BER Research Highlights

Search Date: March 30, 2017

34 Records match the search term(s):


December 28, 2009

Abbott-American Society for Microbiology (ASM) Lifetime Achievement Award to Stanford's Lucy Shapiro

The 2010 Abbott-ASM Lifetime Achievement Award, ASM's premier award for sustained contributions to the microbiological sciences will be presented to Lucy Shapiro, Director, Beckman Center for Molecular and Genetic Medicine, Stanford University. For three decades Shapiro has studied Caulobacter cresentus, a microbe that tolerates high concentrations of uranium and other heavy metals and could play a role in contaminant remediation. Research with C. cresentus provides the most thorough understanding of the cell cycle in any bacterium, critical to understanding all aspects of its physiology. Shapiro's research has shown that the cell is an integrated system in which its transcriptional circuitry is interwoven with the three-dimensional deployment of key regulatory and morphological proteins. The award will be presented at the annual ASM meeting in San Diego, California May 23 - 27, 2010. Shapiro's work has been supported in recent years by DOE's Genomic Science Program.

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

Division: SC-23.2 Biological Systems Science Division, BER


December 28, 2009

Designing Aptamers to Control Chemical Reactions

Aptamers are short single stranded molecules made up of nucleic acids (RNA and DNA) or peptides that bind, like antibodies, to specific target molecules. However, unlike antibodies they can be completely engineered and synthesized in a test tube for a variety of functions. Marit Nilsen-Hamilton's research group at the Ames Laboratory has led to a new approach for controlling metabolic pathways using aptamers. They discovered that it is possible to develop aptamers, using computational modeling of the aptamer structure, that completely protect target molecules from chemical modification. These results suggest that aptamers might be engineered for use inside cells to alter the flow of chemicals through metabolic pathways with the potential to alter plants or microbes for improved production of biofuels.

Reference: T. Wang, et al., "Computational and Experimental Analyses Converge to Reveal a Coherent Yet Malleable Aptamer Structure That Controls Chemical Reactivity," Journal of American Chemical Society (2009) 131, 14747-14755.

Contact: Prem Srivastava, SC-23.2, (301) 903-4071
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


December 28, 2009

Newly Engineered Organism Produces High Levels of Isobutanol

DOE-funded researchers from UCLA and UC Davis have engineered a cyanobacterium, Synechococcus elongatus, to convert carbon dioxide into isobutanol (a good gasoline substitute) and isobutyraldehyde using sunlight. One gene from a bacterium commonly used to make cheese and three genes from two common laboratory bacteria were spliced into S. elongates, enabling it to synthesize these biofuels. The conversion capabilities of the re-engineered microbe compare very favorably with bacterial production of hydrogen and ethanol, and algal production of biodiesel. The "contaminating" isobutyraldehyde has a high vapor pressure and low boiling temperature so it should be possible to remove continuously with minimal energy input during fermentation. It can also be easily converted to isobutanol.

Reference: Atsumi, S., Higashide, W. & Liao, "Direct photosynthetic recycling of carbon dioxide to isobutyraldehyde," J.C. Nat Biotechnol. vol 27 December 2009

Contact: John Houghton, SC-23.2, (301) 903-8288
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Division: SC-23.2 Biological Systems Science Division, BER


December 14, 2009

Hot Springs Bacterium Converts Broad Range of Biomass Sugars

Cellulose and hemicellulose, long cross-linked chains of simple five and six carbon sugars make up over 70% of the dry weight of plant biomass and are the starting material for production of a range of biofuels. Relatively few microorganisms are capable of breaking down these large, complex polymers, and those with the ability to consume multiple types of sugars are even rarer. Researchers at North Carolina State University affiliated with the DOE Bioenergy Science Center (BESC) at Oak Ridge National Lab have shown that the cellulose/hemicellulose degrading hot spring bacterium Caldicellulosiruptor saccharolyticus can simultaneously consume a broad range of carbohydrates found in plant biomass derived sugars, producing hydrogen as a major end product. The ability of C. saccharolyticus to consume a broad range of biomass sugars and to grow at high temperatures (up 75°C) make it an attractive candidate for further development as a biofuel producing organism.

Reference: VanFossen, A.L., et al. 2009. "Carbohydrate Utilization Patterns for the Extremely Thermophilic Bacterium Caldicellulosiruptor saccharolyticus Reveal Broad Growth Substrate Preferences," Applied & Environmental Microbiology 75, 7718-24.

