Biological and Environmental Sciences Directorate
2004 Research Highlights
Genomics: GTL Program
DOE's
Genomics: GTL (Genomes to Life) program is using new genomic data
and high-throughput technologies for studying the proteins encoded
by the genome to explore the amazingly diverse natural capabilities
in microbes. During the first 18 months of this DOE-funded project
at ORNL, the Center for Molecular and Cellular Systems (CMCS)
team evaluated various technologies for performing protein complex
pulldowns and analysis, assembled and validated capabilities,
and initiated the "pipeline." To date, the pipeline
has operated for 37 weeks with an average of 4 pulldowns per week,
including replicates, controls, and blanks. The ORNL pipeline,
which uses the endogenous pulldown method, is integrated with
the Pacific Northwest National Laboratory (PNNL) pipeline that
uses exogenous pulldowns. ORNL has lead responsibility for the
integration of the entire CMCS project, which, in addition to
ORNL and PNNL, includes researchers from Argonne National Laboratory,
Sandia National Laboratories, the University of Utah, and the
University of North Carolina.
M. B. Strader, N. C. VerBerkmoes, D. L. Tabb, H. M. Connelly, J. W. Barton, B. D. Bruce, D. A. Pelletier, B. H. Davison, R. L. Hettich, F. W. Larimer, and G. B. Hurst. "Characterization of the 70S ribosome from Rhodopseudomonas palustris using an integrated 'top-down' and 'bottom-up' mass spectrometric approach," Journal of Proteome Research 3(5): 965-978, American Chemical Society (2004).
First Text on Microbial Functional Genomics
Microbial
Functional Genomics, the first book
with a focus on microbial functional genomics, was published this
year. As the first comprehensive treatment of its subject, the
624-page book provides a timely synthesis and summary of the principles,
approaches, and applications of microbial functional genomics.
It also identifies research gaps, challenges, and experimental
directions in the field and points out the advantages and limitations
of recently developed high-throughput genomic technologies, notably
DNA microarrays and proteomic tools.
Microbial Functional Genomics begins with a chapter that attempts to codify and distinguish various aspects of functional genomics by defining the purpose and the scope of genomics; and it ends with a chapter that speculates on genomics beyond single-cell boundaries, focusing on studies of microbial genomics within the context of microbial populations, communities, and ecosystems. Chapter topics range from a discussion of computational and genomic-scale tools for gene expression analysis to the impact of functional genomics on such established research areas as microbial evolution, bacterial pathogenesis, antimicrobial drug discovery, and microbial detection.
J. Zhou, D. K. Thompson, Y. Xu, J. M. Tiedje,. A. S. Beliaev, T. Palzkill, and R. Hettich. Microbial Functional Genomics, John Wiley and Sons (www.wiley.com), 2004.
Nature Biotechnology features R. pal work
An
article by Frank Larimer and his colleagues on their work with
Rhodopseudomonas palustris (R. pal) was published
in Nature Biotechnology, and the cover featured their work.
The publication is a major step toward understanding how this
bacterium coordinates and expresses its many metabolic capabilities
in response to changing environmental conditions.
The article describes the genome sequence of R. pal, which consists of a 5,459,213-base-pair (bp) circular chromosome with 4836 predicted genes and a plasmid of 8427 bp. This work represents one of the first genomes of anoxygenic photobacteria to be finished. The sequence reveals genes that confer a remarkably large number of options within a given type of metabolism, including three nitrogenases, five benzene ring cleavage pathways, and four light harvesting 2 systems. R. pal encodes 63 signal transduction histidine kinases and 79 response regulator receiver domains. Almost 15% of the genome is devoted to transport. This genome sequence is a starting point to use R. pal as a model to explore how organisms integrate metabolic modules in response to environmental perturbations.
