BER Research Highlights

Search Date: April 27, 2017

34 Records match the search term(s):


December 15, 2008

Cover Article in Chemical & Engineering News (C&EN) Features DOE BioEnergy Research Center (BESC) at Oak Ridge National Laboratory (ORNL)

The December 8, 2008 edition of C&EN provides extensive coverage of DOE's bioenergy research.  The cover story, "Genes to Gasoline," focuses on ORNL research to covert biomass to fuels by efficient and economical processes.  The article explains challenges to the biological production of biofuels, especially the recalcitrance of lignocellulosic material to degradation.  Martin Keller, BESC Director, and Brian Davison and Charles Wyman, BESC scientists, are quoted.  Other DOE-funded scientists conducting biofuels research are also mentioned.  The shortcomings of current biomass pretreatment and conversion options are described as a backdrop for BESC's research programs to develop a one-pot process (combining biomass deconstruction and fuel synthesis in one reactor vessel), a capability to conduct high throughput screening of potential biomass samples, and the opportunity to discover microbes with new enzymes in locations such as hot pools in Yellowstone.  The role of DOE's Joint Genome Institute in facilitating this research is described.  The cover shows a fluorescence micrograph of a switchgrass cross section. 

The cover story "Genes to Gasoline," by Steve Ritter, for the December 8 issue is at: [website]

The cover shows a micrograph of switchgrass credited to DOE/NREL/BESC.

Topic Areas:

Division: SC-23 BER
      (formerly SC-23 OBER)


November 24, 2008

Two New Data Analysis Tools Developed for Proteomics Researchers

Proteomics researchers from the Pacific Northwest National Laboratory (PNNL), the University of Texas, and the University of Wisconsin-Madison have collaborated to develop and deploy new data analysis tools to further the field of proteomics research. Better tools for protein identification are vital to solving intractable problems such as converting agricultural waste into fuels, detecting bio-based threats and quickly detecting and treating disease. These tools are available free of charge through a publicly available website (link expired). Making new proteomics tools available at no cost to the scientific community allows more researchers to enter the proteomics field without investing in expensive tools or needing to develop their own. DAnTE (Data Analysis Tool Extension) was developed as a statistical and visualization software tool that scientists can use to perform data analysis steps on large-scale proteomics data, but it also performs well on genomics microarray data. The second tool, a "bottom-up" data analysis strategy that can detect thousands of peptides over time, has been demonstrated on data from a time-course study of Rhodobacter sphaeroides, an environmentally important photosynthetic microorganism under study in DOE's Genomics:GTL program. These tools were funded by several of the National Institutes of Health as well as DOE's Office of Science. Portions of the research for both tools were performed in the Environmental Molecular Sciences Laboratory, a DOE scientific user facility located at PNNL. Additional details are available at:  [website].

References: Du X, SJ Callister, NP Manes, JN Adkins, RA Alexandridis, X Zeng, JH Roh, WE Smith, TJ Donohue, S Kaplan, RD Smith, and MS Lipton. 2008. "A Computational Strategy to Analyze Label-Free Temporal Bottom-Up Proteomics Data." Journal of Proteome Research 7(7):2595-604.

Polpitiya AD, WJ Qian, N Jaitly, VA Petyuk, JN Adkins, DG Camp II, GA Anderson, and RD Smith. 2008. "DAnTE: A Statistical Tool for Quantitative Analysis of -omics Data." Bioinformatics 24(13):1556-8.

Contact: Paul Bayer, SC-23.1, (301) 903-5324
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER


November 17, 2008

Capturing Carbon in the Oceans: Second Diatom Genome Sequenced at DOE-Joint Genome Institute (JGI)

In the November 13, 2008, issue of Nature, a 77-person team of researchers from 31 scientific institutions including the JGI, reports the complete sequence of a second diatom, Phaeodactylum tricornutum, and an initial comparison with the first sequenced diatom, Thalassiosira pseudonana, also sequenced at the DOE-JGI. Responsible for up to 40% of CO2 capture in the oceans, diatoms play major roles in global carbon sequestration and processing. Preliminary analysis of the P. tricornutum genome suggests a significant degree of acquisition of large sets of genes (perhaps more than 5%) from prokaryotic organisms with subsequent adaptation to the needs of the diatom for carbon and nitrogen processing.

Contact: Daniel Drell, SC-23.2, (301) 903-4742
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


November 03, 2008

Science News Focus Article Features DOE Bioenergy Research Scientists

The October 24, 2008, issue of Science contains a feature article that discusses the bio­logi­cal production of next-generation liquid transportation fuels.  Jay Keasling, Director of the DOE Joint Bioenergy Research Center, explains how his experience using syn­thetic biology to produce large amounts of artemisinin (an antimalarial drug that is expensive to obtain from plant sources) makes him optimistic about the potential for synthetic biology to create biological replacements for gasoline and jet fuel at competi­tive prices.  James Liao of the University of California, Los Angeles-DOE Institute of Genomics and Proteomics describes his pathway engineering approaches to produce isobutanol, which is a better transportation fuel than ethanol because of its higher energy density.  Several experts from startup companies are also interviewed about the future of synthetic biology to provide transformational changes to biofuel production. 

