DOE Joint Genome Institute in the News

Permafrost study referenced in ScienceNews

2012-01-17T11:15:00.000-08:00

In Nature in December, a team of researchers at the Department of Energy’s Joint Genome Institute in Walnut Creek, Calif., and colleagues reported one such microbe’s draft genome — put together from DNA acquired from the semifrozen dirt in an Alaskan black spruce forest. The Alaskan microbe carries genes tuned to transform organic matter into methane, a finding that may one day help provide a vivid picture of what will happen as soil conditions change.

DOE JGI Science Highlights: A toolkit for T. reesei

2012-01-13T14:00:00.000-08:00

The availability of anorganism’s genome sequence is useful for improving downstream applications suchas large-scale biofuel production, but it isonly the first step on this path. In the case of the fungus Trichoderma reesei, whose genomesequence was published by the DOE JGI in 2008, the cellulases in T. reesei have multipleindustrial applications, but fungal strains have traditionally been developedby random mutagenesis.

T. reesei (Image by Irma Salovuori, VTT Biotechnology)

1000 Fungal Genomes project in The Daily Barometer

2012-01-12T16:07:00.000-08:00

Joey Spatafora, an associate professor at Oregon State University, is leading an international project to sequence the genomes of a thousand fungi, a project aptly named 1000 fungal genomes. "It's a really, really exciting time in fungal biology because we can sequence fungal genomes more easily than we could ten years ago," Spatafora said.

Cotton project in the Delta Farm Press

2012-01-07T12:09:00.000-08:00

An international consortium, led by Professor Andrew Paterson of the University of Georgia, has made publicly available the first ‘gold-standard’ genome sequence for cotton. Cotton was among the first plants studied at the molecular level, and the sequence obtained by Paterson and his team is the culmination of a 20-plus year effort in the analysis of cotton genes and genomic DNA.

DOE JGI Science Highlights: Cyanobacteria shed light on carboxysome complexity

2011-12-16T13:17:00.000-08:00

Found in temperate andtropical oceans, Prochlorococcus cyanobacteria are considered theworld’s most abundant photosynthetic organisms, able to convert sunlight toenergy at depths of 200 meters. Despite their size, they are estimated tocontribute up to half of the marine biological carbon sequestration.

Prochlorococcusis a unicellular cyanobacterium that dominates the temperate andtropical oceans.

(Image courtesy of C.Ting, J.King, S.W.Chisholm, 1999)

Permafrost metagenome study on VOA Special English report

2011-12-13T17:22:00.000-08:00

The researchers say one gram of the soil could contain thousands of different kinds of microbes and billions of cells. They say these organisms had never before been cultured in a laboratory.

JANET JANSSON: “So more than ninety percent of those bacteria and other microorganisms in permafrost, we had no idea what they were.”

Read the full story and listen to the report from VOA Special English

DOE JGI Science Highlights: Boosting knowledge of nitrogen-fixing bacteria

2011-12-09T13:45:00.000-08:00

No plant is an island;interactions with complex microbial communities both above the ground and belowthe ground shape the plant’s growth rates and overall health. Understandingthese plant-microbe interactions can lead to improvements in plant health andproductivity and carbon sequestration, which can be applied toward DOE missionsin bioenergy and biogeochemistry.

Dark-fieldphoto of Frankia vesicle clusters (single plant cellsfilled with the filamentous organism)

that have broken free from nodules in theplant Coriaria arborea.

(Image courtesy of David Benson,University of Connecticut)

Tanja Woyke: Genome Technology 2011 Young Investigator

2011-12-05T09:05:00.001-08:00

What inspired Tanja Woyke to pursue her current area of focus is also what makes it possible: single-cell genomic technology. "It allows one to sequence the genome of one individual microbial cell by amplifying its genome a billion-fold using a process called multiple displacement amplification," she says. "I find this quite fascinating. Such an approach was unthinkable 10 years ago."

DOE JGI Science Highlights: Engineering bacteria to produce biodiesel

2011-12-02T14:46:00.000-08:00

Biodiesel productiontypically starts with oil-rich energy crops such as soybean, palm or rapeseed,which are harvested and then converted into fatty acids for use as fuel. Thecost of expanding oilseed crop production is a limiting factor in allowing biodieselto compete with fossil fuel sources.

Electronmicrograph of an E.coli bacterial cluster

(Image by Eric Erbe;Colorization, Christopher Pooley. USDA)

Spider mite genome project in CBC News

2011-11-28T08:57:00.001-08:00

"They can change the repertoire [of genes] that they're using in order to be able to feed on hosts that they would not be adapted to," said Miodrag Grbic, a University of Western Ontario biologist, who led an international project to sequence the spider mite's genome. The results were published this week in the journal Nature.

DOE JGI Science Highlights: Mite genome to help protect bioenergy feedstocks

2011-11-23T14:06:00.001-08:00

The tiny two-spottedspider mite extracts nutrients from the leaves of 1,100 plant species includingbioenergy feedstock crops. The global cost of chemically controlling this pest isestimated to be around $1 billion annually.

SEMimage of the two-spotted spider mite T. urticae.

(Imageby Stephane Rombauts and Wannes Dermauw, Ghent University, Belgium)

Spider mite genome project in GenomeWeb

2011-11-23T12:29:00.000-08:00

The spider mite, named for its ability to spin webs, belongs to an arthropod sub-group comprised of so-called chelicerates and is capable of consuming more than 1,100 plant species. This trait, coupled with its ability to develop resistance to most commonly used pesticides, have made it a potent pest, known for damaging ornamental plants and a range of field and greenhouse crops, from corn or soybean crops to strawberries or tomatoes.

DOE JGI Science Highlights: New tools for the IMG/M analysis system

2011-11-18T14:02:00.000-08:00

Since the initialrelease of the Integrated Microbial Genomes with Microbiome samples (IMG/M) system in 2007 to support the comparativeanalysis of metagenomic data sets, DOE JGIresearchers have made several updates in order to keep pace with the rapidincrease in data set generation due to advances in sequencing technologies.

Victor Markowitz (left) and Nikos Kyrpides (right)

DOE JGI research featured in io9

2011-11-16T12:31:00.001-08:00

Last month I was lucky enough to visit one of the biggest genomics labs in the world. At the Joint Genome Institute (JGI) in Walnut Creek, CA, huge rooms full of genome sequencing machines work 24/7 to crunch the codes that create life. And the research here, funded by the US Department of Energy, has a purpose. The biologists and geneticists at JGI, several of whom helped sequence the first human genome in the 1990s, are trying to unlock the secret of sustainable biofuels that enhance the environment.

DOE JGI Science Highlights: Microbial response to the thawing Arctic

2011-11-11T13:56:00.000-08:00

The frozen Arcticsoils keep an estimated 1,672 billion metric tons of carbon out of the Earth’satmosphere, more than 250 times the amount of greenhouse gas emissionsattributed to the United States in the year 2009. Rising global temperatureshave led to increasing concerns on the potential impacts of thawing permafrostupon the carbon cycle.

