Professional Development Opportunities this Summer

This summer we are offering two professional development workshops: GenomeSolver and Bioinformatics: Unlocking Life through Computation.  Both explore bioinformatics, microbial diversity and the implementation in the undergradauate or high school classrooms. 

The GenomeSolver workshop trains faculty on genome analysis. Workshop attendees will learn about general methodologies, standards, and processes used to annotate and analyze microbial genomes. The workshop contents will be available to aid the faculty in developing teaching modules. In addition, extensive documentation on methodologies and tools will be available via the online environment created for this project. On online web portal Genome Solver (www.genomesolver.org) will be a virtual space for development and sustaining of community. Genome Solver will assist faculty with technical issues and curricular design, as well as an online environment for the ongoing sharing of information including publication of student work. 

http://www.jcvi.org/cms/education/prodev/genome-solver-annotation-workshops

Bioinformatics: Unlocking Life through Computation is a new opportunity for high school teachers. Genomics and biotechnology are valuable tools in our quest to understand life and nature. However, introducing the science classroom to the computational and mathematical underpinnings of biology can be challenging. The goal of this workshop is to introduce a curriculum for mathematics and science education in the area of genomics (with a focus on the fascinating world of microbes). Educators will be introduced to the various analysis and computational challenges that arise in this discipline. Workflow examples illustrating comparative genomic analysis will be made available through the JCVI Metagenomics Report (METAREP) software infrastructure. The eventual aim is for the educational material to be integrated with local high school curricula requirements to expose students to both hypothesis-driven and discovery-based science.

 http://www.jcvi.org/cms/education/prodev/bioinformatics-unlocking-life-through-computation/

JCVI Hosts South African Scientists to Share Microbiome Research Techniques

Two scientists from the University of Cape Town, South Africa have joined Dr. Bill Nierman’s lab for the next month as part of NIH’s Human Heredity and Health in Africa (H3Africa) Initiative, a training program designed to build out technical biological skills in the African research community. This training relates specifically to developing techniques around the area of microbiome analysis, a relatively new field in the biological sciences.

Microbiome analysis for the collaborative study is looking at entire community of microorganisms in the respiratory tract of South African infants to better understand how the microbiome is associated with infant pneumonia and wheezing episodes. The expectation is that the organisms that reside in the infant respiratory tract will provide protection from or a predisposition to the pneumonia or wheezing episodes.

 

The Nierman Group

The Nierman group left to right Sarah Lucas, Bill Nierman, Shantelle Claassen, Mamadou Kaba and Stephanie Mounaud (unpictured Jyoti Shanker and Lilliana Losada) welcomes visiting scientists Ms. Classeen and Dr. Kaba from University of Cape Town for a month long training in microbiome sequencing and analysis.

Mamado Kaba, MD, PhD and colleague Shantelle Claassen from the University of Cape Town will be working closely under the guidance of JCVI’s Stephanie Mounaud who is functioning as the project manager and coordinating the laboratory components of a similar project at JCVI studying the microbiomes of inafnts in the Philippines and also in South Africa. These studies are sponsored by the Bill and Melinda Gates Foundation. The training will focus initially on preparing samples for DNA sequencing on a modern DNA sequencing platform, the Illumina MiSeq instrument. Once the sequence reads are off the sequencer, the instructional focus will shift to analysis of the reads by means of an informatics pipeline that develop phylogenies, or family trees, of the microbes that are obtained from the infant respiratory tract so that the abundance and relatedness of the microbes can be established. The bioinformatics training will be provided by Jyoti Shankar, the statistical analyst working on the Gates Foundation Project.

Mamadou Kaba is a Wellcome Trust Fellow working in the Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town. Mamadou’s research interests include the molecular epidemiology of infectious diseases and the study of human microbiome in healthy and disease conditions. He has contributed in establishing a new research group conducting studies on how the composition of the upper respiratory tract, gastrointestinal, and the house dust microbial communities influences the development of respiratory diseases.

Prior to joining the University of Cape Town, Mamadou worked as Research Associate at the Laboratory of Medical Microbiology, Timone University Hospital, Marseille, France, where he studied the epidemiological characteristics of infection with hepatitis E virus in South-eastern France.

Shantelle Claassen is pursuing a Masters degree in the Division of Medical Microbiology at the University of Cape Town. She has completed a BSc (Med) Honours degree in Infectious Diseases and Immunology at the University of Cape Town, during which she examined the relative efficacy of extracting bacterial genomic DNA from human faecal samples using five commercial DNA extraction kits. The DNA extraction kits were evaluated based on their ability to efficiently lyse bacterial cells, cause minimal DNA shearing, produce reproducible results and ensure broad-range representation of bacterial diversity.

Mamadou and Shantelle are currently involved in an additional prospective, longitudinal study of which the primary objective is to investigate the association between fecal bacterial communities and recurrent wheezing during the first two years of life.

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.

Amazon Expedition

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 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.

Sampling: US to the Azores

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.

Crew leaving Morehead City, NC.

Crew leaving Morehead City, NC. From the left: Sarah Fawcett, Amandine Sabadel, Malcolm Woodward, and Bess Ward.

R/V Endeavor

R/V Endeavor

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.

North Atlantic Transect, north of Sorcerer II transect to the Azores in 2009.

North Atlantic Transect, north of Sorcerer II transect to the Azores in 2009.

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.

CTD Controls

CTD Controls

CTD Controls

CTD Controls

CTD1

CTD1

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.

CTD Profile

CTD Profile

Dry Lab

Dry Lab

 

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!

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.

The Next Generation Science Standards are Ready for Review

The second draft is ready for public comment through January 29th. Please be sure to take some time to review.

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

Plant Bioinformatics Workshop

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!

JCVI-1