BER Research Highlights

Search Date: February 24, 2017

13 Records match the search term(s):


December 18, 2002

Berkeley Hosts Workshop on Automation of Synchrotron-Based Protein Crystallography: Advances Reported in all Areas

A workshop was held in early December at the

Advanced Light Source at the Lawrence Berkeley National Laboratory that brought together many leading researchers in automation of protein crystallography for high throughput determination of protein structure. The topics included protein production and purification, crystallization of proteins, automation of beamlines for remote manipulation of sets of crystals, and data collection, management, and solution of structures in an integrated fashion. The speakers reported substantial advances in each area. For example, optimum conditions for crystallization of a protein now can be identified through highly automated screening systems that include continuous monitoring with cameras that feed into image databases for later analysis and identification of the best means of crystallizing a particular protein with minimal human intervention during a study. The 100 attendees came from all four Department of Energy (DOE) synchrotrons and the Photon Factory in Japan, several other DOE laboratories, universities, research institutes and companies in the pharmaceutical, biotechnology and laboratory instrumentation fields.

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)


December 11, 2002

U.S. - German Research Consortium Sequences Genome of Versatile Soil Microbe, Pseudomonas putida

In a transatlantic collaboration, scientists at The Institute for Genomic Research (TIGR) in Rockville, Maryland, and at four research centers in Germany have completed the sequence and initial analysis of a bacterium, Pseudomonas putida, with potential for remediation of organic pollutants in soil, promoting plant growth, and fighting plant disease. The December 2002 issue of Environmental Microbiology is devoted to this and related microbes. The P. putida project was supported by grants from the U.S. Department of Energy's Office of Science and from the German research ministry, the BMBF and is the microbial 24th genome to be sequenced by the DOE Microbial Genome Program. Knowing the complete DNA sequence of this microbe will aid in the development of new ways to use this and related microbes to clean up organic pollutants. In 1982, P. putida was designated by a National Institutes of Health advisory panel as the first "biosafety" host strain for gene cloning in soil bacteria. Comparisons of the genomes of P. putida and another member of the Pseudomonas genus, P. aeruginosa, an opportunistic pathogen that is the leading cause of death for cystic fibrosis patients, has also provided new insights that will enable us to better identify the features in the P. aeruginosa genome that contribute to making it a pathogen.

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)


December 11, 2002

Understanding Microbial Polarity

Microbes are not just "bags of salt water" in which everything floats freely and is evenly distributed inside a spherical cell. Instead, microbes establish and maintain the unequal distribution of their internal components, i.e., they have "polarity." Polarity enables a microbe to move in the direction of a nutrient or away from a toxin, divide unequally into daughter cells that can display different behaviors (one can swim off looking for a new place to live and eat and the other may stay behind), or from structures that push the cell in one direction or another. A Stanford University research team is studying polarity in a microbe, Caulobacter crescentus, whose DNA was sequenced with Biological and Environmental Research support and that can remediate heavy metals in aquatic environments. A review article in the December 6, 2002, issue of Science, surveys the establishment of polarity in this and other microbes. This is a key step towards understanding the reality of complex microbial biology and the eventual use of microbes to address DOE needs in energy and the environment.

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 20, 2002

International Diatom Annotation Jamboree and Phytoplankton Sequencing Workshop Held at DOE Joint Genome Institute Surprises Revealed

Twenty-seven scientists from the U.S. and six other countries met at the DOE Joint Genome Institute in Walnut Creek, California, on October 21-24 to annotate the newly sequenced genome of the diatom Thalassiosira pseudonana. Annotation of the genome revealed some surprises, including the presence of genes coding for compounds called siderophores that bind iron. Low iron concentrations limit the growth of phytoplankton, and thus carbon fixation, in large regions of the world's oceans. The discovery of these genes has profound implications for our understanding of how the ocean carbon cycle is regulated. Diatoms are of primary importance to the "biological pump" of carbon in the world's oceans. They fix carbon dioxide into their cells, then sink to the deep ocean where the carbon may be sequestered for decades or longer. Diatoms are also of keen interest to the biotechnology industry because of their ability to produce silica cell walls in highly complex patterns. A second meeting on October 25 brought together world experts in marine phytoplankton to generate a list of top candidates for future genomic sequencing. Four high priority candidates were selected, including other diatom species and a colony forming alga called Phaeocystis, that are important in ocean carbon sequestration.

Contact: Anna Palmisano, SC-75, (301) 903-9963
Topic Areas:

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


November 06, 2002

The Sequence of Bioremediation Microbe Shewanella oneidensis Published

The November 2002 issue of Nature Biotechnology includes the publication of the complete 4.9 million base pair, 4,758 predicted gene containing, sequence of the genome of Shewanella oneidensis MR-1. This non-pathogenic microbe displays astonishing metabolic diversity and versatility, having the ability to use more than ten different elements (among them iron, manganese, sulfur, oxygen, chromium and uranium) to generate energy and in the process modifying both the chemical form and subsequent environmental behavior. Shewanella renders uranium immobile in sediments and could prevent leaching into nearby rivers. Continued research on the microbe is underway to explore the potential for bioremediation of DOE legacy wastes.

