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    Maize can produce a cocktail of antibiotics with a handful of enzymes. (Sam Fentress, CC BY-SA 2.0)
    How Maize Makes An Antibiotic Cocktail
    Zealexins are produced in every corn variety and protect maize by fending off fungal and microbial infections using surprisingly few enzymes.

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    The genome of the common fiber vase or Thelephora terrestris was among those used in the study. (Francis Martin)
    From Competition to Cooperation
    By comparing 135 fungal sequenced genomes, researchers were able to carry out a broader analysis than had ever been done before to look at how saprotrophs have transitioned to the symbiotic lifestyle.

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    Miscanthus grasses. (Roy Kaltschmidt/Berkeley Lab)
    A Grass Model to Help Improve Giant Miscanthus
    The reference genome for M. sinensis, and the associated genomic tools, allows Miscanthus to both inform and benefit from breeding programs of related candidate bioenergy feedstock crops such as sugarcane and sorghum.

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    Poplar (Populus trichocarpa and P. deltoides) grow in the Advanced Plant Phenotyping Laboratory (APPL) at Oak Ridge National Laboratory in Tennessee. Poplar is an important biofuel feedstock, and Populus trichocarpa is the first tree species to have its genome sequenced — a feat accomplished by JGI. (Image courtesy of Oak Ridge National Laboratory, U.S. Dept. of Energy)
    Podcast: Xiaohan Yang on A Plantiful Future
    Building off plant genomics collaborations between the JGI and Oak Ridge National Laboratory, Xiaohan Yang envisions customizing plants for the benefit of human society.

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    Expansin complex with cell wall in background. (Courtesy of Daniel Cosgrove)
    Synthesizing Microbial Expansins with Unusual Activities
    Expansin proteins from diverse microbes have potential uses in deconstructing lignocellulosic biomass for conversion to renewable biofuels, nanocellulosic fibers, and commodity biochemicals.

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    High oleic pennycress. (Courtesy of Ratan Chopra)
    Pennycress – A Solution for Global Food Security, Renewable Energy and Ecosystem Benefits
    Pennycress (Thlaspi arvense) is under development as a winter annual oilseed bioenergy crop. It could produce up to 3 billion gallons of seed oil annually while reducing soil erosion and fertilizer runoff.

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    Artistic interpretation of CheckV assessing virus genome sequences from environmental samples. (Rendered by Zosia Rostomian​, Berkeley Lab)
    An Automated Tool for Assessing Virus Data Quality
    CheckV can be broadly utilized by the research community to gauge virus data quality and will help researchers to follow best practices and guidelines for providing the minimum amount of information for an uncultivated virus genome.

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    Unicellular algae in the Chlorella genus, magnified 1300x. (Andrei Savitsky)
    A One-Stop Shop for Analyzing Algal Genomes
    The PhycoCosm data portal is an interactive browser that allows algal scientists and enthusiasts to look deep into more than 100 algal genomes, compare them, and visualize supporting experimental data.

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    Artistic interpretation of how microbial genome sequences from the GEM catalog can help fill in gaps of knowledge about the microbes that play key roles in the Earth's microbiomes. (Rendered by Zosia Rostomian​, Berkeley Lab)
    Podcast: A Primer on Genome Mining
    In Natural Prodcast: the basics of genome mining, and how JGI researchers conducted it in IMG/ABC on thousands of metagenome-derived genomes for a Nature Biotechnology paper.

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    Scanning electron micrographs of diverse diatoms. (Credits: Diana Sarno, Marina Montresor, Nicole Poulsen, Gerhard Dieckmann)
    Learn About the Approved 2021 Large-Scale CSP Proposals
    A total of 27 proposals have been approved through JGI's annual Community Science Program (CSP) call. For the first time, 63 percent of the accepted proposals come from researchers who have not previously been a principal investigator on an approved JGI proposal.

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    MiddleGaylor Michael Beman UC Merced
    How to Successfully Apply for a CSP Proposal
    Reach out to JGI staff for feedback before submitting a proposal. Be sure to describe in detail what you will do with the data.

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    Click on the image or go here to watch the video "Enriching target populations for genomic analyses using HCR-FISH" from the journal Microbiome describing the research.
    How to Target a Microbial Needle within a Community Haystack
    Enabled by the JGI’s Emerging Technologies Opportunity Program, researchers have developed, tested and deployed a pipeline to first target cells from communities of uncultivated microbes, and then efficiently retrieve and characterize their genomes.

