JCVI Blog

Summit on Systems Biology, June 15-17, 2011

Published by Phil Goetz on 12 July 2011 in Bioinformatics.

I attended the Summit on Systems Biology hosted by Virginia Commonwealth University in Richmond, VA June 15-17. So, judging from the talks given, what is systems biology?

Systems biology is non-linear and/or multi-step. Heavy math does not make something systems biology if it’s directly solvable. Taking a big gene expression matrix, using principle component analysis on it, and coming up with a linear equation for the contributions of a list of biomarker genes, is not systems biology. The same microarray expression experiment, coupled with pathway analysis in order to reduce candidate genes and so do a less stringent multiple-hypothesis-testing-correction and so have fewer false negatives, is. So is a non-linear model of how just a few genes interact over time.
Standard bioinformatic analysis seeks correlations. Systems biology goes beyond that to seek cause and effect. Thus, most systems biology work involves time series, and sometimes simulation.

What data and techniques do systems biologists use?

Large datasets of all types. Microarray time-series, genomes, SNPs, protein-protein interactions, automated protein annotation – anything that comes in gigabytes instead of kilobytes.
There was marked interest in protein-protein interaction networks, and in micro RNAs (which inhibit translation of multiple target mRNAs).
There were several papers using reverse-phase protein microarrays. RPMAs can distinguish phosphorylated (which usually means active) from unphosphorylated proteins, which helps understand protein interaction dynamics.
There were several papers using weighted gene co-expression network analysis. WGCNA analyzes modules of co-expressed genes, rather than individual genes. This gives more statistical power from sparse data. Brian Sayre of VSU identified disease-resistance genes in livestock and crop species using single-nucleotide polymorphisms (SNPs) from related species. We might know about some goats that are resistant to a disease that also affects sheep; but sheep don’t have the same SNPs as goats. His group categorized the SNPs into genes, and the genes into pathways common across species, then looked for pathways associated with disease resistance in other species, and hypothesized that the same pathways would be involved in disease resistance in the target species.

What do people do with systems biology?

Medical applications predominated. The main areas of interest were cancer, aging, cell simulation, eukaryotic model organisms, genome-wide association studies, pathway analysis, and immunology.
There were no talks about industrial applications or synthetic biology.
There were no talks on prokaryotes, except one on host-pathogen interactions. This struck me as odd, since eukaryotes are more difficult to analyze or simulate than prokaryotes, and we haven’t done these things with prokaryotes yet.
There were no talks on metagenomics. This also struck me as odd; bacterial communities seem like a natural systems biology problem.

What does the future hold for systems biology?

Omniomics: We don’t want just a protein’s sequence – we want to know where and when it is expressed, what regulates it, what it interacts with, and what parameters describe those interactions. Soon, annotating a genome will not mean producing a list of genes and their functions – it will mean producing a simulation.
We need to learn to think at a higher level of abstraction. If you have tens or hundreds of thousands of genes, transcripts, proteins, small molecules, and structures interacting, you need to figure out what it is you’re really interested in (e.g., “How did this cancer bypass the G1 cell-cycle restriction checkpoint?”), how to specify that precisely enough to ask the computer for an answer, and not to insist on understanding all the details if the answer checks out.
There is a growing gap between research and practice. We can make more and more detailed analyses of diseases, especially in cancer, where each patient has a unique disease at the genetic level. Meanwhile, the FDA approval process is so long and expensive that even in diseases (for example, Alzheimer’s and FTLD) for which there are millions of patients and a handful of known causes, pharmaceutical companies don’t try to develop three to four separate therapies for those three to four causes. And the gap is growing wider: Even as we are coming up with ways to combine weak information from across an entire genome, the FDA is considering proposals to regulate genomic sequencing that would forbid doctors from acquiring a full sequence.

1 Comment Tags: Bioinformatics, systems biology.

Insights gained from influenza genomic sequence data: viral diversity within human populations

Published by Rebecca Halpin on 4 April 2011 in Infectious Disease.

