to use validation software (autoTasker) more efficiently.

Promoter of Bat Genome

During the past year we have found that novel viruses, repetitive genomes, and mixed infection samples could not be easily integrated with our high-throughput assembly pipeline. We have developed an assembly and finishing process that utilizes components of the high-throughput pipeline and combines them with manual reference selection and editing. Using this approach we completed novel adenovirus genomes and mixed-infection avian influenza genomes, and improved assemblies of previously unknown arbovirus genomes. We are currently working on optimizing and automating this new pipeline.

Consed Representation of Mixed Viral Sample

Repetitive genomes have long been known to present great challenges during assembly and finishing. We are presenting a new approach to assembly and finishing of repetitive varicella genome that is based on separating it into overlapping PCR amplicons followed by merging sequenced amplicons during assembly.

To streamline our viral pipelines, we have fully integrated them with JCVI’s LIMS and JIRA Workflow Management to create a semi-automated tracking interface that follows the progress of viral samples from acquisition through to NCBI submission. This allows us to process a large volume of samples with limited manual interaction and, at the same time, gives us flexibility to work on challenging and novel genomes.

Acknowledgements

The JCVI Viral Genomics Group is supported by federal funds from the National Institute of Allergy and Infectious Disease, the National Institutes of Health, and the Department of Health and Human Services under contracts no. HHSN272200900007C.

Bat coronavirus project is collaboration with Kathryn Holmes and Sam Dominguez, University of Colorado Medical Center.

The authors would like to thank members of the Viral Genomics and Informatics group at JCVI.

References

Viral genome sequencing by random priming methods. Djikeng A, Halpin R, Kuzmickas R, Depasse J, Feldblyum J, Sengamalay N, Afonso C, Zhang X, Anderson NG, Ghedin E, Spiro DJ. BMC Genomics. 2008 Jan 7;9:5A virus discovery method incorporating DNase treatment and its application to the identification of two bovine parvovirus species.  Allander T, Emerson SU, Engle RE, Purcell RH, Bukh J.

Note

This post is based on a poster by Nadia Fedorova, Danny Katzel, Tim Stockwell, Peter Edworthy, Rebecca Halpin, and David E. Wentworth.

Etching of Dr. J. Craig Venter on Biowalk of Fame

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.

Biowalk of Fame tour sign

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.

Dr. J. Craig Venter's plaque on the Biowalk of Fame

Biowalk of Fame

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!

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.

Relocating Torrey Pine trees at JCVI La Jolla

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.

Caterpillar D-9 at Work

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?

Building forms for architectural concrete mock-ups

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.

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.

Influenza Genome Amplification Directly From Clinical Specimens (Zhou, B., M. E. Donnelly, D. T. Scholes, K. St.George, M. Hatta, Y. Kawaoka, and D. E. Wentworth. 2009. J.Virol. 83:10309-10313.).

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.

New Live Attenuated Vaccine Approaches. Figure shows influenza RNA polymerase activity (GFP) at various temperatures. Mutations engineered into the genome (PB1-Mut3, PB2-Mut4) synergize and inhibit replication at higher temperatures of the lung (37 C) or fever (39 C).

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.”

David Wentworth DEW checking a hive in the late Spring.

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!

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!

More than six years in the making, the JCVI La Jolla project has developed a reputation for pushing the envelope in terms of sustainability and energy efficient laboratory design.  The project aspires to achieve carbon neutrality while also demonstrating the benefits of sustainable building practices.  Both of these are lofty yet we felt achievable goals.

From the beginning, UCSD Chancellor Marye Anne Fox was an enthusiastic supporter of the project, encouraging scientific collaborations with JCVI and sharing JCVI’s sustainability goals.  UCSD’s Resource Management and Planning team, including Vice Chancellor Gary Matthews, Nancy Kossan, Boone Hellmann, Brian Gregory, and many others offered invaluable advice and assistance.

In 2006, we began a nationwide search for an architect to lead the project.  We came to a startling conclusion:.  while the entire industry talked the “green building” talk, very few had actually walked the walk.  Fortunately, there was one firm who had both designed some great laboratory buildings and whose passion for sustainability matched our own.  Zimmer Gunsul Frasca Architects (ZGF) in Los Angeles officially joined the team in February of 2007 under the leadership of Ted Hyman and Doss Mabe.

But having the best architects wasn’t enough, we needed a highly efficient mechanical, electrical, and plumbing (MEP) design to allow us meet our “net zero” energy goals, given the  energy intensive nature of laboratories.  While interviewing another architectural firm, we met Peter Rumsey, a mechanical engineer who was rethinking energy efficiency in buildings and promoting novel alternatives to traditional MEP design.  I recall Peter describing one project where he had replaced all of the 90 degree piping bends in a building with swept radius connectors, reduced the system’s overall resistance, and eliminated the need for dozens of pumps and their associated energy consumption. As if this approach to engineering wasn’t enough of a selling point, we were delighted to discover his firm had just completed the first LEED Platinum certified laboratory at UC Davis’s Tahoe Center.  Rumsey Engineers (now Integral Group) joined ZGF and began assembling the world-class design team that would bring JCVI La Jolla to life on paper.

The first several months of the design process were beyond exciting.  The hand-picked team of green building experts all exuded a noticeable sense of excitement every time we sat around the table to discuss ideas for the project.  The creativity floodgate had been opened and was materializing itself in all aspects of the building’s design from lighting systems to on-site water treatment.  Sustainability became the team’s mantra not only from an environmental perspective, but also for the research that would take place in the laboratories.  The labs had to support not only the science of today, but the science of tomorrow.  As a result, we focused on flexibility to ensure the building could adapt to the occupants’ needs over time.  Late in 2007, ZGF presented an architecturally stunning building that not only met the original design intent of achieving carbon neutral operation through “net zero” energy use, but also employed a constructed wetland to treat waste-water for reuse, and exceeded the USGBC’s LEED Platinum rating criteria.

Fast forward to today.  The design team has spent the past 10 months working relentlessly to incorporate hundreds of pages of detail into the original design and develop a set of construction documents from which the project will be built.  Coordination meetings have been held on a regular basis to ensure every element of the building meets JCVI’s operational needs.  In many cases, the original design was improved after the design team took a second look.  For example the original lab layout was modified to provide more bench area and increase flexibility of the support areas.  What started as one large open lab became a series of “neighborhoods” separated by highly configurable rooms that can adapt to a wide array of equipment configurations.

While the architects prepared drawings, we began checking off the long list of items needed for ground breaking.  Applying the same level of scrutiny used in selecting the architect and engineers, we began interviewing builders to join the team.  McCarthy Building Companies came onboard early in 2011 and immediately began providing valuable input about constructability and delivering the highest levels of quality throughout the construction process.

In parallel with our design efforts, we worked with many UCSD offices and individuals to complete numerous environmental studies, perform plan reviews, and provide community outreach about the project.  The entire UCSD community has been a great supporter of both JCVI and the sustainability goals of the project.  We are grateful for UCSD’s support and guidance throughout the multi-year development process.

Today we stand poised to begin mass excavation for the foundation in late November.  Until then, we are busy working to mobilize work trailers, install temporary power, water, and data at the site, and construct a temporary road between the construction site and Expedition Way.

2011 Rendering of JCVI La Jolla