BER Research Highlights

Search Date: June 29, 2017

14 Records match the search term(s):


December 27, 2004

Two BER supported Scientists Named in Science's Top 10 for 2004

In an article in the December 17, 2004, issues of Science, entitled, "Genes, Genes Everywhere" the work of the Office of Biological and Environmental Research-funded scientists Craig Venter and Jill Banfield was highlighted as one of the top science stories of 2004. Venter has studied the Sargasso Sea, "deciphering genomes from life in 1500 liters of water" and turning up more than a million new genes that had never been seen before. One startling result is the suggestion that a gene whose product had hitherto been thought of as a light receptor is used by many marine bacteria to process carbon. Venter is now retracing Charles Darwin's voyage on the Beagle to explore diversity in the oceans from around the globe. Another team of environmental genomicists headed by Jill Banfield at the University of California in Berkeley has focused on a small microbial community more than a kilometer down, inside an abandoned mine, where local pH values are less than 1 and there is no light. These organisms, classified into only 5 major species, get their energy by processing iron compounds. The repertoire of enzymes found in each of the five microbes indicated that they had a close relationship. Additional communities are now under study. This story spotlights ongoing work on environmental genomics which takes the most advanced genome sequencing technologies and focuses them on the genomes of entire communities. Much of this work was pioneered by DOE investments in sequencing complex community DNA samples.

Contact: Dan Drell, SC-72, (301) 903-4742
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER
      (formerly SC-72 Life Sciences Division, OBER)


November 29, 2004

NIH Director's Pioneer Award Given to Office of Science Supported Researcher

Xiaoliang Sunney Xie, Ph.D., Professor of Chemistry in the Department of Chemistry and Chemical Biology at Harvard University was among the group of distinguished scientists receiving the newly created National Institutes of Health (NIH) Directors Pioneer Award. Professor Xie was formerly on the staff at Pacific Northwest National Laboratory and his research on the application of single molecule techniques to biological problems has been financially supported by the Office of Biological and Environmental Research for a number of years. The award cited research: (1) to understand conformational and chemical dynamics of biomolecules such as enzymes through single-molecule spectroscopic studies; (2) to study biochemical activities of macromolecules in living cells, gene expression in particular, at the single-molecule level; (3) to develop new microscopy techniques for cellular imaging. The NIH award is designed to support individual scientists and thinkers with highly innovative ideas and approaches to contemporary challenges in biomedical research.

Contact: Arthur Katz, SC-72, (301) 903-4932
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER
      (formerly SC-72 Life Sciences Division, OBER)


November 22, 2004

Walter J. Weber, Jr., Honored with Festshrift Issue of Environmental Science & Technology

The November 15, 2004, issue of the American Chemical Society journal Environmental Science & Technology honors Dr. Walter J. Weber, Jr, Distinguished University Professor of Civil and Environmental Engineering at the University of Michigan. Dr. Weber has been a faculty member at the University for more than 40 years and is director of the Concentrations in Environmental Sustainability (ConsEnSus) program there. He has been a Principal Investigator in the Environmental Management Science Program since its inception in 1996, with his current research in this program focused on engineered natural geosorbents for immobilizing environmental contaminants. The journal features a photograph of Dr. Weber on the cover, an article "Walter J. Weber, Jr.'s Unique Legacy," and a dozen research papers by his present and former students. The article is available at http://pubs.acs.org/subscribe/journals/esthag-a/38/i22/pdf/111504feature_petkewich.pdf

Contact: Roland F. Hirsch, SC-73, (301) 903-9009
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER
      (formerly SC-73 Medical Sciences Division, OBER)


November 15, 2004

Comparative Microbial Genomic Comparisons on Single DNA Molecules

Optical mapping is a technology developed by David Schwartz (University of Wisconsin) to directly image a "stretched-out" molecule of genomic DNA using the unique locations of restriction enzyme cut sites as orientation marks along the length of the DNA. Schwartz and collaborators have now used this powerful technology to directly compare single genomic DNA molecules from a series of different bacteria in order to identify and annotate DNA alterations between bacterial strains represented by several species. These results, published in the November issue of Journal of Bacteriology (v. 186 (22), pp. 7773-7782, 2004), suggest that genomic rearrangements and chromosomal breakpoints can be readily identified and annotated against a prototypic sequenced strain by using the tools of optical mapping. This will contribute to analysis of microbial genomes by comparative genomics which uses information derived from previously sequenced microbial species. To gain further insights, new sequencing efforts are now dealing with the variety of strains or isolates that gives a species definition and range; however, this number vastly outstrips our ability to sequence them.

