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    A vertical tree stump outdoors with about a dozen shiitake mushrooms sprouting from its surface.
    Tracing the Evolution of Shiitake Mushrooms
    Understanding Lentinula genomes and their evolution could provide strategies for converting plant waste into sugars for biofuel production. Additionally, these fungi play a role in the global carbon cycle.

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    Soil Virus Offers Insight into Maintaining Microorganisms
    Through a collaborative effort, researchers have identified a protein in soil viruses that may promote soil health.

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    Data yielded from RIViT-seq increased the number of sigma factor-gene pairs confirmed in Streptomyces coelicolor from 209 to 399. Here, grey arrows denote previously known regulation and red arrows are regulation identified by RIViT-seq; orange nodes mark sigma factors while gray nodes mark other genes. (Otani, H., Mouncey, N.J. Nat Commun 13, 3502 (2022). https://doi.org/10.1038/s41467-022-31191-w)
    Streamlining Regulon Identification in Bacteria
    Regulons are a group of genes that can be turned on or off by the same regulatory protein. RIViT-seq technology could speed up associating transcription factors with their target genes.

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    A panoramic view of a lake reflecting a granite mountain.
    Genome Insider: Methane Makers in Yosemite’s Lakes
    Meet researchers who sampled the microbial communities living in the mountaintop lakes of the Sierra Nevada mountains to see how climate change affects freshwater ecosystems, and how those ecosystems work.

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    A light green shrub with spiny leaves, up close.
    Genome Insider: A Shrubbier Version of Rubber
    Hear from the consortium working on understanding the guayule plant's genome, which could lead to an improved natural rubber plant.

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    The switchgrass diversity panel growing at the Kellogg Biological Station in Michigan. (David Lowry)
    Mapping Switchgrass Traits with Common Gardens
    The combination of field data and genetic information has allowed researchers to associate climate adaptations with switchgrass biology.

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    iPHoP image (Simon Roux)
    iPHoP: A Matchmaker for Phages and their Hosts
    Building on existing virus-host prediction approaches, a new tool combines and evaluates multiple predictions to reliably match viruses with their archaea and bacteria hosts.

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    Abstract image of gold lights and squares against a black backdrop
    Silver Age of GOLD Introduces New Features
    The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives.

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    Graphical overview of the RNA Virus MetaTranscriptomes Project. (Courtesy of Simon Roux)
    A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks
    Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity.

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    Green plant matter grows from the top, with the area just beneath the surface also visible as soil, root systems and a fuzzy white substance surrounding them.
    Supercharging SIP in the Fungal Hyphosphere
    Applying high-throughput stable isotope probing to the study of a particular fungi, researchers identified novel interactions between bacteria and the fungi.

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    Digital ID card with six headshots reads: Congratulations to our 2022 Function Genomics recipients!
    Final Round of 2022 CSP Functional Genomics Awardees
    Meet the final six researchers whose proposals were selected for the 2022 Community Science Program Functional Genomics call.

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    croppe image of the JGI helix sculpture
    Tips for a Winning Community Science Program Proposal
    In the Genome Insider podcast, tips to successfully avail of the JGI's proposal calls, many through the Community Science Program.

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    2022 JGI-UC Merced interns (Thor Swift/Berkeley Lab)
    Exploring Possibilities: 2022 JGI-UC Merced Interns
    The 2022 UC Merced intern cohort share how their summer internship experiences have influenced their careers in science.

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    image from gif that shows where in the globe JGI fungal collaborators are located.
    Using Team Science to Build Communities Around Data
    As the data portals grow and evolve, the research communities further expand around them. But with two projects, communities are forming to generate high quality genomes to benefit researchers.

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    Cow Rumen and the Early Days of Metagenomics
    Tracing a cow rumen dataset from the lab to material for a hands-on undergraduate research course at CSU-San Marcos that has since expanded into three other universities.

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Home › Items tagged with: LBNL

Content Tagged "LBNL"

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September 14, 2012

Berkeley Lab Seeking Licensees in GenomeWeb

“This is a general method to get DNA out from any kind of sample, but with higher sensitivity, we think, than current methods, and more … versatility in terms of product models,” Youn-Hi Woo, a staff scientist at Berkeley Lab and one of the method’s inventors, told PCR Insider this week.”  Read more on GenomeWeb (subscription may… [Read More]

February 13, 2012

A new approach for improve genome assembly

Assembling a genome from fragments of DNA sequence is often compared to assembling a puzzle. One of the problems researchers face with the increasing use of next-generation sequencing technologies is that the pieces of DNA sequence generated by the 454 or Illumina platforms are much smaller and far more numerous than those produced by the… [Read More]

January 17, 2012

Permafrost study referenced in ScienceNews

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… [Read More]

December 14, 2011

Permafrost metagenome study on VOA Special English report

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… [Read More]

November 7, 2011

Permafrost soil metagenome study in UK Press Association

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… [Read More]

November 7, 2011

Permafrost soil metagenome study in GenomeWeb

“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… [Read More]

October 17, 2011

Berkeley Lab Open House recap on Today at Berkeley Lab

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. Read more at Today at Berkeley Lab [Read More]

October 6, 2011

Of Soil Carbon and Climate Change

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… [Read More]

July 8, 2011

DOE JGI/JBEI collaboration in DomesticFuels.com

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… [Read More]

May 27, 2011

JGI Science @ the Lesher: “The Deal with Microbes” video

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.)… [Read More]
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