Contact: Joseph Graber, SC-23.2, (301) 903-1239
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


December 07, 2009

A Resource for Grass Cell Wall Genes

The lignocellulosic biomass contained within the cell walls of grasses makes these plants key candidates for renewable biofuel feedstocks. A major hurdle to utilizing this biomass is in deconstructing the cell walls. Researchers at the National Renewable Energy Laboratory in collaboration with scientists at Purdue University and University of Florida now have constructed a database of over 750 maize (corn) genes involved in cell wall biogenesis. A high throughput spectroscopic screening method was developed during this research to identify mutant plants with unusual cell wall composition and architecture that cannot be distinguished through visual examination alone. Such mutants will be very useful in elucidating the functions of the grass cell wall biogenesis genes, which in turn will facilitate efforts to improve biomass yield and quality in grass bioenergy species. An article on their new resource appears in the December 2009 issue of the journal Plant Physiology.

Reference: Penning, B. W., et al. 2009. "Genetic Resources for Maize Cell Wall Biology," Plant Physiology 151, 1703-28.

Contact: Cathy Ronning, SC-23.2, (301) 903-9549
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Division: SC-23.2 Biological Systems Science Division, BER


December 07, 2009

Getting the Word Out on Advances in Bioenergy Research

A critical issue for the DOE Bioenergy Research Centers is to make all scientific information developed in these large multi-institution collaborative programs readily available across the project. The Berkeley Lab's Joint BioEnergy Institute (JBEI) has made a major step in this direction by building a comprehensive electronic laboratory notebook (ELN) system around a commercial Laboratory Information Management System provided by the prominent data management software developer, GenoLogics. The JBEI system ensures that both the raw data and the scientific context are recorded for every experiment done anywhere in JBEI. The ELN stores researchers' notes, electronic data files, documents and images. Researchers can easily search and retrieve this information using any web browser. The JBEI digital timestamping and notebook synchronization software innovations in this system have the potential for non-exclusive licensing to third parties interested in commercial distribution. Two companies, Surety and CustomWare, have already approached JBEI to license and distribute JBEI copyrighted software.

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


November 24, 2009

Zaida Luthey-Schulten named a Lycan Professor at University of Illinois

Professor Zaida (Zan) Luthey-Schulten, a professor in the Department of Chemistry at the University of Illinois Urbana-Champagn, was invested on October 27 as a William H. and Janet G. Lycan Professor at UIUC. This is one of the highest academic honors at that University. Luthey-Schulten, along with colleagues Carl Woese (a molecular biologist) and Nigel Goldenfeld (a theoretical physicist), are studying mechanisms of protein translation with funding from the Office of Biological and Environmental Research. Her elevation to this named Chair was to honor her for her many contributions to protein chemistry during her career, a career far from over as she explores energy landscapes of proteins involved in protein translation.

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

Division: SC-23.2 Biological Systems Science Division, BER


November 23, 2009

New Microbes Found that Help Leaf Cutter Ants Breakdown Biomass

Tropical leaf cutter ants cultivate specific fungi to efficiently break down cellulosic plant biomass to serve as food for ant colonies. However, plant materials harvested by the ants contain relatively small amounts of nitrogen, a crucial nutrient that limits the growth of the ants' fungal gardens and thus breakdown of plant biomass. In a paper in the November 20 issue of Science, researchers at the DOE Great Lakes Bioenergy Research Center (GLBRC) describe how bacteria colonizing the ant gardens convert atmospheric nitrogen gas into ammonia, a form of nitrogen that can be used by both the fungi and the ants. The group, led by Cameron Currie of the University of Wisconsin, Madison, estimates that over half of the nitrogen requirements of the system are met by these bacteria and that the colonies fertilize the surrounding soil, contributing to overall ecosystem productivity. These results highlight the importance of natural community interactions in the deconstruction of biomass, and suggest potential approaches for consolidated bioprocessing for biofuel production.

Reference: Pinto-Tomás, A. A., et al. 2009. "Symbiotic Nitrogen Fixation in the Fungus Gardens of Leaf-Cutter Ants," Science 20(5956), 1120-23. DOI: 10.1126/science.1173036.

Contact: Joseph Graber, SC-23.2, (301) 903-1239
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Division: SC-23.2 Biological Systems Science Division, BER


November 16, 2009

"The Electric Microbe" Named one of 50 Best Inventions of 2009 by TIME Magazine

TIME Magazine has named a microbe commonly found in the subsurface at sites often contaminated by metal and radioactive wastes as the 20th best invention of 2009. The microbe, Geobacter sulfurreducens, can generate electricity from mud and wastewater using its tiny hairlike extensions called pili. DOE-funded scientist Derek Lovley and his team of researchers at the University of Massachusetts at Amherst have engineered a strain of Geobacter that is eight times more efficient than other strains at producing power. Lovley's team hopes to create novel Geobacter-based fuel cells that can generate cheap, clean electricity.