Contact: Dan Drell, SC-72, (301) 903-4742
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER
      (formerly SC-72 Life Sciences Division, OBER)


November 15, 2004

Methane-Producing Microbe Sequenced by Team at University of Washington

A team of 31 scientists, headed by John Leigh of the University of Washington in Seattle, including Miriam Land and Frank Larimer of the Oak Ridge National Lab, has sequenced, annotated, and analyzed the complete genome of a methane-producing microbe, Methanococcus maripaludis. M. maripaludis generates energy (and "waste" methane) by combining hydrogen and CO2. This Archaeon, a representative of the possibly oldest branch of the tree of life, contains 1,722 protein-coding genes in a single circular chromosome of 1,661,137 bp. Of the protein-coding genes (open reading frames [ORFs]), 44% were assigned a function, 48% were conserved but had unknown or uncertain functions, and 7.5% (129 ORFs) were unique to M. maripaludis. Genes for most of the previously known functions and pathways were identified. For example, a full complement of enzymes for using hydrogen to make methane was identified. Methane (natural gas) is a commonly used, very low polluting energy source in municipal bus fleets in a number of cities and microbial production of methane is a possible option for generating this renewable energy source.

Contact: Dan Drell, SC-72, (301) 903-4742
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER
      (formerly SC-72 Life Sciences Division, OBER)


October 12, 2004

Draft Sequence of Marine Diatom Determined at JGI

Diatoms are simple single-celled algae, covered with elegant and often very beautiful casings sculpted from silica. They share biochemical features of both plants and animals and are related to the organisms that make up the well known White Cliffs of Dover in England. A team of 45 biologists, lead by oceanographer Virginia Armbrust of the University of Washington in Seattle, and including members of the DOE Joint Genome Institute, has taken a big step toward resolving the paradoxical nature of these odd microbes. They have sequenced the genome of the marine diatom Thalassiosira pseudonana. The draft genome consists of 34 million bases on 24 chromosomes and is published in the October 1, 2004, issue of Science. The genome contains about 11,500 genes in all. Analyses of these genes and the proteins they encode confirm that diatoms, in their evolutionary history, apparently acquired new genes by engulfing microbial neighbors. Somewhere along this line, perhaps the most significant acquisition was an algal cell that provided the diatom with all the machinery necessary for photosynthesis. Diatoms date back 180 million years, and remnants of their silica shells make up a porous rock called diatomite that is used in industrial filters. Today diatoms occupy vast swaths of ocean and fresh water, where they play a key role in the global carbon cycle. Diatom photosynthesis yields 19 billion tons of organic carbon, about 40% of the marine carbon produced each year; by processing these amounts of carbon dioxide into solid matter, they represent a key defense against global warming. In addition, the newly analyzed genome is beginning to shed light on how a diatom constructs its intricately patterned glass shell. So far, a dozen proteins involved in the deposition of the silicon have been found and more are expected. Such progress could be a boon to materials scientists as well as climate change scientists.

Contact: Dan Drell, SC-72, 301-903-4742
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER
      (formerly SC-72 Life Sciences Division, OBER)


September 27, 2004

Genomics:GTL Researcher, Colin Hill, Wins MIT's Technology Review "World's 100 Top Young Innovators" Award as well as Black Enterprises' Rising Star Award

Colin Hill, CEO and founder of Gene Network Sciences (a leading company in systems biology), has been named to the 2004 list of the world's 100 Top Young Innovators by Technology Review, Massachusetts Institute of Technology's (MIT) Magazine of Innovation. Hill was also named as the winner of Black Enterprise's Rising Star Award, which recognizes an individual under the age of 35 whose outstanding skills, professionalism, and perseverance have established him as a future business leader. Profiles of Hill will appear in the October issue of both magazines. Gene Network Sciences is conducting a grant funded by the Office of Biological and Environmental using computational models to infer signal transduction pathways and gene expression networks in prokaryotes.