The advent of large amounts of influenza genomic sequence data produced by the Influenza Genome Sequencing Project (IGSP) has led to new concepts regarding influenza viral diversity. It was previously believed that a single influenza lineage entered a human population at the start of an influenza season and gradually spread over time; however, recent analyses of influenza genomes revealed that multiple viral lineages co-circulate within individual populations throughout an influenza season. These different lineages appear to be continuously introduced which provides the opportunity for frequent intra-subtype reassortment. Interestingly, similar levels of influenza diversity exist within populations of both large metropolitan cities and small towns (E.C. Holmes, 2009). Multiple, diverse viral lineages of the same subtype have been observed co-circulating in urban locations comprised of expansive travel networks and rural locations that are geographically isolated.

Additional analyses of complete influenza genomes have led to a ‘source-sink’ model of influenza seasonality. In this model, a global, human ‘source’ population of influenza viruses is thought to be responsible for the antigenic variants that ignite seasonal epidemics in the ‘sink’ populations of the Northern and Southern hemispheres (A. Rambaut, 2008; E. C. Holmes, 2009). The geographic regions of East and Southeast Asia have been hypothesized as potential sources of influenza due to the large, dense human populations which would allow influenza viruses to antigenically evolve with maximum efficiency. These locales may be the focus of future surveillance efforts aimed at identifying emergent influenza viruses that have evolved mechanisms to evade current vaccines.

1 Comment Tags: GSC, Viral Group.

NASA and JCVI host symposium on the evolution of Earth and Life

Published by Chris Dupont on 24 March 2011 in Bioinformatics, Microbial & Environmental Genomics and Synthetic Biology & Bioenergy.

On May 12^th and 13^th, the J. Craig Venter Institute in San Diego will be hosting a NASA Astrobiology Institute-funded symposium titled “Paleobiology in the genomics era.” Paleobiology is the study of the origins and evolution of life and, by nature, is interdisciplinary. The goal is to bring together scientists united by this common interest but differentiated by expertise. A major intellectual challenge to paleobiology is the close interaction between environment and life. As life evolved, it changed the environment and suffered the consequences. One of the most extreme examples is the invention of oxygenic photosynthesis by blue-green algae cyanobacteria; the sunlight-fueled production of dramatically changed the availability of crucial elements of life, like nitrogen, sulfur, iron, zinc, copper, and other trace metals. Genome-based analyses showed that these environmental changes modulated the emergence of metal-requiring proteins. For example, proteins that bind Fe evolved when the earth was Fe rich. Essentially, one biological event changed the environment, which in turn induced a subsequent biological change; a feedback cycle between biota and planet.

In order to study these interactions in a robust fashion, numerous lines of evidence must be integrated, despite originating from disparate fields like organic and inorganic geochemistry (oils and metals in rocks), micropaleontology (tiny fossils), and evolutionary biology. Recent years have observed the emergence and maturation of synthetic biology and computational biology, two fields with tremendous potential for the formulation and testing of hypotheses about the evolution of life. To facilitate a dialog between these fields, myself, along with Ariel Anbar from Arizona State University, and John Peters and Eric Boyd from Montana State University, have invited experts to present their work as it pertains to paleobiology. The topic list almost appears schizophrenic, with numerous hard-core geochemical talks being followed presentations on molecular genetics, synthetic biology, metagenomics, and comparative genomics. This was intentional. I hope to feel intellectually challenged in the fashion of a 1^st year graduate student and further hope that I’m not the only one. A major wild card at the moment is the identity of over 2/3^rd of the attendees. With travel grants available for graduate students, post-doctoral researchers, and faculty, we hope to incorporate novel perspectives not covered by the confirmed speakers.

