BER Research Highlights

Search Date: August 16, 2017

15 Records match the search term(s):


December 03, 2003

A Marriage Between the Jelly Fish and the Immune System

A new method, just published in the journal Nature, has been developed that could greatly speed the development of antibodies (Ab), molecules that can detect, locate, and quantify parts of cells for use in basic research and diagnostic medicine. Finding or making the Abs of interest for a specific task has never been easy since it often requires sorting through billions of different Ab to find the one of interest. Once a specific Ab tag is available a second molecule, known as a reporter, is needed to provide a detectable signal that tells scientists when the Ab bound to its target. One of the best reporters has been a molecule isolated from jelly fish, green flourescent protein (GFP), that fluoresces when an Ab finds its target. Now, Andrew Bradbury of the Los Alamos National Laboratory has devised a new molecule that combines parts of Ab molecules with GFP molecules, without disrupting its fluorescence, to give a more efficient tagging and reporting method. This new Ab-GFP molecule was inserted into a harmless bacterial virus and these Ab-GFP viruses produce billions of different fluorescently labeled Ab tags. Once a virus with the desired tag is identified it can be isolated and grown to produce unlimited amounts of the diagnostic tag. This new technology has important implications for diagnostic medicine and for basic research, including BER's Genomics:GTL program with a goal to identify and characterize the multi protein molecular machines found inside cells.

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)


November 12, 2003

Protein Crystallography with Neutrons Featured in Physics Today

Research at the new protein crystallography station at the Los Alamos Neutron Science Center (LANSCE) has demonstrated that neutron crystallography can reveal information about the structure of proteins that is not accessible by x-ray crystallography. A scientific team led by Gerald Bunick of the Oak Ridge National Laboratory (ORNL), and including researchers from the University of Tennessee, the Fox Chase Cancer Center, and the Los Alamos National Laboratory has determined the precise arrangement of hydrogen atoms on key amino acids of the enzyme D-xylose isomerase. This protein is a bimetallic enzyme that catalyzes the conversion of glucose into fructose by hydrogen atom transfer. It is widely used in the manufacture of high-fructose corn syrup for use in foods. Understanding the structure of the enzyme could lead to design of a modified enzyme that is more efficient in the production of fructose from glucose. Information obtained through neutron crystallography will enhance our knowledge of the mechanism of proton transfer in enzymes of this type as well as in other related enzymes involved in several important metabolic pathways. The new study is highlighted in an article about neutron crystallography of proteins in the November 2003 issue of Physics Today. A scientific paper on the research has just been accepted for publication in Acta Crystallographica D.

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)


October 01, 2003

UCLA-DOE Institute Proteomics Research Highlighted in Chemical & Engineering News

Research directed by Dr. Joseph A. Loo in the UCLA-DOE Institute for Genomics and Proteomics is studying protein machines in Methanosarcina species, a group of microbes that generate methane. Most functions of living cells are carried out by macromolecular machines that contain ten or more protein molecules. Characterizing the structure of these complexes is a key to understanding their functions, and mass spectrometry is becoming a preferred technique for identifying how protein machines are organized. Dr. Loo's research on the proteasome of Methanosarcina thermophila is highlighted in the September 29, 2003, issue of Chemical & Engineering News as part of a report on the 16th International Mass Spectrometry Conference just held in Edinburgh, Scotland. The proteasome contains 28 protein molecules and breaks down proteins that are defective or no longer needed by the cell, serving, as Loo puts it, as the cellular "garbage disposal." His mass spectrometric studies have identified binding of inhibitor molecules to the proteasome and have determined how stepwise breakdown of the proteasome results in loss of the inhibitor molecules. Other protein complexes are also being characterized by Loo, including a complex of ribonucleic acid (RNA) and proteins that is known as "vault" and has a mass of 13 million Daltons.

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)


September 03, 2003

Publication of Ocean Microbe Sequences Elicits Over a Dozen Stories

The publications, in the most recent issues of Nature and Proceedings of the National Academy of Sciences, of the sequences of 4 photosynthetic ocean microbes that have major roles in temperate zone ocean capture of atmospheric carbon dioxide (an important greenhouse gas) has stimulated over a dozen stories in the news media just within the first week after the appearance of these stories. (Several quote Office of Science Director Dr. Raymond Orbach). Reuters, MSNBC, and ABC News are only three of the roughly 14 (so far) that have run stories on the sequencing of Prochlorococcus marinus (3 species) and Synechococcus (1 strain) by teams at MIT and Scripps Institution, both working closely with the DOE Joint Genome Institute. This work was funded by the Office of Science's Office of Biological and Environmental Research.

