BER Research Highlights

Search Date: March 30, 2017

9 Records match the search term(s):


November 07, 2001

BITS 2001

A workshop "Beyond the Identification of Transcribed Sequences: Functional and Expression Analysis" will be held November 9-12, 2001, (see [website] for more information). This 11th international "BITS" workshop rotates back to the US this year and is being held in Reston, VA. During the past few BITS meetings, there has been a progressive shift in emphasis from the characterization of the RNA messages towards an analysis of gene function and expression. This new emphasis will help explain, for example, differences between our body's tissues, their developmental history, and their adaptive responses. Among this year's presentations by DOE-supported scientists, Dr. Richard Smith of Pacific Northwest National Laboratory (PNNL) will describe the development of technology for high through put characterization of gene (protein) products made possible by the unique mass spectroscopy resources at PNNL.

Contact: Marvin Stodolsky, SC-72, 3-4475
Topic Areas:

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


August 01, 2001

Historic Microbe Sequenced in BER Microbial Genome Program.

The complete 3.94 million base pair genome of the historic, chemical solvent-producing microbe, Clostridium acetobutylicum, has been sequenced by Douglas Smith at Genome Therapeutics Corp and annotated by Michael Daly of the Uniformed Services University of the Health Sciences. The research supported by grants from the Biological and Environmental Research (BER) Program, has been published in the latest issue of Journal of Bacteriology. In 1916, Dr. Chaim Weizmann, working in Britain, discovered that C. acetobutylicum could manufacture acetone (desperately needed during World War 1 for munitions production) and British Prime Minister David Lloyd George's gratitude to Weizmann figured importantly in the decision of the British government in 1917 to issue the Balfour Declaration supporting a Jewish homeland in Palestine. When the state of Israel was founded in 1948, Weizmann became its first President. C. acetobutylicum, which can make ethanol and butanol as well as acetone, is the 10th complete microbial genome sequenced under BER Microbial Genome Program grants and published. An additional 9 microbial genomes have been completed but not yet published.

Contact: Dan Drell, SC-72, 3-4742
Topic Areas:

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


June 06, 2001

DOE Microbial Sequencing Results Described in Natural History.

The June issue of Natural History magazine, the publication of the American Museum of Natural History in New York, includes an article by Roberta Friedman called "Bacterial Revelations." Of the five vignettes on recent microbiological findings emerging from genome sequencing, two of them describe work based on DOE Microbial Genome Program efforts. The first centers on the metal reduction abilities of Ralstonia metalliredurens, a microbe studied by John Dunn at the DOE Brookhaven National Laboratory and recently sequenced by the DOE Joint Genome Institute in Walnut Creek, CA . The second centers on two strains of the marine microbe, Prochlorococcus marinus, also sequenced at the DOE Joint Genome Institute, which may account for up to half of the photosynthetic carbon dioxide fixation in the Pacific Ocean. Both vignettes dramatize the impact of the DOE Joint Genome Institute's sequencing efforts as new investigations into the roles of bacteria in environmental processes become possible based on knowing the content of their genomic "parts list."

Contact: Dan Drell, SC-72, 3-4742
Topic Areas:

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


June 06, 2001

Natural and Accelerated Bioremediation Research (NABIR) Findings Published in Science.