USGSresearchers tap the Arctic permafrost for soil samples that can be studied toassess

their microbial composition and the impact of these populations bythawing conditions.

(Courtesy of Mark Waldrop, USGS Soil Carbon Research)

Danforth Center highlights plant projects for CSP 2012

2011-11-10T10:52:00.001-08:00

The U.S. Department of Energy (DOE) Joint Genome Institute (JGI) has selected two projects from a highly competitive pool of applications, submitted by Danforth Plant Science Center Principal Investigators, Dr. Thomas Brutnell and Dr. Todd Mockler as part of its 2012 Community Sequencing Program (CSP).

Read more at the Danforth Center News site.

Permafrost soil metagenome study in Wired UK

2011-11-09T11:18:00.000-08:00

As permafrost thaws, trapped frozen organic matter becomes accessible for microbes to degrade, releasing greenhouse gases as a byproduct. Understanding what sorts of microbes are in the ice is key to predicting the impact of the melting of permafrost soils.
The US Department of Energy has teamed up with the Joint Genome Institute, the Earth Sciences Division of Berkeley Lab and the US Geological Survey to understand how microbes found in the permafrost might respond to a warming environment.

Permafrost soil metagenome study on Voice of America

2011-11-09T09:13:00.000-08:00

Lead author Janet Jansson, senior scientist at the Lawrence Berkeley National Laboratory in California says the trapped microorganisms in permafrost are still active.
Jansson and colleagues at the U.S. Geological Survey and the Joint Genome Institute at the Department of Energy set out to identify microbes in permafrost and find out what they would do once thawed.

Permafrost soil metagenome study on Medill News Reports

2011-11-08T17:05:00.000-08:00

Microbes frozen for thousands of years can spring to life and digest the carbon to release heat-trapping gases into the atmosphere, amplifying warming and melting. Scientists can't yet predict how much of the carbon stored in Arctic permafrost will reach the atmosphere, but microbes could play a pivotal role.

DOE JGI sequencing capabilities in InSequence

2011-11-08T14:14:00.000-08:00

The US Department of Energy's Joint Genome Institute is tweaking its sequencing technology lineup as it gears up to produce more than 47 trillion bases of DNA sequence in the 2012 fiscal year, with more than half that sequencing output slated to go toward its largest user program, the Community Sequencing Program.

Permafrost soil metagenome study on Examiner.com

2011-11-07T16:12:00.000-08:00

The carbon dioxide contained in the polar caps is estimated to be 1,672 billion metric tons. The slow but steady melting of the polar regions from global warming has and will continue to release more carbon as carbon dioxide as the ice sheets melt.More interesting and more potentially dangerous is the effect that melting ice sheets can have on the microbes and bacteria that live in the permafrost. There are literally thousands if not millions of unknown species of microbes and bacteria that inhabit the permafrost.

CSP 2012 project on Science Codex

2011-11-07T16:08:00.000-08:00

Dan Lindner, a research plant pathologist with the Northern Research Station's Center for Forest Mycology Research (CFMR), is one of 13 scientists participating in the '1000 Fungal Genomes' project, which in collaboration with the Department of Energy's (DOE) Joint Genome Institute will sequence two species from every known fungal family. The project is a first step in creating an encyclopedia of all fungi, which will one day help researchers understand not only what they do, but how fungi operate.The '1000 Fungal Genomes' project was one of 41 research projects awarded funding through the Department of Energy's 2012 Community Sequencing Program (CSP), the DOE announced November 3.

Permafrost soil metagenome study in Gizmodo

2011-11-07T14:21:00.000-08:00

A team of researchers from Berkeley took chunks of permafrost soil from Alaska, and shipped them back to the lab to thaw them out in controlled conditions. As they woke up, the gassy little microorganisms trapped in the melting ice spewed out more methane than the contestants in a bean-eating competition.

Permafrost soil metagenome study in Alaska Dispatch

2011-11-07T14:19:00.000-08:00

Researchers have carted chunks of Alaska permafrost off to California, where have learned that allowing the once frozen soil to thaw wakes up hungry microbes, according to newscientist.com, which also offered a cautionary tale.

Permafrost soil metagenome study in Discover

2011-11-07T13:33:00.001-08:00

What’s the News: Melting permafrost in a warming world could mean lots of greenhouses gasses, especially methane, released into the atmosphere. But it also means an unusual community of soil bacteria coming out of hibernation, so to speak. A new study looks at what those permafrost microbes do, exactly, as their environment warms up.

Permafrost soil metagenome study in Time

2011-11-07T13:32:00.000-08:00

One of those wild cards is the 1,672 billion tonnes of carbon equivalent trapped in the form of methane in the Arctic permafrost, the soils kept frozen by the far North's extreme temperatures. Methane is a powerful greenhouse gas—it has 20 times the warming effect of carbon dioxide—and the total amount of carbon equivalent in the Arctic permafrost is 250 times greater than annual U.S. greenhouse gas emissions. As the Arctic warms—which it's doing rather rapidly—there's a risk that the permafrost could become less than permanent, releasing some of that trapped methane into the air, which would then accelerate warming, leading to more Arctic melt, more methane emissions...so on and so on. Climate scientists call this a "feedback loop"—and if it happens soon, you could just call us screwed.

Permafrost soil metagenome study on LiveScience

2011-11-07T09:48:00.000-08:00

"Nobody has looked at what happens to microbes when the permafrost thaws," said Janet Jansson, a senior staff scientist at Lawrence Berkeley National Laboratory in California. She led a study that recorded what happened when chunks of Alaskan permafrost thawed for the first time in 1,200 years.

Permafrost soil metagenome study in UK Press Association

2011-11-07T09:25:00.000-08:00

At the testing laboratories, US researchers extracted almost 40 billion elements of raw DNA, reflecting high microbial diversity in the soil.The scientists were also able to piece together the genetic code, or genome, of a previously unknown methane-producing "methanogen" that was present in large numbers. Reporting their findings in an early online edition of the journal Nature, the researchers led by Dr Janet Jansson, from the Lawrence Berkeley National Laboratory in California, wrote: "This is the first example of a successful assembly of a draft genome of a novel methanogen.

Permafrost soil metagenome study in GenomeWeb

2011-11-07T09:16:00.000-08:00

"Currently in climate models, it's not really taken into account adequately what the microorganisms are doing," senior author Janet Jansson, a researcher affiliated with the Lawrence Berkeley National Laboratory and the US Department of Energy's Joint Genome Institute, told GenomeWeb Daily News. "The hope is to get enough information at the microscopic level that we'll have enough understanding to be able to inform climate models."