Reference: Time Magazine, November 23, 2009 (published November 16, 2009)

Contact: Dan Drell, SC-23.2, (301) 903-4742
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Division: SC-23.2 Biological Systems Science Division, BER


November 09, 2009

DOE Bioenergy Center Characterizes Cell Wall Proteins in Poplar Tree

Developing improved plant feedstocks for bioenergy requires an understanding of plant growth and adaptation and knowledge of the underlying molecular pathways of plant cell wall biosynthesis. Scientists at the DOE Bioenergy Science Center (BESC) report the most comprehensive characterization to date of the proteome, or protein complement, of xylem tissues from poplar, a tree commonly cited as a promising feedstock for bioenergy. The study, featured on the cover of the journal Proteomics, used mass spectrometry-based proteomics as a tool to study wood and secondary cell wall formation. Approximately 6,000 proteins from developing poplar xylem tissue were isolated and identified. They included several newly identified proteins thought to regulate cell wall formation in woody tissues of poplar and many proteins of unknown function. Measuring differences in whole proteomes between different poplar variations will increase our understanding of the fundamental properties that underlie the recalcitrance of woody biomass to degradation. This technology will provide new pathways for the potential improvement of poplar as a bioenergy feedstock.

Reference: Kalluri UC, Hurst GB, Lankford PK, Ranjan P, Pelletier DA. 2009. "Shotgun proteome profile of Populus developing xylem," Proteomics 9 (21):4871-80.

Contact: Cathy Ronning, SC-23.2, (301) 903-9549
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Division: SC-23.2 Biological Systems Science Division, BER


October 26, 2009

DOE Joint Genome Institute (JGI) Breaks the Terabase Barrier

The JGI is a national user facility located in Walnut Creek, CA. In FY 2009, the JGI promised that it would sequence 253 billion (253 Gigabases, Gb) bases of DNA from microbes, plants, and complex biological communities engaged in biology relevant to DOE missions in bioenergy, biogeochemistry, and carbon cycling. They didn't just reach this goal. Instead, aided by new sequencing technologies, they sequenced 1003.9 billion, or a trillion base pairs (a Terabase) of DNA, exceeding their FY 2009 goal by a factor of 4 and their entire FY 2008 production by a factor of 8. The power of these sequencing technologies is being focused on mission relevant projects, including sequencing for the three DOE Bioenergy Research Centers and user-driven microbial, fungal and plant projects. The extraordinary new capacity also is the foundation for the JGI's sequencing of the complete DNA of multi-species natural biological communities, through which many microorganisms are being identified which cannot be isolated from the community for sequencing. All resulting data are rapidly made freely available to the public.

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

Division: SC-23.2 Biological Systems Science Division, BER


October 13, 2009

Genome Standards Consortium Proposes Common Practices for Sequence Reporting

Led by scientists from the DOE Joint Genome Institute, representatives from major high-throughput sequencing centers have jointly published new standards for published genome sequences in the October 9 issue of the journal Science. The proposal posits a tiered set of community-defined categories that increase in rigor and should better reflect the quality of the genome sequences being released. The proposal avoids rigid numerical thresholds in order to remain responsive to rapidly changing sequencing technologies. The proposal also accommodates a growing list of alternative types of genome sequencing projects, such as environmental (metagenomic) or single-cell sequencing. Responses from genome database repositories have been positive and implementation of these standards as a requirement for genome submissions is expected. This common currency in defining the products of genome projects will enable better management of expectations and allow users of genomic data to assess the quality of the deposited available sequences and decide whether these meet their needs.

