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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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    (PXFuel)
    Designer DNA: JGI Helps Users Blaze New Biosynthetic Pathways
    In a special issue of the journal Synthetic Biology, JGI scientific users share how they’ve worked with the JGI DNA Synthesis Science Program and what they’ve discovered through their collaborations.

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    A genetic element that generates targeted mutations, called diversity-generating retroelements (DGRs), are found in viruses, as well as bacteria and archaea. Most DGRs found in viruses appear to be in their tail fibers. These tail fibers – signified in the cartoon by the blue virus’ downward pointing ‘arms’— allow the virus to attach to one cell type (red), but not the other (purple). DGRs mutate these ‘arms,’ giving the virus opportunities to switch to different prey, like the purple cell. (Courtesy of Blair Paul)
    A Natural Mechanism Can Turbocharge Viral Evolution
    A team has discovered that diversity generating retroelements (DGRs) are not only widespread, but also surprisingly active. In viruses, DGRs appear to generate diversity quickly, allowing these viruses to target new microbial prey.

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    Photograph of a stream of diatoms beneath Arctic sea ice.
    Polar Phytoplankton Need Zinc to Cope with the Cold
    As part of a long-term collaboration with the JGI Algal Program, researchers studying function and activity of phytoplankton genes in polar waters have found that these algae rely on dissolved zinc to photosynthesize.

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    This data image shows the monthly average sea surface temperature for May 2015. Between 2013 and 2016, a large mass of unusually warm ocean water--nicknamed the blob--dominated the North Pacific, indicated here by red, pink, and yellow colors signifying temperatures as much as three degrees Celsius (five degrees Fahrenheit) higher than average. Data are from the NASA Multi-scale Ultra-high Resolution Sea Surface Temperature (MUR SST) Analysis product. (Courtesy NASA Physical Oceanography Distributed Active Archive Center)
    When “The Blob” Made It Hotter Under the Water
    Researchers tracked the impact of a large-scale heatwave event in the ocean known as “The Blob” as part of an approved proposal through the Community Science Program.

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    A plantation of poplar trees. (David Gilbert)
    Genome Insider podcast: THE Bioenergy Tree
    The US Department of Energy’s favorite tree is poplar. In this episode, hear from ORNL scientists who have uncovered remarkable genetic secrets that bring us closer to making poplar an economical and sustainable source of energy and materials.

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    HPCwire Editor's Choice Award (logo crop) for Best Use of HPC in the Life Sciences
    JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences
    The HPCwire Editors Choice Award for Best Use of HPC in Life Sciences went to the Berkeley Lab team comprised of JGI and ExaBiome Project team, supported by the DOE Exascale Computing Project for MetaHipMer, an end-to-end genome assembler that supports “an unprecedented assembly of environmental microbiomes.”

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    With a common set of "baseline metadata," JGI users can more easily access public data sets. (Steve Wilson)
    A User-Centered Approach to Accessing JGI Data
    Reflecting a structural shift in data access, the JGI Data Portal offers a way for users to more easily access public data sets through a common set of metadata.

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    Phytozome portal collage
    A More Intuitive Phytozome Interface
    Phytozome v13 now hosts upwards of 250 plant genomes and provides users with the genome browsers, gene pages, search, BLAST and BioMart data warehouse interfaces they have come to rely on, with a more intuitive interface.

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    screencap from Amundson and Wilkins subsurface microbiome video
    Digging into Microbial Ecosystems Deep Underground
    JGI users and microbiome researchers at Colorado State University have many questions about the microbial communities deep underground, including the role viral infection may play in other natural ecosystems.

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    Yeast strains engineered for the biochemical conversion of glucose to value-added products are limited in chemical output due to growth and viability constraints. Cell extracts provide an alternative format for chemical synthesis in the absence of cell growth by isolating the soluble components of lysed cells. By separating the production of enzymes (during growth) and the biochemical production process (in cell-free reactions), this framework enables biosynthesis of diverse chemical products at volumetric productivities greater than the source strains. (Blake Rasor)
    Boosting Small Molecule Production in Super “Soup”
    Researchers supported through the Emerging Technologies Opportunity Program describe a two-pronged approach that starts with engineered yeast cells but then moves out of the cell structure into a cell-free system.

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    These bright green spots are fluorescently labelled bacteria from soil collected from the surface of plant roots. For reference, the scale bar at bottom right is 10 micrometers long. (Rhona Stuart)
    A Powerful Technique to Study Microbes, Now Easier
    In JGI's Genome Insider podcast: LLNL biologist Jennifer Pett-Ridge collaborated with JGI scientists through the Emerging Technologies Opportunity Program to semi-automate experiments that measure microbial activity in soil.

