Monthly Archive for February, 2010

High Impact Science in Antarctica

The Mertz Glacier as seen in 2007, extending 75 km out into the Southern Ocean

Antarctica was in the news this weekend when a 97 kilometer long iceberg the size of Luxembourg collided with the floating Mertz Glacier, breaking the famous glacier off at the base and generating a 2500 sq. kilometer iceberg. Each of these behemoths weigh several hundred billion tons, so the impact must have been quite a crunch!

Iceberg B9B collides with Mertz Glacier Tongue

At right is an image taken February 20th, several days after the impact: the broken Mertz Glacier Tongue is on the left side of the photo, and the colliding B9B iceberg is near the center-right.   The Mertz Glacier, which was sheared off at the base, was a significant barrier to westward drifting sea ice.  The Mertz Glacier is on the George V coast of East Antarctica, a region is famous for its high-velocity katabatic winds: sustained wind velocities at nearby Dumont D’Urville have reached 199 m.p.h!  These winds blow the pack ice out to sea, and because of the blocking geometry of the Mertz Glacier, this area generally remains ice-free all winter.

Fluorescence map of the Mertz Polynya in December 2007 (mertz Glacier is in lower right). Surface blooms are in red, and marine metagenomic samples were taken in areas marked with a star.

In the Austral summer of 2007, scientists from the J. Craig Venter Institute visited this ice-free area, or polynya, as part of the International Polar Year’s Census of Antarctic Marine Life (CAML). Because sunlight can freely penetrate the water column, polynyas are areas of enhanced productivity. Diatoms and other phytoplankton form massive springtime blooms, supporting whales, penguins, and much of the Antarctic food chain.  Above is a fluorescence ‘bloom map’ of the Mertz Polynya, just west of the Mertz Glacier. Our expedition on board the Aurora Australis attempted to capture a biological snapshot of the entire region, and Jeff Hoffman and I were able to collect samples ranging from thick blooms of  Phaeocystis antarctica to oligotrophic cold-water upwellings at the base of the Mertz Glacier.

CTD Rosette being deployed at the base of the Mertz Glacier to collect a sample from 1320m deep

CTD Rosette being deployed at the base of the Mertz Glacier to collect a sample from 1320m in depth

The region around the Mertz Glacier is equally famous as one of three regions where Antarctic Bottom Water is formed (the other two are the Ross and Weddell Seas).  Bottom water is created where saline water is extruded from newly formed sea ice.  This cold dense water sinks from the surface and becomes distributed into all of the world’s major ocean basins. Because the sea-ice in a polynya is continuously formed and blown out to sea, there is near continual production of brine and bottom water.  While in the Mertz Ploynya, Jeff and I used the ships 24-bottle CTD rosette to sample some of this bottom water, and one of the samples came from Buchanan Bay, right next to the area where the glacier split.  This sample came from a depth of 1320m, and may yield insight into bacterial activities at the base of the water column.  Additional deep water samples were taken in the Adelie Depression , the Mertz Bank, and the Mertz Depression, and one sample came from a depth of 3,690 m in the Southern Ocean.

Almost half of the water samples we collected have been sequenced using 454 sequencing technology and are in the process of annotation.  This biological data will form an important baseline as this region undergoes rapid change: loss of the protective geometry of the Mertz Glacier will likely cause changes in the formation of the Mertz Polynya, influencing both the biology of the annual spring bloom and the dynamics of bottom water formation.  Stay tuned for more updates on this exciting event and on the microbiology of the region.

Tafelbergs floating in the morning light, Mertz Polynya, December 2007

Rocky Hill MS Explodes with Science

Mrs. Jill Maisch is the 7th Grade Science teacher at Rocky Hill Middle School who is responsible for the explosion with Science in Clarksburg MD. She, along with new teachers and veteran teachers to the DiscoverGenomics! Science Education Program attended our annual professional development this past summer.  The workshop not only exposes the teacher to genomics but prepares them for our mobile lab visits during that school year.  The teachers are key to preparing their students for an exciting opportunity to learn about advance techniques in the DiscoverGenomics! Science Education Program.  We commit to four visits with the DG! Mobile Lab to our middle schools when teachers participate in our workshop, as a result it makes for an explosive team!

