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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: Simon Prochnik

Content Tagged "Simon Prochnik"

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July 12, 2010

Volvox carteri project on Medical News Today

The evolution of multicellularity occurred repeatedly and independently in diverse lineages including animals, plants, fungi, as well as green and red algae. “This transition is one of the great evolutionary events that shaped life on earth,” says co-first author Simon E. Prochnik, Ph.D., a Computationial Scientist at the DOE Joint Genome Institute. “It has generated… [Read More]

July 12, 2010

Volvox carteri project on Web Newswire

The evolution of multicellularity occurred repeatedly and independently in diverse lineages including animals, plants, fungi, as well as green and red algae. This transition is one of the great evolutionary events that shaped life on earth, says co-first author Simon E. Prochnik, Ph.D., a Computational Scientist at the DOE Joint Genome Institute. It has generated… [Read More]

July 12, 2010

Volvox carteri project on ACED

One of the most pivotal steps in evolution-the transition from unicellular to multicellular organisms-may not have required as much retooling as commonly believed, found a globe-spanning collaboration of scientists led by researchers at the Salk Institute for Biological Studies and the US Department of Energy’s Joint Genome Institute. Read more on ACED [Read More]

July 12, 2010

Volvox carteri project on redOrbit

One of the most pivotal steps in evolution-the transition from unicellular to multicellular organisms-may not have required as much retooling as commonly believed, found a globe-spanning collaboration of scientists led by researchers at the Salk Institute for Biological Studies and the US Department of Energy’s Joint Genome Institute. A comparison of the genomes of the… [Read More]

July 12, 2010

Volvox carteri project on NCTimes

Multicellularity is one of life’s great innovations. The ability of many individual cells to work together as a single being is so profound that scientists have regarded it as an immensely complicated process, requiring a huge amount of genetic retooling. But the process may have been simpler than previously thought, according to a new study… [Read More]

July 12, 2010

Volvox carteri project on EurekAlert

One contribution that may inform biofuels research is reported in the July 9 issue of Science (http://bit.ly/aSGJc3), where researchers led by the DOE Joint Genome Institute (JGI) and the Salk Institute present the 138 million nucleotide genome of Volvox carteri, a multicellular alga that captures light energy through photosynthesis. The DOE is supporting research into… [Read More]

July 9, 2010

Volvox carteri project on GenomeWeb

In this week’s issue of Science, research led by investigators at the Department of Energy’s Joint Genome Institute examines the organismal complexity of the multicellular green alga Volvox carteri. Simon Prochnik et al. sequenced the Volvox genome to 11.1-fold coverage using a whole-genome shotgun approach; when compared to Chlamydomonas reinhardtii, its unicellular relative, the team… [Read More]

March 30, 2010

Naegleria genome project on UC Davis News Service

N. gruberi is harmless to humans, but it does have a relative called Naegleria fowlerii that lives in murky water and can — rarely — swim up your nose and eat your brain. Sequencing was carried out at the U.S. Department of Energy’s Joint Genome Institute in Walnut Creek. The joint first authors on the… [Read More]

March 16, 2010

Naegleria genome project on SpaceDaily

“In a sense, analyzing the Naegleria genome shows us what it would be like to be on this planet more than a billion years ago, and what kind of organisms were around then and what they might have looked like,” said Simon E. Prochnik, a JGI and UC Berkeley bioinformaticist and coauthor of the Cell… [Read More]

March 8, 2010

Naegleria genome project on Medical News Today

Scientists have now sequenced the genome of a weird, single-celled organism called Naegleria gruberi that is telling biologists about that transition from prokaryotes, which function just fine with all their proteins floating around in a soup, to eukaryotes, which neatly compartmentalize those proteins? The sequence, produced by the Department of Energy Joint Genome Institute (JGI),… [Read More]
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