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    A view of the mangroves from which the giant bacteria were sampled in Guadeloupe. (Hugo Bret)
    Giant Bacteria Found in Guadeloupe Mangroves Challenge Traditional Concepts
    Harnessing JGI and Berkeley Lab resources, researchers characterized a giant - 5,000 times bigger than most bacteria - filamentous bacterium discovered in the Caribbean mangroves.

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    In their approved proposal, Frederick Colwell of Oregon State University and colleagues are interested in the microbial communities that live on Alaska’s glacially dominated Copper River Delta. They’re looking at how the microbes in these high latitude wetlands, such as the Copper River Delta wetland pond shown here, cycle carbon. (Courtesy of Rick Colwell)
    Monitoring Inter-Organism Interactions Within Ecosystems
    Many of the proposals approved through JGI's annual Community Science Program call focus on harnessing genomics to developing sustainable resources for biofuels and bioproducts.

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    Coloring the water, the algae Phaeocystis blooms off the side of the sampling vessel, Polarstern, in the temperate region of the North Atlantic. (Katrin Schmidt)
    Climate Change Threatens Base of Polar Oceans’ Bountiful Food Webs
    As warm-adapted microbes edge polewards, they’d oust resident tiny algae. It's a trend that threatens to destabilize the delicate marine food web and change the oceans as we know them.

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Home › Items tagged with: GEBA

Content Tagged "GEBA"

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November 8, 2013

New tool helps find gene markers in microorganisms

Researchers have devised a novel method to exploit relationships between bacteria and archaea for a new set of gene markers The Science The researchers developed a new way to identify gene markers in bacteria and the primitive microorganisms classified in the kingdom known as Archaea. Dubbed, PhyEco (for phylogenetic and phylogenetic ecology) this strategy can… [Read More]

January 4, 2013

DOE JGI Science Highlight: Benefits of “diversity-driven genome sequencing” in CyanoGEBA

Despite their miniscule size, cyanobacteria play significant roles in the global carbon and nitrogen cycles. Researchers are also looking at utilizing them for biofuel and biotechnology applications. In an effort to learn more about the diverse strains in this phylum, DOE Joint Genome Institute scientist Cheryl Kerfeldis leading an effort called CyanoGEBAto increase the number… [Read More]

July 14, 2012

Maturing Metagenomics Needs Ground Rules

For every known star in our universe, there are billions of microbes here on Earth. But scientists are unable to culture most of these species in the lab. One approach to getting to know these beguiling bugs is to look at the big picture of their community. Metagenomics aims to characterize the overall genomic profile… [Read More]

July 6, 2012

GEBA Gets More Cellulase

[Read More]

May 6, 2012

Mount Marty College students wrap first project with DOE JGI’s “Interpret a Genome” program

“Annotating genes is a lot of work, and you have to pay a lot of attention to detail,” said April Knapp, one of seven students who presented findings from the class’s research Friday. “But it’s also very interesting because bioenergy and biofuel is such a high-needs fields. To know that the research we did here… [Read More]

July 6, 2011

UCLA microbiologists find energy-efficient structures in archaeon

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… [Read More]

May 8, 2011

JGI Science @ the Lesher in Contra Costa Times

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 —… [Read More]

March 26, 2011

Eisen blogs Twitter wrap-up of the DOE JGI User Meeting

Off to another meeting so don’t have time to write up details of the JGI User Meeting that just ended.  But I am posting my tweets and some related tweets here.  Also, apparently videos of the talks will be available soon. Will try to clean up the style of the posts ASAP but on the… [Read More]

March 24, 2011

Alfred University selected for DOE JGI Undergraduate Research Program in Microbial Genome Annotation

Alfred University is one of only 21 institutions in the country to be selected for the federal Joint Genome Institution (JGI) Undergraduate Research Program in Microbial Genome Collaboration. What that means, explains Jean Cardinale, professor of biology in the College of Liberal Arts & Sciences, is Alfred University students will have a unique opportunity to… [Read More]

March 15, 2011

Jonathan Eisen named 2011 Benjamin Franklin Laureate

Jonathan Eisen, a renowned open access advocate is awarded the tenth annual Benjamin Franklin award. This award, voted for by members of Bioinformatics.org, recognizes those providing free and open access to materials and methods in science.  More information here. [Read More]
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