31 March 2011
Partnership to advance understanding of personal genomic variation
By Robert Sanders, Media Relations, UC Berkeley
Despite the fact that more than 3,000 people have had at least a portion of their genomes sequenced, and that a growing number of personal genomics companies are urging you to be next, scientists still have a poor understanding of what the differences in your genome really mean.
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Posted by Pinar Aybar at 5:58
17 July 2010
CE Specialist Honored with Lifetime Achievement Award
Dr. Peggy Lemaux, Cooperative Extension Specialist in the Department of Plant and Microbial Biology, was presented with The Society of In Vitro Biology Lifetime Achievement Award for 2010.
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Posted by Eva St. Clair at 1:57
08 July 2010
Exposing the Student Body: Stanford Joins U.C. Berkeley in Controversial Genetic Testing of Students
By: Ferris Jabr, Scientific American
This week, the University of California, Berkeley will mail saliva sample kits to every incoming freshman and transfer student. Students can choose to use the kits to submit their DNA for genetic analysis, as part of an orientation program on the topic of personalized medicine. But U.C. Berkeley isn't the only university offering its students genetic testing. Stanford University's summer session started two weeks ago, including a class on personal genomics that gives medical and graduate students the chance to sequence their genotypes and study the results.
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Posted by Pinar Aybar at 0:58
13 May 2010
Professor Awarded Prestigious BREAD Grant
The National Science Foundation and the Bill and Melinda Gates Foundation have awarded Professor Brian Staskawicz a BREAD Program grant. Staskawicz is the current chair of the department of plant and microbial biology at the College of Natural Resources. He is one of 15 grantees in the US being funded by the NSF-Gates partnership. He will receive a $1.3M grant to support his project on the bacterial blight disease of cassava.
BREAD is a new five-year program jointly funded by the National Science Foundation (NSF) and the Bill & Melinda Gates Foundation. The two entities are partnering to support innovative scientific research designed to address key constraints to smallholder agriculture in the developing world.
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Posted by Eva St. Clair at 0:39
03 October 2000
CNR Joins in Agricultural Genomics Institute
Governor Gray Davis has allocated $300 million to fund the creation of three new research initiatives on University of California campuses, to be known as the California Institutes for Science and Innovation. The College of Natural Resources, in partnership with the Riverside and Davis campuses, is participating in an effort by the University of California to create a California Institute for Agricultural Genomics.
The proposed Agricultural Genomics Institute was selected as one of six finalists eligible to submit a fully developed proposal. If established the Institute will unite more than 200 scientists with expertise in plant and microbial biology, nutrition and animal science from the three campuses in efforts to improve agricultural efficiency, minimize crop loss due to pests and disease and develop nutritional and bio-based products to promote health and well-being. Full proposals are due October 6, 2000. Funding decisions are expected in late November.
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Posted by Eva St. Clair at 4:02
13 December 2000
CNR professor shares success of sequencing first plant genome
By Catherine Zandonella, Media Relations
In a major step for plant biology and agricultural science, scientists have completed the sequencing of the first plant genome, that of a mustard weed known as Arabidopsis thalania. The announcement, published Thursday, Dec. 14, in the journal Nature, marks the completion of a five-year effort that included key contributions from plant molecular biologist Athanasios Theologis, an adjunct professor in the Department of Plant & Microbial Biology at the University of California, Berkeley, and a senior scientist at the UC Berkeley/USDA Agricultural Research Service Plant Gene Expression Center in Albany, Calif.
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Posted by Eva St. Clair at 4:01
12 March 2001
Jumping Genes Stabilize GM Cereals
Continue reading "Jumping Genes Stabilize GM Cereals" » | Permalink
Posted by Eva St. Clair at 3:54
24 July 2003
Research Challenges Theory that Microbes Follow Different Evolutionary Rules as Higher Organisms
by Sarah Yang
Berkeley - A new study led by researchers at the University of California, Berkeley, has found genetic differences in a sampling of a species of hot spring-loving microbes from around the world.
The findings, published online today (Thursday, July 24) by the journal Science, at the Science Express website, challenges the prevailing theory of microbial biodiversity.