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 27, 2003

Second IEEE International Computational Systems Bioinformatics Conference Dedicates Session to Genomes to Life

The Genomes to Life (GTL) program was the subject of an entire session at the Second International Institute of Electrical and Electronics Engineers, Inc., Computational Systems Bioinformatics Conference, held August 11-14, at Stanford University. The meeting, in general, focused on the role of informatics in addressing today's pressing biological and medical issues. This Office of Science (SC) workshop was the first presented on the west coast as part of its ongoing effort to inform scientists from many disciplines of the critical need for bioinformatics and computing research in the GTL program. Dr. Marvin Frazier, SC Life Sciences Division Director, was one of three key note speakers. GTL scientists from Oak Ridge National Laboratory, Sandia National Laboratory, Lawrence Berkeley National Laboratory, and the University of Massachusetts--Amherst spoke at the meeting. The meeting was partially sponsored by the Office of Advanced Scientific Computing Research.

Contact: Marvin Frazier, SC-72, (301) 903-5468
Topic Areas:

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


August 20, 2003

Meeting on Joint Genome Institute's (JGI) Conversion to a User Facility

A meeting of 30 senior scientists and scientific managers from universities, DOE national laboratories, and other federal agencies was held on July 29, 2003, in Pacifica, California, to review the Joint Genome Institute's plan for converting its Production Genomics Facility (PGF) to a user facility. The JGI staff presented a comprehensive description of the operation of the PGF as a user facility, including a new organizational structure and a process for user project selection and interaction with the JGI staff. During the meeting, senior management of the Advanced Light Source (Lawrence Berkeley National Laboratory (LBNL), a National Institute of Health Genotyping Facility, and LBNL's National Energy Research Scientific Computing Division presented their experience as operators of user facilities. Current scientific collaborators (including representatives from industry, the Department of Agriculture, the Environmental Protection Agency, frog researchers, other major sequencing centers, and microbial scientists), members of the JGI Policy Board, and user facilities operators all reviewed and commented on JGI plans. Suggestions were made to improve some aspects of the process but overall the plan was well received. The PGF is scheduled to complete its transition to a user facility in FY 2004.

Contact: Marvin E. Frazier, SC-72, (301) 903-5468
Topic Areas:

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


August 06, 2003

Natural and Accelerated Bioremediation Research (NABIR) Highlighted in the San Francisco Chronicle

The July 14 edition of the San Francisco Chronicle featured an article in the Science section devoted to bioremediation research funded by the Office of Science NABIR program. "Mining bacteria's appetite for toxic waste : Researchers try to clean nuclear sites with microbes," was authored by well-known science writer, David Perlman. The article noted that scientists are exploiting the "unusual appetites" of some microbes as a way to clean up nuclear sites. Dr. Craig Criddle, an environmental engineer at Stanford University, is working with microorganisms that can convert soluble uranium into an insoluble form. Criddle's work includes research at the NABIR Field Research Center at the Oak Ridge Reservation. In collaboration with ORNL scientists, he is identifying and controlling environmental factors that might inhibit or enhance the process of uranium precipitation. Criddle hopes that "after bacteria consume radioactive waste, the uranium can be separated from water like sand, and gathered like a common mineral." The article also describes NABIR funded research by Dr. Derek Lovley of the University of Massachusetts at Amherst. Lovley is currently performing a field experiment at a Uranium Mill Tailing Remedial Action (UMTRA) site in Rifle, CO. The goal of the experiment is to enhance the growth of naturally-occurring microbes called Geobacter to bioremediate uranium-polluted ground water at the site. The article noted that genomes of several species of Geobacter have been sequenced by The Institute for Genomic Research and the DOE Joint Genome Institute. The genome sequencing was funded by the DOE Microbial Genome and Genomes to Life Programs.