Contact: John Houghton, SC23.2, (301) 903-8288
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


November 03, 2008

Computer Simulations Reveal How Anti-Freeze Proteins Work

Research lead by Jeremy Smith of Oak Ridge National Laboratory (ORNL) has yielded new insight into the mechanism of how anti-freeze proteins, found in a wide range of organisms, prevent ice formation.  Utilizing the high performance computational resources at ORNL, the molecular dynamics simulations reveal that at lower temperatures the anti-freeze protein serves a dual purpose: preconfiguring the water to ease ice binding to one face of the protein while disordering the water on the other faces to prevent ice propagation.  ORNL researchers term the preconfiguration effect "pre-ordering-binding" and suggest that the mechanism may be generally applicable to processes occurring at disordered or amorphous surfaces.  A similar simulation approach is planned to examine water structure in lignocellulosic biomass, as similar hydration effects may form a barrier to cellulosic ethanol production.  This work is sponsored in part by DOE's Office of Science.  Details can be found in the October issue of the J.  Am.  Chem.  Soc., 130 (39), 13066-13073, 2008.  The article was featured as a Research Highlight in the September 2008 edition of Nature Chemistry.

Contact: Susan Gregurick, SC-23.2, (301) 903-7672
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Division: SC-23.2 Biological Systems Science Division, BER


November 03, 2008

Nanostructure-Initiator Mass Spectrometry Highlighted in Science and Nature

Nanoscience and mass spectrometry have been combined to produce a new, high throughput method to determine the functions of biologically active molecules, e.g., identification of particular metabolites as evidence that a particular cellular energy pathway is active. Developed by Genomics:GTL scientists Gary Siuzdak and Trent Northern of the Scripps Institute and the Lawrence Berkeley National Laboratory, this new research tool is highlighted in a Perspective article in the September 19 issue of Science. The underlying technology called nanostructure-initiator mass spectrometry (NMIS) is also spotlighted in a Technology Feature article in the October 2 issue of Nature. The technique, called Nimzyme analysis, involves the tagging of the biological molecule(s) to be tested with a fluorous tag that gets embedded in the perfluorosiloxane "initiatior" compound that fill nanosized holes on a specially-prepared surface. This methods allows an array of many embedded molecules of interest to be exposed to a solution containing a specific enzyme or mixtures of other biological molecules of interest followed by a laser pulse or beam of ionizing energy. The irradiation vaporizes the material in the nanoholes, releasing the biological molecules for rapid analysis by mass spectrometer to determine any molecular changes in the florous tagged molecules. The approach has the potential for what the Science Perspective article characterized as "high throughput bioprospecting applications."

References:

Perspective: D. Curran, Science, 321, 1645 (based on article, T. R. Northen et al., Proc. Nat. Acad. Sci. U.S.A. 105, 3678 (2008)).

Technology Feature: N. Blow, Nature 455, 697-700

Contact: Arthur Katz, SC-23.2, (301) 903-4932
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Division: SC-23.2 Biological Systems Science Division, BER


October 27, 2008

Cheaper DNA Sequencing of Very Large Genomes

Complete Genomics, Inc., has announced a new technology for sequencing extremely large genomes at low cost. The system is an evolution from DOE-funded sequencing research carried out at Argonne National Laboratory (ANL) in the 1990s by Rade Drmanac. He continued technology developments with a focus on cost reduction through miniaturization and multiplexing sequence readouts on target DNAs with support from the DOE SBIR program and other sources. Over the years, the scale of data readouts (and the corresponding need for expensive reagents) has gone from square meter membranes to the current implementation involving minute volumes of reagents on microscope slides. On these slides a target genome is redundantly represented as dense arrays of DNA mini-spheres. The new methodology could provide substantial cost reductions for DOE mission needs for sequencing plant genomes, that often are much larger than mammalian genomes. Drmanac's accomplish­ments are described in an article in the October 2008 issue of Nature Biotechnology, and the new instrumentation has been highlighted in an article in the October 6 issue of the New York Times.

Contact: Marvin Stodolsky, SC-23.2, (301) 903-4475
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


October 27, 2008

Enhanced Ethanol Tolerance Achieved in a Lignocellulose Degrading Microbe

Improving microbial tolerance for high concentrations of the biofuels they produce is highly desirable. Increased tolerance means that more fuel can be produced in smaller microbial culture volumes, with considerable savings as well in the distillation of the fuel from the culture medium. The microbe Clostridium phytofermentans degrades lignocellulose and produces alcohol and is being commercialized by DOE SBIR Phase II grantee Sunethanol. George Church, funded by DOE's Genomics: GTL program at Harvard Medical School, is providing scientific expertise in synthetic biology and metabolic engineering to the company.  The two groups are applying their complementary capabilities to biofuels research [sunethanol.com/site/news/2008-06-12/].  A beneficial initial outcome of this collaboration is a doubling of ethanol tolerance of the microbe to 8% by volume. 