It is well accepted in evolutionary science that species of animals and plants are more closely related when they are geographically near each other. When it comes to the tiny world of microbes, however, most scientists believe that different evolutionary rules apply.
"The current dogma has been that, for microbes, what determines diversity is not geographic distance but specific environments," said John Taylor, professor of plant and microbial biology at UC Berkeley's College of Natural Resources and the head of the lab where the study was conducted. "The motto for microbes has been, 'Everything is everywhere, but the environment selects.' "
To test this theory, Rachel Whitaker, a UC Berkeley graduate student in Taylor's lab and lead author of the paper, trekked around the globe - by helicopter in some remote areas - to collect samples of a microbe called Sulfolobus islandicus, which thrives in the extreme environments of geothermal hot springs and volcanic vents. Sulfolobus microbes belong to the domain archaea - discovered in the 1970s - and can withstand highly acidic conditions and temperatures as high as 180 degrees Fahrenheit.
The samples were collected from the Mutnovsky Volcano and the Uzon Caldera-Geyser Valley region on the Kamchatka Peninsula in eastern Russia, the Lassen Volcanic and Yellowstone national parks in North America, and the volcanic region of western Iceland.
The researchers' analysis also includes a large portion of previously collected Sulfolobus samples that were provided by co-author Dennis Grogan, associate professor of biological sciences at the University of Cincinnati.
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Posted by Eva St. Clair at 1:21
30 October 2003
Scientists Accurately Map Plant Genome, Which Could Lead to New Generation of Hybrid Crops
by Sarah Yang
Berkeley - In a study led by researchers at the University of California, Berkeley, and the Salk Institute in La Jolla, Calif., scientists have accurately mapped the genes of the common mustard weed, Arabidopsis. The achievement may lead to the next generation of genetically modified crops that can grow faster, produce more food and resist disease.
The study, which appears in the Oct. 31 issue of Science, reveals the existence of nearly 6,000 genes, about one-third of the genes that exist in Arabidopsis. Knowing these genes and how they work can allow researchers - in a short period of time - to use them to change the characteristics of other plants.
"Arabidopsis has all the genes a plant needs," said Joe Ecker, Salk professor of plant biology. "All flowering plants are closely related, and so the genes that encode various traits are also shared. It's possible, then, to take a gene for flowering from Arabidopsis and insert it into rice or poplar, and have that gene function."
Ecker and Athanasios Theologis, adjunct professor at UC Berkeley's College of Natural Resources and senior scientist at the Plant Gene Expression Center, are the principal investigators on the project, which includes a team of 72 scientists from nine institutions in the United States and Japan. The Plant Gene Expression Center is a collaboration between UC Berkeley's Department of Plant and Microbial Biology and the USDA's Agricultural Research Service.
The findings revealed some shortcomings of computer-based gene prediction programs, including those that have been used to sequence the human genome and the Arabidopsis plant - the plant biologists' equivalent of the fruit fly for genetics research.
The researchers point out that computer algorithms can't always distinguish whether a piece of code corresponds to a single gene or to two overlapping genes. And while the programs have become increasingly accurate in recent years, the researchers added, computer programs may still put genes' parts in the wrong places, find genes that aren't really there, or miss genes altogether. What researchers say they often get from an initial sequence of a genome is a "best-estimate" lineup of transcription units.
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Posted by Eva St. Clair at 5:56
02 February 2004
Scientists Obtain First Genomes of Microbes Directly from Environment
by Robert Sanders
Berkeley - In the first triumph of a field dubbed "environmental genomics," scientists at the University of California, Berkeley, in collaboration with the Joint Genome Institute, have for the first time sequenced the genomes of the most abundant members of a community of organisms - not one at a time, but simultaneously.
The researchers took a simple community of microbes from a pink slick on the floor of an abandoned mine, ground them up, and shotgun sequenced the lot. As they put the pieces of DNA back together, the snippets fell easily into five distinct genomes, four of them unknown until now.
"This is the first recovery of a genome from an environmental sample," said Jillian F. Banfield, professor of earth and planetary science and of environmental science, policy and management at UC Berkeley. "This ushers in a whole new way of exploring and understanding our environment, allowing us to determine how organisms work as individuals and together, and how they contribute to geochemical processes."
