BER Research Highlights

Search Date: June 28, 2017

10 Records match the search term(s):


November 21, 2005

Science Article Provides Insights About Ribosome

In the November 4, 2005 issue of the journal Science, LBNL researcher Dr. James Cate and collaborators provided important new insights into the operation of the ribosome, the molecular complex that manufactures proteins in the cell. Dr. Cate and his colleagues determined two high resolution ribosome crystal structures resulting in the first detailed view of the interface between ribosome subunits as well as its center for producing proteins. The research is part of the Genomics:GTL effort to develop strategies to label complexes to track their operation in microbial cells. The National Institutes of Health partially supported this work.

Contact: Arthur Katz, SC-23.1, (301) 903-4932
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER
      (formerly SC-23.1 Life Sciences Division, OBER)


May 23, 2005

An Electrifying Discovery

NABIR-supported researcher Dr. Derek R. Lovley of the University of Massachusetts, Amherst, has made a remarkable discovery that will be published in the journal Nature in mid-June. Dr. Lovleys group has found that the metal-reducing microorganism Geobacter produces nanotube projections called pili on the outer cell surface that appear to function as electron conducting nanowires. The data indicates these conductive pili are conduits by which Geobacter transfers electrons onto iron oxides during the process of dissimilatory iron reduction. This is of importance because Geobacter species are detected as a dominant species in the subsurface during stimulated uranium bioremediation, where iron oxide reduction is a dominant process. Discovery of this fundamental mechanism of microbial metal reduction could lead to better models for subsurface bioremediation processes but may also have implications for the electronics field because the conducting pili can be mass produced and pili composition can be altered via genetic manipulation.

Contact: Arthur Katz, SC-23.1, (301) 903-4932
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER
      (formerly SC-23.1 Life Sciences Division, OBER)


May 23, 2005

ORNL Environmental Microbiologist Honored by Microbiology Academy

Dr. Jizhong (Joe) Zhou, Distinguished R&D Staff Scientist in the Microbial Genomics and Ecology Group, Environmental Sciences Division at Oak Ridge National Laboratory, has been elected to the American Academy of Microbiology (AAM) as a Fellow. AAM is the honorific leadership group within the American Society for Microbiology (ASM), which is the world's oldest life science organization. This honor recognizes Dr. Zhou's many contributions to environmental microbiology in support of DOE mission aims in a variety of BER-funded programs in microbial genomics and environmental restoration.

Contact: Dan Drell, SC-23.1, (301) 903-4742
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER
      (formerly SC-23.1 Life Sciences Division, OBER)


May 09, 2005

Paper on "Community Proteomics of a Natural Microbial Biofilm" to Appear in May 5 Issue of Science

Communities made up of different microbes play key roles in Earth's biogeochemical cycles. However, our knowledge of these communities is limited because we have only been able to study them when the microbes could be grown in the laboratory, limiting our ability to explore critical community and environmental interactions. In the May 5, 2005, issue of Science, a BER-funded group lead by Dr. Jill Banfield of UC Berkeley studied a natural microbial biofilm community collected from an acid drainage site at Iron Mountain, near Redding, California. These biofilms grow under very acidic conditions (pH ~0.8) and in the presence of high concentrations of iron, zinc, copper, and arsenic. Using a combined genomic and proteomic approach 2,033 proteins were identified in this five microbe community, including 48% of the proteins predicted from the previous DNA sequence analysis of the dominant organism in the community. Proteins involved in protein refolding and response to oxidative stress appeared to be highly expressed, suggesting that damage to biomolecules is a key challenge for survival by this microbial community. This is the first time that genomic and proteomic approaches have been used on a naturally occurring microbial community to characterize the "community genome" as well as the "community proteome" promising insights into potential biological strategies for remediation of these toxic materials.

