Office of
Biological and Environmental Research Weekly Report
December 15,
2008
New Genome-Based Tools Improve Description
of Uranium Bioreduction in the Environment. Environmental microbes play an important
role in the remediation of contaminants such as uranium by converting them from
mobile to immobile forms. However, we do
not have accurate or reliable tools to predict the role that microbes will play
in remediation of contaminants at a site.
Researchers at the University
of Massachusetts have
developed a genome-enabled approach for assessing the metal-reducing activity
of members of the Geobacter
family involved in acetate stimulated uranium reduction in the environment. This new approach couples laboratory studies with
in silico
modeling of microbial metabolism and gene expression (mRNA) analyses from the dominant
Geobacter
species at a site to explain how the microbes respond to acetate injected into
the subsurface to stimulate uranium reduction.
The new tools can, for example, provide crucial data on rates of acetate
uptake useful in mechanistic, in silico, models of microbial growth and activity. The current study is an example of how
genome-enabled studies of environmentally-relevant microbes can lead to more
mechanistic descriptions of microbial metabolism in the environment.
Reference:
Microbiology, 2008, vol 154:2589-2599.
Media Interest:
No
Contact: Robert T. Anderson, SC-23.1, (301) 903-5549
Cover Article in Chemical & Engineering News (C&EN) Features
DOE BioEnergy Research
Center (BESC) at Oak Ridge National Laboratory (ORNL). The December 8, 2008 edition of C&EN provides extensive coverage of DOE’s bioenergy research. The cover story, “Genes to Gasoline,” focuses
on ORNL research to covert biomass to fuels by efficient and economical
processes. The article explains
challenges to the biological production of biofuels,
especially the recalcitrance of lignocellulosic
material to degradation. Martin Keller,
BESC Director, and Brian Davison and Charles Wyman, BESC scientists,
are quoted. Other DOE-funded scientists
conducting biofuels research are also mentioned. The shortcomings of current biomass pretreatment
and conversion options are described as a backdrop for BESC’s
research programs to develop a one-pot process (combining biomass deconstruction
and fuel synthesis in one reactor vessel), a capability to conduct high
throughput screening of potential biomass samples, and the opportunity to
discover microbes with new enzymes in locations such as hot pools in
Yellowstone. The role of DOE’s Joint Genome Institute in facilitating this research
is described. The cover shows a
fluorescence micrograph of a switchgrass cross
section.
The cover story “Genes to Gasoline,” by Steve Ritter, for
the December 8 issue is at:
http://pubs.acs.org/cen/coverstory/86/8649cover.html
The cover shows a micrograph of switchgrass
credited to DOE/NREL/BESC:
http://pubs.acs.org/cen/coverstory/86/8649aboutcover.html
Media Interest: No
Contact: Roland Hirsch, SC23.2, (301) 903-9009; John
Houghton, SC23.2,
(301) 903-8288
Training the Next Generation of
Scientists in Advanced Data Assimilation Techniques. The use and analysis of complex data sets is
an integral part of many scientific disciplines today including climate modeling. DOE-funded researcher
Professor Eugenia Kalnay organized an Intensive
Course on Data Assimilation at the School
of Sciences of the University of Buenos Aires
and the Center for Atmospheric and Ocean Research. Approximately 100 young scientists were provided
a solid foundation to understand current approaches for in situ and remotely
sensed data assimilation
Following the training course, an international workshop on
‘Ensemble Kalman Filter Inter-comparisons’ was held
at the same venue November 10-13, 2008, to encourage scientific discussions to
better understand data assimilation methods used by current researchers in the
field and to engage the next generation of scientists. The workshop focused on intercomparisons
of two widely-used data assimilation methods, incorporating both theoretical
considerations as well as practical implementations, with a special emphasis on
atmospheric data assimilation. The
discussions should provide a solid scientific basis underpinning decisions by meteorological
agencies.
Media Interest: No
Contact:
Anjuli Bamzai, SC-23.1, (301) 903-0294
Hybrid Numerical Methods Improve Computer
Modeling of Geochemical Processes. Geochemically
important reactions governing the transport of contaminants in groundwater are
often influenced by processes occurring at very small scales (microscales). Simulating
and extrapolating these phenomena to larger scales is computationally
inefficient. Hybrid numerical methods
can improve extrapolation from microscale process
models to coarser scale models by coupling the models only where needed rather
than across the entire computational domain thereby improving computational
efficiency. Researchers at the Pacific
Northwest National Laboratory, Idaho National Laboratory, and the University of
California/San Diego describe the use of hybrid numerical methods to simulate
mineral precipitation in a mixing front between two geochemically reactive
solutions. The results have important
implications for linking microscale mechanisms
influencing the mobility and reactivity of contaminants in groundwater to field
scale predictions of contaminant transport.
This work is jointly funded by Biological and Environmental Research and
Advanced Scientific Computing Research under the Scientific Discovery through
Advanced Computing (SciDAC) program.
Reference:
SIAM
JOURNAL ON SCIENTIFIC COMPUTING, 2008, 30 (6): 2799-2816.
Media Interest:
No
Contact: Robert T. Anderson, SC-23.4, (301) 903-5549