F. W. Larimer, P. Chain, L. Hauser, J. Lamerdin, S. Malfatti, L. Do, M. L. Land, D. A. Pelletier, J. T. Beatty, A. S. Lang, F. R. Tabita, J. L. Gibson, T. E. Hanson, C. Bobst, J. L. T. Y. Torres, C. Peres, F. H. Harrison, J. Gibson, and C. S. Harwood. "Complete genome sequence of the metabolically versatile photosynthetic bacterim Rhodopseudomonas palustris," Nature Biotechnology 22(1): 55-61 (2004).
ISI "New Hot Paper"
A
scientific study of carbon turnover in fine roots conducted at
the ORNL and Duke University Free Air CO2 Enrichment
sites was listed as an ISI Essential Science Indicators "new
hot paper" in the field of Environment and Ecology for November
2004. The ESI Special Topics Web Site recognizes selected papers
that are of special current interest.
ORNL's
Richard Norby was among the authors of the paper.
The paper shows that differences between tree species in carbon allocation to roots and root dynamics help determine soil carbon sequestration potential. The study found that fine roots of some forest tree species live years longer than the 1-year lifespan estimates often used to calculate the carbon-storing capability of forests. Trees that regenerate fine roots more often deposit more atmospheric carbon into the soil than trees with longer-lived fine roots, the findings suggest. By using a uniform, 1-year turnover time for fine roots, past studies may have overestimated the amount of CO2that the forests of the world can sequester each year.
R. Matamala, M. A. Gonzalez-Meler, J. D. Jastrow, R. J. Norby, and W. H. Schlesinger. "Impacts of fine root turnover on forest NPP and soil C sequestration potential," Science 302: 1385-1387, November 21 (2003).
CSiTE Evaluates CO2 Sequestration Potential
The
Consortium for Research to Enhance Carbon Sequestration in Terrestrial
Ecosystems, or CSiTE, has described an approach to assessing promising
techniques for removing
CO2 from the atmosphere through
management of terrestrial ecosystems. CSiTE is a group of researchers
led by Wilfred Post of ORNL, Cesar Izaurralde of the Pacific Northwest
National Laboratory, and Julie Jastrow of the Argonne National
Laboratory. According to CSiTE, agriculturally-based options for
reducing net greenhouse gas emissions by increasing carbon sequestration
in soils should be evaluated for competitiveness with other options
such as renewable energy and
CO2 capture with geologic storage.
W. M. Post, R. C. Izaurralde, J. D. Jastrow, B. A. McCarl, J. E. Amonette, V. L. Bailey, P. M. Jardine, T. O. West, and J. Zhou. "Carbon sequestration enhancement in U.S. soils," Bioscience 54(10): 895-908 (2004).
AmeriFlux Ecoregion-scale Analysis
The
AmeriFlux network, established in 1996, consists of a network
of instrumented towers across the country that provide continuous
observations of ecosystem-level exchanges of
CO2 , water, energy, and momentum.
Its purpose is to quantify variation in
CO2 and water vapor exchange
between terrestrial ecosystems and the atmosphere and to clarify
underlying mechanisms responsible for observed fluxes and carbon
pools.
A new ecoregion-scale analysis of the AmeriFlux network reveals that although central continental environments are well represented, additional flux towers are needed to represent environmental conditions in south Texas, the Sonoran Desert, and the Pacific Northwest.
The new analysis is based on a set of statistically derived ecoregions produced for the lower 48 states, using a multivariate clustering process. Because of the small cell size and the large number of cells, the cluster analysis was performed in parallel on a supercomputer.
DOE is currently selecting additional tower sites in the upper Midwest region. In terms of representing conditions within the lower 48 states, however, the regional analysis suggests adding sites in the Pacific Northwest or south Texas would improve representation more.
W. E. Hargrove, F. M. Hoffman, and B. E. Law. "New analysis
reveals representativeness of the AmeriFlux network," EOS
84(48) (December 2, 2003).