Contact: Marvin Stodolsky, SC-23.2, (301) 903-4475
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


October 13, 2008

"Bold Traveler" Microbe Makes its Own Ecosystem Nearly 2 Miles Underground

From 2.8 kilometers deep in the Mponeng Mine in South Africa a novel microbe has been found that reduces sulfates and fixes carbon and nitrogen apparently in the absence of any other form of life, comprising by itself, the first known single-species ecosystem. In the October 10 issue of Science, researchers Terry Hazen and Adam Arkin at the Lawrence Berkeley National Lab, with colleagues from other DOE labs and several academic institutions, describe the discovery, DNA sequence, and initial characterization of microbe. Named, Desulforudis audaxviator, or "Bold Traveler" in a reference to Jules Verne's Journey to the Center of the Earth, this microbe exploits hydrogen and sulfate produced by the radioactive decay of uranium. Its genome sequence, determined at the DOE-Joint Genome Institute, revealed greater genetic diversity than expected given the homogeneity and stability of its environment. Significantly, its genome contains genes equipping it to get carbon (and energy) from carbon monoxide, carbon dioxide, bicarbonate, formate, and other nonbiological sources that may provide useful biological capacities for future bioenergy developments.

Contact: Daniel Drell. SC-23.2, (301) 903-4742
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


October 13, 2008

A Public Resource for Functional Analysis of Metagenomes

The advent of high capacity sequencing of microbial genomes creates new possibilities for the sequencing of whole microbial communities. This emerging field of metagenomics, the sequencing and analysis of environmental samples, provides new insights into, for example, the genomes of organisms involved in the fate and transport of containment materials, carbon sequestration, or biomass conversion. However metagenomics also creates new challenges in the analysis of massive datasets. Researchers at Argonne National Laboratory have responded to this challenge by developing a freely available, open-source analysis platform, MG-RAST ([website]) which provides a new paradigm for the functional annotation of metagenomic data. By combining high performance computing with analysis software and new methods for the control of these datasets, researchers are able to break the analysis bottleneck and achieve high throughput annotation of metagenomic samples. This work is sponsored in part by DOE's Office of Science. Details can be found in BMC Bioinformatics 2008, 9:386.

Contact: Susan Gregurick, SC-23.2, (301) 903-7672
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


October 06, 2008

Science Magazine Policy Forum Discusses Biofuels Sustainability

The October 3, 2008, issue of Science contains a Forum contribution led by Phil Robertson of Michigan State University.  Robertson is the lead sustainability investigator for the DOE Great Lakes Bioenergy Research Center and a scientific advisor to the upcoming October 28 DOE/USDA Sustainability workshop.  In the article, Robertson and coauthors describe potentially harmful environmental impacts resulting from fuel uses of grain-based ethanol and suggest ways to reduce them. Production of ethanol and other biofuels from cellulosic biomass appears to have substantial sustainability advantages compared to grain-based ethanol, but the authors caution that an expanded research agenda and careful policy consideration will be required to realize the potential benefits. The authors conclude that "sustainable biofuel production systems could play a highly positive role in mitigating climate change, enhancing environmental quality, and strengthening the global economy, but it will take sound, science-based policy and additional research effort to make this so."

Contact: John Houghton, SC-23.2, (301) 903-8288
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


September 29, 2008

Nature Interviews DOE Joint Genome Institute Scientist on Metagenomics

On the tenth anniversary of the coining of the term metagenomics, two leading scientists affiliated with the DOE-Joint Genome Institute (JGI), Phil Hugenholtz (UC Berkeley and the DOE-JGI) and Gene Tyson (MIT), were interviewed in the Q & A section of the September 25 issue of Nature. Metagenomics is the science of sequencing and analyzing the composite genome of a microbial community, the way microbes are commonly found and work in nature. Hugenholtz and Tyson pioneered microbial community sequencing, first studying a biofilm from an acid mine drainage site in Northern California and recently the microbial community in the hind gut of the wood-digesting termite. By employing the techniques of metagenomics we can go beyond the identification of specific players to creating an inventory of the genes in that environment, said Hugenholtz. The promise of metagenomics is that microbial communities carrying out DOE mission relevant processes (bioenergy production, waste cleanup, carbon processing) can now be studied at their genomic level. This knowledge can lead to inventories of genes and proteins and their metabolic potentials that are present in these communities, as well as studies of how these change over time, how they are impacted by human activities, and how we can use them to further DOE mission needs.