DOE JGI science in the Washington Post

2011-11-05T12:43:00.000-07:00

JGI director and geneticist Eddy Rubin is a pioneer in the field of “metagenomics,” the study of how the DNA in many creatures can work together to create ecosystems. Right now, he and his team are studying microbes that live in a cow’s rumen, the stomach-like organ that the animals use to break down grasses into fuel. All their results are published publicly online, for scientists and entrepreneurs to mine for ideas and to prevent unnecessary duplication of research.

DOE JGI Science Highlights: A metagenomic approach to analyzing rice endophytes

2011-11-04T14:21:00.000-07:00

During the call for 2012 proposals for the DOE JGI’s Community Sequencing Program, one of the areas of focus researchers were asked to consider was that of plant-microbe interactions. Microbes that live in plants or in the rhizosphere where plant roots and soil interact can play crucial roles in plant health. This is of particular interest to bioenergy researchers who want to develop feedstock crops for cellulosic biofuels production.

by jonrawlinson

With this in mind, an international team of researchers including DOE JGI Microbial Genomics Program Lead Tanja Woyke conducted the first metagenomic analysis of a microbial community of endophytes found inside rice plant roots. The study was published online October 4, 2011 in Molecular Plant-Microbe Interactions.

Read more »

CSP 2012 announcement in GenomeWeb Daily News

2011-11-04T13:34:00.000-07:00

The Department of Energy's Joint Genome Institute has chosen 41 research projects out of 152 applicants to use its sequencing services under its 2012 Community Sequencing Program, JGI said Thursday.Researchers for this year's CSP program, which provides the scientific community with access to JGI's high-throughput sequencing technologies, proposed projects to study plant-microbe interactions, how microbes are involved in carbon capture and greenhouse gas emission, and metagenomics.

DOE JGI Science Highlights: Tension wood study helps tailors bioenergy feedstock

2011-10-28T13:04:00.000-07:00

When the DOE JGIpublished the poplar genome sequence analysis in 2006, it bolstered severalresearch efforts to fully develop that tree’s potential as a candidate bioenergy feedstock.

Poplarstems (left) respond to bending stress by producing tension wood.

Electronmicrographs from a comprehensive BESC study reveal how tension wood (bottomright)

develops a secondary cell wall layer, in contrast to normal wood (topright). (Image courtesy of ORNL)

In a report publishedonline October 4, 2011 in Energy & Environmental Science, DOE JGI’s Gerald Tuskan at Oak Ridge NationalLaboratory, theproject lead on the poplar genome project, and colleagues at the BioEnergy Science Center at ORNL turned theirattention on a characteristic of poplar trees that could be useful forincreasing available sugars and ultimately, biofuelsyield from trees.

DOE JGI Science Highlights: UV treatments for contaminated MDA reagents

2011-10-21T11:59:00.000-07:00

Single cell genomicsis a method used by researchers to get around the research roadblock thrown upby the need for large amounts of microbial DNA in order to do traditionalsequencing techniques. In this process, a single cell isolated from anenvironmental sample is amplified to make millions of copies of the microbialgenome for sequencing.

Sequencesderived from the single amplified genomes in the study were mapped to
referencegenomes such as P.fluorescens (Image by Ninjatacoshell/Wikimedia Commons)

Berkeley Lab Open House recap on Today at Berkeley Lab

2011-10-17T11:12:00.000-07:00

At DOE JGI's metagenomics of restored wetlands exhibit

Most notable among the crowd of thousands was the number of youngsters who were in attendance. Families were enthralled by the terrific science, engineering, and operations efforts presented at the various booths.

Director Rubin on corngrass1 for biofuel

2011-10-12T09:23:00.000-07:00

Up to now, the fast-growing switchgrass, because of its tough lignin, an organic polymer, has required heavy chemical treatment before it can be turned to ethanol as biofuel. Chuck's gene transfer experiments have shown that because the improved switchgrass keeps the plants young, the lignin content of their cells is minimal and would need no chemical treatment, he reported.

DOE JGI Science Highlights: Fungal enzymes to improve biomass pretreatment processes

2011-10-07T13:58:00.000-07:00

Many of the enzymescurrently being used in the pretreatment processes for cellulosic biofuels production come fromspecies that thrive at temperatures comfortable to humans (68°F-95°F).

To speed up thisprocess of converting polysaccharides to fermentable sugars, a goal driven bythe nation’s Renewable Fuels Standard requirement that calls for the annualproduction of 36 billion gallons of biofuelby 2022, researchers propose raising the temperature of the reaction. Thisproposed change in the process in turn requires enzymes from species that cantolerate hotter environments.

Thermophilic fungus M. thermophila

(Micrograph by Ronald de Vries, CBS-KNAW Fungal Biodiversity Centre. Image enhanced by Michelle Wyse)

Of Soil Carbon and Climate Change

2011-10-06T10:10:00.000-07:00

Thanks to genome sequencing techniques such as those at the Department of Energy’s Joint Genome Institute in Walnut Creek, California, we now have a much better idea of what microbes are in soil, what they’re doing, and what proteins they’re producing. That’s important, because a handful of soil can teem with millions of microbes, some of which break down soil organic matter.

Read more at the Berkeley Lab Newscenter

Thermophilic fungi in Scientific American

2011-10-05T11:39:00.000-07:00

Heat-loving fungi could provide a key enzyme for making low cost biofuel, and a team of "mushroom detectives" from the Department of Energy's Joint Genome Institute think they've just nailed their man - er, fungus.

Thermophilic fungi in energyNOW!

2011-10-04T14:48:00.000-07:00

Next-generation biofuel refining is based on tweaking enzymes to break down plant walls and convert biomass to fermentable sugars. The research has two main goals. One is to find ways to cut down the energy input needed for biofuel processing.

Thermophilic fungi in Walnut Creek Patch

2011-10-03T14:30:00.000-07:00

Research on fungi at the Joint Genome Institute in Walnut Creek is heating up the nation's efforts to develop biofuels as an alternative to fossil fuels.

DOE JGI Science Highlights: Structural Analysis of Cow and Hoatzin Microbial Communities

2011-09-30T14:18:00.000-07:00

Inside the guts ofmany animals, microbes break down the plant fibers ingested as part of theirdiet. These microbes are of interest to bioenergy researchers who want to learn from nature and apply these cellulosicdegradation capabilities toward biofuelproduction. To this end, at the DOE JGI, several sequencing projects havefocused on the microbial communities in the guts of organisms such as termites,cows, and Tammar wallabies.

Hoatzin(Image by Maria G. Dominguez-Bello, University of Puerto Rico)

DOE JGI Science Highlights: Genomic analysis of self-fertilizing fungi

2011-09-23T14:00:00.000-07:00

Filamentous fungi helpdecay plant material, a process which has applications for producing biofuels and other products.The model organism for filamentous fungi is Neurospora tetrasperma, a plant pathogenthat is also self-fertilizing.