While the content of the meeting is exciting, the format is pretty sweet too. As part of NASA’s Workshop Without Walls series, the meeting will be webcast live with an accompanying live stream chat. Thus, people will be able to see the presentations and pose questions and comments during the attendant discussions. Previous workshops have often had hundreds of live viewers throughout the meeting, despite only dozens of in situ attendees. The actual energy savings for a single meeting are modest in isolation; imagine 250 people not flying 500 miles and you basically have a single 737 flight that remains grounded. However, the future of environmentally-friendly science requires important preliminary steps to change dominant trends. Similarly, the talks will be streamed live without charge and deposited in the open access scientific podcast site, Scivee.tv; economic barriers to information exchange are removed.

Needless to say, I’m looking forward to this meeting. Organizing something like this is an absolute undertaking. The number of details that need attention is astounding. And if you think I actually could do that, you don’t know me. Numerous people at JCVI have provided invaluable assistance, including Matt LaPointe and Jasmine Pollard, Robert Friedman, Dave Negrotto, and Jody Wilson. It would also have no chance of happening if it not for Pat Goley, who has handed the numerous (re: uncountable) details I’ve lapsed on.

Check out the NASA page for the meeting and webcast registration.

http://astrobiology.nasa.gov/nai/geobiology2011

Closed

JCVI Supports Human Mircrobiome Body Site Experts with Shotgun Data Analysis

Published by Johannes Goll on 24 February 2011 in Bioinformatics, Genomic Medicine and Microbial & Environmental Genomics.

Members of the Human Microbiome Project (HMP) Consortium (see http://commonfund.nih.gov/hmp and http://www.hmpdacc.org for more information on the project and partners) including human microbiome body site experts gathered for a virtual Jamboree January 19th. The fully online-based Jamboree has been set-up to communicate initial data products and tools best suited for analysis, primarily to make the data amendable/consumable in a user-friendly way for body site exerts. 61 participants followed the Jamboree agenda with presenters given access to a common desktop that was shared via the internet using an online collaboration tool. Results from the Data Analysis Working Group (DAWG) were presented in the areas of 16S rRNA gene sequence (16S DAWG) and metagenomic whole-genome shotgun analysis (WGS DAWG). The efforts of the 16S DAWG focus on marker-gene based approaches to estimate biological diversity and how marker variability is associated with patient meta-data. The WGS DAWG complements results from the 16S marker based analysis with comprehensive sequencing of random pieces of genomic DNA from the collection of microorganisms which inhabit a particular site on, or in, the human body (microbiome). These analyses allow researchers to investigate among other questions what microorganisms are present, and the nature and extent of their collective metabolism, at a particular body site. Ultimately researchers want to relate this information to healthy versus diseases states in humans.

METAREP tutorial presented as part of the HMP Virtual Jamboree

The current survey comprises more than 700 samples from hundreds of individuals taken from up to 16 distinct body sites. Illumina sequencing has yielded more than 20 billion Illumina reads and annotation data produced from the sequences exceeds 10 terabytes. In anticipation of such data volumes, we have developed JCVI Metagenomics Reports (METAREP), an open source tool for high-performance comparative analysis, in 2010. The tool enables users to slice and dice data using a combination of taxonomic and functional/pathway signatures. To demonstrate how the tool can be used by body site experts, we picked and loaded sample data from 17 oral samples and presented a quick tutorial on how users can view, search, browse individual samples and compare multiple samples (see video). The functionality was very well received and body site experts asked JCVI to make all the 700+ samples available. As a result of the Jamboree, JCVI in agreement/collaboration with the HMP Data Analysis and Coordination Center and the rest of the HMP consortium, will soon set-up a dedicated HMP METAREP instance that will allow body-site experts and eventually other users to analyze the DAWG data in a user-friendly way via the web.

Closed Tags: HMP, human microbiome project, metagenomics, metarep.

The Microbiome of Esophageal Cancer

Published by Manolito Torralba on 19 January 2011 in Genomic Medicine.