Contact: John Houghton, SC-72, (301) 903-8288
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER
      (formerly SC-72 Life Sciences Division, OBER)


September 13, 2004

New Sequence-Based Approach to Environmental Genomics Published in Science

In a recent issue of Science (9/3/04), Ed DeLong (MIT) and colleagues, including scientists from the DOE Joint Genome Institute in Walnut Creek, California, describe the use of genome based analyses of methane-oxidizing Archaea (evolutionarily ancient microorganisms) from deep-sea sediments to study the biological mechanisms controlling anaerobic methane oxidation. This will lead to a better understanding of the significant impacts on the flux of greenhouse gases from ocean to atmosphere and the roles of these microorganisms in those processes which, in turn, may illuminate the ways oceanic microbes participate in global carbon cycling and climate processes. One current model suggests that relatives of methane-producing Archaea developed the capacity to reverse methanogenesis and thereby to consume methane to produce cellular carbon and energy. The results published today show that nearly all of the genes that are typically associated with methane production are present in one specific group of these methane-consuming organisms, but appear to be "run backwards" so that rather than generating methane, they consume it instead. A significant contribution to this science came from the DOE Joint Genome Institute that carried out the sequencing of genomic libraries constructed from deep-sea sediment organisms, without a requirement for individual growth and culturing of each organism in the sediments. These genome-based observations provide a foundation for metabolic modeling of methane oxidation in the absence of oxygen in the deeper parts of the oceans.

Contact: Dan Drell, SC-72, (301) 903-4742
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER
      (formerly SC-72 Life Sciences Division, OBER)


August 02, 2004

Genomics:GTL Research to be Highlighted at 10th Annual Symposium of the International Society for Microbial Ecology

Genomics:GTL scientists Terry Hazen and Adam Arkin from Lawrence Berkeley National Laboratory have organized a session on August 24, 2004, to teach participants how a microbe with a sequenced genome can be annotated and how this information can be used to guide an experimental program in ecological physiology. A key objective of this type of research is to develop sufficient basic knowledge to enable the use of genome sequence information for predicting the metabolic and physiological state of a microorganism under different environmental conditions and, in turn, predicting how that organism would respond to stress. Understanding and modeling functional microbial community structure and stress responses in subsurface environments has tremendous implications for our fundamental understanding of biogeochemistry and the potential for natural attenuation or bioremediation of contaminated sites. The international symposium will be held in Cancun, Mexico, August 22-27, 2004.

Contact: David Thomassen, SC-72, (301) 903-9817
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER
      (formerly SC-72 Life Sciences Division, OBER)


July 26, 2004

Environmental Remediation Sciences and Genomics:GTL Researcher in the News

Dr. Derek Lovley of the University of Massachusetts was recently highlighted in a syndicated Knight-Ridder newspaper article for his work with the microbial Geobacter species. Geobacter species conserve energy to support growth via the enzymatic reduction of metals such as iron and uranium. Lovley's group, in collaboration with PNNL researcher Philip E. Long, demonstrated that native Geobacters are associated with the in situ removal of uranium from contaminated groundwater. This bio-based, in situ technique could lead to more cost effective means to remove contaminant metals from groundwater. In addition to its potential as a remediation tool, the novel attributes of Geobacter metabolism that enable it to reduce solid phase metals also enable it to reduce electrodes and produce electricity when cultured in microbial fuel cells. While the power outputs are small from such cells the efficiency of the process is quite high. Lovley maintains that further advances should enable practical use of microbial fuel cells for low power energy needs.