Neurospora tetrasperma rosette (Image by Namboori B. Raju, Stanford University)

Selected for the DOE JGI’s 2007 Community Sequencing Program, the fungi is of interest to researchers such as studying lignindegradation, and its genome allows for broader comparative analyses with otherorganisms that range in genomic divergence by nearly 100 million years.

DOE JGI's Tringe in PopSci's Brilliant 10

2011-09-20T08:53:00.000-07:00

Susannah Green Tringe of the DOE Joint Genome Institute (DOE JGI) has been named one of 2011’s "Brilliant 10," the annual list compiled by Popular Science magazine of top young researchers. In adding her name to the list, which appears in the October issue, the magazine recognized her $2.5 million grant from the DOE Early Career Research Program to study the role of microbial communities in restored wetlands in the San Francisco Bay-Delta region of California and their impact on long-term carbon sequestration.

Read more of the DOE JGI's announcement.

DOE JGI Science Highlights: Soil biocrust microbial genome

2011-09-16T13:30:00.000-07:00

One of the DOE JGI’s 2011 Community Sequencing Program projects involves studying biological soil crusts tounderstand their role in the global carbon cycle. Found in arid lands whichmake up nearly half of the planet’s total land mass, communities of lichens,mosses and cyanobacteria use soil particles toform biocrusts less than half aninch in depth.

Biologicalsoil crusts are specialized communities of cyanobacteria, mosses, and lichens.

(Image courtesy of USGS Canyonlands Research Station/soilcrust.org)

DOE JGI Science Highlights: High-temperature enzymes for biomass breakdown

2011-09-09T17:27:00.000-07:00

To overcome thechallenge of breaking down cellulosic biomass for commercial biofuel production, whichinvolves the application of high temperatures, a team of researchers includingDOE JGI’s Martin Allgaier, now at theLeibniz-Institute of Freshwater Ecology and Inland Fisheries in Germany, andPhil Hugenholtz, now director of the Australian Centre for Ecogenomics at the University of Queensland in Australia, focused on microbial communities in a composting bioreactor thatare used to extreme conditions.

Bioenergy candidate feedstock switchgrass in Nebraska. (Image by Stephen Ausmus, USDA-ARS)

Dry rot (Serpula) genome project in BasqueResearch.com

2011-09-07T17:30:00.000-07:00

Science journal has published research work on the sequence of the genome of the Serpula lacrymans fungus and in which the Public University of Navarre (UPNA) lecturers Gerardo Pisabarro de Lucas and José Antonio Oguiza Tomé, professor and senior lecturer in Microbiology respectively, participated. The research, largely funded by the US Department of Energy through the Joint Genome Institute (JGI) in California, was carried out by an international consortium and aimed to find out what strategies the fungus uses to degrade the lignin part of wood. The elimination of this component of trees is required for the extraction of cellulose, from which alcohol is obtained and with which the idea is to produce biofuels.

Dark ocean project in Climate Action

2011-09-06T10:15:00.000-07:00

To understand the world's climate, we must understand how the 70% of the Earths surface that is covered with water behaves. Very little is known about the processes below 200m, or the area where photosynthesis is not possible due to the lack of light penetration. Scientists from the U.S. Department of Energy Joint Genome Institute (JGI) have found that the amount of carbon being absorbed at these depths is greater than can be attributed to Archaea alone and that some bacteria must be operating at immense depths.

DOE JGI Science Highlights: Capturing carbon in the dark ocean

2011-09-02T12:18:00.000-07:00

The oceans cover morethan half of the planet’s surface, and as such play an important role in theglobal carbon cycle, trapping 50 times more carbon than the atmosphere.However, the process by which carbon fixation takes place deep underwater wherethe sunlight does not penetrate has not yet been fully explained.

Throughsingle cell genomics, novel bacteria in the dark ocean that may help explainthe carbon budget of the oceans were identified. (Image from the VERTIGOexperiment on lbl.gov)

DOE JGI Science Highlights: A mechanism for de novo intron insertion

2011-08-31T10:30:00.000-07:00

Introns are the parts of a gene sequence that are not expressed in the protein. In the August 30 issue of Nature Communications, a team led by DOE JGI’s Eukaryote Program head Dan Rokhsar and Uffe Hellsten describe a potential mechanism by which introns have been added to a genome sequence since what they refer to as “the original genomic invasion of introns” millions of years ago. Unlike other previously described mechanisms by which introns have been inserted into a gene sequence, they said, this method does so precisely and without disrupting the surrounding coding sequence.

The genome of Strongylocentrotus purpuratus was among the sequences compared for this study

(Image by Minette Layne/Wikimedia Commons.)

DOE JGI Science Highlights: A “meraculous” way to conduct whole-genome assemblies

2011-08-19T08:38:00.000-07:00

The dramatic shift in sequencing technologies that allows genome researchers to generate the equivalent of a single human genome in days rather than the decades it took multiple organizations to complete a single one has also shifted the bottleneck from sequence production to sequence assembly. For example, the Sanger platform routinely produced reads 700 basepairs long while the Illumina platform generates reads 35-100 basepairs in length, making the assembly process challenging.

Pichia stipitis (Image by Thomas Kuster, USDA, Forest Products Laboratory.)

DOE JGI researchers led by Eukaryote Program head Dan Rokhsar and Jarrod Chapman, have developed an efficient way to do short-read assemblies of eukaryotic genomes using a computer algorithm referred to as meraculous.

DOE JGI's Prochnik in Discovery News

2011-08-18T16:45:00.000-07:00

"This one-celled organism hunts and eats bacteria as an amoeba, swims around looking for a better environment as a flagellate, and then hunkers down and waits for good times as a cyst," said Simon Prochnik, a computational scientist at the U.S. Department of Energy’s Joint Genome Institute. "It is a very rare process to go from amoeba to flagellate like this."

Xylose-fermenting yeast project in Ethanol Producer

2011-08-18T09:37:00.000-07:00

Using Mother Nature as their teacher, researchers at the U.S. DOE’s Great Lakes Bioenergy Research Center, along with the DOE’s Joint Genome Institute, have sequenced the genomes of two types of yeasts found in bark beetles and then compared and contrasted the results with other yeasts’ genome sequences to determine which can best convert the elusive C5 sugars of cellulosic material to ethanol. What they found surprised and encouraged them, and left them with more than enough work to fill the next several years.

Read more in Ethanol Producer magazine

DOE JGI Science Highlights: Toward a Better Understanding of Soil-Microbe Interactions

2011-08-12T13:36:00.000-07:00

In the August 2011 issue of the Journal of Bacteriology, a team of researchers led by DOE JGI’s Patrick Chain at Los Alamos National Laboratory focused on a microbe that can help or harm as the case may be.