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 04, 2002

Protein Crystallography Station at Los Alamos Neutron Science Center Begins First External User Run

A new experimental station for studying the three-dimensional structure of proteins using neutron beams has just been opened to the national structural biology community at the Los Alamos National Laboratory. Protein crystallography with neutron beams enables locating the hydrogen atoms in many proteins with greater precision than when x-ray beams are used. Time at the station is allocated on the basis of peer-reviewed proposals from potential users; requests for this first user run were for three times the number of available hours of the station. Several experiments will compare the results of neutron crystallography with x-ray crystallography for determining the structure of specific proteins. Development and operation of this station is funded by the Office of Science's Biological & Environmental Research program. The station is part of the Short Pulse Spallation Source Enhancement Project at the Los Alamos Neutron Science Center (LANSCE), which also includes two experimental stations funded by the Office of Science's Basic Energy Sciences program.

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)


August 21, 2002

PNNL Team Determines Majority of "Conan the Bacterium's" Proteome

Scientists at the Department of Energy's Pacific Northwest National Laboratory have obtained the most complete analysis of the total set of proteins (the proteome) of any organism to date using the microbe Deinococcus radiodurans. This microbe has been called "Conan the Bacterium" by the media for its ability to withstand high doses of radiation and its astonishing DNA repair capabilities and has even been listed in the Guinness Book of World Records as the world's toughest bacterium. This research could open up new opportunities to harness this remarkable bacterium for helping to clean up contaminated DOE sites. While the genomic DNA sequence of this microbe was published three years ago, that information by itself has not allowed researchers to understand the DNA damage repair system. Information was needed about which genes are expressed when the microbe is exposed to radiation, about the proteins that are expressed in increased amounts under the radiation stress, and about how these proteins are involved in the highly effective damage recognition and repair system of D. radiodurans.

In a study published in the August 20 issue of the Proceedings of the National Academy of Sciences (PNAS), a team lead by Richard Smith identified more than 60% of the proteins in the possible set of proteins (the proteome) predicted for D. radiodurans from its genome, the most complete analysis of the proteome yet done by any group. The results include identification of proteins that are highly expressed by this microorganism under environmental stresses, and discovery of functional classifications for proteins that previously were uncharacterized. These unprecedented studies were conducted on the unique 11.4 tesla mass spectrometer at the Biological and Environmental Research's Environmental Molecular Sciences Laboratory (EMSL).

The research was directed by Richard D. Smith of the EMSL, with his colleague Mary Lipton as the lead author on the article, and with collaborators from Louisiana State University and the Uniformed Services University of the Health Sciences. Funding was provided by the Office of Science Natural and Accelerated Bioremediation Research and Genomes to Life programs. The PNAS research article is accompanied by a commentary written by Jan Mrázek of Stanford University.

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)


July 24, 2002

Presidential Early Career Award in Science and Engineering (PECASE) awarded for BER funded research

Dr. Jizhong Zhou of the Environmental Sciences Division of Oak Ridge National Laboratory has won the prestigious PECASE award for his leadership in the fields of functional genomics and microbial ecology. In separate ceremonies on June 11 and 12, Dr. Zhou received congratulations and citations from Secretary Abraham and from President Bush. Dr. Zhou has made significant contributions to a wide range of BER programs. Dr. Zhou was specifically cited for his "pioneering application of genomic and molecular technologies to environmental studies." Dr. Zhou and his research group have developed nucleic acid-based microarrays that can be used to analyze microbial community structure and functioning at levels of detail never before achieved. His research findings will be critical to a wide range of DOE mission areas, including bioremediation of legacy wastes, carbon sequestration, and biofuel production, as well as advancing the overall field of biotechnology.

Contact: Anna Palmisano, SC-75, 3-9963 and Dan Drell, SC-72, 3-4742
Topic Areas:

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


June 18, 2002

BER Supports Conference on Genomics and Homeland Security

The American Academy of Microbiology (AAM), with support in part from the Office of Biological and Environmental Research (BER) Life Sciences and Environmental Sciences Divisions, convened a colloquium entitled "Microbial Forensics: A Critical Assessment" on the applications of genomics in the response to bioterrorist acts. The colloquium was organized at the request of the Federal Bureau of Investigations (FBI), and involved scientists from Los Alamos National Laboratory, U.S. Department of Agriculture (USDA), and academia. The colloquium was held during the week of June 3, 2002, in Burlington, VT. The Academy's key recommendations regarding microbial forensics will be summarized in a report to be issued in August 2002. This report will describe specific research and development needs in basic science (select agent identification, comparative genomics, and ecophysiology) and in applied science (development of new, legally-admissible protocols for sample handling; quality assurance and quality control). The Academy is the only honorific organization devoted entirely to microbiologists and the science of microbiology; fellows are required to demonstrate scientific excellence, originality, and leadership; high ethical standards; and scholarly and creative achievement. BER's involvement in the colloquium bridges the Department of Energy's missions in biodefense and biological research, supports coordination of scientific activities among federal agencies (such as FBI and USDA), and publicizes its commitment to high-quality science leading to greater use of new molecular technologies.