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)


July 23, 2003

New Phase II SBIR Awards Support Genomes to Life Program (GTL)

Three of the 2003 Phase II SBIR winners may produce products that will speed scientific discovery for the GTL program. Most microbes cannot be grown as pure cultures in the laboratory yet many of these microbes have biochemical capabilities that could be used to address DOE energy and environmental needs. Information on any microbe's biochemical capabilities can be obtained from its DNA sequence yet it is difficult to get enough DNA and big enough pieces of DNA from microbes that can't be grown in laboratory cultures. Phase II SBIR awards to Molecular Staging Inc. and to Lucigen Corporation will provide scientists with new tools needed to get large quantities and large pieces of DNA from unculturable microbes for DNA sequence analysis. A third Phase II SBIR award to Genomatica, Inc., will provide scientists with new software that will speed the assembly of information on the functions of individual genes in a genome, obtained from DNA sequencing, into networks of genes that work together to carry out an organism's various biochemical processes. All three of these new research awards support core needs of the GTL program.

Contact: Marvin Stodolsky, SC-72, 301-903-8521
Topic Areas:

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


June 25, 2003

'Mail-in' Crystallography at Brookhaven National Laboratory Highlighted in Nature

Scientists with the protein crystallography (PX) program at Brookhaven National Laboratory (BNL) have solved a major obstacle to wider use of synchrotron light sources by the structural biology community. Synchrotron radiation has become essential for solving structures of proteins and other biological macromolecules and complexes using x-ray diffraction. Yet there are only five of these facilities in the U.S. where such experiments can be done. Thus most scientists must travel a considerable distance to carry out a structural study, often spending more time on travel than on the actual experiment. Over the past four years Robert Sweet and Howard Robinson of BNL's Biology Department and their colleagues have developed a service by which scientists can send frozen crystals to Brookhaven and have the local BNL staff carry out the PX data collection at the National Synchrotron Light Source (NSLS). The service is described in an article in the June 19, 2003, issue of the widely-read journal Nature. The article points out that some 50 research groups are using this service annually, half of them being molecular biologists with little previous crystallography experience. The service enables these scientists to get results in weeks instead of having to wait for months for an opportunity to run experiments at the NSLS themselves. In turn, the available beam time is used much more efficiently, since expert BNL staff are running the experiments instead of novice users. The article notes that the European Synchrotron Radiation Facility is now offering a similar service and that several other synchrotrons in the United States are considering setting one up.

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)


June 04, 2003

Office of Science Research Shines at American Society for Microbiology Annual Meeting

The annual meeting of the American Society for Microbiology was held in Washington, DC, the week of May 19. In a meeting that was, overall, dominated by medical microbiology, Office of Science research comprised about 11% of all posters present (some 200 out of a total of about 1800 posters) and about 10% of all oral presentations (nearly 40 of just under 400 presentations). Office of Science staff co-chaired (Marvin Frazier, SC-72; Sharlene Weatherwax, SC-14; Dan Drell, SC-72) or spoke (Ari Patrinos, SC-70) at scientific sessions as did SC-funded scientists. Office of Science research programs that were represented included the Microbial Genome Program, the Natural and Accelerated Bioremediation Research Program, the Genomes to Life Program, the Environmental Management Science Program, and the Biotechnological Investigations-Oceans Margin Program. Many other presentations at the meeting represented research not directly funded by SC, but enabled by SC's support for the genomic sequencing of a large number of microbial genomes now being used for a diverse array of experiments.

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)


April 23, 2003

DOE Joint Genome Institute and Oregon State University Sequence Key Soil Microorganism in Carbon and Nitrogen Cycles

This microbe, Nitrosomonas europaea (N. europaea), derives all of the energy it needs to grow from the oxidation of ammonia to nitrate. In so doing, N. europaea converts CO2 to cell biomass. This type of carbon sequestration may lead to biologically-based technologies to capture carbon dioxide from the atmosphere. As an editorial in the Journal of Bacteriology, May 2003, points out, the use of ammonia, CO2 and mineral salts to make biomass (more N. europaea cells) essentially means that this microbe makes itself from "almost nothing." Additionally, N. europaea is highly dependent on environmental iron and its genome seems to contain genes that confer upon it the capacity to "steal" iron from surrounding microbes. Consistent with many previously sequenced microbes, about 30 percent of the genetic information in its genome mediates unknown functions in the microbe's biology.