Jill Maisch

Jill hard at work!

Our first visit to Rocky Hill Middle School on January 26th  taught the students how to use one of the many pieces of equipment they will use constantly in the program, the micropipette; as part of our “Practice Measuring Liquids” activity where they learn how to measure small amounts of colored liquid to create the visual spectrum.

Mrs. Maisch’s class was thrilled to learn about the pipette and that one million party goers could in fact share one liter of coke…of course in very, very one microliter small glasses.  Despite the cold and the snow from the two snow storms last week, we still exploded with Science! BOOM! I’m looking forward to our next visit on March 4th and the activity,” Case of the Bloody Crowbar” surely it will be as explosive as our first.

New ways to analyze metagenomics data

Are you looking for new tools to analyze your metagenomics data? Are you using  MG-RAST, IMG/M or MEGAN for your daily metagenomics work?

JCVI is working on a user friendly alternative that you might be looking for -  a new  tool kit  for metagenomics data visualization and analysis  built using the latest web 2.0 technologies.

JCVI’s Metagenomics Reports (METAREP) is a user friendly web interface designed to help scientists browse, compare, view,  and query annotation data derived from ORFs called on metagenomics reads. It supports both functional (Gene Ontology, Enzyme Commission Classification) and browsing of taxonomic assignments. When performing a search, users can either specify fields or logical combinations of fields to flexibly filter datasets on the fly. METAREP provides lists and pie charts of top functional and taxonomic categories for browse and search results. Tools are being developed that focus on the comparative analysis of multiple datasets. The system is optimized to be user friendly and fast .

Currently, an alpha version of METAREP  is used and tested internally at JCVI. In April 2010 , we will release the beta version to a limited set of interested external users.

If you like to see the tool in action,  join us  at the DOE Genomic Science Workshop ( February 9-10, 2010) for our web and poster presentation (5:30 – 8:00 pm on each day) or sign up to become part of the beta testing process at www.jcvi.org/metarep .

DNA microarrays vs RNAseq — The winner and new heavyweight champion is?… It’s a draw.

In the past year or so there have been several articles stating that the death of microarray technology is growing near. These proclamations are due to the more recently introduced methodology referred to as RNAseq. At first glance I wrote these claims off as being silly and premature. Over time though I am starting to appreciate that while the claim is still clearly wrong, the issue isn’t about technology displacement at all. My group works on a wide variety of gene expression problems ranging from the simple in vitro microbial gene expression studies to problems involving metagenomic samples of enormous complexity (http://pfgrc.jcvi.org). In my experience, the decision of whether to use DNA microarrays or RNAseq seems straight-forward and unambiguous. In reality the two technologies couldn’t be more complementary. Given the simple in vitro gene expression study as an example, the low cost, short turn-around time, exceptional quantitative accuracy and ease of data generation all make the glass slide microarray the clear choice.

About three years ago our laboratory began thinking about how to examine gene expression of pathogenic bacteria in the context of host infection. The challenge here is related to assay sensitivity since any RNA preparation derived from such an infection will yield host RNAs in an abundance 100 to 1000 times greater than that obtained from the infectious agent. Labeled RNAs from such an experiment would yield little useful information about the bacterial gene expression using standard DNA microarray procedures. This represents a clear case for RNAseq. The bewildering number of sequence reads we have come to enjoy from NextGen sequencing platforms is only going to get better. The extra bonus of applying RNAseq is that both the host and infectious agent can be profiled at the same time. There are still many technical problems to work out for routine use of RNAseq, such as effective rRNA removal and the development of appropriate data analysis tools, but the effort required seems quite justifiable.