In anticipation of the International Human Microbiome Congress, our group has diligently worked to generate data to present for our HMP demo project studying the microbiome of patients who have developed esophageal cancer, gastrointestinal reflux disease, and barrett’s esophagus. We received a large number of samples in December of 2010 which surveyed four body sites (esophagus, fecal, oral and stomach) of twelve patients. Upon isolation of DNA, we amplified a variable region of the 16S gene for each sample using barcoded PCR primers. Incorporation of the 454 A and B adaptors to our primers also provided minimal loss of sequence data when compared to previous methods that would ligate the adaptors to amplicons after PCR. This method also allowed us to generate sequence reads which are all in the same 5’-3’ orientation. A large dataset with high quality sequence reads was generated and is currently going thru phylogenetic analysis. Metagenomic data is also currently being generated from DNA extracted from esophageal brushings taken from a healthy individual as well as a patient who has developed esophageal cancer. This comparative analysis will be scientifically beneficial in identifying key structural and functional elements that are known to increase pathogenesis of a complex disease such as cancer. We are anxiously awaiting results from the analysis of these sequences and expect to present a thorough investigation on the esophagus microbiome.

Closed Tags: 16S, cancer, esophagus, HMP, metagenomics.

A Look Back at 2010 at the JCVI…

Published by Laura Sheahan on 3 January 2011 in Bioinformatics, Education, Genomic Medicine, Infectious Disease, Microbial & Environmental Genomics, Plant Genomics, Policy Center, Sequencing and Synthetic Biology & Bioenergy.

As the J. Craig Venter Institute (JCVI) soars into its 19th year, we reflect on the past year of highlights and accomplishments to mark the close 2010 and look forward to more significant scientific advances in 2011.

JCVI Top 10 of 2010 …

1. First Synthetic Cell: Fifteen years in the making, 2010 brought to bear with huge anticipation the successful construction of the first self-replicating, synthetic bacterial cell. The work was published in Science in May. The synthetic cell called Mycoplasma mycoides JCVI-syn1.0 is the proof of principle that genomes can be designed in the computer, chemically made in the laboratory and transplanted into a recipient cell to produce a new self-replicating cell controlled only by an artificial genome. Although the first synthetic cell was not designed to produce a specific bioproduct, the team has shown that this can be done and the potential benefits are numerous. The research team, lead by JCVI President Craig Venter, Hamilton Smith, Clyde Hutchison, and Daniel Gibson, envision a future where the rapid design and production of biological products using synthetic biology techniques will be used to produce clean fuels, medicines, and other bioproducts. Throughout the course of this work, the JCVI Policy group has extensively engaged in outside review of the ethical and societal implications of this work, including advising the new Presidential Commission on Bioethics on their recommendations for oversight.

M. mycoides JCVI-syn1

2. Synthetic Vaccines: Following on the heels of the announcement of the first synthetic cell, the company Synthetic Genomics Inc. and JCVI announced in October the formation of a new company, Synthetic Genomics Vaccines Inc. (SGVI). The privately held company is focused on developing next generation vaccines that can be rapidly produced and tested, which is especially important for outbreaks of new infectious diseases. SGVI also announced a three-year collaboration with Novartis to apply synthetic genomics technologies to accelerate the production of the influenza (flu) seed strains required for vaccine manufacturing. The seed strain is the starter culture of a virus, and is the base from which larger quantities of the vaccine virus can be grown. Under this collaboration, Novartis and SGVI will work to develop a “bank” of synthetically constructed seed viruses ready to go into production as soon as WHO makes recommendations on the flu strains. The technology could reduce vaccine production time by up to two months, which is particularly critical in the event of a pandemic.