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    Artistic interpretation of how microbial genome sequences from the GEM catalog can help fill in gaps of knowledge about the microbes that play key roles in the Earth's microbiomes. (Rendered by Zosia Rostomian​, Berkeley Lab)
    Uncovering Novel Genomes from Earth’s Microbiomes
    A public repository of 52,515 microbial draft genomes generated from environmental samples around the world, expanding the known diversity of bacteria and archaea by 44%, is now available .

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    Green millet (Setaria viridis) plant collected in the wild. (Courtesy of the Kellogg lab)
    Shattering Expectations: Novel Seed Dispersal Gene Found in Green Millet
    In Nature Biotechnology, a very high quality reference Setaria viridis genome was sequenced, and for the first time in wild populations, a gene related to seed dispersal was identified.

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    The Brachypodium distachyon-B. stacei-B. hybridum polyploid model complex. (Illustrations credits: Juan Luis Castillo)
    The More the Merrier: Making the Case for Plant Pan-genomes
    Crop breeders have harnessed polyploidy to increase fruit and flower size, and confer stress tolerance traits. Using a Brachypodium model system, researchers have sought to learn the origins, evolution and development of plant polyploids. The work recently appeared in Nature Communications.

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All JGI Features
Home › Items tagged with: UC Berkeley

Content Tagged "UC Berkeley"

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December 16, 2011

Cyanobacteria shed light on carboxysome complexity

Found in temperate and tropical oceans, Prochlorococcus cyanobacteria are considered the world’s most abundant photosynthetic organisms, able to convert sunlight to energy at depths of 200 meters. Despite their size, they are estimated to contribute up to half of the marine biological carbon sequestration. Prochlorococcusis a unicellular cyanobacterium that dominates the temperate and tropical oceans. … [Read More]

October 12, 2011

Director Rubin on corngrass1 for biofuel

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… [Read More]

April 7, 2011

DOE JGI’s Cheryl Kerfeld among 2011 ASBMB awardees in Washington DC

Cheryl A. Kerfeld, a structural biologist and the head of the Department of Energy Joint Genome Institute’s Education and Structural Genomics Program, won the ASBMB Award for Exemplary Contributions to Education. Kerfeld, who also serves as an adjunct professor at the University of California, Berkeley, was named the winner for encouraging effective teaching and learning… [Read More]

January 12, 2011

UC Berkeley’s CNR reports Cheryl Kerfeld’s ASBMB Award

“The integration of bona fide research and development of critical thinking skills into undergraduate education has no greater or more effective advocate than Cheryl Kerfeld,” said Kathleen Scott, an associate professor at the University of South Florida, who supported Kerfeld’s nomination for the award. Colleagues underscore that Kerfeld has pushed the envelope for education both… [Read More]

August 30, 2010

Sponge genome project on Cosmos magazine

It’s just a blob, with no eyes, no nervous system, no muscle, no gut, no circulatory system, no tissues of any sort really – just cells embedded in a jelly matrix. They’re not even considered true animals. Yet according to the Nature report the sponge genome, which was read by researchers at the University of… [Read More]

August 16, 2010

Sponge genome project on Inside Science

According to the new study, which was based on a species of sponge found on the Great Barrier Reef off the coast of Australia, the creature has some 18,000 genes. This is fewer than the number of genes humans possess (currently estimated at about 20,500 genes) — but not far off. A few years ago,… [Read More]

August 12, 2010

Sponge genome project on U Wire

A team of scientists – led by Daniel Rokhsar, UC Berkeley professor of molecular cell biology and physics and program head for computational genomics at the U.S. Department of Energy’s Joint Genome Institute – assembled a draft genome sequence of the Amphimedon queenslandica, a sponge native to the Great Barrier Reef, which researchers said provides… [Read More]

August 10, 2010

Sponge genome project on the Daily Californian

A team of scientists – led by Daniel Rokhsar, UC Berkeley professor of molecular cell biology and physics and program head for computational genomics at the U.S. Department of Energy’s Joint Genome Institute – assembled a draft genome sequence of the Amphimedon queenslandica, a sponge native to the Great Barrier Reef, which researchers said provides… [Read More]

August 6, 2010

Sponge genome project on redOrbit

“Though we think of a sponge as a simple creature whose skeleton we take to the bathtub, it has a lot of the major biochemical and developmental pathways we associate with complex functions in humans and other more complex animals,” she said. “But there are certain missing components. Future studies will reveal how sponges operate… [Read More]

August 6, 2010

Sponge genome project at UC Berkeley Newsroom

“Our hypothesis is that multicellularity and cancer are two sides of the same coin,” said Rokhsar, program head for computational genomics at JGI and a professor of molecular and cell biology and of physics at UC Berkeley. “If you are a cell in a multicellular organism, you have to cooperate with other cells in your… [Read More]
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