Banfield and graduate student Gene W. Tyson from UC Berkeley's Department of Environmental Science, Policy and Management, with colleagues from UC Berkeley and the U.S. Department of Energy's Joint Genome Institute (JGI) in Walnut Creek, Calif., report their feat this week in the Advance Online Publication of the journal Nature.
Banfield and her students, post docs and colleagues are primarily interested in how the microbes, obtained from the Richmond Mine in Iron Mountain, Calif., one of the largest Superfund sites in the country, interact with minerals to produce acid mine drainage.
"Acid mine drainage is one of the most pressing long-term environmental problems worldwide, and it's caused by microbial processes," Banfield said. "This study has dramatically improved our understanding of the microorganisms involved and has opened the way for development of much more highly refined models of acid mine drainage systems."
"If we understand the organisms and how they cause this environmental problem, we can try to do something about it in the long run," Tyson added.
"This represents an important example of how the production sequencing capacity developed by the Department of Energy at the JGI for the human genome program can provide fundamental insights into vital environmental problems," said JGI Director Eddy Rubin.
Understanding the biofilm ecosystem also may be relevant to the search for life on Mars, since it's conceivable that the iron and sulfur-rich surface of Mars could harbor microbes that eat iron, similar to those in iron and sulfur-rich pyrite mines like the Richmond Mine.
For the past nine years, Banfield has been studying a pink microbial biofilm that sits like scum on the surface of green pools of water, as acidic as battery acid, in the dark depths of the Richmond Mine, located nine miles northwest of Redding. Her goal is to understand how the extremophiles - microbes that live in extreme environments - live together and generate the acid drainage that makes such mines toxic hazards. The green runoff from the mine, captured and treated by the Environmental Protection Agency, is not only acidic, but also contains high levels of toxic metals - zinc, iron, copper and arsenic - and is a piping 108 degrees Fahrenheit.
In this low-light, low-oxygen, high-acid and toxic environment about 1,400 feet into the mountain, the microbes thrive. They fix carbon and nitrogen from the carbon dioxide and nitrogen in the air, eat iron by oxidizing it with oxygen, and in the process dissolve the iron pyrite (iron sulfide, also known as fool's gold) to create sulfuric acid.
Previously, researchers have studied microbial communities, such as those in hot springs or in the ocean, either by isolating individual organisms or strains, culturing them and sequencing the cultured population; or by plucking bits and pieces of genes from the various members of the community.
A big problem is that only about one in 100 microbes can be cultured sufficiently to extract its genome. Even if a microbial genome is known, however, this still doesn't tell researchers how it interacts with other microbes in its environment.
Banfield and other researchers have been looking at a more daring approach - sequencing the whole community at once, a technique Banfield prefers to call "community genomics." That's like surveying the species in the African veldt by grinding up lions, zebras, elephants and an unknown number of other animals, cutting the genes into tiny pieces, and trying to sort them into distinct genomes.
But it works, Banfield said, "at least with the small number of distinct organisms in this community."
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Posted by Eva St. Clair at 0:31
12 October 2009
Professor Honored for Outstanding Contributions to California Forestry
The California State Board of Forestry and Fire Protection presented the Francis H. Raymond Award for Outstanding Contributions to California Forestry to Dr. William Libby on October 7, 2009.
Dr. Libby is Professor Emeritus of Forest Genetics, having taught forestry at the College of Natural Resources in the Department of Environmental Science, Policy, and Management between 1962 and 1994. His pioneering work in the field of forest tree genetics is internationally recognized and respected. Dr. Libby has practiced forestry on several continents and is well known for his work with California’s coast redwood and Monterey pine trees.
Though he officially retired in 1994, Dr. Libby has continued to educate and enlighten across the borders of country and perspective. He currently sits on the Board of the Save the Redwoods League with a focus on promoting research on redwood forest disturbance effects and the impacts of climate change on California’s coast redwood and giant sequoia forests. Dr. Libby’s observations on state and national forest policy are reflective of his insight and intellectual curiosity. His dedication in service to the forests of California and elsewhere is inspirational.
