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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: Eddy Rubin

Content Tagged "Eddy Rubin"

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November 15, 2012

DOE JGI Director Rubin’s keynote at the UCSF Institute for Human Genetics 2012 Symposium

The [UCSF Institute for Human Genetics 2012] symposium led off with geneticist Eddy Rubin, MD, PhD, whose presentation demonstrated that genetic studies are being applied to human problems that extend even beyond the realm of medicine. Rubin – a scientist who oversaw the sequencing and analysis of 13 percent of the human genome as part of the… [Read More]

November 16, 2011

DOE JGI research featured in io9

Last month I was lucky enough to visit one of the biggest genomics labs in the world. At the Joint Genome Institute (JGI) in Walnut Creek, CA, huge rooms full of genome sequencing machines work 24/7 to crunch the codes that create life. And the research here, funded by the US Department of Energy, has… [Read More]

November 5, 2011

DOE JGI science in the Washington Post

JGI director and geneticist Eddy Rubin is a pioneer in the field of “metagenomics,” the study of how the DNA in many creatures can work together to create ecosystems. Right now, he and his team are studying microbes that live in a cow’s rumen, the stomach-like organ that the animals use to break down grasses… [Read More]

October 12, 2011

Director Rubin on corngrass1 for biofuel

Up to now, the fast-growing switchgrass, because of its tough lignin, an organic polymer, has required heavy chemical treatment before it can be turned to ethanol as biofuel. Chuck’s gene transfer experiments have shown that because the improved switchgrass keeps the plants young, the lignin content of their cells is minimal and would need no… [Read More]

July 1, 2011

Efficiency Improvements in Biofuels Production

To overcome the difficulties of converting cellulosic biomass into high energy-content fuel, researchers have been seeking to improve various stages of the process. One big obstacle that stands in the way is that most enzymes are inefficient at breaking down biomass when in the presence of ionic liquids, solvents that have proven effective at treating the… [Read More]

May 23, 2011

DOE JGI Director honored by Middlebury College

Waddell, who was presented the honorary degree, doctor of humane letters, was one of six people to receive honorary degrees at this year’s commencement ceremonies. The others were economics scholar and international adviser to political leaders Padma Desai, doctor of laws; Vermont’s long-serving senator, Patrick Leahy, doctor of laws; local volunteer and activist Dorothy Bigelow Neuberger… [Read More]

March 24, 2011

DOE JGI as ‘Genomics Foundry’ in GenomeWeb

The Joint Genome Institute plans to transition from a sequencing center to a “genomic foundry” — a one-stop shop for large-scale functional annotation, single-cell genomics and transcriptomics, high-throughput custom sample prep, and analysis expertise, among other proposed services, said Eddy Rubin at JGI’s sixth annual User Meeting in Walnut Creek, Calif. Ultimately, Rubin said, he… [Read More]

January 31, 2011

Cow rumen metagenome study in EarthSky

Enter: the cow. If cows are good at anything, it’s digesting plant material until it turns into sugar; Dr. Rubin noted that cows have been eating grass for a few million years. That’s why Rubin’s team decided to do major genetic analysis of microbes inside the stomachs of cows. He explained that he was interested… [Read More]

January 28, 2011

Cow rumen metagenome study on BBC World Service: Science in Action

Growing crops to make bio-fuel is controversial – they can take up valuable land and resources that could be used for food production and in the case of oil palms, large tracts of rainforest have been cleared to make way for this cash crop. But the second generation of bio-fuels hope to make use of… [Read More]

January 28, 2011

Rumenating on improving biofuel production

Developing alternative fuels from plants has been challenging in part due to the high costs associated with processing plant biomass to more easily convert it into sugars and from there into biofuels. Ruminants such as the cow, however, can eat more than a hundred pounds of plant matter a day and break it down.  Switchgrass… [Read More]
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