Contact: Dan Drell, SC-23.2, (301) 903-4742
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


September 22, 2008

DOE Scientist Featured at National Advisory Research Resources Council Meeting

Dr. Richard D. Smith of Pacific Northwest National Laboratory presented the science lecture at the September 16 meeting of the advisory council for the National Center for Research Resources (NCRR) of the National Institutes of Health (NIH). His topic was “New Proteomics Technologies: From Systems Biology Research to Broad Clinical Application.” Smith directs the NCRR-funded Proteomics Research Resource for Integrative Biology at PNNL. He explained how this program builds on technologies developed for DOE missions. The importance of DOE’s Environmental Molecular Sciences Laboratory for his program was noted. The NCRR is a cross-disciplinary unit of NIH with an annual budget of $1.1 billion. It is responsible for providing resources used by large numbers of biomedical scientists. Several of the resources are located at DOE National Laboratories. Smith’s talk and the other presentations at the meeting can be found at: http://www.ncrr.nih.gov/about_us/advisory_council/presentations_sept08.asp

Contact: Roland F. Hirsch, SC-23.2, (301) 903-9009
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Division: SC-23.2 Biological Systems Science Division, BER


August 11, 2008

Feature Article in Nature on "Genomics of Cellulosic Biofuels" by Director of DOE Joint Genome Institute

The August 14 issue of Nature has an invited review, "Genomics of Cellulosic Biofuels," by Eddy Rubin, Director of the DOE Joint Genome Institute. The article describes the enormous promise for development of new routes to cellulosic biofuels from genomic sequencing of plants (sources of biomass precursors of liquid fuels) and microbes (sources of enzymes and pathways to convert biomass to liquid fuels). Rubin lays out a path for how emerging genomic technologies will contribute to a substantially different biofuels future compared to todays corn-based ethanol industry, mitigating, in part, the food-versus-fuel debate. Rubin concludes that Genomic information gathered from across the biosphere, including potential energy crops and microorganisms able to break down biomass, will be vital for improving the prospects of significant cellulose biofuel production. This describes a key foundation of SCs Bioenergy Research Centers and the Genomics:GTL program.

Contact: Dan Drell, SC-23.2, (301) 903-4742
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


July 21, 2008

Biofuels Researcher Receives Fulbright Senior Research Award

Dr. Kenneth E. Hammel, research chemist at the US Forest Service, Forest Products Laboratory, has been named recipient of a Fulbright Senior Research Award by the German-American Fulbright Program. Dr. Hammel, a SC-supported researcher, studies mechanisms of lignin degradation by fungi, a key step in the conversion of lignocellulose into a chemical form that can be more easily converted into biofuels. He is using new solution-state Nuclear Magnetic Resonance (NMR) spectroscopy as well as isotope enrichment strategies to characterize the fundamental biochemical mechanisms used by a variety of fungi to degrade lignin. Dr. Hammel will spend 10 months abroad studying newly discovered fungal enzymes that have an important role in carbon cycling in forest soils. These enzymes also have potential applications in the development of biotechnology solutions for selective oxidations of chemicals.

Contact: Arthur Katz, SC-23.2, (301) 903-4932
Topic Areas:

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


July 21, 2008

LBNL Researchers Win R&D 100 Award for Phylochip Development

Tools for rapid characterization of complex microbial communities are needed to detect and identify microorganisms in a variety of environmental samples. SC researchers at LBNL have developed a microarray technique known as the Phylochip that can detect and identify thousands of different species of microorganisms very rapidly. The Phylochip provides the capability for unprecedented detection and identification in a device about the size of a quarter. The Phylochip was developed by Gary Andersen, Todd DeSantis, Eoin Brodie and Yvette Piceno from LBNLs Earth Sciences Division. The device has been used to identify airborne bacterial species as part of a biodefense project, to assess microbial communities involved in environmental cleanup projects, and will help to advance the understanding of microbial processes involved in biofuel production and carbon sequestration. The prestigious R&D 100 awards are given in recognition of the top 100 significant technological advances over the past year.

Contact: Robert T. Anderson, SC 23.1, (301) 903-5549; Dan Drell, SC 23.2, (301) 903- 4742
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Division: SC-23.2 Biological Systems Science Division, BER
      (formerly SC-23.2 Medical Sciences Division, OBER)


July 14, 2008

DOE Investigators Review Article Featured on Cover of Chemical Physics Letters

DOE investigator Dr. Haw Yangs (LBNL and UC-Berkeley) review article, Progress in Single-Molecule Tracking Spectroscopy was highlighted on the cover of the May 27, 2008 issue of Chemical Physics Letters. Yang is a leader in the field of 3D tracking spectroscopy for single molecules. Normally, measurements are made in biological systems on the average properties of many molecules of a specific type, not on single molecules. However, the average properties of a specific molecular species does not capture the range of reactivity of the individual molecules that may be critical to illuminating mechanisms that control important cellular processes. Dr. Yang is pioneering the development of experimental approaches that will track single molecule movement in cells, correlating the location of a molecule with its biological and chemical actions, and producing insights about how specific systems function in cells. He is currently developing spectrometric techniques to track individual fluorescent molecules as they move in three dimensions. This technology will be used to reveal the detailed behavior of the Cellulosome, the molecular complex that plays a fundamental role in the degradation of cellulose, as it interacts with cellulosic plant material.