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Posted by Eva St. Clair at 7:59
02 July 2009
Tougher controls sought for DNA ancestry testing
As the popularity of take-home DNA kits to trace ancestry or calculate the risk for serious medical conditions grows, there is an increasingly critical need for federal oversight of "direct-to consumer" genetic testing, as well as of the use of DNA samples for research, according to researchers from the University of California, Berkeley, and several other academic institutions.
In the past year, scientists, sociologists and bioethicists, among others, have come to agree that the technology of these direct-to-consumer tests, which run between $100 and $1,000 apiece, is problematic and that the test results can be misleading and lead to problems including skewed ethnic data and questionable membership claims to Native American tribes.
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Posted by Cyril at 5:29
06 July 2009
Growing young scientists in Tahiti
A University of California, Berkeley, project to catalog nearly every living thing on the Polynesian island of Moorea is enlisting the help of the island's 5th graders and showing them that science is not for foreigners only.
While conducting research for his thesis and for the Moorea Biocode Project, ESPM graduate student Brad Balukjian has been teaching 5th graders at the Paopao Primary School about biodiversity and introducing them to the scientific study of the plants and animals they see every day.
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Posted by Cyril at 5:22
30 October 2008
Indonesian biodiversity grant, CNR toxicologist seeks to discover human health solutions in Indonesian biodiversity
University of California scientists have received a five-year, $4 million grant to study the biodiversity of fungi, bacteria, plants, insects and vertebrates on the Indonesian island of Sulawesi, a southeast Asian island threatened by the loss of biodiversity in its tropical forests.
An international team of collaborators will conduct biodiversity surveys, screen microbes and plants for applications to human health and energy needs, recommend strategies to conserve endangered species, and develop and encourage local conservation. The project is organized into six associate programs -- five led by UC Davis scientists while one program, focusing on discovery of human health solutions is being led by Len Bjeldanes, professor of toxicology at CNR.
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Posted by Cyril at 2:01
27 February 2009
UC Berkeley researchers explain key mechanism of inheritance that defies Mendel’s first law of genetics
FOR IMMEDIATE RELEASE
Researchers at the University of California, Berkeley, have discovered a key mechanism responsible for a curious type of genetic inheritance that has been one of the great, unsolved mysteries in biology. The new findings, to be published today (Friday, Feb. 27) in Science, help explain the phenomenon of paramutation, in which certain alleles are heritably altered while their DNA sequences remain unchanged.
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Posted by Cyril at 1:50
09 September 2008
$1.4 M grant funds PMB researcher's work on "jumping genes"
Damon Lisch, Ph.D., a research professional in the Department of Plant and Microbial Biology was recently awarded a grant from the National Science Foundation’s Plant Genome Research Program.
The four-year, $1.4 million award supports research on the ways in which genomes recognize and inactivate “jumping genes,†or transposons.
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Posted by Cyril at 0:34
16 April 2008
Sudden Oak Death pathogen is evolving, says new study that reconstructs the epidemic
BERKELEY – The pathogen responsible for Sudden Oak Death first got its grip in California's forests outside a nursery in Santa Cruz and at Mt. Tamalpais in Marin County before spreading out to eventually kill millions of oaks and tanoaks along the Pacific Coast, according to a new study led by researchers. It provides, for the first time, evidence of how the epidemic unfolded in this state.
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Posted by Cyril at 0:33
22 May 2008
Rapid escalation characterizes arms race between virus and host
BERKELEY – The interaction between a virus and its host is often portrayed as an arms race, with each new viral attack parried by the host and each new defense by the host one-upped by the virus.
Researchers have for the first time documented this arms race within the genes of both the virus and its host.
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Posted by Cyril at 0:15
10 July 2008
Genes could solve pollution mysteries
Researchers have for the first time identified environmental pollutants by looking at the genes of a small, freshwater crustacean. This new gene-based technique could lead to better and faster lab tests for pinpointing pollutants in contaminated ecosystems.
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Posted by Cyril at 9:14
06 December 2007
$5.2 million grant from Moore Foundation funds ambitious project to barcode an entire ecosystem
In the middle of the South Pacific, about 12 miles west of Tahiti, is a tropical island that soon will emerge as a model ecosystem, thanks to the efforts of a U.S.-French research team led by University of California, Berkeley, biologists.
