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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: biofuel

Content Tagged "biofuel"

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September 4, 2009

T. reesei research on Checkbiotech

The current study complements last year’s publication of the T. reesei genome, which was sequenced at the DOE JGI. The authors looked at the sequence of the reference strain named for the Army quartermasters, QM6a, noted Baker. “Now we’re looking at strains such as RUT C30, which is a parent strain for many cellulase producing… [Read More]

September 4, 2009

T. reesei research on e Science News

During World War II, T. reesei frustrated American Army quartermasters in the South Pacific by speeding up the rate at which canvas supplies wore out. Now the same fungus is a key producer of industrial enzymes that are used, among other applications, to break down biomass for biofuel production. Part of the makeover can be… [Read More]

September 4, 2009

T. reesei research on Brightsurf

In half a century, one fungus has gone from being the bane of the Army quartermasters’ existence in the Pacific to industry staple and someday, as part of the U.S. Department of Energy’s mission to promote national energy security through clean, renewable energy development, a biofuel producers’ best friend. Trichoderma reesei’s makeover is due in… [Read More]

August 21, 2009

Looking beyond biotech companies for microbe-based biofuels

If you’re feeling ill trying to keep up with all the strange biofuel news these days, you might want to have some lab tests run. You could have a form of E. coli poisoning, a cyanobacteria outbreak, or maybe you accidentally ingested some highly toxic fire moss or perhaps bumped into a desert locust –… [Read More]

July 14, 2009

DOE JGI’s Phil Hugenholtz at “Microbes at UQ” Symposium

Keynote speaker Dr Phil Hugenholtz will be describing recent advances in the metagenomic analysis of the microbial communities within the termite hind-gut, following on from work published in Nature in 2007. The stomachs of termites actually harbor a gold mine of microbes that have now been tapped as a rich source of enzymes for improving… [Read More]

July 7, 2009

UW-M/JGI ant collaboration on Cleantech.com

Scientists from the University of Wisconsin, the Joint Genome Institute and Emory University have been tracking the symbiotic relationship between the three groups of organisms in the rainforest. Together, the three can consume 880 pounds of dry leaves a year, maximizing the energy harnessed from the leaves through a bioreactor process refined over 50 million… [Read More]

July 6, 2009

NZ’s Federated Farmers comments on AgResearch/JGI project

“Ultimately this is about taking the gas out of the gas,” said Don Nicolson, Federated Farmers President. “By identifying what organisms and enzymes are involved in an animal’s digestive process, there’s real potential to see less waste but more productivity from farm animals. “AgResearch deserves major credit for working with JGI to undertake this research… [Read More]

July 6, 2009

JGI/UW-M leaf cutter ant project on Discovery News

The genomes of 17 different ants, fungi and bacteria that eat through hundreds of pounds of leaf matter a year could ultimately lead to new techniques for making biofuels. Scientists from the University of Wisconsin, the Joint Genome Institute and Emory University are sequencing the first-ever community genome, searching for clues to how what’s essentially… [Read More]

July 1, 2009

JGI collaboration on pine beetle research in Biomass magazine

Genomics and proteomics research organizations Genome Canada, Genome British Columbia and Genome Alberta will help fund a $7.8 million research project designed to create tools for the prediction and guarantee of sustainable biomass feedstocks for Canadian biofuel production. The University of Alberta and the U.S. DOE’s Joint Genome Institute will also co-fund the project. The… [Read More]

June 5, 2009

“Craig Venter Has Algae Biofuel in Synthetic Genomics’ Pipeline”

In his Joint Genome Institute keynote speech in March, Venter said “the new algae” is something that “secretes whatever lipid size we want to engineer. This changes algae from what everybody’s been looking at as a farming problem into a manufacturing problem. So we are trying to get algae to go into a continuous production… [Read More]
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