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

Division: SC-23.2 Biological Systems Science Division, BER


September 28, 2009

National Institutes of Health Recognizes DOE Scientists

NIH has announced the recipients of the highly competitive Transformative and New Innovator research grant awards. Three of the 97 new grants in these two programs are to DOE-funded scientists who will develop new applications of their advanced technologies. Wei-Jun Qian of the Pacific Northwest National Laboratory has made significant contributions to advancing mass spectrometry instrumentation for proteomics. The NIH New Innovator grant will enable him to seek a thousand-fold improvement in sensitivity of these experiments while increasing the speed so that a hundred or more experiments can be carried out each day on an instrument. Jerilyn Timlin of Sandia National Laboratories has developed new techniques for imaging living cells with high spatial resolution.She will use her New Innovator grant to combine imaging of the dynamics and interactions of proteins in living cells currently studied one at a time into a single, multiplexed technique capable of studying five or more proteins simultaneously. Sunney Xie of Harvard University also has pioneered techniques for imaging, in his case Stimulated Raman Scattering (SRS), which allows studying single molecules in complex biological systems, without having to label them to make them detectable. His Transformative research grant will enable him to extend the SRS technology to study the dynamics of lipids in living cells. These scientists have major support for their technological research from the Offices of Biological and Environmental Research and Basic Energy Sciences. Their NIH-funded research will seek new technologies that will also have applications in DOE bioenergy research.

Contact: Arthur Katz, SC-23.2, (301) 903-4932; Susan Gregurick, SC-23.2, (301) 903-7672
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Division: SC-23.2 Biological Systems Science Division, BER


September 28, 2009

Restarting a Microbial Genome after its Modification in Yeast

Many microbes grow extremely slowly in their native environments, and because of this have been difficult to adapt for DOE missions through genetic engineering. A team at the Venter Institute has developed a solution to this difficult problem.They have shown previously that a small bacterial genome can be transferred into a much larger yeast host and maintained therein. The bacterial genome can then be modified by methods that are routine in the yeast host. The new development demonstrates that the engineered genome can be transferred back into a bacterial shell with intact function. This success opens a pathway for modifying the genomes of many bacteria that could be valuable for addressing bioenergy and environmental missions.

Reference: Carole Lartigue, et al., "Creating Bacterial Strains from Genomes That Have Been Cloned and Engineered in Yeast," Science, Volume 325, pages 1693-1696 (September 25, 2009).

 

Contact: Marvin Stodolsky, SC-23.2, (301) 903-4475
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Division: SC-23.2 Biological Systems Science Division, BER


August 17, 2009

New Approach for Putting Algae to Work on Energy Challenges

In the August issue of the journal Nature Methods, a team of DOE-funded researchers at the University of Virginia and Harvard Medical School publish findings on a new systems biology based method for simultaneous metabolic network modeling and verification of gene function.  Using the alga Chlamydomonas reinhardtii as a model system, the researchers were able to produce a refined annotation of gene function and a significantly more robust and experimentally validated metabolic network reconstruction.  The results of this study provides new targets for metabolic engineering of biofuels production by C. reinhardtii and related algae as well as a powerful new tool for studying functional properties of biological systems. 

Contact: Joseph Graber, SC-23.2, (301) 903-1239
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


August 10, 2009

Measuring Chemical Changes Inside Living Cells at the Advanced Light Source (ALS)

Understanding how microbes adapt to changing chemical environments is a critical aspect of being able to "put microbes to work" solving DOE challenges.  Berkeley Lab scientists have now shown that Fourier transform infrared (FTIR) spectromicroscopy at the ALS can follow cellular chemistry within living microbes in real time.  The synchrotron FTIR technique provides a powerful new tool to understand the response of living cells to chemical stresses involved in synthesis of biofuels compounds, breakdown of cellulosic biomass, and a wide variety of other systems relevant to DOE missions.  Being able to make these dynamic measurements continuously inside selected living cells dramatically increases the usefulness and reliability of information that traditionally is derived from cells that have been killed and broken apart.  A new experimental station is nearing completion at the ALS to enable further biological and environmental applications of the technology.

Reference: Hoi-Ying N. Holman, Eleanor Wozei, Zhang Lin, Luis R. Comolli, David A. Ball, Sharon Borglin, Matthew W. Fields, Terry C. Hazen, and Kenneth H. Downing "Real-time molecular monitoring of chemical environment in obligate anaerobes during oxygen adaptive response," Proceedings of the National Academy of Sciences (USA), 106:12599-12604; (August 4, 2009). 