Rhizosphere, magnified 10,000X (Image by Sandra Silvers, USDA-ARS)

Ochrobactrum anthropi thrives in a variety of habitats including polluted soil, plants and even higher mammals. One strain of O. anthropi can degrade the compounds used as slow-release nitrogen fertilizer, while another strain can enhance tea plant growth and decrease the incidence of brown root rot in the same plant. Still another strain is an opportunistic pathogen in hospitalized patients.

DOE JGI Science Highlights: Another Brown Mercury Producer Genome Sequenced

2011-08-05T17:42:00.000-07:00

In the August edition of The Journal of Bacteriology, a group of scientists including several DOE JGI researchers and longtime collaborator Judy Wall of the University of Missouri described the genome for Desulfovibrio africanus, a sulfate-reducing bacterium isolated from Namibia that doesn’t require oxygen for its survival. Like the Desulfovibrio species sequenced as recently as this year but dating back to 2006, the bacterium is able to produce brown (methyl) mercury, a human neurotoxin that also contaminates terrestrial and aquatic ecosystems.

A bacterium called Desulfovibrio desulfuricans strain ND132 can transform elemental mercury into methylmercury, a human neurotoxin (Courtesy of Oak Ridge National Laboratory)

DOE JGI Science Highlights: Sweetening the Biofuels Production Process

2011-07-29T16:42:00.000-07:00

Spathaspora passalidarum, one of the fungi sequenced for this paper
(Courtesy of Thomas Kuster at USDA, Forest Products Lab)

Currently, converting cellulosic biomass into biofuels is inefficient and costly. One of the barriers to reducing costs and yields is that xylose, a five-carbon sugar that represents nearly half of available sugars in plant (in the form of hemicellulose), is extremely difficult and time-consuming to break down using enzymes sourced from conventional yeast strains.

Eucalyptus genome project on Science in Public

2011-07-26T09:52:00.000-07:00

The genome of one of Australia’s biggest Eucalyptus trees, the Flooded Gum or Eucalyptus grandis, has now been mapped, allowing scientists and conservationists an insight into the secrets of an important piece of Australiana.
Eucalyptus has become the most popular plantation tree in the world – with millions of hectares planted in Africa, America, Europe and Asia. That’s one of the reasons that the global community chose a eucalyptus species to map.

DOE JGI Science Highlights: Ethanol Contaminant Could Assist Production Efficiency

2011-07-25T09:48:00.000-07:00

An Ethanol plant in Bairstown, Iowa

(Courtesy of USDA)

In the August edition of The Journal of Bacteriology, researchers led by long-time collaborator David Mills of the University of California Davis, and including DOE JGI’s Alex Copeland, Olga Chertkov and Lynne Goodwin, announced the completed genome sequence of Lactobacillus buchneri and has now been made publically available.

Dry rot (Serpula) genome on ScienceNewsline

2011-07-24T21:22:00.000-07:00

As reported online July 14 in Science Express, an international team of scientists including DOE JGI researchers compared the genome of Serpula lacrymans, the second brown rot fungus to have its genome sequenced, against 10 other published fungal genomes. The DOE JGI sequenced seven of these genomes among them Postia placenta, the first brown rot fungus sequenced.

DOE JGI Science Highlights: Destroyer of Houses Harnessed for Biofuel Production

2011-07-20T16:55:00.000-07:00

A variant of Serpula lacrymans causes dry rot. (Dave Brown

via Flickr/ Creative Commons Attribution 2.0)

Although people rarely see the positives when their wooden houses begin to rot, scientists at the DOE JGI have found a silver lining in this destructive phenomenon. Through DNA sequencing and a comparative analysis with other fungi that DOE JGI has characterized, researchers have homed in on the mechanisms that the brown rot, Serpula lacrymans, employs to break down biomass and published the results of this enzyme discovery project online in Science Express on July 14.

Dry rot (Serpula) genome project on eNews Park Forest

2011-07-19T09:07:00.000-07:00

In 2007 the US Department of Energy’s Joint Genome Institute sequenced Serpula lacrymans in order to see if the way it breaks down cellulose in wood could be harnessed for biofuel production. An international team analysing the genome have found the enzyme mechanisms that could explain the aggressive decay caused by this form of dry rot. These may help develop new pretreatments for biofuel production from agricultural wastes.

Dry rot (Serpula) project in Biofuels Journal

2011-07-15T13:03:00.000-07:00

"For example, if you go back far enough in time to the period when trees were developing, there was no way to break lignocellulose down, which led to the coal seams we tap today.
"When the fungi figured out how to break down lignocellulose, the coevolution of the fungi and trees kick-started the carbon cycle again."

Dry rot (Serpula) genome project on Greenwire

2011-07-15T11:14:00.000-07:00

Researchers have sequenced the genome for brown rot -- also known as dry rot -- in a step that could have applications for biofuels and better understanding of forest carbon cycling.

Dry rot, a scourge of homeowners, is a fungus that decays wood by attacking its sugars -- cellulose and hemicellulose -- and working around the tough lignin cells that give it its structure.

Dry rot (Serpula) genome project on WalesOnline

2011-07-15T09:01:00.000-07:00

WELSH scientists are looking at harnessing the power of the virulent fungus which causes dry rot to help make biofuels of the future.

Closer examination of the damaging fungus Serpula lacrymans as part of an international project led by Swansea University could also hold the key to protecting buildings from dry rot.

Serpula genome project on MyCor Fungal Web Genomics

2011-07-15T08:57:00.000-07:00

The other good news of this Bastille Day: our paper on the Serpula lacrymans genome is reported online July 14 in Science Express.

The Domestic Dry Rot (Serpula lacrymans, Basidiomycete, Coniophoraceae) comprises two subgroups, S. lacrymans varshastensis, found in montane conifer forests in the Himalayan foothills, and S. lacrymans var lacrymans, cause of building dry rot, which diverged in historic time [Kauserud et al. (2007) Mol. Ecol.16: 3350-3360].

DOE JGI's role in national quest for cellulosic biofuels in the New York Times

2011-07-13T15:21:00.000-07:00

The rumen is like a huge bathtub, he said, holding about 50 large soda bottles' worth of fluid redolent with bacteria. Relying on these symbiotic microbes, cows eat up to 150 pounds of grass a day, a food inedible to most animals, including humans. Hess was after those microbial secrets, and the placid heifer was happy to oblige.
"You can just do your experiment," he said later. "The cows don't really care."

Mycosphaerella genome project in Capital Press

2011-07-11T16:21:00.000-07:00

Septoria typically infects young seedlings that have recently emerged, creating lesions, and spreading to the higher leaves. It can affect yield and quality, Goodwin said. Control methods are typically fungicide sprays, he noted.

Igor Grigoriev, of the U.S. Department of Energy's Joint Genome Institute in Walnut Creek, Calif., has been sequencing the genomes of other fungi in the same class.

