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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 › Archives for Leila Hornick
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September 15, 2010

HudsonAlpha involved in cacao genome project

Excerpted from EurekAlert!: “Mockaitis, a biochemist-turned-genomicist, joined the project in early 2009, and quickly set to work with her collaborators to tackle the challenge of sequencing and accurately pasting together the approximately 400 million base pairs of the tree’s genome. Mockaitis’ Cacao Genome Group partners at the U.S. Department of Agriculture’s Subtropical Horticulture Research Station… [Read More]

September 10, 2010

New clues for understanding a novel cellulolytic process

Fibrobacter succinogenes is an anaerobic bacterium that breaks down plant cell wall biomass in ruminants and converts the cellulose into glucose. Sequenced at the DOE JGI for the Great Lakes Bioenergy Research Center (GLBRC), the 3.8 million base genome was completed and the information submitted to the National Center for Biotechnology Information in late 2009…. [Read More]

September 3, 2010

Bacterial lessons in rare metal recovery

One of the goals of the DOE’s Genomics:GTL Program is understanding how microbes and microbial communities perform the functions that have helped them thrive in a wide variety of environments and which have applications in the DOE mission areas of bioenergy, carbon cycling and biogeochemistry. British scientists applied information gleaned from Desulfovibrio genomes sequenced by… [Read More]

August 30, 2010

Brachypodium genome project on The Warsaw Voice

Brachypodium distachyon, commonly called purple false brome, is a model grass that enables researchers to more easily and thoroughly study temperate cereals, such as wheat, barley, rye and oats. These grasses are one of the most important groups of domesticated plants. The sequencing of the nuclear genome of Brachypodium is a big step towards intensified… [Read More]

August 30, 2010

Sponge genome project on Cosmos magazine

It’s just a blob, with no eyes, no nervous system, no muscle, no gut, no circulatory system, no tissues of any sort really – just cells embedded in a jelly matrix. They’re not even considered true animals. Yet according to the Nature report the sponge genome, which was read by researchers at the University of… [Read More]

August 27, 2010

Standardizing metagenomic classifications

A five-tier metagenome classification system would  enable genomic researchers to better extract and understand data. (Image from Ivanova et al. Env Microbiol. 2010: 12(7):1803-1805.) Studying the genomes of microbial communities, or metagenomics, has been facilitated in the last few years by advances in sequencing technologies. However, as the DOE JGI’s Natalia Ivanova, Susannah Tringe, Dino… [Read More]

August 20, 2010

A bacterium for biohydrogen production

Breaking down organic wastes typically involves microbial communities of bacteria and archaea working in concert with methanogens, which remove the hydrogen generated during the degradation process. The interactions between these syntrophic communities are being studied to understand the roles these microbes play individually and and as whole. In the August 2010 issue of the journal… [Read More]

August 16, 2010

Sponge genome project on Inside Science

According to the new study, which was based on a species of sponge found on the Great Barrier Reef off the coast of Australia, the creature has some 18,000 genes. This is fewer than the number of genes humans possess (currently estimated at about 20,500 genes) — but not far off. A few years ago,… [Read More]

August 13, 2010

Updating Genomics and Bioinformatics Courses for Undergraduates

Responding to the National Research Council of the National Academies’ call to “involve students in working with real data and tolls that reflect the nature of life sciences research in the 21st century,” the DOE JGI’s Education Program, headed by Cheryl Kerfeld, collaborated with faculty members from several universities around the country to develop bioinformatics… [Read More]

August 13, 2010

Syntrophic communities sequencing project on SciGuru

In work published in the advanced online version of the International Society for Microbial Ecology (ISME)’s Journal on August 5, an international team of scientists including DOE JGI researchers report the first metagenome analysis of a microbial community grown in an anaerobic methanogenic (methane producing) bioreactor. The microbial community is syntrophic, i.e., certain organisms live… [Read More]
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