Contact: Arthur Katz, SC-23.2, (301) 903-4932; Joseph Graber, SC-23.2, (301) 903-1239; Roland F. Hirsch, SC-23.2, (301) 903-9009
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Division: SC-23.2 Biological Systems Science Division, BER


August 10, 2009

Prestigious Award Given to SLAC Scientist

The International X-ray Absorption Society (IXAS) announced its 2009 Awards for achievement in the field of XAFS (x-ray absorption fine structure). Professor Britt Hedman, a member of the SLAC Photon Science faculty and Deputy Director of SSRL, was named as co-recipient of the IXAS Outstanding Achievement Award. The Award is shared with Professor Frank de Groot, Utrecht University, Netherlands. This is the highest award of the International XAFS Society and is given every three years for outstanding accomplishments across all x-ray absorption spectroscopy disciplinary areas, including experimental and theoretical studies. The award, formally named the IXAS Edward Stern Outstanding Achievement Award, recognizes the contributions of Dr. Hedman in the development of technology and methodologies for low- and hard- energy XAFS and extensive applications to the study of metalloprotein active sites. Dr. Hedman's research has been carried out primarily at SSRL, within its Structural Molecular Biology program, which is funded by DOE-BER and NIH-National Center for Research Resources.

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


July 27, 2009

DOE Funded Researchers Win R&D 100 Award for Design of GeoChip

A team of investigators led by Jizhong Zhou of the University of Oklahoma has been selected to receive an R&D 100 Award for development of the GeoChip, a tool for screening functional characteristics of complex microbial communities in the environment.  The GeoChip is microarray of DNA probes that allows detection of over 10,000 genes involved in functions of interest to DOE including metal reduction, stress tolerance, nutrient acquisition, and degradation of carbon compounds by wide range of microbes.  These microbial functions can be used to develop microbe-based remediation strategies. 

Contact: Joseph Graber, SC-23.2, (301) 903-1239
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


July 27, 2009

Progress in Developing Highly Stable Enzymes for Biofuel Production

Large scale processing of biomass will require enzymes that work at the high temperatures to efficiently and effectively break down the biomass feedstock. Researchers at the DOE Joint BioEnergy Institute (JBEI) have just announced significant progress toward meeting this need by determining the three-dimensional structure of an enzyme that degrades cellulose at elevated temperatures. They observed unique structural features such as patterns of internal bonding and incorporation of metal ions that suggest how the enzyme retains its activity at high temperatures where the function of most enzymes is destroyed. The structural information is guiding bioengineering of new forms of the enzyme that will work at still higher temperatures or in harsh chemical environments and with enhanced efficiency.

Reference: Acta Crystallographica D, volume 65, pages 744-750 (August 2009)

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

Division: SC-23.2 Biological Systems Science Division, BER


July 20, 2009

New Approach to Analysis of Lipids for Biofuel Research

A new technique has been developed that applies mass spectrometry to overcome obstacles to measurement of uncharged lipid molecules, a critical group of products of cellular metabolism in systems being studied for production of biofuels. Researchers at the Berkeley Lab led by Trent Northern have developed a method for converting these charge-neutral molecules to positively charged ions, without losing information about the chemical structure of the molecules. The ions can easily be identified and measured in widely used instruments, such as electrospray ionization mass spectrometers, which cannot directly measure neutral molecules. This development is important for study of neutral lipids (i.e. fatty alcohols, glycerolipids, and sterols), which represent a large and important class of metabolites for biofuel research which often go undetected. This new technique will allow detection of these metabolites with high sensitivity.

Reference: Hin-Koon Woo, Eden P. Go, Linh Hoang, Sunia A. Trauger, Benjamin Bowen, Gary Siuzdak, and Trent R. Northen, "Phosphonium labeling for increasing metabolomic coverage of neutral lipids using electrospray ionization mass spectrometry" Rapid Communications in Mass Spectrometry, (2009), volume 23 pages 1849-1855.

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


July 13, 2009

19th Annual Meeting of US-EC Biotechnology Task Force

Since 1990, the US-EC Task Force on Biotechnology Research has been coordinating transatlantic efforts to promote research on biotechnology and its applications for the benefit of society. The 19th meeting of the Task Force was held May 21-22, 2009 at Lawrence Berkeley National Laboratory (LBNL). Drs. Anna Palmisano and David Thomassen represented the DOE and reported, respectively, on working group on Environmental Biotechnology and on Biobased Products and Bio-Energy. The Task Force took tours of DOE's Molecular Foundry, DOE's nanoscience user facility at LBNL, and the Joint Bioenergy Institute (JBEI), DOE's bioenergy research center at LBNL. More information on the Task Force can be found here.

