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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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All JGI Features
Home › Items tagged with: Chlamydomonas

Content Tagged "Chlamydomonas"

Page 1 of 212»

June 17, 2011

GreenCut2: Algorithm to ID Plant Protein Functions

Researchers use genome sequencing to inform various cellular processes in land plants and algae, including the details of photosynthesis.  Despite the access to an increasing number of plant genomes (most of which have been generated by the DOE JGI), it remains difficult to correlate protein information with function, until now.  For example, identifying the role… [Read More]

May 9, 2011

Selaginella genome project on redOrbit

Grigoriev noted that the Selaginella genome helps fill in a large gap in plant evolution from the unicellular green alga Chlamydomonas, sequenced at the DOE JGI and published in 2007, to flowering plants with vascular systems. “Selaginella occupies a phylogenetically important position for which we had no reference,” he said. “On one end of the… [Read More]

July 16, 2010

Volvox carteri project on Astrobiology magazine

“If you think of proteins in terms of lego bricks, Chlamydomonas already had a great lego set,” says James Umen, assistant professor in the Plant Molecular and Cellular Biology Laboratory at the Salk Institute. “Volvox didn’t have to buy a new one, and instead could experiment with what it had inherited from its ancestor.”  Read… [Read More]

July 16, 2010

Volvox carteri project on NCTimes.com Blog

The study was published in the July 9 issue of Science. It may also be pertinent to the ongoing development of algae as a biofuel petroleum replacement, a major focus of research in San Diego and at the federal level. The team compared the genome of Volvox, a multicellular spherical algae, with that of the… [Read More]

July 16, 2010

Volvox carteri project in Algae Industry Magazine

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

July 15, 2010

Volvox carteri project on Biology News Net

Prochnik points to both Volvox and Chlamydomonas as experimentally tractable model organisms where the information will be widely used, even by researchers who are not necessarily interested in Volvox biology. “Having the Volvox genome is a fantastic resource for directing further research towards our target areas of interest. With this pair of algal genomes in… [Read More]

July 15, 2010

Volvox carteri project on Genetics Times

“The fundamental developmental biology interest in studying the Volvocine algae is that a single cell ancestor has evolved multicellularity and complicated cellular processes in a short evolutionary period,” explained DOE JGI bioinformaticist and co-first author Simon Prochnik. What the team found, he said, is “an astonishing lack of innovation” in the Volvox genome when compared… [Read More]

July 14, 2010

Volvox carteri project on CORDIS Wire

This is due the fact that within the green algal order Chlamydomonadales there are closely related uni- and multicellular species, such as the two-flagellated unicellular model alga Chlamydomonas reinhardtii and its sister taxon Volvox carteri, the latter being made up of more than 2,000 cells and having a much more complex life cycle on top… [Read More]

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 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]
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