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)


April 23, 2003

Two Office of Science/Biological and Environmental Research (SC/BER) Supported Scientists Win Major Microbiology Awards

At the annual meeting of the American Society for Microbiology (ASM) in Washington, DC, May 18-22, two SC/BER supported microbiologists will receive prestigious ASM awards. Dr. Kenneth Nealson of the University of Southern California will receive the Proctor and Gamble Award in Applied and Environmental Microbiology for his contributions to our knowledge of the microbiology of marine, freshwater, terrestrial, and other environments where microbes are found. One key finding was quorum sensing, the chemical basis for how microbes sense local cell density. He is well known for developing technologies to detect microbial life in unconventional environments, attracting National Aeronautics and Space Administration interest as potentially valuable for life detection on Mars probes. Nealson is a grantee in the DOE Genomes to Life Program. Also being honored is Dr. Gary Olsen of the University of Illinois, who will receive the United States Federation for Culture Collections and J. Roger Porter Award. Olsen has made many fundamental contributions to microbial taxonomy, analyses of microbial diversity, and the use of small RNA sequences to build the presently understood "tree of life" in the microbial world. Olsen is a grantee in the DOE Microbial Genome Program.

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)


April 02, 2003

National Awards in Analytical Chemistry to Biological & Environmental Research Scientists

The American Chemical Society (ACS) Division of Analytical Chemistry has announced the recipients of its 2003 awards. J. Michael Ramsey, head of the Laser Spectroscopy and Microinstrumentation Group at Oak Ridge National Laboratory, will receive the Award in Chemical Instrumentation, sponsored by the Dow Chemical Company Foundation, for his accomplishments in microfabricated instrumentation for chemical measurements, detection of single atoms, and characterization of aerosol particles. Norman Dovichi, Endowed Professor of Analytical Chemistry at the University of Washington, will receive the Award in Spectrochemical Analysis for his contributions to ultrasensitive spectrochemical detection of single molecules, capillary array DNA sequencing and single cell protein fingerprinting. Dr. Ramsey's research is supported in part by the Environmental Management Science Program in the Office of Biological & Environmental Research (BER) and Dr. Dovichi by the BER Genomes to Life Program. The awards include a stipend of $4000 and will be presented at the ACS National Meeting in New York in September.

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)


February 05, 2003

Novel Microchip Enables Optical Observation of Single Molecules in Their Natural State

Research at Cornell University has created a microchip that isolates individual biological macromolecules such as enzymes and enables observation of their behavior as they interact with other molecules, one at a time. The nanostructured chip has holes that constrain laser illumination to just 2500 cubic nanometers of the solution, such that only about one small soluble molecule and one molecule of the enzyme of interest are contained in it. A laser beam interrogates each hole, producing a fluorescence signal only when the enzyme is interacting with a small soluble molecule. The rate of this reaction can be followed in real time for each enzyme molecule, which enables a clearer understanding of the reaction than when only data averaged over many hundreds or thousands of molecules are available. The research, which is funded in part by the Genome Program in the Office of Biological & Environmental Research, is highlighted on the cover of the January 31, 2003, issue of Science. The principal investigators of the project, professors of engineering and applied physics Watt W. Webb and Harold Craighead, note that the technique may enable rapid genome sequencing using just a single molecule of DNA, reading strands of DNA tens of thousands of base pairs long. This would overcome a significant limitation of the best current techniques which only can sequence up to about 1000 base pairs at a time.

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)


January 08, 2003

Robots Enhance Protein Crystallography Throughput at Stanford Synchrotron Radiation Laboratory (SSRL)

An experimental run in October 2002 with manual handling of the crystals required 24 hours to screen 100 crystals of a protein complex, with several crystals being damaged or lost. A run by the same group two weeks later, but this time using the new SSRL robotic system, saw 130 crystals screened in less than eight hours, with no crystal being damaged or lost. Clearly the coming widespread implementation of robotics at crystallography beamlines will enable a substantial increase in the number of users that can be accommodated. The process of obtaining the x-ray crystallographic data needed for solving the three dimensional structure of a protein or other biological macromolecule involves screening of numerous crystals of a molecule to find the ones that give the best resolution. Until recently this required manual handling of each of 100 or more crystals, with the researchers having in the process to carry out a multi-step protocol to shut off the x-ray beam into the experimental hutch, gain access to the diffractometer station in the hutch, change the crystal, leave the hutch, and open the beam shutter. All of the Department of Energy synchrotron light sources are implementing automated systems for carrying out these steps. The recent experience of a prominent structural biology research group at SSRL illustrates the benefits these systems will bring.

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)