Contact: David Thomassen, SC-23, 301-903-9817
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Division: SC-23 BER


June 22, 2009

Advance in Raman Microscopy Highlighted in Nature Magazine

Degradation of lignocellulosic materials in biomass is a critical step in production of biofuels, but the process is also extraordinarily difficult to follow experimentally in real time. A new technique, Stimulated Raman Scattering (SRS) microscopy, overcomes some of the limitations of existing technologies for imaging the degradation of biomass. SRS microscopy enables improved measure­ment of cellulose and lignin distribution at the surface and varying depths in plant cell walls. Developed by Sunney Xie of Harvard University with DOE funding, SRS microscopy is being used in collaboration with scientists at the National Renewable Energy Laboratory to image changes in plant cell walls during their degrada­tion. SRS microscopy will make it easier to follow cellulose and lignin as cell wall degradation proceeds. The new technique is the subject of a feature article in the June 4, 2009, issue of Nature.

Reference: H. Ledford, "The Naked Microscope," Nature (2009) 49, 636.

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


June 22, 2009

Merrifield Award Presented to Steven Kent

Dr. Steven Kent of the University of Chicago has made major contributions in automating the synthesis of specialized protein derivatives and for providing synthetic strategies for proteins that cannot be prepared by biological routes. His DOE-funded research has promising applications in developing new ways to analyze specific functions of plants and microbes relevant to biofuels research. The R. Bruce Merrifield Award was presented to Dr. Kent during the 21st American Peptide Society Symposium in recognition of the lifetime achievements of a peptide scientist and memorializing the Nobel Laureate who pioneered solid-phase peptide synthesis. His Merrifield Lecture, Inventing chemistries to reveal how proteins work, was presented during the Symposium.

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

Division: SC-23.2 Biological Systems Science Division, BER


June 01, 2009

DOE Synchrotron Light Sources Reveal Structure of Key Enzyme in Metabolism of Carbohydrates

Acetoacetate decarboxylase is used by bacteria for a critical step in the conversion of starches to alcohols and acetone, a key step in biofuels production.  Now the structure of the enzyme in three dimensions has been solved, allowing scientists to understand the mechanism by which the conver­sion takes place. This, in turn, will help development of improved enzyme variants through protein engineering, including enzymes that could be used in the production of biofuels. The studies were carried out by a research group based at Boston University using x-ray crystallography stations at the National Synchrotron Light Source and a small angle x-ray scattering station at the Stanford Synchrotron Radiation Lights Source. 

Reference: Meng-Chiao Ho, Jean-François Ménétret, Hiro Tsuruta and Karen N. Allen, "The origin of the electrostatic perturbation in Acetoacetate decarboxylase," Nature, 459, 393-397 (21 May 2009)

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

Division: SC-23.2 Biological Systems Science Division, BER


June 01, 2009

Plugging Microbial Activities and Genomes into the Energy Grid.

An Office of Science sponsored  symposium at the May general meeting of the American Society for Microbiology (ASM) in Philadelphia discussed microbial genomics and systems biology research aimed at the development of new biofuels and bioenergy sources.  Tim Donohue and Jennie Reed of the DOE Great Lakes Bioenergy Research Center at the University of Wisconsin convened the symposium.  The symposium also featured Martin Keller of the DOE Bioenergy Sciences Center at Oak Ridge National Laboratory, James Liao of the UCLA-DOE Institute of Genomics and Proteomics, and Andreas Schirmer of LS9, Inc., a biotechnology company focusing on biofuels research.  Donohue, Keller, Liao, and Schirmer also participated in a press conference at the meeting highlighting the symposium.  Follow up news articles appeared on the websites Genomeweb.com and Greenwire on May 19th, and further print articles are expected to follow.

Contact: Joseph Graber, SC-23.2, (301) 903-1239
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


May 04, 2009

Sustainability of Biofuels Workshop Report Issued

The joint USDA-DOE Office of Science Sustainability of Biofuels Workshop, held October 28-29, 2008, stimulated an interactive discussion among a wide range of experts on the state of the science and research needed to establish sustainable production and utilization of cellulosic biofuels. The workshop report has just been issued and is available at (/biofuels/sustainability/). It summarizes the workshop and presents a series of new and critically important areas of research. Interdisciplinary teams involving scientists from the agricultural, ecological, socioeconomic, and information system communities will be required to fill knowledge and technology gaps and provide integrated solutions that effectively target specific challenges. This research, however, must maintain a holistic view of the entire biofuel production system and its socioecological impacts. DOE, USDA, and other federal agencies now have a unique opportunity to use the workshop recommendations to develop an integrated research agenda that addresses the environmental, economic, and social dimensions of cellulosic biofuels across multiple scales and ensures that this emerging industry has the information needed to grow sustainably.

