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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.

    Read more

    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
Home › News & Publications › Publications › 2005 Publications

2005 Publications

Alexandrino, J. et al. (2005) Strong selection against hybrids at a hybrid zone in the Ensatina ring species complex and its evolutionary implications. Evolution 59(6), 1334-1347.
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Boore, J. L. et al. (2005) Sequencing and comparing whole mitochondrial genomes of animals. Molecular Evolution: Producing the Biochemical Data, Part B 395, 311-348. Doi 10.1016/S0076-6879(05)95019-2
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Dehal, P. et al. (2005) Two rounds of whole genome duplication in the ancestral vertebrate. Plos Biology 3(10), 1700-1708. ARTN e314 DOI 10.1371/journal.pbio.0030314
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Foster, J. et al. (2005) The Wolbachia genome of Brugia malayi: Endosymbiont evolution within a human pathogenic nematode. Plos Biology 3(4), 599-614. ARTN e121 DOI 10.1371/journal.pbio.0030121
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Francino, M. P. et al. (2005) An adaptive radiation model for the origin of new gene functions. Nature Genetics 37(6), 573-577. Doi 10.1038/Ng1579
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Gatesy, J. et al. (2005) Hidden likelihood support in genomic data: Can forty-five wrongs make a right?. Systematic Biology 54(3), 483-492. Doi 10.1080/10635150590945368
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Jansen, R. K. et al. (2005) Methods for obtaining and analyzing whole chloroplast genome sequences. Molecular Evolution: Producing the Biochemical Data, Part B 395, 348-384. Doi 10.1016/S0076-6879(05)95020-9
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Keys, D. N. et al. (2005) A saturation screen for cis-acting regulatory DNA in the Hox genes of Ciona intestinalis. Proceedings of the National Academy of Sciences of the United States of America 102(3), 679-683. Doi 10.1073/Pnas.0408952102
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Leebens-Mack, J. et al. (2005) Identifying the basal angiosperm node in chloroplast genome phylogenies: Sampling one's way out of the felsenstein zone. Molecular Biology and Evolution 22(10), 1948-1963. Doi 10.1093/Molbev/Msi191
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Macey, J. R. et al. (2005) Plethodontid salamander mitochondrial genomics: A parsimony evaluation of character conflict and implications for historical biogeography. Cladistics 21(2), 194-202. Doi 10.1111/J.1096-0031.2005.00054.X
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Macey, J. R. et al. (2005) The complete mitochondrial genome of a gecko and the phylogenetic position of the Middle Eastern Teratoscincus keyserlingii. Molecular Phylogenetics and Evolution 36(1), 188-193. Doi 10.1016/J.Ympev.2005.03.025
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Medina, M. et al. (2005) Genomes, phylogeny, and evolutionary systems biology. Proceedings of the National Academy of Sciences of the United States of America 102, 6630-6635. Doi 10.1073/Pnas.0501984102
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Medina, M. et al. (2005) Phylogeny of sea hares in the Aplysia clade based on mitochondrial DNA sequence data. Bulletin of Marine Science 76(3), 691-698.
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Mueller, R. L. et al. (2005) Molecular mechanisms of extensive mitochondrial gene rearrangement in plethodontid salamanders. Molecular Biology and Evolution 22(10), 2104-2112. Doi 10.1093/Molbev/Msi204
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Noonan, J. P. et al. (2005) Genomic sequencing of Pleistocene cave bears. Science 309(5734), 597-9. 10.1126/science.1113485
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Parham, J. F. et al. (2005) A reassessment of the referral of sea turtle skulls to the genus Osteopygis (Late Cretaceous, New Jersey, USA). Journal of Vertebrate Paleontology 25(1), 71-77. Doi 10.1671/0272-4634(2005)025[0071:Arotro]2.0.Co;2
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Place, A. R. et al. (2005) Genetic markers in blue crabs (Callinectes sapidus) II. Complete mitochondrial genome sequence and characterization of genetic variation. Journal of Experimental Marine Biology and Ecology 319(1-2), 15-27. Doi 10.1016/J.Jembe.2004.03.024
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Richards, S. et al. (2005) Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution. Genome Research 15(1), 1-18. Doi 10.1101/Gr.3059305
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Rojas, A. et al. (2005) Gata4 expression in lateral mesoderm is downstream of BMP4 and is activated directly by Forkhead and GATA transcription factors through a distal enhancer element. Development 132(15), 3405-3417. Doi 10.1242/Dev.01913
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Tringe, S. G. et al. (2005) Comparative metagenomics of microbial communities. Science 308(5721), 554-557. Doi 10.1126/Science.1107851
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Vrdoljak, G. et al. (2005) Characterization of a diesel sludge microbial consortia for bioremediation. Scanning 27(1), 8-14.
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Weng, L. et al. (2005) Lack of MEF2A mutations in coronary artery disease. Journal of Clinical Investigation 115(4), 1016-1020. Doi 10.1172/Jci24186
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Wolf, P. G. et al. (2005) The first complete chloroplast genome sequence of a lycophyte, Huperzia lucidula (Lycopodiaceae). Gene 350(2), 117-128. Doi 10.1016/J.Gene.2005.01.018
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