3. Hydra Genome – one of the animal kingdom’s earliest common ancestors: JCVI scientists along with more than 70 other researchers from around the world, have sequenced and analyzed the genome of Hydra magnipapillata, a fresh water member of the cnidaria– stinging animals that include jellyfish, sea anemones and corals. The research, published in the March 14 edition of Nature, was co-led by Ewen F. Kirkness, JCVI, Jarrod A. Chapman, Department of Energy Joint Genome Institute, and Oleg Simakov, University of California, Berkeley. This is the second sequenced cnidarian genome, following that of a sea anemone, Nematostella vectensis, in 2007. The ancestors of these two species diverged more than 500 million years ago, and comparison of their genomes has revealed common features of the earliest animals that gave rise to the diversity of animals on Earth today. The team found clear evidence for conserved genome structure between the Hydra and other animals, like humans. Unexpectedly, the sequencing also revealed a novel bacterium that lives in close association with the Hydra.

4. Uncovering the Human Microbiome: Microbes are living within and on the human body and this collective community is called the human microbiome. JCVI Scientists, as one component of the large scale NIH Roadmap Human Microbiome Project, and along with colleagues at three other genome centers sequenced the genomes of ~180 microbes from the human body, published in the May 21 edition of Science. At the JCVI we anticipate sequencing an additional 400 species over the next few months. Colleagues at the JCVI are also using single cell approaches to isolate new strains that have not been cultured – isolates whose genomes will also be completely sequenced. The role these microbes play in human health and disease is still relatively unknown and these approaches are allowing us to gain a greater understanding of these enigmatic species.

5. Body Louse Genome: A global research team led by Ewen Kirkness and colleagues from JCVI published a study in the Proceedings of the National Academy of Sciences in June describing the sequencing and analysis of the human body louse, Pediculus humanus humanus, a human parasite responsible for the transmission of bacteria that cause epidemic typhus, relapsing fever and trench fever. Detailed analysis of the genome was then conducted by a large international group of 71 scientists, coordinated by Barry Pittendrigh, University of Illinois, and Professor Evgeny Zdobnov, University of Geneva Medical School. Comparative studies of the body louse genome with other species revealed features that will enhance our understanding of the relationships between disease-vector insects, the pathogens they transmit, and the human hosts. In addition to the targeted louse genome, the project unexpectedly yielded the complete genome sequence of a bacterial species, Riesia, that lives in close association with lice, and which is essential for survival of the insects. The researchers believe that the genome will be a valuable reference for evolutionary studies of insect species, especially in the areas related to insect growth and development.

6. Castor Bean Genome Sequencing: A research team co-led by Agnes P. Chan and colleagues from JCVI and Jonathan Crabtree and others at the Institute for Genome Sciences, University of Maryland School of Medicine, published the sequence and analysis of the castor bean (Ricinus communis) genome in Nature Biotechnology in August. Because of the potential use of castor bean as a biofuel and its production of the potent toxin ricin, the team focused efforts on analysis of genes related to oil and ricin production. The analyses could be important for comparative studies with other oilseed crops, and could also allow for genetic engineering of castor bean to produce oil without ricin. Identifying and understanding the ricin–producing gene family in castor bean will be important in preventing and dealing with potential bioterrorism events. Genomics enables enhanced diagnostic and forensic methods for the detection of ricin and precise identification of strains and geographical origins. As a next step, the group suggests further comparative genomic studies with the close relative cassava, a major crop in the developing world, to further elucidate their disease resistance aspects.

7. Science Education: JCVI was an Official Partner of the inaugural USA Science and Engineering Festival held on the National Mall in Washington, DC in October. The Festival, which was the country’s first national science festival, included over 500 of the country’s leading science and engineering organizations with the aim to reignite the interest of our nation’s youth in the sciences. The JCVI ‘Discover Genomes’ Bus was showcased during a two-day expo and some of the research being done at JCVI was presented to around 1700 visitors by our scientists and staff.

There were lines all day!

