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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: Hellsten

Content Tagged "Hellsten"

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August 31, 2011

A mechanism for de novo intron insertion

Introns are the parts of a gene sequence that are not expressed in the protein. In the August 30 issue of Nature Communications, a team led by DOE JGI’s Eukaryote Program head Dan Rokhsar and Uffe Hellsten describe a potential mechanism by which introns have been added to a genome sequence since what they refer… [Read More]

August 4, 2010

Sponge genome project in New Scientist

Sponges are primitive creatures with a body plan unlike that of any other living organism. They are also our most distant animal cousins. Now that their genetic make-up has finally been sequenced, it could explain one of the greatest mysteries of evolution: how single-celled organisms in the primordial oceans evolved into complex multicellular animals with… [Read More]

July 21, 2010

Frog genome project on NIH Research Matters

A team of scientists led by the U.S. Department of Energy (DOE) Joint Genome Institute and the University of California, Berkeley, set out to add to the set of X. tropicalis research tools by sequencing its genome. The team, which included researchers from NIH’s National Library of Medicine (NLM) and National Cancer Institute (NCI), was… [Read More]

May 26, 2010

Frog genome project on BBC

“When human genome work was wrapping up around 2002, we were discussing what should be next,” JGI’s Uffe Hellsten told BBC News. “At that time there were a couple of furry mammals in the pipeline, and the chicken and at least two fish – but there seemed to be a gaping hole in the branch… [Read More]

May 24, 2010

Frog genome project on ScienceNews

A new study, published April 30 in Science, lays out the genetic blueprint of the Western clawed frog, Xenopus tropicalis. A larger cousin of X. tropicalis, called Xenopus laevis, is a popular laboratory organism for studying development. But with a genome about half the size of X. laevis’, the Western clawed frog has easier DNA… [Read More]

May 10, 2010

Frog genome project on QB3

When the Joint Genome Institute decided to sequence a frog genome, however, the Xenopus research community recommended X. tropicalis over X. laevis because tropicalis has half the genome size. While X. tropicalis is diploid, with two copies of each gene on 10 pairs of chromosomes, the X. laevis genome has undergone duplication and could have… [Read More]

May 10, 2010

Frog genome project on UPI

Sater said the frog is extremely important for studies of embryonic development and the regulation of cell division since its genes are highly similar to those in mice and humans. Other similarities include the frog’s molecular communication pathways that serve as lines of communication between cells and are critical for the maintenance and differentiation of… [Read More]

May 10, 2010

Frog genome project on 7th Space

“Sequencing and assembling a genome is basically science infrastructure – the equivalent of building roads and bridges – and once the infrastructure is in place, everyone can benefit,” Sater said. “This work is an enormous contribution to research now in progress throughout the world, and essentially every study that uses Xenopus as a research animal… [Read More]

May 6, 2010

Frog genome project on Medical News Today

The findings published in Science are based on the DNA of a single African clawed frog whose DNA was broken down into small pieces that were replicated many, many times, then sent to laboratories around the world for analysis. The project sprang from a meeting of researchers in Walnut Creek, Calif., in 2002, when the… [Read More]

May 6, 2010

Frog genome project on the Courier-Journal

The frog is cousin to the Western clawed frog (Xenopus laevis), which is often used to study embryo development and cell biology and having its genome will make sequencing laevis easier to do, said Harland.   Because frogs are especially sensitive to minute amounts of chemical that mimic hormones and can disrupt their endocrine system,… [Read More]
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