Atp 10c Gene Controls Obesity, Metabolic Problems
Research
has shown that deleting a specific gene in mice leads to obesity
and associated metabolic problems. Mice lacking the Atp10c gene
are heavier and fatter and develop non-alcoholic fatty liver disease
over time.
Atp10c is believed to function in the transport of lipids in fat cells. It is a novel type IV P-type ATPase and a putative phospholipid transporter. The study assessed the overall effect of the heterozygous deletion of Atp10c on obesity-related phenotypes and metabolic abnormalities in mice fed a high-fat diet. Heterozygous mice with maternal inheritance of Atp10c were compared with heterozygous mice with paternal inheritance of Atp10c and wild-type controls.
Mutants inheriting the deletion from their mothers had significantly higher body weight; adiposity index; and plasma insulin, leptin, and triglyceride concentrations than sex- and age-matched male control mice fed a 10% fat diet and female mice fed a 45% fat diet. Glucose and insulin tolerance tests after 4 and 8 weeks on the diets showed mutants had altered glucose tolerance and insulin response compared with the controls, suggesting insulin resistance in both sexes.
Mice were killed at 12 weeks, and routine gross and histological evaluations of the liver, pancreas, adipose tissue, and heart were performed. Histological evaluation showed more severe micro- and macrovesicular lipid deposition within the hepatocytes in the mutant mice. Although gender differences were observed, our data suggest that heterozygous deletion, along with an unusual pattern of maternal inheritance of the chromosomal region containing the single gene Atp10c, causes obesity, type 2 diabetes, and nonalcoholic fatty liver disease in these mice.
M. S. Dhar, C. S. Sommardahl, T. Kirkland, S. Nelson, R. Donnell, D. K. Johnson, and L. W. Castellani. "Mice heterozygous for Atp10c, a putative amphipath, represent a novel model of obesity and type 2 diabetes," Journal of Nutrition 134(4): 799-805 (April 2004).
New Cesium Extractants Promising for Cleanup
A
proof-of-principle experiment has shown that a prototype generation
of new pH-switchable cesium extractants offers up to three-fold
greater stripping efficiency. In principle, if this single-stage
improvement is propagated in a multi-stage flowsheet, a smaller,
more efficient, and less expensive plant for cleanup of high-level
waste could be designed.
The results were recently published in a journal article describing extraction experiments using new calixarene-crown ether extractants bearing amino substituents. Except for the amino substituents, the new extractants closely resemble BOBCalixC6, the calixarene-crown targeted for use in the Salt Waste Processing Facility being designed for cleanup of high-level waste at the Savannah River Site starting in 2010.
Under acidic stripping conditions, the amino groups in the new extractants become protonated, and it is thought that the resulting charged ammonium groups repel the bound cesium, resulting in its release. Experiments will aim at testing this hypothesis, improving the pH-switching efficiency, and increasing the solubility and robustness of this exciting new family of extractants.
E. Bazelaire, M. G. Gorbunova, P. V. Bonnesen, B. A. Moyer, and L. H. Delmau. "pH-switchable cesium nitrate extraction with calix[4]arene mono- and bis(benzocrown-6) ethers bearing amino functionalities," Solvent Extr. Ion Exch. 22(4): 637-661 (2004).
HLW Glass Model Reproduces Key Chemical Behaviors
A
model of high-level-waste (HLW) base glass has been developed
that reproduces key melting points and chemical behavior, information
critical for predicting the behavior of glass in melters and for
dealing with problems such as the precipitation of crystals that
clog melters. The glass models will also be important as source
terms for predicting leaching and stability in waste repositories,
and they can provide the initial point for models of radionuclide
transport within geologic media. The modeling results have already
found commercial utility, in particular in projects with the glass
companies Visteon and PPG.
For this work, Dr. Theodore Besmann was honored with the Spriggs Phase Equilibria Award.