Contact: Brendlyn Faison, SC-74, 3-0042
Topic Areas:

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


April 24, 2002

Genetic Engineering News Highlights Microbial Genome Gateway Site

The April 15, 2002, issue of Genetic Engineering News (GEN) has spotlighted, with high praise, the BER-supported (Biological and Environmental Research) ORNL-maintained (Oak Ridge National Laboratory) Microbial Genome Gateway web site microbialgenomics.energy.gov. GEN notes that this site "will make you sit up and smell the coffee, however, with an extensive collection of links to both [microbial sequencing] projects underway and completed." GEN goes on to note that "The site is more than just a collection of sequences, however, with sections devoted to education, links, images, and program descriptions." The review notes the "excellent coverage of topic" and the complete absence of weak points. This site is part of the BER Microbial Genome Program that focuses on sequencing genomes of, and supporting biological research into, microbes of mission interest to the Department of Energy, i.e. capable of cleaning up legacy wastes, fixing carbon dioxide, and producing biofuels.

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)


February 13, 2002

First Tree Genome Sequenced

The genome of Populus balsamifera ssp. trichocarpa, commonly known as the black cottonwood, a species of Poplar tree distributed from the Kenai Peninsula of Alaska to Baja, California, east to Nevada, Utah, Wyoming, Idaho, Montana, North Dakota, and Alberta, will be the first tree genome ever sequenced. The Populus Genome Scientific Steering committee and the BER Joint Genome Institute (JGI) in Walnut Creek, California, are leading the sequencing of this Poplar species. This international research project has representatives from the University of Washington, Oregon State University, Pennsylvania State University, the British Columbia Genome Sequence Center, the Swedish University of Agricultural Sciences, the National Center for Genome Research, the JGI, the Oak Ridge National Laboratory, and other institutions. Dr. Toby Bradshaw (chair of the Science Steering Committee) from the University of Washington and Dr. Jerry Tuskan from Oak Ridge National Laboratory are the principal scientists from the Populus genetics and molecular biology scientific communities who are providing genetic material and technical coordination of the sequencing effort and working with the JGI in California. Scientists working on tree genetics and tree productivity and product utilization are wildly enthusiastic about the sequencing of this tree species because it represents an important first step in understanding the genome of a common, commercially important tree species. Scientific significance and industrial interest in the Poplar sequencing project are described in a press release that appears in the Science Daily web site and the project is also reported in other science media.

[website]

Contact: Roger C. Dahlman, SC-74, 3-4951
Topic Areas:

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


January 30, 2002

The World and I Highlights BER Microbial Genome Program

The January 2002 issue of The World and I prominently features results from the DOE Biological and Environmental Research (BER) Microbial Genome Program in a major article titled "Great Expectations of Small Genomes" by staff writer Dinshaw Dadachanji, and boldly notes that "Ongoing efforts to sequence the DNA of various microorganisms are fueled by the promise that the information gained will boost advances in such areas as medicine, energy production, environmental cleanup, and industrial processes." The focus of BER's Natural and Accelerated Bioremediation Research (NABIR) program includes microbial bioremediation as a particular emphasis and the majority of the microbes sequenced under the sponsorship of the Microbial Genome program have demonstrated relevance to bioremediation, energy production, and global climate processes. The article further notes that "Shewanella oneidensis, a bacterium that can grow in water and soil, can consume toxic organic wastes and precipitate certain heavy metals--including radioactive uranium--from solution. This ability could be used to trap and remove uranium from a contaminated stream." BER-supported researchers at the DOE Oak Ridge National Laboratory are now placing hundreds of its DNA segments on microarrays to find genes that might be useful for environmental remediation.

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)


January 09, 2002

BER Funds Microbial Research at Michigan State University

The DOE Office of Public Affairs has published a press release that describes a Biological and Environmental Research-funded Michigan State University (MSU) grant for Microbial Research. Dr. George Garrity and colleagues will conduct research on the patterns of microbial evolution and the relationships among species. Secretary of Energy Spencer Abraham is quoted as saying, "This research will provide scientists valuable information as they try to understand the biology and the potential uses of newly discovered species of microbes. Application of this information could lead to improved pollution cleanup techniques and more efficient bio-energy production." Dr. Garrity, the principal investigator for the two-year grant, is a professor of microbiology at Michigan State University and the Editor-in-Chief of Bergey's Manual, a widely-used, international reference work for bacterial taxonomy. MSU researchers and their colleagues will use a variety of powerful statistical analytic methods to cluster more accurately microbial species so that their relationships to each other are clearer and more consistent with what is known about their biology. With rapidly growing data sets and an even more rapidly growing number of relationships among the data, powerful computers are required to carry out the research. An organism's evolutionary relationship can be represented in a number of different ways that are not mutually consistent, depending on just which DNA sequence pieces are used. The research will work to resolve apparent paradoxes such as this. This research is funded as part of the Microbial Genome Program.

Contact: John Houghton, SC-72, 3-8288
Topic Areas:

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