Contact: Arthur Katz, SC-23.2, (301) 903-4932
Topic Areas:

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


June 30, 2008

Bioenergy Center Director Authors Most Cited Articles in ACS Chemical Biology

Dr. Jay Keasling, Director of DOEs Joint BioEnergy Institute (JBEI) and member of LBNL and UC Berkeley, had the first and fifth most cited articles published in ACS Chemical Biology in the first quarter of 2008. Keaslings review article, Synthetic Biology for Synthetic Chemistry in January 2008 was the most cited and an article by Keasling and other members of JBEI, Addressing the Need for Alternative Transportation Fuels: The Joint BioEnergy Institute, was the fifth most cited. The review article explains the potential for synthetic biology (the design and construction of new biological components and assembly into integrated systems) to aid biofuel and drug production as well as biological remediation of contaminants. The article on JBEI describes the goals of the DOE Bioenergy Research Center and explains the research thrusts on feedstocks, deconstruction, synthesis of next generation fuels, and technology development.

Contact: John Houghton, SC-23.2, (301) 903-8288
Topic Areas:

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


June 30, 2008

Great Lakes Bioenergy Center Scientists Featured in Congressional Briefing

On June 11, the Ecological Society of America hosted House and Senate briefings on The Sustainability of Cellulosic Biofuels. Speakers included Dr. Phil Robertson, Michigan State University (MSU) and Sustainability Thrust Lead for the Great Lakes Bioenergy Research Center (GLBRC), Dr. Doug Landis, MSU and the GLBRC, and Dr. Madhu Khanna, University of Illinois, who conducts research with the BP Energy Biosciences Institute. They described the superiority, measured by energy return, of cellulosic biofuels as compared with grain-based sources, such as corn.

Dr. Robertson, the chief scientist for an OBER/USDA Sustainability Workshop planned for October 2008, described other advantages of cellulosic crops, including its ability to grow on land not suitable for food crops, its potential to mitigate carbon dioxide emissions, and its benefits for clean water and air. Dr. Landis spoke about the environmental value of maintaining high levels of biodiversity through the use of cellulosic crops, and Dr. Khannabiofuel spoke about the need to align energy policy and climate policy to properly guide cellulosic production. A summary handout including links to the presentations is available at http://www.esa.org/pao/policyActivities/briefing062008.php.

Contact: John Houghton, SC-23.2, (301) 903-8288
Topic Areas:

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


June 16, 2008

Journal of Structural Biology Cover Article on X-ray Imaging of Cells at Advanced Light Source (ALS)

X-ray tomography has determined the structure of organelles in yeast cells during different stages of the cell cycle, providing for the first time three-dimensional images that show how the cells change during the cycle. The research is reported in the June issue of the Journal of Structural Biology, with selected images shown on the cover. The authors show that use of the soft X-rays at the ALS enables imaging of cellular components without having to expose the cells to potentially damaging staining reagents. They were able to determine how the yeast responds to changes in its environment. They note that the new X-ray microscope being commissioned at the ALS for biological studies will enable further improvements in spatial resolution that should reveal fine structure of microtubules and other components of the cell. This new imaging technique is ideally suited to imaging bioenergy-relevant organisms. The research was led by Dr. Carolyn A. Larabell of the Lawrence Berkeley National Laboratory and the University of California-San Francisco.

Contact: Roland F. Hirsch, SC-23.2, (301) 903-9009
Topic Areas:

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


June 16, 2008

SC Investigator’s New Approach to Capturing Multiprotein Complexes Highlighted in Journal of Proteome Research

A LBNL project led by Dr. Mark Biggin has developed an enhanced approach to rapidly separate intact multiprotein complexes from cells. These multiprotein complexes, often called molecular machines, play critical roles in every aspect of the biochemistry of the cell but are often difficult to isolate and study intact. Traditionally, these complexes are captured using biological tags that are genetically and laboriously inserted into different proteins in the complex one at a time. The new approach eliminates the need for these tags. The “tagless” approach involves removing the cell’s soluble content followed by several gentle chromatographic steps that leave the complexes intact. The complexes are separated from one another based on properties such as electric charge and molecular weight. At the end of the process there is a high probability that only one complex is clustered in one or a small number of related fractions. Mass spectrometry is used to confirm the identity of the proteins. The separation approach is being automated, providing researchers with a new tool to rapidly determine how these complexes and their associated biological processes change in a microbe or a plant exposed to different environmental conditions or genetic modifications. This work was highlighted in the Journal of Proteome Research.

Contact: Arthur Katz, SC-23.2, (301) 903-4932
Topic Areas:

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


June 09, 2008

Genomics:GTL Researchers Use Metagenomics to Tap Environmental Diversity of Viruses

In a study published in the May 23rd issue of Science, researchers led by Jill Banfield at the University of California, Berkeley, used an innovative metagenomics approach to sample the diversity of viruses present in a natural microbial community inhabiting acidic mine drainage (AMD). Viruses are highly abundant in nature and have large impacts on structure and function of microbial communities, both via predation and by mediating the exchange of genetic material among species. However, relatively few genome sequences from viruses that infect bacteria and archaea are currently available. The Banfield team took advantage of a set of short virus-derived sequences, found in many bacteria and archaea, that serves as an immune system thought to confer an ability to resist viral infection. With support from DOEs Joint Genome Institute and Genomics:GTL program, the researchers focused on these elements in AMD biofilm DNA sequences, which allowed both the identification of, and then partial reconstruction of, sequences of viral origin. This then led to the matching of specific viruses to their AMD hosts and suggested new insights into the evolutionary arms race occurring between host defense systems and viruses in these AMD populations. This is an important and novel tool for the study of community-level interactions between viruses and their bacterial (or archaeal) hosts, which will be critical to understanding how microbial communities involved in DOE mission-relevant processes change over time and how such shifts might affect community composition and function.