Models of HLW glass composition, processing schemes, limits on waste loading, and corrosion/dissolution release depend on an accurate knowledge of liquidus (melting point) temperatures and thermochemical values. Unfortunately, existing models for liquidus temperatures are empirically based, depending on extrapolation of experimental information. In addition, present models of the leaching behavior of different glass waste forms use simplistic assumptions of the thermochemistry, or experimentally measured values obtained under nonrealistic conditions. There is thus a critical need for more accurate and more widely applicable models for HLW glass behavior. These models were developed based on the associate species approach.
T. Besmann. "Thermochemical modeling of oxide glasses,"J. Am. Ceram. Soc. 85(12): 2887-94 (2002).
New Phytologist Highlights Biological, Environmental Research
Work
sponsored by the Office of Biological and Environmental Research
was prominent in the May 2004 issue of the international plant
sciences journal New Phytologist, which featured the theme "ecosystem
function in response to elevated CO2 and temperature
in terrestrial ecosystems."
The special issue developed from an April 2003 workshop on interactions between increasing CO2 and temperature in terrestrial ecosystems, organized and chaired by ORNL's Richard Norby. Norby also serves as environment editor of New Phytologist. The workshop and the journal issue were strongly influenced by research sponsored by BER's Program for Ecosystem Research and Terrestrial Carbon Processes.
A prestigious Tansley review by Robert Nowak, David Ellsworth, and Stanley Smith focuses on responses observed in DOE's network of Free Air CO2 Enrichment (FACE) experiments. A review by Norby and Yiqi Luo addresses the issues of multi-factor interactions and data-model fusion that are foci of the Program for Ecosystem Research. Research articles describe results from the FACE experiments at ORNL, Duke University, and the Nevada Test Site, as well as ORNL research on CO2 and temperature interactions and research sponsored by the National Institute for Global Environmental Change in Colorado.
The
special issue is available online at http://www.blackwell-synergy.com/links/toc/nph/162/2,
and the workshop is described at
http://gcte-focus1.org/activities/activity_11/teracc/tahoe2003summary.html.
Bio-based Synthesis of Silica Nanostructures
Natural
systems excel in directing the synthesis of inorganic material for
various functional purposes. One of the best-studied systems is
silica synthesis, such as occurs in diatoms and marine sponges.
ORNL has successfully used poly-L-lysine to promote the synthesis
of silica in neutral, aqueous solution and then immobilize it onto
a silicon support structure. The resulting structures show silica
particles on the order of 30 nm across that eventually fuse to form
an interconnected coating. The surface patterning technique offers
a route to integrate conventional silicon-patterning technologies
with biologically-based material synthesis. This combined fabrication
enables controlled assembly over multiple length scales and an understanding
of silica synthesis in natural systems.
E. A. Coffman, A. V. Melechko, D. P. Allison, M. L. Simpson, and M. J. Doktycz. "Surface patterning of silica nanostructures using bio-inspired templates and directed synthesis," Langmuir 20(20): 8431-8436 (2004).
Protonation States of D-xylose-isomerase Revealed
Research
on the protonation states of D-xylose isomerase (XI) conducted
by Dr. Gerry Bunick and his colleagues has been published in the
open literature and presented at the 2004 American Crystallographic
Association.
To demonstrate the effectiveness of time-of-flight (TOF) neutron diffraction in biology, crystallographers used spallation neutrons at the Los Alamos Neutron Science Center Protein Crystallography Station (PCS) to reveal the protonation states of XI, an important industrial enzyme. These publications are a major step toward validating the PCS and TOF macromolecular neutron diffraction. In addition, XI is one of the largest biological macromolecules ever studied at high resolution using neutron TOF techniques. Most important, this research provides strong justification for funding a macromolecular diffractometer (MaNDi) at the Spallation Neutron Source at Oak Ridge National Laboratory.
B. L. Hanson, P. Langan, A. Katz, X. Li, J. M. Harp, J. P. Glusker, B. Schoenborn, and G. J. Bunick. "A preliminary time-of-flight neutron diffraction study of Streptomyces rubiginosus D-xylose isomerase," Acta Crystallographica D60: 241-249, 2004.