8. Viral Genomics– In 2010 the JCVI has published over 1600 influenza genomes and over 75% of all published flu genomes to date have been sequenced by the JCVI, totaling over 6000 genomes. This year the diversity of viral genomes we have sequenced has significantly expanded under the NIH Genomic Sequencing Center for Infectious Diseases contract. Some of the projects include viruses causing diseases such as measles, mumps, rubella, encephalitis, SARS, and the common cold, just to name a few. The viral group has annotated and published 79 Rotavirus (stomach flu) and 33 Coronavirus genomes (includes SARS and common cold) this year and many more will be published in 2011. The pace of sequencing and finishing genomes has also increased this year as a result of adoption of nextgen platforms (e.g. Illumina/454 and Illumina/Solexa) and the development of more efficient methodologies to increase productivity while reducing costs.

9. Marine Microbial Genome Sequencing Project: JCVI scientists have continued their quest to isolate and sequencing microbes living in global ocean waters to discover new genes and enzymes, and to help understand the role microbes play in the ocean ecosystem. Shibu Yooseph, Kenneth Nealson and colleagues at JCVI published an analysis of 137 known marine microbial genomes living in the global ocean surface in Nature in November. These genomes were compared to metagenomic samples of ocean waters of 10.97 million sequences of JCVI’s Sorcerer II Global Ocean Sampling (GOS) metagenomic data and thousands of 16S rRNA sequences. The marine genomes were collected as part of the Gordon and Betty Moore Foundation-funded Marine Microbial Genome Sequencing Project, a project coordinated by JCVI that has a primary goal of obtaining whole genome sequences of ecologically important microbes from a variety of diverse, global marine environments. The work provides a good example of combining metagenomic data with sequenced genomes data to study microbial communities and to generate testable hypotheses in microbial ecology.

10. Sorcerer II Global Ocean Sampling Expedition: On December 17th 2010 Sorcerer II arrived in Florida after spending the last two years with her crew collecting samples in The Baltic, Mediterranean and Black Seas. Funded generously by the Beyster Family Foundation Fund, The San Diego Foundation, and Life Technologies Foundation, Sorcerer II has sailed ~28,000 nautical miles since departing San Diego in March 2009. During this time 212 samples were collected and over 5,100 liters of sea water was filtered and sent to JCVI for analysis of the microbial life contained within these samples. The JCVI established strong collaborations with scientists in all 16 countries in which samples were collected, which will lead to joint publications and future collaborative studies in the new year. Read more.

Sunrise in the Ligurian Sea

Looking Forward to 2011…

Ten-year anniversary of the Human Genome Project: To commemorate the anniversary of the publications of the first human genome sequences in 2001, JCVI and Nature are hosting a conference and celebration in February 2011 titled – Human Genomics: The Next 10 Years. The conference will look forward to the promises of human genomics for the next 10 years, with sessions on medical advances related to genomics; the technological and ethical challenges of human genomics; personalized and familial genomics; the human microbiome project; variation in the human genome; and making sense of the genetic code. This conference will be a great way to jump into the new year and inspire the grandiose ideas and achievements that genomic scientists will accomplish over the years to come.

1 Comment

Holiday Art

Published by Stephanie Mounaud on 23 December 2010 in Infectious Disease.

In a relatively unknown place, on the 3rd floor of JCVI in Rockville, MD, is a small fungal room where art meets science (and of course where all our fungal research takes place). Fungus often gets such a bad reputation for being gross and somewhat ‘standard’. We fungal folks know better and I am hoping to educate others with the underlying beauty that fungi possess, in a funky way. I recognize that beauty is in the eye of the beholder but I felt this might convince some that fungus can be fun and not just something that grows in the back of your fridge or a nuisance that contaminates your plates. Please enjoy these funky fungal holiday art forms.

Fungal Christmas tree. Top: Talaromyces stipitatus; Tree: Aspergillus nidulans; Ornaments: Penicillium marneffei; Trunk: Aspergillus terreus.

Fungal snowman. Hat, Eyes, Mouth, Buttons: Aspergillus niger; Arms: Aspergillus nidulans; Nose: Aspergillus terreus with Penicillium marneffei; Body: Neosartorya fischeri.

Fungal Christmas Tree.

I am open to suggestions and only limited by my own creativity (and of course my current work load) but never by the diversity of the very cool fungal world.