"We think we will be able to derive those features that make them pathogens," Grigoriev said.

DOE JGI Science Highlights: Wallaby Yields Insight Into Limiting Methane

2011-07-08T17:38:00.000-07:00

Research published in the June 30 edition of Science Express features an analysis of the microbial content of the Tammar wallaby gut, which may inform strategies for diminishing greenhouse gas emissions from other ruminants.

Tammar wallaby (photo by Mehgan Murphy, Smithsonian’s National Zoo)

Selected as a sequencing target by the DOE JGI’s Community Sequencing Program (CSP) in 2007, scientists had became interested in these mini kangaroos because of their similar digestive systems to cows, in addition to the fact that they release lower amounts of methane, and thus less of a carbon footprint. In 2009, the U.S. Environmental Protection Agency calculated that 20 percent of the nation’s human-related methane emissions were attributable to livestock digestive processes. In Australia, livestock emissions account for 12 percent of the country’s annual total greenhouse gas emissions.

DOE JGI/JBEI collaboration in DomesticFuels.com

2011-07-08T14:10:00.000-07:00

Researchers from the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) and the Joint BioEnergy Institute (JBEI) at DOE’s Lawrence Berkeley National Laboratory are trying to discover salt-loving organisms that may be more efficient in treating biomass and improve sugar yield for biofuel production. The class of solvents known as ionic liquids, are liquid forms of salt that will inactivate enzymes by interfering with the folding of polypeptides—the building-blocks of proteins. These solvents are useful for breaking down biomass; however, they can also hinder the ability of cellulases used to produce sugars after pretreatment.

UCLA microbiologists find energy-efficient structures in archaeon

2011-07-06T09:45:00.001-07:00

a type of Archaea known as Methanosprillum hungatei contains incredibly efficient energy-storage structures.

The findings are published in the July 5 issue of the journal Environmental Microbiology.

M. hungatei is of considerable environmental significance because of its unique ability to form symbiotic relationships with syntrophic bacteria to break down organic matter and produce methane gas. Yet while their important role in the food chain has been studied, little has been known about how they generate and store energy.

Read the rest of the release at the UCLA Newsroom

DOE JGI Science Highlights: Efficiency Improvements in Biofuels Production

2011-07-01T16:40:00.001-07:00

To overcome the difficulties of converting cellulosic biomass into high energy-content fuel, researchers have been seeking to improve various stages of the process. One big obstacle that stands in the way is that most enzymes are inefficient at breaking down biomass when in the presence of ionic liquids, solvents that have proven effective at treating the biomass and enhancing conversion to fermentable sugars that come from the plant.

The Great Salt Lake in Utah (Courtesy of Charles Uibel, GreatSaltLakePhotos.com)

However, researchers from the DOE JGI and Joint BioEnergy Institute (JBEI) have partnered to create a solution to this problem. Published online July 1 in the journal Green Chemistry, these scientists, including DOE JGI director Eddy Rubin, targeted halophilic (salt-tolerant) enzymes, specifically those living in the Great Salt Lake,

DOE JGI/JBEI collaboration in Green Car Congress

2011-07-01T16:26:00.000-07:00

Such salt-tolerant enzymes, particularly cellulases, offer significant advantages for industrial utility over conventional enzymes, they said. The group plans to expand this research to develop a full complement of enzymes that is tailored for the ionic liquid process technology with the goal of demonstrating a complete biomass-to-sugar process, one they hope can enable the commercial viability of advanced biofuels.

DOE JGI Science Highlights: Consortium Drives Genome Standards

2011-06-24T16:37:00.000-07:00

As technology for sequencing genomes has become cheaper and more widely accessible, there is a greater urgency to institute a standardized, comprehensive language for researchers to share their findings. The Genomic Standards Consortium (GSC), an open-membership organization, is building a culture of collaboration to achieve greater efficiencies by spending less time combing through and interpreting inconsistent information, thus maximizing the field’s potential for yielding more substantial findings.

The 8th GSC meeting was hosted at the JGI DOE in 2009

DOE JGI Science Highlights: GreenCut2: Algorithm to ID Plant Protein Functions

2011-06-17T16:32:00.000-07:00

Researchers use genome sequencing to inform various cellular processes in land plants and algae, including the details of photosynthesis. Despite the access to an increasing number of plant genomes (most of which have been generated by the DOE JGI), it remains difficult to correlate protein information with function, until now. For example, identifying the role proteins play in the evolution of chloroplasts and how the photosynthetic apparatus responds under different conditions.

Soybean, one of the plants studied using GreenCut (Scott Bauer, USDA)

DOE JGI bioinformaticist Simon Prochnik and collaborators at UCLA and the Carnegie Institution at Stanford have developed and deployed a computer algorithm that can distinguish proteins involved in photosynthesis present in plant and green algal genomes, but not in non-photosynthetic organisms.

GreenCut algorithm in Crop Biotech Update

2011-06-17T14:37:00.000-07:00

Grossman and colleagues revealed that many of the GreenCut proteins are also present in ancient cyanobacteria, red algae, and diatoms. Further assessment of these proteins is expected to bring more discoveries about their functions in photosynthetic cells, and how the photosynthetic cells might be adapted to survive various environmental conditions.

Read more in ISAAA's Crop Biotech Update

GreenCut algorithm in e! Science News

2011-06-17T09:58:00.000-07:00

Using advanced computational tools to analyze the genomes of 28 different plants and photosynthetic organisms, Grossman and his colleagues at the University of California in Los Angeles and the Joint Genome Institute of the Department of Energy were able to identify 597 proteins encoded on plant and green algal genomes, but that are not present in non-photosynthetic organisms. They call this suite of proteins the GreenCut.

Cassava project in Bloomberg View

2011-06-17T07:56:00.000-07:00

Over the past few years, the U.S. Department of Energy’s Joint Genome Institute has taken up the challenge to sequence additional starches that could make a significant difference in developing nations where corn and soybean are less important than such staples as foxtail millet, sorghum and cassava. Such crops, if engineered to be more nutritious, as well as cheaper to grow in large quantities, could combat hunger in the poorest parts of Africa and Asia.

Read the full Bloomberg View column. More information about the genome sequences of foxtail millet, sorghum and cassava, as well as other plants, is available on Phytozome.net

Mycosphaerella project in Media Newswire

2011-06-15T11:39:00.000-07:00

Enzymes often break down plant cell walls and begin removing nutrients, leading to the plant's death. M. graminicola, however, enters the plant through stomata, small pores in the surface of leaves that allow for exchange of gases and water.

Goodwin said the fungus seems to lay dormant between plant cells, avoiding detection. It later infects the plant, removing necessary nutrients and causing disease.

