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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: algae

Content Tagged "algae"

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June 24, 2013

Ehux – The Alga of Many Faces

Known by the researchers who sequenced it at the Department of Energy Joint Genome Institute as “The Beast”, and considered the “Flowers of the Ocean” by others, Emiliania huxleyi has proved to be a single-celled coccolithophore of many faces. The third most abundant group of phytoplankton, Ehux is the basis of most ocean food chains,… [Read More]

June 18, 2013

Ehux pangenome project in San Diego Union-Tribune

The algae are the third most abundant phytoplankton, and are a key component of the ocean food chain, nourishing animals including crustaceans, shellfish and other filter feeders.They’re characterized by their intricate shells, composed of interwoven lattices of calcium carbonate.“We kind of think of them as flowers of the ocean,” Read said. Read the full story… [Read More]

June 14, 2013

Ehux pangenome project in redOrbit

 “The Ehux genome is incredibly variable,” said study co-author Dr. Uwe John and biologist with the Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research (AWI). “For example, if the genetic information of two humans is compared, an agreement of about 99 per cent is found. However, if, for example, we take two Ehux strains from… [Read More]

September 14, 2012

Targeted metagenomics approach pins down role of “wild” alga

Marine microbes play key roles in cycling carbon between the atmosphere and the ocean depths, but little is known about their populations throughout the waters. As global temperatures change, so do these populations, which in turn impacts their contributions to the carbon cycle. Researchers want to learn more about these effects, but one of the… [Read More]

August 31, 2012

Algal Lipid Pathways Linked to Those in Plants and Fungi

Red algae play an important role in carbon and nitrogen cycles in the ocean, and are potential biomass for biofuel production. However, few red algae have been studied at the genomic level to date. An international collaboration of researchers has found that some species of the extremophilic red algae Porphyra have a pathway similar to… [Read More]

June 17, 2011

GreenCut algorithm in Crop Biotech Update

Grossman and colleagues revealed that many of the GreenCut proteins are also present in ancient cyanobacteria, red algae, and diatoms. Further assessment of these proteins is expected to bring more discoveries about their functions in photosynthetic cells, and how the photosynthetic cells might be adapted to survive various environmental conditions. Read more in ISAAA’s Crop… [Read More]

June 17, 2011

GreenCut algorithm in e! Science News

Using advanced computational tools to analyze the genomes of 28 different plants and photosynthetic organisms, Grossman and his colleagues at the University of California in Los Angeles and the Joint Genome Institute of the Department of Energy were able to identify 597 proteins encoded on plant and green algal genomes, but that are not present… [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]

March 21, 2011

Aureococcus genome project in Knoxville News Sentinel

The research team’s study focused on one particular strand of harmful algal blooms: Aureococcus anophagefferens. Originally, the team thought this strand would be found in the deep oceans, but the researchers discovered instead that it actually thrived in the human-affected conditions of the coastal regions. Read more at knoxnews.com [Read More]

February 25, 2011

DOE JGI Highlight: First genome of a Harmful Algal Bloom species

Algae play key roles in the global carbon cycle, helping trap carbon emissions. But some algal species can bloom, discoloring coastal waters and reduce the amount of light and oxygen available in the ecosystem. To describe these events, the term “harmful algal blooms” (HABs) was introduced two decades ago to note that accumulation of algal… [Read More]
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