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JBEI, Synthetic Biology Featured in Publication
JBEI chart
A feature article about the Joint BioEnergy Institute (JBEI), the six-institution partnership led by Berkeley Lab that’s one of three new DOE Bioenergy Research Centers, appears in the latest issue of the American Chemical Society’s ACS Chemical Biology. The VIMSS Computational Core and MicrobesOnline is the support base of the JBEI partnership featured in the bioenergy article mentioned in LBLToday.
Gary Andersen   Stage Grante to Help Trace Beach Pollution
Marin beaches will soon get regular high-tech testing to detect and identify sources of possible bacterial pollutants. The county Board of Supervisors recently approved using an $848,000 state grant to hire Berkeley Lab to conduct high-tech DNA testing that can help pinpoint the source of pollutants. The monitoring — which utilizes a PhyloChip — can differentiate between bacteria caused by humans, cows, deer, seals, birds or other species. Gary Andersen, with the Lab’s Earth Sciences Division, is the project’s principal investigator. Full story.
Keasling & Somerville  

Keasling, Somerville Get BayBio Awards
In front of several hundred biosciences industry leaders, Berkeley Lab’s Jay Keasling and Chris Somerville were honored together on stage at the BayBio Pantheon Awards Dinner last month. The duo received this year’s Visionary Award for their roles (respectively) in bringing the Joint BioEnergy Institute (JBEI) and the Energy Biosciences Institute (EBI) to Berkeley. BayBio is a trade association serving the life science industry in Northern California. Each year the group recognizes achievement and honors excellence in the field. Go here for the complete list of honorees.

Microbes Online Team Featured in Today at Berkeley Lab
Faster Protein Scanning Tool Developed at Lab
Microbes Online Team

To analyze the millions of new genes found by DNA sequencing projects, biologists search for similarities to known protein families, usually using commericial tools, such as InterProScan. The MicrobesOnline group with Berkeley Lab’s Physical Biosciences Division has developed a tool that is up to 40 times faster than InterProScan. Their FastHMM analyzed 2.5 million proteins on a 20-CPU cluster in just a week. FastHMM will allow research groups to analyze the flood of new DNA sequences without the need of supercomputers. Learn more about FastHMM here

Aindrila Mukhopadhyay  

Aindrila Mukhopadhyay, a Berkeley Lab physical bioscientist and member of the DOE Genomics: GTL project, will speak at the Human Genome Conference in Los Angeles Thursday and Friday (Oc 25 & 26, 2007).

The conference was organized by the African American Genetics Education Project. Mukhopadhyay will talk on the discovery of metal ion-reducing bacteria in waste sites and the development of effective biocontainment strategies. One such bacterium is Desulfovibrio vulgaris, which were selected for sequencing and annotation by the Department of Energy.

keasling   Another Keasling Honor:
It may not be the most flattering of designations, but Berkeley Lab Physical Biosciences Division Director Jay Keasling has been selected by the international version of Newsweek magazine as one of its “10 Hottest Nerds.” The group, which also includes scientists like Eric Lander, J.Craig Venter and Svante Paabo, was asked what the current biosciences revolution means for the 21st century. Keasling’s reaction when told of his new status? “Well, I am a nerd,” he said. Read his (see last entry) and the other nerds’ comments here.
uctv   Berkeley Lab’s 2007 summer lectures will begin airing nationally in October on University of California Television. First up is Bill Collins’ talk on the future of the Earth’s climate on Oct. 1, followed by Terry Hazen’s lecture on bioremediation on Oct. 8. More lectures will air in November.
Jon Davies   Tri-City teachers broaden horizons
Teacher Brings Lab Technology to Classroom: Jonathon Davies
Go here for the story.
DOE JBEI logo   DOE Names JBEI as One of Three New Bioenergy Research Centers
Secretary of Energy Samuel W. Bodman has announced that a partnership between Berkeley Lab and five other institutes has been chosen to host one of three bioenergy research centers (BRCs) being funded through its Biological and Environmental Research Genomics:GTL research program in the Office of Science. This new center will be known as the DOE Joint BioEnergy Institute (DOE JBEI) and it will be headquarted in the East Bay. It is expected to receive $125 million in DOE funding over the next five years. “The selection of DOE JBEI is a major vote of confidence in the Bay Area’s growing leadership in the national effort to develop new and cleaner sources of renewable energy,” said Jay Keasling, director of Berkeley Lab’s Physical Biosciences Division and a UCB Professor of Chemical Engineering, who has been designated as DOE JBEI’s Chief Executive Officer. For more information, go here.
Michael Cipriano   Programmer by Day, Six-Legged Robot Inventor on the Weekend

