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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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News & Publications
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June 1, 2015

Meraculous: Genome Assembly from Months to Minutes

“Using the parallelized version of Meraculous, we can now assemble the entire human genome in about eight minutes using 15,360 computer processor cores. With this tool, we estimate that the output from the world’s biomedical sequencing capacity could be assembled using just a portion of NERSC’s Edison supercomputer,” says Evangelos Georganas, a UC Berkeley graduate… [Read More]

April 27, 2015

Launching the JGI Diversity & Inclusion Initiative

On April 3, 2015, JGI and Genomics Division supervisors took part in a half-day retreat on diversity & inclusion. “About 50 supervisors from Genomics and the Joint Genome Institute (JGI) gathered earlier this month at the retreat for talks and discussions on implicit biases, what an inclusive workplace looks like, how to implement processes in recruiting… [Read More]

April 10, 2015

Soil bacteria and Setaria in R&D Magazine

“Our results show that healthy growth can be achieved by combining certain soil bacteria with grasses, even when plants are grown in extremely nitrogen-deprived soil,” said study coauthor Richard Ferrieri, director of Brookhaven Lab’s Radiochemistry and Biological Imaging Program. “We plan to apply this method to other crop systems, including bioenergy grasses like sorghum, switchgrass,… [Read More]

April 7, 2015

A science ambassador at the NSBE Convention

Steve Wilson at NSBEAs part of Berkeley Lab Director Paul Alivisatos’ Diversity & Inclusion Initiative, our own Steve Wilson served as a Lab science ambassador to the National Society of Black Engineers’ (NSBE) 41st Annual Convention on March 25-29, 2015 in Anaheim, CA. Wilson was part of a delegation including representatives from the Workforce Development & Education and Human Resources… [Read More]

April 1, 2015

Operations Deputy Ray Turner on Why Diversity Matters

“What I’ve found over the last nine years working in a more liberal and diverse environment at the JGI is that there are huge benefits from diversity in the workplace, the main one being that you just simply get better ideas with a more diverse group of people within your department or organization.” Our Operations… [Read More]

March 31, 2015

Potential new bacterial phylum in The Scientist

At the US Department of Energy (DOE) Joint Genome Institute User Meeting held in Walnut Creek, California, last week, researchers announced the genomic identification of a potential new bacterial phylum, Candidatus Kryptonia, based on their study of samples isolated from four hot springs located in North America and Asia. A talk presented by our postdoc… [Read More]

March 2, 2015

Ultra-small bacteria project in Huffington Post

“These newly described ultra-small bacteria are an example of a subset of the microbial life on earth that we know almost nothing about,” says Jill Banfield, a Senior Faculty Scientist in Berkeley Lab’s Earth Sciences Division and a UC Berkeley professor in the departments of Earth and Planetary Science and Environmental Science, Policy and Management…. [Read More]

March 2, 2015

Congressman DeSaulnier Visits JGI

(Left to right): Ray Turner, Jim bristow, Susannah Tringe, Rep. Mark DeSaulnier, and Susie Theroux.On Friday, February 20, first-year Congressman Mark DeSaulnier, whose 11th District spans from Antioch in east Contra Costa County to Richmond in the west, visited the landmark energy and environmental genomics user facility at his District’s geographic center, the DOE Joint Genome Institute in Walnut Creek. The Representative and his staffer Pat Joyce met with… [Read More]

February 24, 2015

March 4: DOE JGI-EMSL Collaborative Science Google+ Hangout

JGI-EMSL G+ Hangout graphicHave questions about or plan to submit a Letter of Intent to the DOE JGI-EMSL Collaborative Science Initiative? Now is your chance to learn more about these national scientific user facilities funded by the U.S. Department of Energy and the collaborative science capabilities they offer the global research community. The DOE Joint Genome Institute (JGI) and… [Read More]

February 23, 2015

Mycorrhizal fungi project in ScienceNews

“Long before the fungi engaged in trade with their plant hosts, though, their fungal ancestors primarily were decomposers, breaking down wood from dead trees. So how did this mutually beneficial relationship with live plants evolve?” The ScienceNews article ran on February 23, 2015. Learn more about the DOE JGI’s role in understanding the symbiotic relationship… [Read More]
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