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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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August 12, 2014

High quality reference Brassicales genomes

The Brassicaceae constitute not only one of the most diverse plant families, but also one rich in agronomically-important vegetable and oilseed crops. Several species have been domesticated and include different cabbages, broccoli, turnip, rapeseed, horseradish, and several mustards. Brassicaceae include a number of species that are current and emerging biodiesel crops. Researchers plan to generate… [Read More]

August 12, 2014

Reducing methane emission from peatlands

Peatlands harbor up to one third of the world pool of soil carbon and are estimated to be responsible for as much as 20 percent of the global emission of the greenhouse gas methane.  Sequencing the metagenome and metatranscriptome of peat soil, and in particular, the rare peatland Desulfosporosinus species, as well as potentially novel… [Read More]

August 12, 2014

Metagenomic consequences of Amazon deforestation

The Amazon rainforest plays an essential role in global ecological processes. It is the largest terrestrial carbonsequestering ecosystem in the world, controlling global temperature and precipitation, and balancing the flux of atmospheric gases. It is also the largest repository of plant and animal species on Earth. Despite its importance, it is one of the least… [Read More]

August 12, 2014

Developing a thermophilic fungal model group

Thermophilic fungi have been an important source of industrial enzymes for decades but research and development efforts have historically focused on the identification and characterization of cellulolytic genes from just a few strains. This approach has produced advanced enzymes over time, but recent genomics-based investigation has almost instantaneously yielded a diverse palette of novel, thermostable,… [Read More]

August 12, 2014

1000 Fungal Genomes

More than any other group of eukaryotic microbes, fungi are essential biological components of the global carbon cycle. Collectively, fungi are capable of degrading almost any naturally occurring biopolymer and numerous human-made ones. The use of fungi for the continued benefit of humankind, however, requires an accurate understanding of how they interact in naturally and… [Read More]

August 12, 2014

Investigating the Serpentinite-hosted Subsurface Biosphere

Serpentinization is the aqueous alteration of ultramafic rocks, characteristic of the Earth’s mantle, and results in the generation of highly-reducing, hydrogen- and methane- rich fluids with extremely high pH’s (commonly greater than 11). Microbial communities hosted within serpentinites may be important mediators of carbon and energy exchange between the deep Earth and the surface biosphere…. [Read More]

August 12, 2014

Functional genomics in Coprinopsis cinerea

While most basidiomycetes are difficult to cultivate in the laboratory, Coprinopsis cinerea is a notable exception in that it can complete its life cycle on artificial media in just two weeks. The C. cinerea genome is well-characterized, and both forward and reverse genetic approaches are now standard, allowing enormous scope for experimental manipulation in this… [Read More]

August 12, 2014

Defining the Populus Microbiome

Populus is considered the model organism for the study of woody perennials, and represents the first tree genome to be fully sequenced. Populus is also one of only a few species that are capable of establishing associations with both arbuscular mycorrhizal (AM) and ectomycorrhizal (EM) fungi, as well as various specific endophytic and rhizosphere associated… [Read More]

August 12, 2014

Dark ocean microbial single cell genomics

Considered one of the largest biomes on Earth, the dark ocean is comprised of the water column below the epipelagic, including meso-, bathy- and abyssopelagic and the hadal zones. It contains an active and metabolically diverse microbial assemblage that is responsible for about half of marine organic carbon mineralization. A large-scale single cell genomics study… [Read More]

August 12, 2014

Developing Schizophyllum commune as a model system

The study of wood breakdown into simple sugars is an important field of research due to its possible application in biofuel production. Developing S. commune as a model system to study the processes of wood degradation would allow researchers to study roles of enzymes in a fungus for which exist many protocols for studying genes… [Read More]
Page 1 of 612345...»Last »

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