Adam Arkin


  Arkin, Keasling Elected To Microbiology Academy
Lab life scientist Adam Arkin and Physical Biosciences Division Director Jay Keasling have been elected to the American Academy of Microbiology (AAM). They are among 54 newly elected fellows announced yesterday. The AAM is the honorific leadership group within the American Society for Microbiology. Fellows are elected annually using a peer-reviewed process, based on scientific achievements and contributions that have advanced microbiology.
ESME cover  

GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes

bugs   Microbes Online Highlighted in Today at Berkeley Lab
Microbes Online, a website for comparative and functional genomics of prokaryotes, now boasts over 420 complete genomes, with nearly 1.5 million genes assigned to more than 60,000 protein families. A recent upgrade of the website features an interactive tree browser for protein family phylogenies, a maximum-likelihood species tree, tools for discovering regulatory sequences, and profile searches and visualization of gene expression data. Microbes Online was created in 2003 by the Computational Core of the Virtual Institute for Microbial Stress and Survival (VIMSS), led by Lab life scientist Adam Arkin.
ASTAR   Lab Hosts Science
Boot Camp for Judges

Fifty-five state and federal judges are attending a science training session at Berkeley Lab this week. The conference’s goal is to give the judges an orientation on emerging trends in science, and enhance their ability to preside over cases involving novel scientific evidence. It is organized by the Advanced Science & Technology Adjudication Resource Center (ASTAR), which seeks to improve the capacities of the nation’s courts in resolving highly technical cases. The judges will tour Berkeley Lab and meet with Lab Director *Steve Chu* and leading Lab scientists *Mark Alper*, *Terry Hazen*, *Jay Keasling*, *Carolyn Larabell*, and *George Smoot*, among others. In addition, they’ll participate in several mock trials related to nanotechnology and other relevant topics. Go here for more on ASTAR.
keasling   BP selects UC Berkeley to lead $500 million energy research consortium with partners Lawrence Berkeley National Lab, University of Illinois
The BP grant will expand on and further leverage existing collaborations (including VIMSS/ESPP2 Functional Genomics and Computational Core team members) between UC Berkeley and the Lawrence Berkeley National Lab to explore ideas for clean fuels. UC's center of bioengineering research, Jay Keasling's lab, is housed within LBNL's Berkeley West Biocenter; also home to VIMSS/ESPP2.
UC Berkeley News article
hazen   Successful ERSP proposal awards
Terry Hazen will work with Pacific Northwest National Laboratory scientists to explore meta-proteogenomics at the Hanford 100H Site. Read about the awards here.
Gary, Eoin & Todd   Want biodiversity? Look no further than the air around you. It could be teeming with more than 1,800 types of bacteria, according to a first-of-its-kind census of airborne microbes recently conducted by Berkeley Lab. Earth scientist Gary Andersen and colleagues used an innovative DNA test to catalog the bacteria in air samples taken from the Texas cities of San Antonio and Austin. Surprisingly, they found a widely varied bacterial population that rivals the diversity found in soil. They also found naturally occurring relatives of microbes that could be used in bioterrorist attacks — although many of these relatives are harmless. Full story.
David Stahl  

Abelson Advancing Science Seminar at AAAS Explores the Planet of the Microbes

"It's definitely time for microbes to have their due," said David Stahl, a professor of environmental engineering and science at the University of Washington and a keen student of the microbial world. "We live on the planet of the microbes," he said, with very large numbers of those organisms controlling the key cycles of planetary chemistry that produce such essentials to life as oxygen and organic forms of carbon and nitrogen.


keasling   Which scientist had the greatest impact in the past year?
For his breakthroughs in the field of synthetic biology, including treatments for malaria, AIDS, and cancer as well as discoveries of new fuel resources, DISCOVER is awarding University of California at Berkeley’s Jay Keasling with its prestigious Scientist of the Year award on November 15th in New York City. Bob Guccione, Jr., CEO of DISCOVER media, says, “Dr. Keasling is a visionary whose ingenuity merits special recognition. DISCOVER believes what separates Dr. Keasling from other scientists, who also have done groundbreaking work, is his spirit and his determination to help those who cannot help themselves. He is a true humanitarian.”