Contact: Robert T. Anderson, SC-75, (301) 903-5549
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER
      (formerly SC-75 Environmental Remediation Sciences Division, OBER)


April 19, 2004

The Institute for Genomic Research Partners Complete Sequence of Corrosive Bacterium Desulfovibrio vulgaris

A team of scientists led by the Institute for Genomic Research (TIGR) has sequenced the genome of Desulfovibrio vulgaris, a sulfate-reducing bacterium that can damage oil and natural gas pipelines and corrode oilfield equipment. The microbe takes part in a process called microbially influenced corrosion (MIC), in which bacteria act together to create a biofilm that covers metal pipelines or equipment. MIC has caused "staggering" economic losses at industrial sites around the world, according to TIGR. It is expected that analysis of the microbe's genes will help minimize such damage. In their analysis of the D. vulgaris genome, scientists found a network of c-type cytochromes-proteins that facilitate electron transfer and metal reduction during energy metabolism and are thought to give the organism a significant capacity for reducing metals. The organism could be used to help remediate metallic pollutants such as uranium and chromium, the researchers said. In addition to TIGR, the sequencing team included scientists from the University of Calgary, the University of Missouri-Columbia, Johns Hopkins University, and George Washington University Medical Center. The study, funded by the U.S. Department of Energy Microbial Genome Program, will be published in the May 2004 issue of Nature Biotechnology.

Contact: Dan Drell, SC-72, (301) 903-4742
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER
      (formerly SC-72 Life Sciences Division, OBER)


February 04, 2004

"Protein Hugs"

On January 20, 2004, the radio show "Earth and Sky," broadcast to over 600 radio stations domestically and more overseas, featured Argonne National Laboratory biologist Lee Makowski who has funding from the Office of Science. Makowski described his research using x-ray scattering to determine the shapes of proteins and the interactions between proteins and small molecules. He explained how molecules in cells don't have cell phones to make meeting arrangements and that they need elaborate "handshakes" to come together to do their work. He also explained that x-ray analysis of proteins requires that proteins be made into rigid crystals, but when proteins interact with small molecules they deform and the crystal structure often unstable. He noted that understanding how proteins deform as they interact with small molecules will likely enable us to design better drugs. This same understanding will enable the Genomics:GTL program to develop biotechnology solutions to address DOE missions. Text of the broadcast and background interviews are available at http://www.earthsky.org/shows/edgeshow.php?t=20040120%22.

Contact: John Houghton, SC-72, (301) 903-8288
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER
      (formerly SC-72 Life Sciences Division, OBER)


February 04, 2004

New Genomic Resource In Press

Before large DNA molecules can be sequenced, they are cut into small pieces and expanded, or cloned, into large numbers of copies using microbial-based 'cloning' vectors. The most commonly used vector for the initial amplification of DNA prior to sequencing is the Bacterial Artificial Chromosome, or BAC, initially developed by Mel Simon at Cal Tech with DOE funds. BACs have had many high profile uses from the isolation of human breast cancer genes to the sequencing of the human genome. A new two volume set of Methods in Molecular Biology gathers methods and protocols for diverse BAC applications. Edited by Shaying Zhao, of The Institute for Genomic Research, and Marvin Stodolsky, of the Office of Science, these volumes will be a valuable reference as BACs continue to be extensively used in genomic research. A summary of past developments and uses of BACs can be found in the preface to these volumes, available on line at [website].

Contact: Marvin Stodolsky, SC-72, (301) 903-4475
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER
      (formerly SC-72 Life Sciences Division, OBER)


January 07, 2004

Genomatica Awarded Prestigious Frost & Sullivan Technology Leadership Award for SimPheny"

Frost & Sullivan, a leading international marketing consulting company, has named Genomatica, Inc., a leader in silico systems biology company, a recipient of the 2003 Technical Insights Award for Technology Leadership. Genomatica received the award for SimPheny", its revolutionary modeling and simulation software platform for the life sciences. SimPheny" is a computer modeling platform designed to make predictions of cellular metabolism and behavior thus speeding research and development for the development of biotechnology products. The Technology Leadership Award is bestowed each year upon the company that has demonstrated excellence in technology leadership within its industry. The recipient company must demonstrate technology leadership by excelling in all stages of the technology life-cycle, including, incubation, adaptation, take-up and maturity. Also considered are elements such as feasibility of product launch, likelihood of customer acceptance and acceptance rates, and estimated time to market. Genomatica has partnered with several recipients of DOE Genomes to Life awards to model metabolic processes in sequenced microbes that carry out reactions of great DOE mission relevance, among them bioremediation and carbon sequestration.

Contact: Dan Drell, SC-72, (301) 903-4742
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER
      (formerly SC-72 Life Sciences Division, OBER)