Contact: John Houghton, SC-23.2, (301) 903-8288; Libby White, SC-23.2, (301) 903-7693
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Division: SC-23.2 Biological Systems Science Division, BER


April 27, 2009

Ant Symbionts May Provide New Approaches to Biofuels Synthesis

Leaf-cutting ants are well-known agriculturalists, cultivating fungus gardens capable of efficiently breaking down lignocellulosic plant material and converting it to food for ant colonies. Cameron Currie, a University of Wisconsin microbiologist at the DOE Great Lakes Bioenergy Research Center (GLBRC), is studying the complex interactions between ants, their cultivated fungi, and the microbial communities that colonize their nests. A news commentary in the April 2nd issue of the journal Nature describes Currie's research and his collaborative effort with the DOE Joint Genome Institute to sequence microbial community genome fragments from ant colonies. The aim of this approach is to prospect for new lignocellulose-degrading enzymes that could be further developed for biofuels production. The idea is that the ants' long evolutionary history may help us in our attempts to break down plant biomass, says Currie.

Contact: Joseph Graber, SC-23.2, (301) 903-1239
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


April 27, 2009

Predicting Biological Behaviors

The cover article for the March 2009 issue of The Scientist highlighted advances made by three DOE scientists developing systems biology approaches to computationally simulate responses of microbes to changes in their environment. Dr. Nitin Baliga (Institute for Systems Biology) and his collaborators developed a computer model that could predict molecular-level responses of a free-living cell to genetic and environmental changes.  Remarkably, the model was able to predict responses to changes that were different from the experimental data used to construct the model. The key to these insights is the normal interconnectedness of biological systems, for example changes in temperature affect solubility. The ability to link and predict novel biological responses represents an important step toward the ultimate goal of an in silico model of cell behavior. While the investigators focused on microbial systems involved in environmental processes of interest to DOE, the methodology has broad applications to all biological systems and is a major step forward in the burgeoning field of systems biology.

Contact: Arthur Katz (SC-23.1, 3-4932) and Susan Gregurick (SC-23.1, 3-7672)
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Division: SC-23.1 Climate and Environmental Sciences Division, BER


April 13, 2009

Comparing Genomes of Two Algae Strains Highlights Genes for Carbon Capture

Scientists from the Monterey Bay Aquarium Research Institute, led by Alexandra Z. Worden, have decoded the genomes of two algal strains, highlighting the genes enabling them to capture carbon and maintain the delicate balance of carbon in the oceans.  The study sampled two geographically diverse isolates of the photosynthetic algal genus Micromonas: one from the South Pacific, the other from the English Channel. Surprisingly, the two isolates had about 90% of their genes in common compared to about 98% for humans and some primates.  Algae such as Micromonas were among the first cells on Earth to acquire the capacity to fix CO2 and use the energy from sunlight to generate biomass (the essential process of photosynthesis).  Worden said that the differences between these algae may make them more resilient compared to more closely related species, enabling them to better survive environmental change and their geographically diverse locations. These results help illuminate cellular processes that could be used to produce algae-derived biofuels. Scientists at DOE's Joint Genome Institute (JGI) played an essential role in the research by carrying out the DNA sequencing and participating in the interpretation of the results. These findings are published in the April 10 edition of the journal Science.

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

Division: SC-23.2 Biological Systems Science Division, BER


April 13, 2009

Defining the Role of Predictive Modeling for Rational Biological Engineering

The field of genomics is moving toward rational re-engineering of microbes that could provide new technologies for DOE's energy and environment missions.  Nitin Baliga and co-authors at the Institute for Systems Biology (ISB) have just published an article in Nature Reviews Microbiology (Volume 7, pages 297-305, April 2009) that discusses current research in genomics and the opportunities for significant advances provided by the integration of new technologies such as synthetic biology, systems biology, and predictive modeling. The authors point out that biological systems do not readily adapt to large changes in their metabolic or regulatory systems that alter the balance of energy or resources.  New strategies are needed to overcome this obstacle that bring together separate efforts in systems biology and synthetic biology using simultaneous global modeling and systems optimization. This multi-scale approach to experimental characterization and redesign of microbial cells and microbial communities will provide a foundation for applying microbial biology to achieve new sources of energy and to solve problems in environmental contamination.

