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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: HudsonAlpha

Content Tagged "HudsonAlpha"

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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 2, 2013

Sinking SOS levels lead to reduced salt tolerance

The Food and Agriculture Organization reported that salt levels in the soil is reducing the world’s agricultural lands at the rate of one percent a year. Concerns over feeding a growing global population with limited arable land have led to interest in developing salt-tolerant crops for food and fuel Found on the seashores of eastern… [Read More]

December 21, 2012

Cotton genome project in AL.com

If researchers’ plans spin out as they hope, King Cotton may get a new title as a Super Plant of the 21st century…. While most U.S. cotton is used in textile production, researchers say it could become an important part of biofuel production and bioremediation.   Full story at AL.com  [Read More]

September 6, 2012

32 papers in one day – ENCODE project’s first reports

The papers published Wednesday recount more than 1,600 experiments involving more than 180 different cell types, said Richard Myers, president of the nonprofit HudsonAlpha Institute for Biotechnology in Huntsville, Ala.“They have shown how the millions of switches in the human genome determine which proteins in the body are going to be made, how they will work together, and how… [Read More]

May 18, 2012

Foxtail Millet Genome an Improved Reference for Switchgrass

The DOE is interested in switchgrass as a prospective biofuels feedstock, but its genome is complicated because it has multiple copies of its chromosomes. As the world leader in sequencing plants and other organisms for their relevance to DOE missions, the JGI has sequenced switchgrass and several other plants that are candidate plant feedstocks; other… [Read More]

May 18, 2012

Foxtail millet project in GenomeWeb Daily News

From Genomics in the Journals: “Bennetzen and colleagues from the University of Georgia, the HudsonAlpha Institute, the Department of Energy’s Joint Genome Institute, and elsewhere used Sanger sequencing complemented by high-throughput sequencing methods to generate a high-quality, 400 million base reference genome for foxtail millet. “ Read more at GenomeWeb Daily News [Read More]

May 17, 2012

Foxtail millet project in Biofuels Digest

In an attempt to piece together the switchgrass genome, the DOE Joint Genome Institute (JGI) in an international partnership with includes the DOE BioEnergy Science Center (BESC) and the DOE Joint BioEnergy Institute (JBEI) has sequenced plant genomes of related candidate bioenergy crops such as sorghum and the model grass Brachypodium but may have found the missing… [Read More]

May 16, 2012

Foxtail millet genome project in AgProfessional

One of the challenges in studying grasses for bioenergy applications is that they typically have long lifecycles and complex genomes. Jeremy Schmutz, head of the DOE JGI Plant Program at the HudsonAlpha Institute of Biotechnology, pointed out that foxtail millet has several advantages as a model. It’s a compact genome roughly half a billion bases… [Read More]

April 15, 2011

Arabidopsis lyrata reference genome now available

Arabidopsis thaliana is a small flowering plant often used as a model system by researchers. As part of the 2006 Community Sequencing Program portfolio, the DOE JGI selected A. thaliana’s close relative A. lyrata for sequencing. By comparing their genomes and the genomes of other, related species, researchers could gain insight into plant genetics, specifically… [Read More]

April 11, 2011

Arabidopsis lyrata genome project in GenomeWeb

The international research team, led by investigators at the Max Planck Institute for Developmental Biology, compared the newly sequenced genome to the much smaller genome of the model organism A. thaliana. Their findings suggest that the pared down version of the genome found in A. thaliana reflects a spate of small deletions — many affecting… [Read More]
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