Posts in category JCVI

Thule, Greenland Year Two

Sequence data from the previous year allowed us to determine the overall microbial population in each site and this year we decided to focus on the Rich Lake site which seem to have representation of nearly all microbes found in the other sites. So lucky for us we only had to work on one site this year rather than six. This in itself had me excited to go back to Thule. After a five-hour flight on a military plane from BWI I finally arrived to Thule Greenland where we were greeted by the Colonel as well as other high ranking military officials at the hanger. Once I cleared the customs processing area, I arrived to the dorm where the other scientists were living. It was a little different from last year’s accommodations but nevertheless the luxuries of WI-FI, Internet and cable TV were all available. As I am anxious to get to the field and see the changes in the Rich Lake site, we were given some interesting news. That day was not a good day to travel to the site because a mother polar bear and her two cubs were spotted nearby not too long ago by military police. However, we managed to get other work done by preparing the schedule for the sampling, cultivation and other labwork.

 

The next few days consisted of preparing culture media, cultivation traps and diffusion chambers, and going out into the field (polar bear spray in hand; yes it’s a real thing!). We were extra careful in the field since there was quite a bit of fog in the area that did not seem to go anywhere and fog happens to be the same color as polar bears. The fog did however make it a bit easier to sleep since most of the sunlight was covered and when there’s 24 hours of daylight from mid-April until September, a little fog can still serve a purpose.

Rich Lake Site

Rich Lake Site

Greenland

Greenland

Scientist Spotlight: Meet Sarah Highlander

Sarah Highlander Ph.D. is an esteemed scientist and professor who joined JCVI in La Jolla this year. She comes from a long line of academically successful Professors, including a great uncle who was a University Dean. As a young child, Sarah was influenced by her parents: her mother was a musician and her father was a Ph.D. chemical engineer. Sarah too was a musician and she still enjoys jazz and the opera. But it was her father’s scientific career that influenced her own decision to pursue scientific research as her career.

Dr. Sarah Highlander

Dr. Sarah Highlander

As a chemical engineer and early IT specialist, he shared his interests with her at the kitchen table by doing mathematical puzzles and simple experiments. They explored the impact light had on grass growth by placing plants in the closet. Then in high school, she had the opportunity to work on a microbiology project with the help of her father. Using agar slants from his colleague’s lab, she looked for antimicrobial features of bacteria in the soil. Even with these opportunities, her focus in the sciences wasn’t fully set until she began working as a technician in a fermentation research lab where she had the opportunity to work with plasmids after completing her bachelor’s degree. At this point, plasmids and restriction enzymes were not readily available and researchers had to isolate them in their labs. She was extremely successful as a technician and even published several papers and secured several patents.

This experience launched Highlander into Medical Microbiology. She went to the Sackler Institute of Biomedical Sciences at the New York University School of Medicine, where she earned her Ph.D. in 1985. With her curious nature and the bourgeoning field of biotechnology, she began to research the replication of DNA plasmids in Staphylococcus. She asked basic but as yet unanswered questions such as, “How are these molecules controlled in the cell?” and “How can they best be manipulated in the laboratory?” Her thesis involved characterizing small RNA molecules that control plasmid copy number.

During her Post-doctoral fellowship, she shifted her focus to infectious diseases and worked on vaccine development for a cattle disease called “shipping fever” at the University of Texas Health Science Center. Shipping fever is the most common and costly problem affecting calves. It accounts for major economic losses to the cattle producer by reducing average daily weight gain, impairs feed efficiency, and diminishes overall performance and health of beef calves. Vaccination is key to reduce the disease and Highlander’s research culminated in the development of a subunit vaccine that is still in use.

After her fellowship, she began her professorship at Baylor’s College of Medicine (BCM), where she continued her research into shipping fever. The primary bacterial agent in this disease is Mannheimia haemolytica, which is the same family as the human respiratory pathogen, Haemophilus influenzae. JCVI scientists were the first to sequence and publish the H flu genome in 1995. Dr. Highlander’s group performed extensive characterization of the M. haemolytica leukotoxin and developed numerous genetic tools for manipulation and tagging of the organism. She holds patents for subunit and live-attenuated vaccines to prevent shipping fever.

In 2002, Highlander founded Prokaryon Technologies, a for-profit company focused on animal health to prevent and control diseases associated with food animals. One of Prokaryon’s lead products was a genomics-derived vaccine to prevent shipping fever in cattle.

While leading and growing her company, Highlander stayed committed to her academic research interests and joined the Human Genome Sequencing Center at Baylor. At BCM, she participated in genome sequencing of several pathogens (including M. haemolytica) and she moved to focus more on human pathogens. From 2006 to 2013, Highlander was a principal investigator for the Human Microbiome Project (HMP), a National Institutes of Health-funded program in which JCVI researchers were also key leaders.

In addition to her research, Highlander was involved in graduate and medical education at BCM. She was the co-director of the departmental graduate program for 15 years and directed and taught courses focused on bacterial physiology and molecular laboratory methods. Preparation for lectures and interactions with students helped her stay on top of new techniques and research, which in turn helped her further her own research. Sarah had the opportunity to mentor many graduate students both formally and informally.

At JCVI, Highlander is continuing her work on the microbes that live in and on the human body. Specifically she and her team are looking at the complex microbial communities that live in the human gut. While many microbes are associated with disease, most in the human body are associated with health. Highlander and her team are working to develop specific healthy bacterial mixtures that could be used treat conditions such recurrent Clostridium difficile diarrhea, inflammatory bowel disease and others. She is also using bioinformatics tools to look for new causes of diarrhea. “I am delighted to be a part of the collaborative environment here at JCVI and to be surrounded by colleagues who share common interests in bacterial genetics, genomics, microbial physiology and pathogenesis. The microbiome group at JCVI is strong and I hope to be able to make significant contributions to ongoing and future projects here”.

Even in her personal life, Sarah researches, through her hobby of tracing her genealogy. She has been able to find family roots dating back to the 1500s. This detective work is challenging but it keeps her mind sharp and detailed oriented. She points out that learning family naming patterns can be critical to genealogy research just as algorithm development is to genomic research.

Never having lost that early scientific curiosity and excitement of discovery that her father instilled in her as a young girl, Sarah loves working in the laboratory at JCVI and asking questions. Her analytical and inquisitive nature is one of her greatest professional strengths. She is fascinated by the complexity of the microbial ecosystem in our bodies and the impact these microbes have on our health. As she says, “Microbes are going to continue to win through evolution. We need to figure out the next step to keep ahead!” Let’s hope Highlander and her team can win this battle.

Building the World’s First Net-Zero Energy Lab [video]

Building the World’s First Net-Zero Energy Lab

And see the construction in time-lapes.

The 2014 Summer Internship Application is Open and Announcing the Genomics Scholar Program

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.

 

 

2013 Intern Poster Session

2013 Intern Poster Session

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.

Thule, Greenland – Day One

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. 

blog2

blog1

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.

DSCF0619

DSCF0622

 

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.

Building a Solid Foundation

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.

5500 gallon rainwater storage tank is lowered into place

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.

Single TES tank arrives by tractor trailer

Two 25,000 gallon TES tanks being installed

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.

 

Erected concrete forms

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.

 

Mock-up of a single office window at the building’s exterior.

Water testing the window system

Biowalk of Fame

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.

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

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

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

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

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!

Moving dirt at JCVI La Jolla

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.

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.

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!