Contact: Dan Drell, SC-23.1, (301) 903-4742
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER
      (formerly SC-23.1 Life Sciences Division, OBER)


April 04, 2005

BER-Funded Scientist Profiled in The Scientist for Metabolic Engineering Work

The March 28, 2005, issue of The Scientist profiles Dr. Jay Keasling of the Lawrence Berkeley National Laboratory and University of California, Berkeley for designing and reengineering the common bacterium E. coli to produce arteminesin, a powerful anti-malarial compound. Arteminesin is a highly effective anti malarial drug that is expensive and difficult to make in conventional ways. Keasling, with support (in part) from the Office of Biological and Environmental Researchs Genomics:GTL program, has been studying how to design and reengineer a bacteriums natural abilities to metabolize nutrients into various products; in this way, he can engineer a bacterial cell into a micro-manufacturing plant for a valuable product that the cell, left to its own devices, would not be able to make. Given the impact of malaria on less developed countries, (1.5 million deaths annually), the Keasling approach not only could benefit people in areas endemic with malaria but may also be useful at enabling microbial production of a variety of other useful and valuable compounds including those with direct GTL relevance. Recently, the Bill and Melinda Gates Foundation provided $42.6 million towards a public-private partnership, built around Keasling's progress, to develop bacterially synthesized arteminesin and following commercialization and regulatory clearance, get it to clinical application where it is needed most.

Contact: Dan Drell, SC-23.1, (301) 903-4742
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER
      (formerly SC-23.1 Life Sciences Division, OBER)


March 28, 2005

GTL Featured in Recent Issues of The Scientist and The Economist

The Office of Biological and Environmental Research's (BER) Genomics:GTL program was the subject of a Vision column by Dr. Ari Patrinos in the March 14, 2005, issue of The Scientist. The column presents a case for being "bullish" on the promise of biotechnology to deliver solutions to the principal Department of Energy (DOE) energy and environmental security missions. The use of bacteria to precipitate uranium out of groundwater, the potential for a synthetic genome to provide organisms with selected characteristics that address DOE needs, and the use of the DNA sequence of the Populus tree to create opportunities for enhancing biomass potential were cited as examples of biotechnology's promise for DOE needs. Additionally, in The World in 2005, a companion publication to The Economist, BER is referenced as leading the way to use microbes for generating energy and cleaning up pollution. The development of a synthetic bacterium from "off-the-shelf" parts in the laboratories of Drs. Craig Venter and George Church offers the promise of synthetic biology to form the basis of important and possibly revolutionary technology.

Contact: John Houghton, SC 23.1, (301) 903-8288
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER
      (formerly SC-23.1 Life Sciences Division, OBER)


March 28, 2005

New BER/JGI Microbial Genome Database Tool Reported in Science

The March 18, 2005, issue of Science reports on the new Integrated Microbial Genomes (IMG) site at the DOE Joint Genome Institute (JGI) (p. 1701, Microbial Get Together.) This new clearinghouse (https://img.jgi.doe.gov/v1.0/main.cgi) from DOE helps researchers analyze the deluge of DNA data on microorganisms. The IMG site currently stores nearly 300 draft or completed genome sequences from archaea, bacteria, and other microbes, along with tools for sifting through the data. Visitors can get acquainted with all 2526 protein-coding genes carried by the marine cyanobacterium Synechococcus, for example. Besides basic information about the gene, its protein, and its function, visitors can summon diagrams illustrating which biochemical pathways the gene influences. Browsing tools make it easy to pinpoint similar genes in different organisms and compare them side by side.

Contact: Dan Drell, SC-23.1, (301) 903-4742
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER
      (formerly SC-23.1 Life Sciences Division, OBER)


February 21, 2005

Novel Insights into Bacterial Radiation Resistance Developed from DOE Microbial Genome Program

In a paper that has been accepted for publication in next month's FEMS Microbiology Reviews, Michael Daly of the Uniformed Services University of the Health Sciences and colleagues (including scientists from Howard University, NIH, Pacific Northwest National Lab, and the University of Minnesota) develop the concept that radiation resistant microbes such as Deinococcus radiodurans (capable of resisting doses up to 2000 times what is lethal for humans) is not due to unusual or extra genes that less resistant bacteria lack, but rather that due to regulatory alterations that permit them to use their repair mechanisms much more efficiently. A characteristic observed in radiation resistant bacteria is the accumulation of high levels of intracellular Manganese (Mn) ions and the relative dearth of Iron (Fe); just the opposite is seen in bacteria that are sensitive to radiation. Mn is known to suppress the formation of oxygen radicals while Fe tends to promote their formation, suggesting a link between radical formation (consequent to normal cell metabolism) and DNA damage. This may lead to the identification of ways to increase radiation resistance by adjusting Mn/Fe ratios in cells prior to radiation exposures.