In the May 18, 2001, issue of the journal Science, NABIR researcher Dr. Terry Beveridge of the University of Guelph, Canada, and collaborators at the Virginia Polytechnic Institute and State University published a paper entitled "Bacterial recognition of mineral surfaces: Nanoscale interactions between Shewanella and alpha-FeOOH." Shewanella oneidensis is a bacterium that can "respire" iron (oxy)hydroxide minerals, as well as metals such as chromium and uranium, in the absence of oxygen. Little is known about how bacteria might use a solid mineral substrate for respiration because of the difficulty in observing molecular level processes at the microbe-mineral interface. The researchers used a novel approach to examine the binding of metal reductases in the outer membrane of the bacterium to the mineral surface. Atomic force microscopy measured the binding strength between the bacterium and the mineral surface in the presence and absence of oxygen. Nanomechanical measurements showed an affinity between Shewanella and the iron containing mineral, goethite. This affinity was not measurable in the presence of oxygen or with minerals that were not respired. Molecular modeling suggested that an iron reductase protein in the outer membrane of the bacterium reduced the iron present in goethite as part of the respiratory process. This study is the first to measure microbe-mineral interactions at a nanoscale, and opens the possibility of combining nanoscale measurements with molecular genetics and mineralogy to identify all components of electron transfer in metal and radionuclide reduction during bacterial respiration.

Contact: Anna Palmisano, SC-74, 3-9963
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER
      (formerly SC-74 Environmental Sciences Division, OBER)


June 06, 2001

Natural and Accelerated Bioremediation Research (NABIR) Highlighted at the American Society of Microbiology.

NABIR investigators had a major impact on the annual meeting of the American Society of Microbiology which was attended by over 15,000 scientists. NABIR research was presented in 12 invited talks and over 50 additional scientific papers. NABIR researchers reported their findings in two sessions on "Bioreduction of Metals and Bioremediation of Metal-Contaminated Soils," as well as at sessions on "Subsurface Microbiology," "Anaerobic Respiration," "Molecular Microbiology Ecology," and "Gene Expression in the Environment." Dr. Gil Geesey, a NABIR investigator from Montana State University, won the most prestigious award in environmental microbiology, the 2001 Procter & Gamble Applied and Environmental Microbiology Award. Dr. Geesey was recognized for his research on bacterial-surface interactions, and he presented a lecture entitled "Surfaces: Catalysts of diverse bacterial cell behavior." Other highlights include a report by Dr. James Fredrickson of Pacific Northwest National Laboratory that the highly radiation-resistant bacterium Deinoccoccus radiodurans is endemic to subsurface soils beneath radioactive waste storage tanks at the Hanford reservation, making this microbe especially promising for in situ bioremediation approaches. Dr. Derek Lovley from the University of Massachusetts reported that during active metal reduction, subsurface microbial communities are dominated by metal- and radionuclide-reducing bacteria called Geobacter. Genomes of both Geobacter and Deinococcus have been sequenced by the BER Microbial Genome Program, and researchers are using this information to better understand the potential of these bacteria for bioremediation of metals and radionuclides at DOE sites.

Contact: Anna Palmisano, SC-74, 3-9963
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER
      (formerly SC-74 Environmental Sciences Division, OBER)


June 06, 2001

Structural Biologist to Receive Welch Award in Chemistry.

The Robert A. Welch Award in Chemistry for 2001 will be given to Professor Roger Kornberg of Stanford University. He is being honored for his research into the structure of the proteins and molecular machines that carry out the conversion of the genetic code into the signals to make specific proteins in living cells. Two cellular components responsible for translating gene sequences have been the major focus of his research: the nucleosome, which contains the cell's chromosomes, and RNA polymerase, which transcribes the genetic information in the DNA sequence into messenger RNA to synthesize proteins. Many of the structural studies have been carried out at the Department of Energy synchrotron light sources, especially at the Stanford Synchrotron Radiation Laboratory (SSRL). Two new papers from the Kornberg group on RNA polymerase II reporting on structures determined at SSRL have just been published in Science. This award is presented annually by the Robert A Welch Foundation of Houston, Texas, in recognition of lifetime accomplishments in the chemical sciences and includes an honorarium of $300,000.

Contact: Roland Hirsch, SC-73, 3-9009
Topic Areas:

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


April 25, 2001

Protein Data Bank Advisory Committee Meets, Assesses Impact of Accelerating Use of Synchrotrons for Protein Crystallography.