Bacteria found living 2 miles underground
Discovery shows life could exist on other planets, scientists say

Scientists descending more than 2 miles into the hot, fractured rocks of a South African gold mine have discovered clans of microbes that have thrived there in total isolation for millions of years. Their quest, the scientists say, reveals more clearly than ever how life can exist in the most extreme environments imaginable: beneath the surface of Mars, perhaps, or on almost any other planet in the galaxy.

"These bugs come from a formation at least 3 million and probably tens of millions of years old," said biologist Terry Hazen, head of the Lawrence Berkeley National Laboratory's Ecology department and a co-author of the report. "They're living happily down there, remote and secluded, and they have the ability to adapt to anything that comes their way."

Mine-Dwelling Microbe Included in Ripley's List
The paper in Science, whose co-authors include Berkeley Lab earth scientists Terry Hazen, Gary Andersen, Eoin Brodie and Todd DeSantis, provided a “strange-but-true” fact for a recent item in Ripley’s Believe It or Not.


Press Release: Microorganisms One Part of the Solution to Energy Problem Says Report, Washington, DC – November 15, 2006 – The answer to one of the world’s largest problems – the need for clean, renewable sources of energy – might just come from some of the world’s smallest inhabitants – bacteria – according to a new report, Microbial Energy Conversion , released by the American Academy of Microbiology.

“Imagine the future of energy. The future might look like a new power plant on the edge of town – an inconspicuous bioreactor that takes in yard waste and locally-grown crops like corn and woodchips, and churns out electricity to area homes and businesses," says Judy Wall of the University of Missouri – Columbia.

View the Press Release here

stahl   The 2006 Procter & Gamble Award in Applied and Environmental Microbiology is presented to David Stahl.
Judy Wall  

New Approaches to Microbial Energy featuring Dr. Judy Wall, VIMSS researcher from the University of Missouri - Columbia. In a world dependent on diminishing fossil fuels, microbes may be the key to the future.

Listen to this podcast from the American Society for Microbiology's MicrobeWorld Radio

green genes   Summer Fellow Makes ‘Greengenes’ Accessible Through New Tutorial
Greengenes is a website used by biologists from around the globe to detect and classify microorganisms from their local environments, based upon easily collected DNA samples. For example, Eoin Brodie of Berkeley Lab’s Earth Sciences Division (ESD) is finding natural soil bacteria that prevent toxic heavy metals from entering waterways. He can rapidly analyze DNA samples from subsurface waters by comparing them against the comprehensive Greengenes database hosted in Terry Hazen's Ecology Department at Berkeley Lab.
  Life Cycle of Operons Yields New Look at Bacterial Genetics
BERKELEY, CA — In a breakthrough that will immediately benefit biologists who study bacteria, and could in the future have bearing on
the advancement of synthetic biology, a team of researchers has determined the life cycle of operons, small groups of genes with
related functions that are co-transcribed in a single strand of messenger RNA. Present in all known bacterial genomes, operons play a
crucial role in gene expression programs that enable microbes to adapt to environmental stresses. This research was conducted by scientists with the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab), the University of California at Berkeley, and the Howard Hughes Medical Institute (HHMI).
  Salt Stress in Desulfovibrio vulgaris Hildenborough: an Integrated Genomics Approach
Article in Journal of Bacteriology
  Intimate Strangers: Unseen Life on Earth, a videocast documentary on microbial life and evolution from the American Society for Microbiology
Episode 04/04/2006: A New Age, features VIMSS co-I, Terry Hazen, on bioremediation

Explore the future of microbes and how they can improve the quality of life on Earth through genetic engineering, bioremediation and electronics. The 21st century challenges us to reclaim our damaged environment and feed a growing population. This hour introduces scientists who are turning to microbes for solutions and the tiny organisms who are making new cleanup technologies possible.

Using Fake Plants to Halt A Real Killer -Jay Keasling
  VIMSS's new website launches. Please send your comments. (02/15/06)
  Site, Microbial Ecology Featured In Symmetry Magazine. (02/05/06)
  Zhili He's VIMSS paper is among the top 20 requested papers published in Applied and Environmental Microbiology between July 2005 - September 2005. (02/05/06)
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