Video: Cataloging an ecosystem |
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Posted by Cyril at 0:24
26 April 2007
Video: Sudden Oak Death expert on KQED Quest
Devastating over 1 million oak trees across Northern California in the past 10 years, Sudden Oak Death is a killer with no cure. But biologists including CNR's Matteo Garbelotto are looking to the trees' genetics for a solution.
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Posted by Cyril at 9:30
13 November 2007
The Secrets in Your Genome
A personal DNA sequence
is not yet practically useful.
But it could be, argues Prof. Steven Brenner, if we had the right resources.
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Posted by Cyril at 1:18
14 March 2007
Mine Runoff Continues To Provide Clues To Microbial Diversification
Pink slime at the surface of water trickling through an old mine in California is proving to be a treasure for researchers in their quest to learn more about how bacterial communities exist in nature.
Continue reading "Mine Runoff Continues To Provide Clues To Microbial Diversification" » | Permalink
Posted by Cyril at 0:44
18 November 2006
Undergrad Laura Lagomarsino maps ancestral relationships using genetics
Lagomarsino, third year in Plant Biology, is using nuclear and chloroplast genes to develop a phylogeny, or map of ancestral relationships between species of the genus Heliconia, a tropical plant. Her mentor, Assistant Professor Chelsea Specht in the department of Plant and Microbial Biology, uses molecular and evolutionary biology to understand lineages of related plants.
SPUR funding has allowed Specht to provide Lagomarsino with necessary laboratory materials to expand her research.
The SPUR program offers students a unique opportunity to develop as scientists with a level of independence that has often been reserved for graduate students. Not only does this help make Berkeley students more competitive, it develops of the kind of creative thinking skills so essential to the success of any scientist. “You learn all the techniques†says Lagomarsino, “But then you are also given a certain amount of freedom, and your thoughts are valued.â€
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Posted by Cyril at 1:19
02 December 2006
Undergrad Matt Stuckey uses DNA to understand butterfly evolution in the Sierra
Matthew Stuckey, fourth year in Environmental Economics and Policy and Conservation Resource Studies, is researching how the butterfly Colias behrii colonized the Sierra Nevada.
Through mentorship with Professor George Roderick and graduate student Sean Schoville, Stuckey has been working on cloning nuclear genes to assess genetic variation within and among populations of C. behrii.
Roderick’s team is using genetics to understand how organisms have colonized new areas. SPUR funds have helped provide chemicals and lab supplies necessary for molecular cloning – a technique essential for Stukey’s research.
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Posted by Cyril at 0:49
02 January 2007
Undergrad Subhajit Poddar researches genetics of green algae
Until he met the slimy green algae called Chlamydomonas, undergraduate Subhajit Poddar didn’t know he was interested in plant biology. “Once I began working with mutant strains of algae, I was totally hooked,†he says.
Poddar, fourth year in Plant and Microbial Biology, studies the green algae Chlamydomonas under the mentorship of Professor Krishna Niyogi. His research has focused on identifying and cloning genes responsible for two compounds involved in photosynthesis.
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Posted by Cyril at 0:33
02 January 2007
Shotgun sequencing finds nanoorganisms
 |
| The smallest form of life known to science could fit into the period at the end of this sentence. |
For 11 years, Jill Banfield has collected and studied the microbes that slime the floors of mines and convert iron to acid, a common source of stream pollution around the world.
Imagine her surprise, then, when research scientist Brett Baker discovered three new microbes living amidst the bacteria she thought she knew well. All three were so small - the size of large viruses - as to be virtually invisible under a microscope, and belonged to a totally new phylum of Archaea, microorganisms that have been around for billions of years.
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Posted by Cyril at 6:24
20 December 2006
New study shows promise of genomics in monitoring environmental toxicology
A new study led by researchers from the Department of Nutritional Sciences and Toxicology identifies specific gene expression changes in a species of water flea in response to contaminants, lending new support for the role of toxicogenomics in environmental monitoring.
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Posted by Cyril at 9:57
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