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)


January 10, 2005

Novel Approach Used to Assign Functions to Previously Unknown Proteins in a Microbe

An interdisciplinary team of scientists at ORNL, PNNL and BIATECH in Seattle used a combination approach mixing experimental and computational analyses in the microbe Shewanella omeidensis. Integrative approaches such as this one offer valuable means to undertake the enormous challenge of characterizing the rapidly growing number of hypothetical proteins continuing to be found in each newly sequenced genome. The bacterium Shewanella oneidensis strain MR-1 is a metabolically versatile microbe that can reduce a wide range of organic compounds, metal ions, and radionuclides and thus offers great promise to help clean up contaminated DOE sites. Similar to almost all other sequenced microbes, about 40% of the predicted 4324 genes in the S. oneidensis genome are unknown and therefore cannot be assigned potential roles and functions in the microbe. The work will be published within the next two weeks in the Proceedings of the National Academy of Sciences. The resulting analyses identified about one-third of the 1600 previously 'hypothetical' genes. The scientists (part of the DOE "Shewanella Federation") were able to identify similar proteins in other sequenced organisms for nearly all of these 538 'hypothetical' proteins, but could confidently assign exact biochemical functions for only 16 of them. Computational and experimental evidence provided less exact but plausible functional assignments or insights for an additional 240 genes. These functional annotations significantly reduce the "search space" within which the exact functions of these genes, about which nothing was previously known, can be experimentally determined and advance our understanding of genes involved in vital cellular processes.

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)


January 10, 2005

Scientists Decipher Genome of Bacterium that Helps Clean Up Major Groundwater Pollutants

Scientists at the Institute for Genomic Research (TIGR) in Rockville, MD, have deciphered the genome sequence of a microbe that can be used to clean up pollution by chlorinated solvents  a major category of groundwater contaminants that are often left as byproducts of dry cleaning or industrial production. The work is to be published in Science on Friday, January 7. The study of the DNA sequence of Dehalococcoides ethenogenes found evidence that the soil bacterium may have developed the metabolic capability to consume chlorinated solvents fairly recently  possibly by acquiring genes from a neighboring microbe in order to survive the increased prevalence of the pollutants. The microbe which was discovered by Steve Zinder at Cornell University at a sewage treatment plant in Ithaca, NY, is the only known microbe that is known to reductively dechlorinate the pervasive groundwater pollutants tetrachloroethelene (PCE) and trichloroethylene (TCE). The end result is a nontoxic byproduct, ethene. Another major collaborator was Lorenz Adrian of the Institute for Biotechnology at the Technical University of Berlin, Germany. The D. ethenogenes project was sponsored by the U.S. Department of Energy's Office of Biological and Environmental Research. Today, environmental consulting companies are using Dehaloccocoides cultures to assure remediation at numerous sites contaminated by PCE or TCE  by one count, there are at least 17 Dehaloccocoides bioremediation sites in ten states, including Texas, Delaware and New Jersey. Dehalococcoides ethenogenes turns out to have 19 different reductive dehalogenases (RDs)  which allow the microbe to "breathe" chlorinated solvents. Those RDs, in combination with the bacterium's five hydrogenase complexes and its severely limited repertoire of other metabolic modes, show that D. ethenogenes is highly specialized for respiratory reductive dechlorination using hydrogen as the electron donor. By comparing the genomic sequence of D. ethenogenes with that of other Dehalococcoides spp. and related organisms that have different capabilities and spectra for dehalogenation, scientists should be able to deepen the understanding of the chemical process and the best ways to use microbes in the bioremediation of sites that are contaminated with halogenated organic compounds. The genome of D. ethenogenes is the first complete sequence from the green nonsulfur group of bacteria. By comparing its genome sequence with that of the more than 50 other species sequenced at TIGR, scientists have learned more about the phylogenetic diversity of microbes.

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)