Mycosphaerella genome project in Agricultural Research

2011-06-10T09:17:00.000-07:00

The pathogen that causes the disease, Mycosphaerella graminicola, has a long "silent period," a latent stage during which it takes nutrition from the living plant and evades the host plant's natural defenses. Scientists previously did not have a good understanding of how the organism infects wheat, or how the wheat plant itself resists the pathogen. Sequencing the genome of the pathogen could help answer these questions, among others.

Mycosphaerella genome project in Farmers Guardian

2011-06-10T09:15:00.000-07:00

SCIENTISTS have cracked the genetic code of septoria tritici - the most important foliar disease of wheat in the UK - and in doing so have gained an insight into how the disease is able to evade wheat’s natural defences.

The researchers, who were funded by the BBSRC and others, hope the study, which reveals the complete genome sequence of the septoria pathogen mycosphaerella graminicola, will enable them to breed resistant crop plants or improve the use of pesticides.

DOE JGI Science Highlights: First Finished Filamentous Fungus

2011-06-10T09:09:00.000-07:00

An international consortium of scientists, including scientists from DOE JGI, have published the analysis for Mycosphaerella graminicola, the first filamentous fungus to be fully finished. Having the 39.7 million nucleotide genome available will enable researchers to learn more about the methods plant pathogens use to attack and damage crops, including those being considered for use as feedstocks for biofuels production.

Septoria tritici blotch on wheat (Courtesy of Gert Kema, Wageningen UR)

As detailed in the June 9, 2011 issue of PLoS Genetics, the fungal pathogen causes leaf blotch disease in wheat. Scientists had recognized the effects of this disease but struggled with understanding the pathogen’s behavior.

DOE JGI Science Highlights: Tagging coral proteins adapting to global climate change

2011-06-03T11:34:00.000-07:00

Over the past two decades, scientists have linked the decrease in the pH levels of the global oceans and the corresponding slowdown in coral growth to the increasing levels of carbon dioxide trapped in the atmosphere and which in turn are being absorbed in the ocean.

Acropora table coral on the Great Barrier Reef

(Image (c) Pete Faulkner, Mission:awareness/Marine Photobank")

As coral reefs are the primary habitat for several marine organisms, their decline has significant impacts on the health of the marine ecosystems and ocean productivity. To better understand how corals contribute to the global carbon cycle, one of the 2007 DOE JGI Community Sequencing Program projects included plans to generate a dataset of expressed sequence tags or ESTs, small portions of a genome that can be used to help identify unknown genes and chart their locations along the sequence, from the reef-building coral Acropora palmata.

Poplar rust genome project on Wisconsin Ag Connection

2011-05-31T15:30:00.000-07:00

The sequencing of the genetic codes of wheat stem rust pathogen (Puccinia graminis) and poplar leaf rust pathogen (Melampsora larici-populina) is expected to help researchers develop control strategies to address worldwide threats to wheat fields and tree plantations. The study, published in the Proceedings of the National Academy of Sciences, was a six-year collaborative effort of USDA's Agricultural Research Service (ARS), the U.S. Department of Energy Joint Genome Institute, the National Science Foundation, the Broad Institute of Harvard and the Massachusetts Institute of Technology, the University of Minnesota and the French National Institute for Agricultural Research.

Read more on the Wisconsin Ag Connection

A.niger genome project on The Bioenergy Site

2011-05-31T15:28:00.000-07:00

Published online ahead of print May 4, 2011 in Genome Research, a team led by Scott Baker of the Pacific Northwest National Laboratory compared the genome sequences of two Aspergillus niger strains to, among other things, better harness its industrial potential in biofuels applications. As more than a million tons of citric acid are produced annually, the production process involving A. niger is a well understood fungal fermentation process that could inform the development of a biorefinery where organic compounds replace the chemical building blocks normally derived from petroleum. Learning more about the genetic bases of the behaviors and abilities of these two industrially relevant fungal strains, wrote senior author Baker and his colleagues in the paper, will allow researchers to exploit their genomes towards the more efficient production of organic acids and other compounds, including biofuels.

DOE JGI Science Highlights: How salt-loving archaea can assist with biofuel production

2011-05-27T11:37:00.000-07:00

Halophilic bacteria thrive in environments with very high concentrations of salt such as the waters and sediments of salt lakes and saline soils. One of the reasons why the DOE JGI has been sequencing halophiles under the Genomic Encyclopedia of Bacteria and Archaea (GEBA) project and the Community Sequencing Program is because they have salt-adapted enzymes that could be used in breaking down complex sugars, a process applicable to biofuel production. Sequencing these extremophiles also provides researchers with more information about their metabolic capabilities.

Published online May 25, 2011 in PLoS ONE, a team of researchers from the DOE JGI, the DSMZ in Germany and INEOS Bio in Arkansas

JGI Science @ the Lesher: "The Deal with Microbes" video

2011-05-27T09:30:00.000-07:00

The May 9, 2011 event at the Lesher Center for the Arts in downtown Walnut Creek featured Jonathan Eisen and Rachel Mackelprang of DOE JGI, and Terry Hazen of Berkeley Lab. KTVU Health and Science Editor John Fowler served as panel moderator.

(Note: There's a short delay before the video starts at the 20-second mark.)

One of the global processes microbes play a key role in is the carbon cycle, which is currently unbalanced. Humans release more carbon into the atmosphere than can be naturally removed. Lawrence Berkeley National Laboratory (Berkeley Lab) launched the Carbon Cycle 2.0 initiative to provide the science needed to restore this balance by integrating the Lab’s diverse research activities and delivering creative solutions toward a carbon-neutral energy future. Microbes play a major role in the management of global carbon. An affiliate of LBNL, the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) has researchers working on some of these solutions.

Thanks to Walnut Creek TV for recording the event.

DOE JGI Director honored by Middlebury College

2011-05-23T10:03:00.000-07:00

Waddell, who was presented the honorary degree, doctor of humane letters, was one of six people to receive honorary degrees at this year’s commencement ceremonies. The others were economics scholar and international adviser to political leaders Padma Desai, doctor of laws; Vermont’s long-serving senator, Patrick Leahy, doctor of laws; local volunteer and activist Dorothy Bigelow Neuberger ’58, doctor of humane letters; geneticist and director of the Department of Energy’s Joint Genome Institute Edward M. Rubin, doctor of science; and civil rights activist Maxine Atkins Smith, doctor of humane letters, who earned a master’s degree in French from Middlebury in 1950 and won the Freedom Award from the Memphis-based National Civil Rights Museum in 2003.

Read more in the Burlington Free Press

DOE JGI Science Highlights: Fungal lessons for large-scale "green" chemical production

2011-05-20T09:50:00.000-07:00

The chemical compound citric acid has been produced on a large-scale basis for decades with the help of the filamentous fungus Aspergillus niger. The fungus also has enzymes that can be used to help break down plant cell walls for biofuel production, and it plays a key role in the carbon cycle.