I can think of only one application that is beginning to take on momentum where an investigator may truly ponder which strategy makes the most sense to apply. The approach is one that mimics EST sequencing as a means of defining genes and gene limits. Our ability to properly identify coding DNA sequences (CDS) in genomes ranges from, very good to relatively poor, depending on the genome in question. Members of the parasite research community, to name one, have struggled with this problem often. Generally speaking, substantial over-calling of genes occurs making it difficult for scientists to begin down the path of functional characterization of their favorite genome. We have worked with such groups recently to provide an independent means of substantiating gene calls via evidence of RNA expression. The design of such studies involves generating RNAs from a wide variety of experimental conditions to enhance the frequency for evidence based gene calls. DNA microarrays designed as a low or high density tiling array can be acquired at a reasonable cost and with good experimental outcomes. The case for applying RNAseq rests on the increased ability to detect transcripts that are expressed at low levels that defy routine detection using DNA microarrays.

In summary, I find very few instances where one might reasonably stop to wonder which technology are best suited for the biological/technical problem at hand. When sensitivity isn’t limiting, use DNA microarrays. When sensitivity is everything, look toward the short read sequencing technologies. In the end it turns out that it wasn’t really a contest at all. We should all feel fortunate that each strategy has its appropriate time and place for use. Those researchers, like myself, that have invested much time and effort working with DNA microarrays have nothing to fear, we just have more options now. This is a good thing to say the least. Most of our gene expression work is supported through a contract from NIAID to the PFGRC under contract N01-A115447.

Scott Peterson http://www.jcvi.org/cms/about/bios/speterson/

Professor, JCVI

Scientific Director, PFGRC at JCVI

Science Festivals

With spring around the corner (or at least we hope), there are several upcoming science festivals. These festivals are designed to provide students and families opportunities to find out what is happening in local science research institutes, universities and companies. These organizations are expanding the text books beyond our imaginations. These are EXCITING times in science – we are just scratching the surface of understanding the diversity of life on our planet, beginning to understand how to boot up synthetic cell, and how to better care for us and our planet.

SDSA High Tech Fair 2009: Dr. Bretschger and students

We are looking forward to participating in the SDSA High Tech Fair, March 9 & 10. Stop by our booth. It should be easy to find – with a unique sulfur odor coming from the sediment battery Dr. Bretschger created related to her work. At the end of March, we will exhibit with SD Science Festival Expo Day, March 27, which brings together over 150 hands-on science activities and stage performances for people of all ages and interest levels!

Switching coasts, April 25, JCVI will be participating at the Rockville Science Day. Another fun day of hands-on science activities and demonstrations! Look for the Mobile Lab there!!

DiscoverGenomics! Mobile Lab

DiscoverGenomics! Mobile Lab

Finally, this fall, we are excited to participate in the first ever USA Science & Engineering Festival Expo on the National Mall! The Mobile Lab will be there with other labs for a mobile lab CONVOY!! Well, maybe not as security might not like that, but we will be there.  Explore science & engineering with hundreds of free, hands-on activities and over 40 science shows on three different stages. The two-day Expo is perfect for teens, children and their families, and anyone with a curious mind who is looking for a weekend of fun and discovery. Build an underwater robot, chat with a Nobel Laureate, explore the science behind the magic of Hogwarts Academy and see a car that drives itself. From bugs to birds, kitchen chemistry to computer games, environmental monitoring to electronic music – the Expo has something for everyone and is completely free of charge. The Expo is the pinnacle event of the inaugural USA Science & Engineering Festival to be held in the greater Washington D.C. area October 10-24, 2010. The USA Science & Engineering Festival is a collaboration of over 500 of the nation’s leading science and engineering organizations. For more information on all Festival events and how you can get involved, visit www.usasciencefestival.org

I hope everyone can make it out to these great events.  If you are scientists or have a science-related career, please be sure to get out there and volunteer.  National Lab Day has provided a great national portal to volunteer.  There are never enough science fair judges, career speakers or mentors, so contact your local school to find out how you can help.