Monthly Archive for June, 2010

Road Sampling Starts in Mar Menor, Spain.

Before sampling  was to resume  on Sorcerer II,  a 2 week multiple-site road sampling trip was planned.  Chris Dupont arrived in Valencia a day after me, in the next two days we would load up a giant rental van and hit the road.  On Wednesday May 5th we drove the 322 kilometers (200 miles) from Valencia to Mar Menor.

Route from Valencia to Mar Menor (To see full image of route click on picture and again when the new window opens)

Mar Menor is a salty lagoon that is separated from the Mediterranean Sea by a 22 kilometer (14 miles) sandbar with a narrow opening on the east side.

Mar Menor Lagoon

On Thursday we were joined by Dr. Francisco Rodriguez-Valera (one of our Spanish collaborators),  Aitor Gonzaga and Dr. Olga Onyshchenko from  Universidad Miguel Hernandez Campus San Juan .  They had taken the 3 hour cruise from Alicante to Mar Menor on Dr. Francisco Rodriguez-Valera personal motor boat.  Chris and I loaded our gear on the boat and motored to the site, which has been monitored for years.  We collected 50 liters of water and took measurements for salinity, pH, temperature dissolved oxygen and turbidity.  We also took sub-samples for Antonio Camacho from the Universitat de València.  After all the samples were collected, we motored back to the marina and setup all our gear to filter the water.

Sampling on dock in Mar Menor. From left to righ, Olga, Francisco and Aitor.

The biomass in Mar Menor is so much greater than the open ocean, so all we needed was 50 liters instead of the normal 400 liters to clog all 3 of the filters.  The Mar Menor sample will be great to compare to the Albufera sample (in the next blog  Karolina  will talk about the Albufera sampling), because they are geographically close but  are very different lagoons in many ways (salinity, fresh/saltwater input,  and nutrient input from surrounding land).

For more pictures from the Mar Menor sampling from Francisco click here.

Return to Sorcerer II, The Mediterranean Season

Hello everyone! On May 2nd I flew from San Diego to rejoin Sorcerer II in Valencia Spain. Sorcerer II has been in Spain since our last sample in November, during that time her crew has been very busy upgrading systems and getting the rig certified. Sorcerer II is looking great and is ready for another successful sampling season.

Mast being removed

Sorcerer II being hauled out of the water

This summer we will be sampling the Mediterranean and Black Seas. We have established some strong collaborations with different Institutes and Universities around the Mediterranean.  While our exact schedule and ports of call haven’t been determined, we are confident that our 2010 GOS expedition in the Mediterranean and Black Seas will include very unique and interesting samples.  So please check the blog often as we plan on blogging and posting pictures on a regular basis.

Docked in Valencia

Looking for a Few Good Genomes (to sequence)!

The JCVI is one of three centers funded by the National Institutes of Allergy and Infectious Disease (NIAID) to provide sequencing and genotyping services to the infectious disease community.  We are continually looking for researchers who would like to have organisms of research interest to them sequenced and become a resource for the community. The costs are covered under the NIAID contract to the JCVI Genome Sequencing Center for Infectious Diseases (GSC) and therefore of no cost to the investigators.

The JCVI GSC provides the infectious disease research community with rapid and cost-effective high-quality sequencing services for pathogenic microorganisms including viruses, bacteria, fungi, protozoa, and invertebrate vectors of disease. The center is focused on NIAID Category A-C priority pathogens, related organisms, clinical isolates, closely related species, and microorganisms responsible for emerging and re-emerging infectious diseases and their hosts. Genotyping services are offered by the Center in order to study the variation in host response. The center also offers expertise in pathogen biology with the ultimate goal to use the sequencing and genotyping data to develop new diagnostics, vaccines, and drugs.  Data generated from the sequencing and genotyping projects will be released to the scientific community in accordance with the NIAID Data and Reagent Sharing and Release Guidelines.

JCVI has completed many projects to date and over 15 are ongoing or about to start. See here for information about these projects and the collaborators.  We are currently in year 2 of our second five year contact and over 70 known publications have resulted from these collaborative efforts.

We particularly encourage multi-collaborator projects that will provide the most impact for the scientific community.  The sequencing and genotyping projects to be conducted by center are selected from white paper proposals that can be submitted by investigators worldwide, including academia, not-for-profit organizations, industry, and government.  Information about the application process is available here.

Please contact us with questions and for advice about developing a white paper proposal.  A JCVI project lead will be assigned to each person/group who submits a white paper to help them with the process and ensure the best chance for success.  We look forward to hearing from you!

Influences of trace metals on biological evolution

Scientists show how trace metal chemistry and global changes in oxygen have influenced the evolution of metalloproteins and the Eukaryotes

June 4, 2010 - A paper is being published in PNAS this week about how the varying abundance of trace metals in the environment has influenced biological evolution. The research team, led by Chris Dupont of the J. Craig Venter Institute and Gustavo Caetano-Anollés at the University of Illinois, correlated environmental changes in metal availability over the past 3 billion years ago with the critical events in the evolution of the three superkingdoms of life (Archaea, Bacteria, and Eukaryota).

Billions of years ago, ocean chemistry was dramatically different from today. Completely devoid of oxygen, trace elements such as iron, manganese, and cobalt were abundant. The evolution of photosynthesis resulted in an increase in atmospheric oxygen around 2.4 billion years ago and prompted a series of chemical changes. Over the next 2 billions years the ocean slowly started to accumulate oxygen, increasing the amount of zinc, copper, and molybdenum that was available. At the same time, iron became very rare.

Nearly all biological pathways require metalloproteins (enzymes that bind metals) that are critical for cellular function. The metals utilized by biological life include: Mg, K, Ca, Fe, Mn, Zn, Cu, Mo, Ni, Se, and Co, yet the utilization of these elements varies between organisms. Of these, Fe, Zn, and Ca are the most utilized. Early life, the authors said, lacked both the structures required to control intracellular metal concentrations and the metal-binding proteins themselves involved in electron transport and redox reactions. Within the timeline of protein structure evolution, the invention of proteins that transport and sense metals coincided with the birth of electron transport, as well as the first unique cells. Essentially, the ability to control intracellular metal concentrations appears to be one of the fundamental definitions of biological life.

The first organisms predominantly used metals that were abundant in the ancient ocean, Fe, Mn, and Co. This bias in utilization is preserved to this day in the Bacteria and Archaea, who still predominantly use ancient protein structures. Later, as the ocean accumulated oxygen, new proteins evolved that bound zinc and copper. So did the Eukaryotic superkingdom, which includes all organisms with a nucleus, from single-cell plankton to humans. The authors found that the new zinc and copper-binding proteins are only found in Eukaryotes, not in the Bacteria and Archaea. The nucleus houses most of the new zinc binding proteins and this unique utilization of zinc is one of the defining features of all Eukaryotes. One speculation advanced by the authors is that zinc concentrations in the ancient ocean were too low to allow for the evolution of the Eukaryotes, at least until global changes in oxygen occurred.

This work was funded by the NASA Astrobiology Institute and Dr. Dupont is a collaborator at the “Follow the Elements” NAI institute at Arizona State University. Co-authors on the study include Andrew Butcher from the University of York (UK) and Ruben Valas and Dr. Phil Bourne at the University of California, San Diego.