Aspergillus niger (Sue Karagiosis, PNNL)

“For biofuels it’s a highly relevant organism since it’s already been scaled up, shown to be safe, and used for enzyme production,” said Scott Baker of DOE JGI partner Pacific Northwest National Laboratory about this A. niger strain selected for sequencing by the DOE JGI in 2005.

DOE JGI microbes on space shuttle Endeavour per Wired UK

2011-05-16T16:28:00.000-07:00

there are also some other passengers on the shuttle, who might not receive the same media attention, sew-on patches and victory parades. Alongside the all-male crew of mission STS-134, six types of microorganism and a bobtail squid will strap in their seat-belts and head into space.

Read more in Wired UK but head for the DOE JGI homepage to find out why Cupriavidus metallidurans and Vibrio fischeri were selected for sequencing

Maize genomics at DOE JGI User Meeting in Genome Technology

2011-05-16T12:45:00.000-07:00

Speaking at the Department of Energy Joint Genome Institute's sixth annual User Meeting, held in Walnut Creek, Calif., in March, Buckler said that while they may not have realized it at the time, maize breeders in Thailand, Mexico, and elsewhere have, since the turn of the 20th century, captured a great deal more genomic diversity with their land practices than those in the US have. Outside of the US, "there's lot of very good, useful variation sitting in these diverse, improved lines that we can really start to harness and use in breeding," Buckler said.

Read more in the May 2011 issue of Genome Technology. Watch the video of Ed Buckler's talk on the DOE JGI's YouTube channel.

Eucalyptus genome sequence in ScienceDaily

2011-05-14T16:30:00.000-07:00

According to Prof Myburg, these scientists, as well as countries with commercial eucalypt plantations will be the primary beneficiaries of the genome sequence now available on the Internet (http://www.phytozome.net/eucalyptus.php). The Eucalyptus research community will continue to add value to the genome sequence in order to make it more accessible to the broader scientific community. Publication of the genome sequence in a scientific journal is expected to take place by early 2012.

DOE JGI Science Highlights: Spikemoss genome aids biofuels researchers and botanists

2011-05-13T09:54:00.000-07:00

The genome of a small plant is providing biofuels researchers with information that could influence the development of candidate biofuel feedstock plants and offering botanists long-awaited insights into plant evolution. Published online May 5, 2011 in Science Express, a team of researchers including DOE JGI’s Dan Rokhsar and Igor Grigoriev used a comparative genomics approach on Selaginella moellendorffii and 14 other plants up and down the phylogenetic tree to identify the core genes likely to be present in a common ancestor to land plants.

Selaginella moelledorffii. (Image by Jing-Ke Weng, Salk Institute)

“When you burn coal, you’re burning Selaginella’s ancestors,” said Purdue University botanist Jody Banks, who led the 2005 DOE JGI Community Sequencing Program project.

Tringe DOE Award in BioPortfolio

2011-05-12T22:28:00.000-07:00

DOE's Office of Science awarded the Early Career Research grant to Susannah Green Tringe, a researcher in the Lawrence Berkeley National Laboratory's Genomics Division, to study how microbial communities in restored wetlands may impact long-term carbon sequestration, from a genomic perspective.

Eucalyptus genome in FirstScience News

2011-05-12T16:25:00.000-07:00

A team of international researchers, led by Prof Zander Myburg from the Department of Genetics and the Forestry and Agricultural Biotechnology Institute (FABI) at the University of Pretoria (UP) – in collaboration with the US Department of Energy (DOE) Joint Genome Institute (JGI) – making available the complete genome sequence of the forest tree species, Eucalyptus grandis. It took the team, who had the support of a network of more than 130 Eucalyptus researchers from 18 countries, four years to complete the genome sequence and annotate more than 40,000 genes contained within it.

Tringe DOE Award in GenomeWeb

2011-05-12T14:08:00.000-07:00

DOE's Office of Science awarded the Early Career Research grant to Susannah Green Tringe, a researcher in the Lawrence Berkeley National Laboratory's Genomics Division, to study how microbial communities in restored wetlands may impact long-term carbon sequestration, from a genomic perspective.

Tringe DOE Award in Technology Today

2011-05-11T16:22:00.000-07:00

Susannah Tringe of the Genomics Division and DOE’s Joint Genome Institute. Tringe investigates the sequencing and characterization of natural communities of microbes and their roles in processes ranging from biomass degradation to efficient production of biofuels from non-food crops. Her Early Career award from the Office of Biological and Environmental Research is for her proposal “Microbial communities in biological carbon sequestration.” (See http://jgi.doe.gov/News/news_11_05_10.html)

Berkeley lab second campus in the Daily Californian

2011-05-11T16:19:00.000-07:00

The six sites that made the final cut from a list of more than 20 potential sites in the Bay Area are Alameda Point in the city of Alameda, Berkeley Aquatic Park West in West Berkeley, Brooklyn Basin in Oakland, properties already occupied by the lab in Emeryville and Berkeley, Golden Gate Fields and Richmond Field Station, which is currently owned by the University of California and was the paradigm for a second campus, according to lab officials.

Poplar rust fungal genome project in Western Farm Press

2011-05-10T17:33:00.000-07:00

The sequencing of the genetic codes of wheat stem rust pathogen (Puccinia graminis) and poplar leaf rust pathogen (Melampsora larici-populina) is expected to help researchers develop control strategies to address worldwide threats to wheat fields and tree plantations. The study, published in the Proceedings of the National Academy of Sciences, was a six-year collaborative effort of USDA's Agricultural Research Service(ARS), the U.S. Department of Energy Joint Genome Institute, the National Science Foundation, the Broad Institute of Harvard and the Massachusetts Institute of Technology, the University of Minnesota and the French National Institute for Agricultural Research.

Poplar leaf rust fungal genome project on KRVN

2011-05-10T16:35:00.000-07:00

Wheat stem rust causes major epidemics of both barley and wheat worldwide. A strain known as Ug99 has spread across Africa and into Central Asia, and has been able to overcome most of the stem-rust-resistant wheat varieties developed over the past 50 years. Poplar leaf rust can cause significant losses in poplar tree plantations. Poplar is an important crop for the wood industry and is becoming increasingly important to the biofuel industry in the United States and Europe because of its rapid and significant production of biomass.

JGI Science @ the Lesher in The Oakland Tribune

2011-05-09T19:54:00.000-07:00

The researchers, who will speak Monday evening at the Lesher Center for the Arts in Walnut Creek, are working with the Joint Genome Institute in Walnut Creek, a federal facility for genetic sequencing of microbes and other life-forms.

The terrestrial ecosystem, meaning everything on land -- from plants to soil and other geological features -- absorbs about one-third of atmospheric carbon. Much of the credit goes to microbes, said Donald DePaolo, an associate lab director who heads the Berkeley Lab's Carbon Cycle 2.0 initiative.