DOE WEEKLY REPORT
OCTOBER 13, 2009
OFFICE OF BIOLOGICAL AND ENVIRONMENTAL RESEARCH
I. This Week’s Accomplishments
An International Effort to Develop a Policy
for ‘Omics Data Sharing. An international effort is
underway to develop a framework to enable the sharing of biological data
generated from a wide variety of experiments.
This week in the journal Science
key stakeholders and members of international funding agencies, including
Dr. Susan Gregurick from the Department of Energy, have published a template for policies related to the sharing of ‘omics data and information. At the heart of this template is the notion that all data and information relevant to published results should be made available to the scientific community in a timely fashion, according to international data standards and in the appropriate scientific databases. This policy follows directly from and is in line with the DOE’s Genomic Science data and information sharing policy of October 1, 2008 (http://genomicsgtl.energy.gov/datasharing/). In order to facility continued development of data sharing policies, a website has been set up to encourage the exchange of ideas and policy comments among funders and researcher (Biosharing, http://biosharing.org/). Details of this article can be found in Science 9 October 2009: 234-236.
ARM Facility Selects 2011 Experiments. DOE’s Atmospheric Radiation Measurement Climate Research Facility (ACRF) has announced its three major campaigns for 2011. These campaigns address major scientific uncertainties, have significant international or interagency collaborations, and will be the first major experiments to incorporate new ACRF capabilities acquired under the Recovery Act. The first mobile facility and G-1 aircraft will support a Ganges Valley (India) Aerosol Experiment to study the impact of increasing aerosols on the Indian Summer Monsoon, specifically the impact on precipitation. Many in-country collaborators will provide valuable complementary measurements. A major campaign at the Manus site (ACRF Tropical Western Pacific site), the ACRF Madden- Julian Oscillation (MJO) Investigation Experiment, will be coordinated with a large international MJO initiation field campaign called CINDY2011 (Cooperative Indian Ocean experiment on intraseasonal variability in the Year 2011). The mechanism and cause of the MJO, an equatorial traveling pattern of anomalous rainfall that is planetary in scale, is not well-understood and has the distinction of not being accurately simulated in any current model. The Mid-latitude Continental Convective Clouds Experiment will be a joint campaign with the NASA Global Precipitation Measurement Project. This experiment, conducted at the ACRF Southern Great Plains site will study cloud and precipitation transitions and environmental quantities that are important for convective parameterization in large-scale models and cloud-resolving model simulations.
Genome
Standards Consortium Proposes Common Practices for Sequence Reporting. Led by scientists from the DOE Joint Genome
Institute, representatives from major high-throughput sequencing centers have
jointly published new standards for published genome sequences in the October 9
issue of the journal Science. The proposal posits a tiered set of
community-defined categories that increase in rigor and should better reflect
the quality of the genome sequences being released. The proposal avoids rigid numerical
thresholds in order to remain responsive to rapidly changing sequencing
technologies. The proposal also
accommodates a growing list of alternative types of genome sequencing projects,
such as environmental (metagenomic) or single-cell
sequencing. Responses from genome
database repositories have been positive and implementation of these standards
as a requirement for genome submissions is expected. This common currency in
defining the products of genome projects will enable better management of
expectations and allow users of genomic data to assess the quality of the
deposited available sequences and decide whether these meet their needs.
Climate Change Lesson Plan Selected for MyHealthySchool.com A lesson plan about climate change in the Arctic was selected by MyHealthySchool.com to join their
collection of online educational resources.
Developed through the DOE’s Atmospheric Radiation Measurement (ARM)
Education and Outreach Program for junior high school students, the lesson plan
called “Bringing Climate Change into the Classroom” covers the greenhouse
effect, sea ice, adaptation, and climate change in the Arctic. The MyHealthySchool.com website provides
teachers, administrators and parents with tools for creating greener,
healthier, more socially responsible schools and children. Their efforts are intended to help children
learn how to make decisions that benefit their communities, the environment and
their own lives. For more learning tools
specific to climate, visit education.arm.gov.
Visualizing Microbial Activity in the Subsurface. The transport of metal and radionuclide contaminants in groundwater can be greatly influenced by microbial activity. Geophysical methods provide a way to detect microbial activity across larger spatial scales in subsurface environments than can be accomplished by point source drilling-intensive techniques. Detection of in situ microbial activity is important for developing realistic conceptual models of contaminant fate and transport at DOE sites. Results obtained from researchers at Lawrence Berkeley National Laboratory, Pacific Northwest National Laboratory and the University of California at Berkeley working at a field test site in Rifle, CO show that geophysics techniques can detect geochemical changes attributable to specific microbial activities in the subsurface across large spatial areas at field sites. These techniques provide a more spatially resolved assessment of microbial activity in the subsurface and can be used to inform conceptual and quantitative models of contaminant transport in the subsurface.
Reference: Environ. Sci. Technol., 2009, 43(17): 6717-6723
II.
Program
Focus for the Week Ahead, includes Major Projects and Initiatives
III.
Public
Events/Meetings
IV.
Recovery
Plan
All six of the BER Recovery Act projects met their planned FY09 4th quarter and end of year performance milestones. The ARM Climate Research Facility project at the Pacific Northwest National Laboratory (PNNL) has awarded $47M worth of contracts, including all of their planned major items of equipment (MIEs). The Environmental Molecular Sciences Laboratory project at PNNL has awarded $20M worth of contracts, including the three longest lead procurements (12 months each). The PNNL project manager for the Integrated Assessment (IA) project and the BER program manager are scheduled to visit the University of Maryland Computer and Space Sciences Complex in College Park, MD on October 13th to assess facility modification and connectivity needs. The Joint Genome Institute (JGI) project at the Lawrence Berkeley National Laboratory (LBNL) has approximately 1/5th of its planned procurements under contract. The Kbase project at Oak Ridge National Laboratory (ORNL) has finalized the agenda for the SC09 workshop and is identifying participants for a workshop at the Plant and Animal Genome conference in San Diego, CA in January 2010. The Joint Bioenergy Research Institute (JBEI) at LBNL has a contract in place for an FTIR confocal microscope. The Bioenergy Science Center (BESC) at ORNL has approximately half of its funding under contract. The Great Lakes Bioenergy Research Center (GLBRC) at the University of Wisconsin has more than half of its funding under contract.
V.
Reform-Based
Actions
VI.
Meetings/Events
VII.
Potential or
Expected Press Stories
VIII.
Legislative
Activity
IX.
Senior
Personnel Announcements
X.
Issues for
Attention