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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: bioenergy

Content Tagged "bioenergy"

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September 13, 2013

Beetle gut microbes bore through woody tissues

Profile of wood-boring beetle’s midgut microbial community identifies candidate genes involved in processes including lignin degradation The Science Metagenomics allowed researchers to conduct a functional analysis of the midgut microbial community in the Asian longhorned beetle (Anoplophora glabripennis), an invasive insect that feeds on lignin in deciduous trees such as poplars and willows. The Impact… [Read More]

May 20, 2013

DOE Early Career Awardee’s work to involve DOE JGI collaboration

O’Malley’s research, which she recently presented at the spring meeting of the American Chemical Society, involves the use of anaerobic gut fungi from horses, sheep, and other large herbivores to convert the cellulose in plants into sugars. Nature has evolved these fungi to break through lignin, a tough biopolymer that surrounds cellulose, and convert that… [Read More]

May 17, 2013

The genetic diversity of the maize microbiome

The rhizosphere is the space in, on and around the plant roots where microbes in the plant interact with the microbes in the soil. The DOE JGI did a study with the plant Arabidopsis. [Read More]

April 19, 2013

Termite diets dictate microbes in their guts

Realtors and homeowners cringe at the thought of termites on their properties, but for bioenergy researchers, these insects are rich harbors of microbial communities that can break down woody lignocellulose. In 2007, the DOE Joint Genome Institute sequenced the microbes in the hindgut of termites from Costa Rica (from the Nasutitermesgenus) to identify the genes… [Read More]

March 29, 2013

A peach of a genome with breeding lessons for biofuels crops

Several plants sequenced by the DOE Joint Genome Institute have been considered “flagship” genomes due to their importance to DOE mission and plant science. Among these plants are poplar, the first tree sequenced and a candidate bioenergy feedstock, and soybean, the primary source of biodiesel in the United States. Other plant genomes are important for… [Read More]

March 25, 2013

Peach genome project in Biofuels Digest

In California, the US Department of Energy Joint Genome Institute (DOE JGI) is working to isolate the “evergreen” locus in peaches, which extends the growing season of the plant. Said Daniel Rokhsar, head of the DOE JGI Eukaryotic Program, “In theory, it could be manipulated in poplar to increase the accumulation of biomass.” Peach genes… [Read More]

March 22, 2013

Large toolset for detecting genetic variation in poplars

Beyond their status as a fast-growing candidate biofuels feedstock. [Read More]

March 15, 2013

Bacterial sequence to help understand ant fungal gardens

Leaf-cutter ants forage for leaves that they use to cultivate a fungus in specialized gardens. (Wikipedia, CC-BY-SA-3.0,2.5,2.0,1.0)Leaf-cutter ant colonies are comprised of millions of ants harvesting hundreds of kilos of leaves annually for use in growing their primary food source, a fungus. The fungal gardens tended by these ants allow them to convert plant biomass on a very large scale. Bioenergy researchers are looking at the microbial composition of the fungal… [Read More]

March 8, 2013

Comparing extremophile isolates from Yellowstone

Researchers isolated and sequenced four species of Hydrogenobaculum. [Read More]

January 25, 2013

Lessons learned from comparing Cochliobolus fungi

Cochliobolus fungi are cereal grain pathogens in the Dothideomycetes class, and many species are known to infect crops such as corn, rice, barley, wheat and oats, causing severe losses at harvest time and to biomass feedstocks for biofuels. In a study published January 24, 2013 in Plos Genetics, one in a series of publications concerning… [Read More]
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