Climate Modeling for IPCC
ORNL
supports climate change studies for the Intergovernmental Panel
on Climate Change (IPCC), an organization established by the United
Nations Environment Program and the World Meteorological Organization.
IPCC climate simulations will document the state of the scientific
understanding of climate change due to anthropogenic greenhouse
gas emissions. As part of this assessment, the computer models
that countries use to make future projections are subjected to
detailed comparison and critique. Collections of studies of future
emissions scenarios have recently been completed using the computing
resources of DOE, the National Science Foundation, and the Japanese
Earth Simulator. This collection will form the basis for many
of the U.S. research communities' contributions to the IPCC.
Over the last year, ORNL's Center for Computational Sciences dedicated 1.5 million CPU-hours of the IBM p690 computer Cheetah toward this completion of the project. Over 1100 years were simulated using the ORNL computers. The simulation model used is jointly developed by the National Center for Atmospheric Research and a consortium of DOE labs. (The SciDAC program of the Office of Science directed this work.) A new release of the Community Climate System Model in June 2004 was specifically designed to provide simulation results addressing the chief scientific questions asked by the IPCC study.
W. Washington, H. Teng, G. Meehl, J. Arblaster, J. Hu, L. Buja.
"Future polar climate change simulations with the CCSM3,"
to appear in http://ams.confex.com/ams/pdfpapers/84955.pdf.
Data set available at http://www-pcmdi.llnl.gov/ipcc/ipcc_data_status.php.
Making the Artificial Retina Safe
DOE
is sponsoring research on development of an artificial
retina to restore vision to victims of retinal disorders. As
part of that effort, the DOE national laboratories are designing
a micro-electronic device that would be implanted on the surface
of the retina. A critical issue associated with multielectrode implants
for artificial sight is operating the electrodes within safe limits
of charge injection and avoiding formation of harmful electrochemical
by-products. One of the most harmful of these by-products is gaseous
hydrogen formed by electrolysis of water. Multielectrode implants
are operated in constant current mode. The compliance voltages can
easily exceed the thermodynamic limits of water electrolysis.
To address this problem, ORNL has developed an original diagnostic analysis system to detect the formation of hydrogen under real-world operating conditions. We have constructed a model "glass eye" that contains synthetic vitreous humor and is operated at 37°C. The system can accommodate virtually any electrode size and geometry. The test "eye" cell is part of a flow system that employs a tin oxide gas-sensitive sensor for hydrogen detection. When hydrogen chemisorbs on the surface of the semiconductor sensor, it causes a change in electrical conductivity. The sensor's great sensitivity and ability to operate in steady-state mode for many hours has been recognized as a valuable contribution to the repertoire of diagnostic tools needed for the successful development of retinal implants.
Surface-enhanced Raman Scattering on Any Surface
Tuan
Vo-Dinh and his colleagues at ORNL have created a nanoprobe that
induces surface-enhanced Raman scattering (SERS) on any surface.
The SERS-inducing probe was 
fabricated
from an optical fiber tapered to a tip 100 nm in diameter. A thin
layer of silver islands was applied to the tip of the tapered
fiber via thermal evaporation to induce the SERS effect. The small
scale of the tip may be amenable to localized, nondestructive
SERS-based analyses of surfaces with high spatial selectivity.
Because the contact probe itself induces the SERS effect, no modification
of the sample is required. Direct analysis at submicrometer spatial
selectivity is therefore possible for analyte compounds on any
type of surface.
The small-scale probe allows SERS detection in nanoscale environments, on localized surfaces, and inside cells. Direct analysis of dry surfaces also is now possible. This could spur renewed interest in SERS as a diagnostic tool.
D. L. Stolzes, Z. H. Chi, and T. Vo-Dinh. "Surface-enhanced-Raman-scattering-including nanoprobe for spectrochemical analysis, Applied Spectrometry 58: 292-298 (March 2004).
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