Contact: Dan Drell, SC-23.2, (301) 903-4742
Topic Areas:

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


May 26, 2008

Office of Science Research Yields Understanding of Key Function of Uranium-Reducing Microbe

Biophysical research has provided an important clue about how bacteria move within radionuclide-contaminated sites, where they can reduce and immobilize these contaminants. Scientists at Argonne National Laboratory determined the three-dimensional structure of sensory domains of two proteins involved in movement of the bacterium Geobacter sulfurreducens. These domains are involved in chemotaxis, the means by which bacteria sense where to move to find nutrients or to avoid harmful chemicals. Binding of a stimulant molecule to a sensory domain on the outside of the cell transmits a signal to the interior of the cell, initiating the expression of proteins that enable the cell to move in response to the external stimulation. The Geobacter family is of particular interest because it is a major component of the microbial community in many subsurface environments contaminated by uranium. The Office of Science is supporting research into how Geobacter affects fate and transport of uranium in order to understand how this contamination could be remediated. The information obtained about the structure of the signaling domains will help to understand not only how microbes sense and move toward locations with higher uranium concentrations, but more generally respond to a variety of chemical changes in their environment. The Argonne research was led by Dr. Marianne Schiffer of the Biosciences Division and made use of the Structural Biology Center's protein crystallography stations at the Advanced Photon Source. It was published in the April 11, 2008, issue of the Journal of Molecular Biology.

Contact: Roland F. Hirsch, SC-23.2, (301) 903-9009
Topic Areas:

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


May 26, 2008

Office of Science Researchers Write Editorial for Special Issue of Science on Microbial Ecology

James Tiedje and Timothy Donohue are authors of the editorial,"Microbes in the Energy Grid." They point to the "incredible metabolic diversity of today's microbial world" as a great resource for developing new routes to energy production from renewable sources and for mitigating climate change by increasing sequestration of carbon from the atmosphere. Microbes have already been identified that can carry out a wide range of chemical transformations that could be harnessed for meeting energy and climate challenges. Yet, as the authors emphasize, the vast majority of species of microbes on Earth are still unknown. Thus research in microbial ecology will undoubtedly identify many new capabilities that will help address societal needs in energy and the environment. They urge the scientific community to "inform the public and policy-makers about the research needed to bring the chemical and catalytic power of microbes to bear on meeting our ever-growing energy needs." Jim Tiedje is professor of microbiology and crop and soil sciences and Director of the Center for Microbial Ecology at Michigan State University and Tim Donohue is professor of bacteriology at the University of Wisconsin, Madison, and Director of the Office of Science's Great Lakes Bioenergy Research Center. The editorial appears in the May 23, 2008, issue of Science.

Contact: John Houghton, SC-23.2 (301) 903-8288
Topic Areas:

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


May 05, 2008

Bacteria Can Eat as Well as Produce Antibiotics

Unexpected new microbial defensive capabilities are emerging from genomic analyses of microbial diversity from the Genomics:GTL program and genome sequencing projects at the DOE Joint Genome Institute. Professor George Church and colleagues at the Harvard Medical School Systems Biology Center report on yet another remarkable example of microbial adaptability in the April 4 issue of the journal Science. It has long been recognized that bacteria living in soils fight to maintain their territory by producing antibiotics against their competitors; such antibiotics (such as streptomycin) have been widely used in medicine to fight infection. In the course of surveying soil microbes for useful capabilities in environmental remediation or bioenergy production, the researchers discovered a further adaptation "some microbes can eat their enemies" ammunition. This means that the original defensive purpose of these microbial antibiotics can be used as a dietary source when other nutrients are lacking. This new result may have implications for the general evolution of antibiotic resistance of microbes in a variety of health and environmental settings.

Contact: Marvin Stodolsky, SC-23.2, (301) 903-4475
Topic Areas:

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


May 05, 2008

BER Scientists Receives Fulbright Senior Research Award

Dr. Kenneth E. Hammel, research chemist at the U.S. Forest Service, Forest Products Laboratory, Madison, Wisconsin, and an associate professor in the Department of Bacteriology, University of Wisconsin-Madison, has been named recipient of a Fulbright Senior Research Award by the German-American Fulbright Program. Dr. Hammel is supported by BER for imaging studies of the mechanisms used by lignin-degrading fungi, a process directly relevant to the processing of feedstocks into a chemical form that can be more easily converted into biofuels. His award allows him to do research that focuses on newly discovered fungal enzymes that have an important role in carbon cycling in forest soils but he will continue to supervise studies for BER. He will be working with Professor Martin Hofrichter at the International Graduate School in Zittau, Germany.