Contact: Susan Gregurick, SC-23.2, (301) 903-7672, Arthur Katz, SC-23.2. (301) 903-4932
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Division: SC-23.2 Biological Systems Science Division, BER


April 13, 2009

New Insights From Computer Simulations May Improve Biomass Deconstruction

Scientists at the DOE BioEnergy Science Center (BESC) have made a significant step in understanding the recalcitrance of biomass to microbial deconstruction. Microbes that break down plant biomass have large extracellular enzyme complexes, known as cellulosomes, that break down plant cell walls.  The BESC team used computational simulations to understand the binding dynamics of two cellulosome proteins that play critical roles in the assembly of the cellulosome.  The simulations included a typical cellulosome complex and one with mutant proteins that cause a major change in protein-protein recognition sites needed for normal assembly of the cellulosome. This information will help BESC researchers redesign cellulosomal modules that can degrade biomass more efficiently than normal cellulosomes. The research, made possible with computational time on the ORNL Kraken Cray XT5 Supercomputer, has just been published online in the journal Protein Science in a paper titled Building a foundation for structure-based cellulosome design for cellulosic ethanol: Insight into cohesin-dockerin complexation from computer simulation, by Jiancong Xu, Michael Crowley, and Jeremy C. Smith.

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


March 02, 2009

A Genomic-Scale Reconstruction of Mycoplasma genitalium

Reconstructing an organism's metabolic pathways is an important step in being able to understand and use those biological capabilities to solve DOE energy and environmental challenges. This rapidly evolving field requires development of sophisticated computational tools to model metabolic networks, tools to bridge gaps in the models, and experiments to resolve inconsistencies. Dr. Costas Maranas of Penn State University describes the systematic reconstruction of pathways involving 40% of the genes in Mycoplasma genitalium, one of the smallest known self-replicating organisms. Their computational model of M. genitalium iPS189 includes 262 biochemical reactions and 274 metabolites and is 87% accurate in capturing genes essential for M. genitalium function. This work provides a roadmap for the automated construction of computer-based metabolic models for other organisms important for DOE mission needs. Details can be found in the journal PLoS Computational Biology, February 2009, Vol. 5 , Issue (2).  This work is jointly sponsored by DOE's Office of Biological and Environmental Science and the Office of Advanced Scientific Computing Research.

Contact: Susan Gregurick, SC-21.1, (301) 903-7672, Christine Chalk, SC-21.1 (301) 903-5152
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Division: SC-23 BER
      (formerly SC-23 OBER)


March 02, 2009

Microbial Production of Methyl-ethyl ketone (MEK)

The path to reduced dependence on foreign oil includes development of biofuels and progressive replacement of petrochemistries. With funding from DOE's Small Business Innovative Research (SBIR) program, Genomatica, Inc. has announced the effective production of MEK by microbes. MEK and its easily made derivatives have diverse usages in plastics and explosives. MEK also is an industrial cleanser widely used prior to assembly of complex metal assemblies such as aerospace components. MEK can be purified in the same distillation plants already used for ethanol production. Genomatica develops computational models of microbial metabolism, beginning with a microbe's DNA sequence, that illuminate the microbe's biochemical repertoire. The models serve to guide genetic engineering of either novel biochemical pathways and/or their optimization for commercial production, including applications to address DOE energy and environmental needs. 

Contact: Marvin Stodolsky, SC-23.2, (301) 903-4475
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Division: SC-23.2 Biological Systems Science Division, BER


February 23, 2009

Third-Generation DNA Sequencing Introduced

Sequencing the genomes of natural mixtures of species (metagenomes) is key to research for DOE's environmental and energy missions. A new generation of DNA-sequencing instruments, based on a concept from DOE-funded scientists Watt Webb and Harold Craighead at Cornell University, that will enable faster, reliable studies of microbial populations will soon be available. The new instrument sequences single strands of DNA directly, rather than large numbers of identical copies. The new instrument was introduced by Pacific Biosciences of Menlo Park, California, at the 10th annual Advances in Genome Biology and Technology conference and will be available later this year. The new technology has two advantages over current high-throughput sequencing instruments.  It can read DNA sequence about 10,000 times faster and can read 1000 or more contiguous base pairs from one DNA, significantly longer than existing capabilities.  Both advantages will benefit DNA sequencing applications for DOE-relevant mission needs.

References: Mathieu Foquet, Jonas Korlach, Warren R. Zipfel, Watt W. Webb, and Harold G. Craighead, Focal Volume Confinement by Submicrometer-Sized Fluidic Channels, Analytical Chemistry (2004) 76 (6), 1618-1626 and articles cited in the paper.

John Eid, et al., Real-time DNA sequencing from single polymerase molecules Science (2009) 323 (1), 133-138 Advances in Genome Biology and Technology

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