14 Comments Tags: Christmas tree, fungus, snowman.

Insights gained from influenza genomic sequence data: frequent intrasubtype reassortment

Published by Rebecca Halpin on 21 December 2010 in Infectious Disease.

Studies using whole genomic influenza sequence data produced by the Influenza Genome Sequencing Project (IGSP) have focused mainly on influenza evolution and epidemiology. For instance, IGSP data has provided important insight into the frequency of intrasubtype reassortment (in which reassortment occurs between different segments of the Influenza genome). The data suggests that reassortment occurs frequently, leading to viruses with altered antigenic properties that may evade current vaccines. Thus, it is useful to study not only the HA and NA segments that produce the hemagglutinin and neuraminidase proteins that sit on the surface of the virion and interact with host cells, but the whole viral genome, as this provides a complete picture of the emergence of the virus (E.C. Holmes, 2009).

The significance of intrasubtype reassortment for strain emergence was shown by the appearance of the new strain of Influenza H1N1 in 2009, which is a reassortant virus containing multiple swine influenza lineages.

In the October 2010 publication by Ilyushina et al, they show that despite the lack of detection thus far in humans, viable seasonal/pandemic Influenza virus reassortants can be generated in a laboratory setting. Their study showed that intrasubtype reassortment is able to occur between seasonal H3N2 and pandemic H1N1 viruses, potentially leading to the emergence of a strain with higher virulence.

1 Comment Tags: GSC, Viral Group.

2011 Internship Program Updated

Published by Lisa McDonald on 2 December 2010 in Education.

The 2011 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 2011 program can be found at http://www.jcvi.org/cms/education/internship-program/

Hopefully this winter, we won’t be hit with two MAJOR snow storms in Maryland that shut all the schools, the federal government and JCVI down for several days the week applications were due! I don’t think they are calling for much snow this year in the Washington Metropolitan Area. Of course, that is not a problem for our colleagues in San Diego.

JCVI Rockville February 2010

Some interesting facts about the summer internships from last year:

366 applicants applied online
44 Interns were selected:

8 high school students
19 undergraduate students
13 graduate students
4 secondary teachers

12 of the 44 were in San Diego and 32 in Rockville

The intern projects ranged across the Institute:

Shewanella oneidensis Growth in Chemostats
Purification and Characterization of a Pyrenoid Localized Decarboxylase
M. mycoides Minimalization: Combinatorial Assembly
Molecular Detection of Temperate Phages and Lysogens in the Marine Environment
Comparing the Performance of Short-Read Genome Assemblers
Phylogenetic Analysis of Cecal Microbiota in Alcohol-Induced Dysbacteriotic Mice, and Comparison of Pyrosequencing and Sanger Sequencing Technologies
Laboratory Research and Environmental Health & Safety (included making a safety video)
The Role of Accounting

Good luck to all the applicants this year!

11 Comments Tags: internship program.

Starting the Atlantic Crossing

Published by Jeff Hoffman on 17 November 2010 in Microbial & Environmental Genomics.

Wednesday November 17^th 2010

On November 10^th Sorcerer II set sail from Valencia Spain to start the sail back to America. The first leg was a 3 day sail down the Spanish coast to Gibraltar.

Coastline to Gibraltar

Valencia Coastline

John showing the delivery crew around Sorcerer II

We spent one night in Gibraltar to get fuel and supplies. The next day we took a very important sample on the Mediterranean Sea side of the Straits of Gibraltar. We collected a surface sample, which should be the lower salinity Atlantic water coming into the Mediterranean Sea. At the same location we collected a deeper sample, this is the saltier Mediterranean water flowing on the bottom into the Atlantic Ocean.

CTD cast from Med. Sea side of the Straits of Gibraltar. Salinity increased from 36 to 38 PSU

After we collected our last Mediterranean Sea sample, we sailed through the Straits of Gibraltar into the Atlantic Ocean and started our way to the Canary Islands.