The Protein Data Bank (PDB) for three-dimensional structures of proteins has been managed since 1999 by the Research Collaboratory for Structural Bioinformatics (RCSB), whose members are Rutgers University, the National Institute of Standards & Technology, and the University of California, San Diego (UCSD). The project receives funding from the National Science Foundation, the National Institutes of Health, and the BER program at DOE.

The PDB Advisory Committee has just held its annual meeting, this year at UCSD. The PDB received 2961 new structure depositions in calendar year 2000, and showed excellent performance in handling the depositions. There is, however, concern that the number of depositions will accelerate rapidly over the next few years, due to several large projects ("structural genomics") that will focus on high-throughput structure determination including the DOE synchrotron light sources. The Advisory Committee urged the PDB management to establish closer ties with the synchrotrons to ensure reliable and efficient transfer of new structural data.

The PDB has improved its international ties. The eleven-member advisory committee includes representatives from England, Japan, The Netherlands, and New Zealand. Structures can now be deposited to partners in England and Japan, and structural data can be retrieved from web sites.

Contact: Roland Hirsch, SC-73, 3-9009
Topic Areas:

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


March 21, 2001

Fourth Annual DOE Natural and Accelerated Bioremediation Research (NABIR) Program Grantee/Contractor Meeting.

The fourth annual NABIR grantee/contractor meeting was held in Warrenton, VA, on March 11-14, 2001. The nearly 140 attendees included bioremediation researchers, BER program managers, and EM managers and staff. In a keynote address, Dr. Gerald Boyd, Deputy Assistant Secretary of Science and Technology for Environmental Management, emphasized the importance of NABIR research to finding solutions to legacy wastes of radionuclides and metals at DOE sites. EM representatives from headquarters and field operations participated in a roundtable organized by Paul Bayer (SC-74) on connecting NABIR research to EM customer needs. A scientific highlight of the NABIR meeting was a session on the use of data from BER's Microbial Genome Program by NABIR researchers. Genomic data have provided new insights into the physiology and ecology of radionuclide-reducing microorganisms, such as Geobacter and Desulfovibrio, and radiation-resistant microbes, such as Deinococcus. Special sessions were also devoted to new field research projects at the NABIR field research site at ORNL, NABIR research at Uranium Mill Tailing Remedial Action sites, and on Bioremediation and its Societal Implications and Concerns. A "town hall" style session was held as part of ongoing strategic planning for the NABIR program. NABIR researchers agreed that the program's focus on immobilization of metals and radionuclides in the subsurface is appropriate, and that communication of NABIR results to regulators and stakeholders was critical to the acceptance of this approach.

Contact: Anna Palmisano, SC-74, 3-9963 and John Houghton, SC-74, 3-8288
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER
      (formerly SC-74 Environmental Sciences Division, OBER)


March 07, 2001

Infrared Spectromicroscopy featured on journal cover.

Researchers at the Lawrence Berkeley National Laboratory are using the infrared spectromicroscopy station on beamline 1.4.3 of the Advanced Light Source (ALS) to study chemical changes in living cells under various physiological conditions and stresses. This research is featured on the cover of the February 2001 issue of Applied Spectroscopy, the premier journal for research applying all forms of spectroscopy to scientific and technical problems. The cover shows a picture of the ALS, a diagram of the beamline and station, a picture of the apparatus, the results of a study of beam sharpness, and pictures representing applications of the new technique in geomicrobiology and cellular biology.

Inside this issue is a research article demonstrating that exposure to the infrared beam from the synchrotron does not appreciably heat a biological sample. This is the first step toward one main objective of the BER-funded research, to determine whether exposure to the beam has any near- or long-term physiological effects on individual living cells. Viability tests on cells exposed to the beam are now being carried out. In a second aspect of the research, an infrared microscope stage that enables incubation of cells under controlled conditions is being developed for application in biomedical research. The principal investigators are Hoi-Ying N. Holman, Michael C. Martin, and Wayne R. McKinney.

Contact: Roland Hirsch, SC-73, 3-9009
Topic Areas:

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