Contact: Arthur Katz, SC-23.2, (301) 903-4932
Topic Areas:

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


March 17, 2008

DOE-JGI Researchers Sequence Genome of Soil Fungus Laccaria bicolor, Symbiotic Colonizer of Plant Roots

In the March 6, 2008, issue of Nature, the DOE-JGI, with French and Swedish collaborators, report the genome sequence of the fungus, Laccaria bicolor, that is intimately involved in rhizosphere colonization and symbiosis for many plants. The availability of this genome provides an unparalleled opportunity to develop a deeper understanding of the processes by which symbionts interact with plants in the carbon and nitrogen cycles, providing new insights to enhance plant productivity. This 65-megabase genome is the largest fungal genome published to date, and contains ~20,000 predicted protein-encoding genes (fewer than in the human genome). The most highly expressed of these accumulates in the proliferating hyphae colonizing the host root and may have a decisive role in the establishment of the symbiosis. Another unexpected observation is that the genome of L. bicolor lacks carbohydrate-active enzymes involved in degradation of plant cell walls, but maintains the ability to degrade non-plant cell wall polysaccharides, a capacity of potential use to bioenergy researchers. This may also enable the fungus to grow within both soil and in living plant roots. The predicted gene inventory of the L. bicolor genome points to previously unknown mechanisms of symbiosis operating in this class of fungi.

Contact: Dan Drell, SC-23.2, (301) 903-4742
Topic Areas:

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


March 10, 2008

Washington Post Story on DOE-JGI-Sequenced Microbe That Degrades Multiple Forms of Biomass

Today's Washington Post, on page B4, carries a story on University of Maryland professors Ronald Weiner and Steven Hutchinson who have been studying a Chesapeake Bay microbe called Saccharophagus degradans 2-40, that contains more carbohydrate-degrading enzymes than any other microbe analyzed so far. The carbohydrates it is known to degrade include agar, chitin, alginic acid, carrageenan, cellulose, B-glucan, laminarin, pectin, pullulan, starch, and xylan. All of these can be found in plant material and point to a potential role for this microbe in degradation of plant biomass as a first step to Bioenergy production (including ethanol) from the sugars in biomass. S. degradans 2-40 also has been seen to digest newspaper and magazine pages, materials presently recycled and often discarded in landfills. (If it can handle used office Xerox paper, energy independence will be ours in no time!) The DOE-Joint Genome Institute determined the complete genome sequence (the parts list) of S. degradans 2-40 in 2006 and a manuscript describing the work is in press. The Washington Post story also noted that Zymetis, a spin-off company from the University of Maryland, will try to exploit S. degradans 2-40 for bioethanol generation highlighting the interest in the private sector in microbial Bioenergy production leveraging DOE investments in genome sequencing.

Contact: Dan Drell, SC-23.2, (301) 903-4742
Topic Areas:

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


March 03, 2008

Nature News Feature on Biofuels Focuses on DOE Research

A four-page article in the February 21, 2008, issue of Nature discusses how biotechnology is seeking innovations that will provide new, appropriate sources of biofuels. Most of the scientists featured in the article are funded by the Office of Biological & Environmental Research's Genomics:GTL program. The article quotes Jay Keasling of the Lawrence Berkeley National Laboratory and Director of BER's Joint BioEnergy Institute about efforts to find biofuel alternatives to ethanol. The article describes research into microbial routes to higher alcohols such as isobutanol by James Liao of the UCLA-DOE Institute of Genomics and Proteomics at the University of California at Los Angeles. The challenges of converting cellulose into sugars that are readily converted to fuel are discussed by Lee Lynd of Dartmouth College and Mascoma Corporation, which is part of BER's BioEnergy Science Center (BESC). Issues of scale-up of new processes for production of fuels are addressed in the article by Craig Venter, founder of Synthetic Genomics and the J. Craig Venter Institute, and Michael Himmel of the National Renewable Energy Laboratory and BESC. There also is an editorial in this issue of Nature about the mandate in the Clean Energy Act of 2007 to switch to cellulose-based biofuels and the research needed to achieve it.

Contact: Roland F. Hirsch, SC-23.2, (301) 903-9009
Topic Areas:

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


February 25, 2008

Open Source DNA Sequencing Software and Instrumentation

Commercial instruments are generally protected by both patents and copyrights for any supporting software. A significant departure from this long term trend is the Polonator, a highly parallelized DNA sequencer supporting whole genome sequencing strategies. Similar to the Open Source computer software philosophy, neither the reagents nor the supporting software are secret. Rather the vision is to enable diverse scientists to both optimize the base system to their individual objectives and to contribute improvements to the system as a whole, see (link expired). The Polonator is but one of numerous inventions and resources flowing from the laboratory of George Church at the Harvard Medical School and his collaborators. They have been exceptionally prolific in spinning off companies which provide equipment and services to the research and commercial communities. This began under the former Human Genome Program and continues with support from the current GTL program. A listing of the commercial spinoffs is available here: [website]

Contact: Marvin Stodolsky, SC-23.2, (301) 903-4475
Topic Areas:

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


February 04, 2008

New Technique for Analysis of Metabolic Flux in Microbial Communities

A new approach has been developed by scientists at the Lawrence Berkeley National Laboratory to overcome the significant challenge of studying a microbe in its natural environment. The ability to develop biotechnology-based strategies for environmental remediation or bioenergy applications with microbes depends on understanding microbial metabolism under rapidly changing conditions. Moreover, the metabolism of a single microbe is difficult to selectively monitor in the presence of many other microbial community species The Lawrence Berkeley scientists engineered a reporter gene encoding the green fluorescent protein (GFP) into a microbe, then fed the microbe glucose labeled with the stable radioisotope carbon-13. Subsequent analysis of the metabolism of carbon-13 label from glucose into amino acid building blocks within the GFP reflected the metabolism of all the proteins in that microbe. This proof of concept of the technique lays the foundation for analysis of a range of metabolic activities within a specific microbe, rather than the entire microbial community in which it is found. The research was directed by Jay Keasling, with funding from the Genomics:GTL program in the Office of Biological & Environmental Research, and was published in the February 1, 2008, issue of the journal Analytical Chemistry.

Contact: Sharlene Weatherwax, SC-23.2, (301) 903-3213
Topic Areas:

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


January 28, 2008

Office of Science Researcher's Model is Featured on the Front Cover of the Journal Cell

A significant step in the development of the field of systems biology, marking the first time researchers have systematically perturbed and accurately predicted a cell's dynamics at the genome scale (for most of the thousands of components in the cell), has been acknowledged by a cover in the prestigious journal Cell. DOE support of a team of biologists led by Nitin Baliga at the Institute for Systems Biology in Seattle, WA, has enabled development of a model mapping a significant number of the circuits that control the biological activities of a whole free living organism, Halobacterium salinarium NRC-1. This detailed model of the pathways that allow the cell to function was extracted by carefully selected experiments involving genetic and environment perturbations and development of algorithms. The result was a model that was able to predict how over 80 percent of the total genome (several thousand genes) responded to stimuli over time, dynamically rearranging the cell's makeup to meet environmental stresses. It is a valuable step in the ultimate goal of in silico prediction of cell behavior with its obvious potential for biofuels and pharmaceuticals. The study represents an important partnership between biologists and computer scientists that now provides experimental, algorithmic and software infrastructure for others to apply this approach to new organisms.

Contact: Arthur Katz, SC-23.2, (301) 903-4932; Susan Gregurick, SC-23.2, (301) 903-7672
Topic Areas:

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


January 07, 2008

DOE-JGI Microbial Genome Sequencing Project Leads to the Discovery of a New Carbon Dioxide Fixation Pathway

The December 14, 2007, issue of Science features a report that reveals a novel fifth pathway for carbon dioxide (CO2) fixation used by the archaeon, Metallosphaera sedula. The real significance of this new finding is that novel additional mechanisms exist in the microbial world for carbon capture and cycling; exploitation of these strategies may lead to new opportunities and technologies to address critical DOE missions in bioenergy and carbon biosequestration. The discovery of this new pathway, distinct from the four previously identified pathways for growth on CO2, including the well-known Calvin cycle that powers photosynthesis in plants and algae, was grounded in the sequencing of the genome of Metallosphaera sedula by the DOE Joint Genome Institute which provided the genetic "parts list" for comparison with genes known to be involved in the four previously known pathways for growth on CO2 as a sole carbon source. Additional genome comparisons revealed that a number of other microbes possess this new pathway and in surveying the Venter Global Ocean Sampling database, an unexpectedly large number of "5th-pathway" genes were observed, suggesting that this mechanism for carbon capture is much more widespread than suspected.

Reference: Ivan A. Berg, Daniel Kockelkorn, Wolfgang Buckel, and Georg Fuchs. 2007. Science 318(5857) 1782.

Contact: Dan Drell, SC-23.2, (301) 903-4742
Topic Areas:

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


January 07, 2008

New Pathways Developed to Higher Alcohols as Biofuels

Although much attention is currently focused on ethanol as a biofuel, other alcohols could be even more valuable, with energy densities closer to that of conventional gasoline (thus providing gas mileage comparable to that of gasoline), and less hygroscopic properties (which would simplify their distribution, for example in pipelines). The difficulty in implementing the use of higher alcohols is that no economical biosynthetic route has been developed to produce them in the large quantities needed (with the possible exception of 1-butanol). Now a research group at the UCLA-DOE Institute for Genomics and Proteomics has shown that straight-chain (such as 1-butanol) and branched-chain alcohols containing four and five carbons atoms can be produced using a common microbe, E. coli, by engineering the needed metabolic pathways to the desired products into the microbe. Their key breakthrough exploited redirection of existing highly efficient amino acid biosynthetic pathways in E. coli to the formation of the desired alcohols. Because of the universal presence of these amino acid pathways in all species, the strategy can be implemented in many different organisms, enabling the use of a large variety of raw materials, from cellulose to carbon dioxide. The research was supported by the Genomics:GTL program in the Office of Biological & Environmental Research, with James C. Liao as principal investigator, and appears in the January 3, 2008, issue of Nature.

Contact: Roland F. Hirsch, SC-23.2, (301) 903-9009
Topic Areas:

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