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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
Home › News & Publications › Publications › 2003 Publications

2003 Publications

Azumi, K. et al. (2003) Genomic analysis of immunity in a Urochordate and the emergence of the vertebrate immune system: "waiting for Godot". Immunogenetics 55(8), 570-581. Doi 10.1007/S00251-003-0606-5
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Boffelli, D. et al. (2003) Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science 299(5611), 1391-1394. Doi 10.1126/Science.1081331
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Bray, N. et al. (2003) Avid: A Global Alignment Program. Genome Research 13(1), 97-102. Doi 10.1101/Gr.789803
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Chain, P. et al. (2003) Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea. Journal of Bacteriology 185(9), 2759-2773. Doi 10.1128/Jb.185.9.2759-2773.2003
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Cheng, J. F. et al. (2003) Comparative and functional analysis of cardiovascular-related genes. Pharmacogenomics 4(5), 571-582. Doi 10.1517/Phgs.4.5.571.23794
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Couronne, O. et al. (2003) Strategies and tools for whole-genome alignments. Genome Research 13(1), 73-80. Doi 10.1101/Gr.762503
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Dubchak, I. et al. (2003) Multi-species sequence comparison: the next frontier in genome annotation. Genome Biology 4(12). Artn 122 Doi 10.1186/Gb-2003-4-12-122
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Feil, H. et al. (2003) Site-directed disruption of the fimA and fimF fimbrial genes of Xylella fastidiosa. Phytopathology 93(6), 675-682. Doi 10.1094/Phyto.2003.93.6.675
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Frazer, K. A. et al. (2003) Cross-species sequence comparisons: A review of methods and available resources. Genome Research 13(1), 1-12. Doi 10.1101/Gr.222003
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Gibson-Brown, J. J. et al. (2003) A proposal to sequence the amphioxus genome submitted to the joint genome institute of the US department of energy. Journal of Experimental Zoology Part B-Molecular and Developmental Evolution 300B(1), 5-22. Doi 10.1002/Jez.B.00042
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Grogan, J. L. et al. (2003) Basal chromatin modification at the IL-4 gene in helper T cells. Journal of Immunology 171(12), 6672-6679.
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Grossman, A. R. et al. (2003) Chlamydomonas reinhardtii at the crossroads of genomics. Eukaryotic Cell 2(6), 1137-1150. Doi 10.1128/Ec.2.6.1137-1150.2003
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Hallam, S. J. et al. (2003) Identification of methyl coenzyme M reductase A (mcrA) genes associated with methane-oxidizing archaea. Applied and Environmental Microbiology 69(9), 5483-5491. Doi 10.1128/Aem.69.9.5483-5491.2003
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Huby, T. et al. (2003) Regulation of the expression of the apolipoprotein(a) gene - Evidence for a regulatory role of the 5 ' distal apolipoprotein(a) transcription control region enhancer in yeast artificial chromosome transgenic mice. Arteriosclerosis Thrombosis and Vascular Biology 23(9), 1633-1639. Doi 10.1161/01.Atv.0000084637.01883.Ca
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Ishida, T. et al. (2003) Endothelial lipase is a major determinant of HDL level. Journal of Clinical Investigation 111(3), 347-355. Doi 10.1172/Jci200316306
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Murphy, M. B. et al. (2003) An improved method for the in vitro evolution of aptamers and applications in protein detection and purification. Nucleic Acids Research 31(18). ARTN e110 DOI 10.1093/nar/gng110
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Nardi, F. et al. (2003) Response to comment on "Hexapod origins: Monophyletic or paraphyletic?". Science 301(5639).
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Nardi, F. et al. (2003) Hexapod origins: Monophyletic or paraphyletic?. Science 299(5614), 1887-1889. Doi 10.1126/Science.1078607
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Nobrega, M. A. et al. (2003) Scanning human gene deserts for long-range enhancers. Science 302(5644), 413-413. Doi 10.1126/Science.1088328
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Palenik, B. et al. (2003) The genome of a motile marine Synechococcus. Nature 424(6952), 1037-1042. Doi 10.1038/Nature01943
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Passamonti, M. et al. (2003) Molecular evolution and recombination in gender-associated mitochondrial DNAs of the manila clam Tapes philippinarum. Genetics 164(2), 603-611.
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Pennacchio, L. A. et al. (2003) Insights from human/mouse genome comparisons. Mammalian Genome 14(7), 429-436. Doi 10.1007/S00335-002-4001-1
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Pennacchio, L. A. et al. (2003) Human-mouse comparative genomics: Successes and failures to reveal functional regions of the human genome. Cold Spring Harbor Symposia on Quantitative Biology 68, 303-309. Doi 10.1101/Sqb.2003.68.303
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Pennacchio, L. A. et al. (2003) Apolipoprotein A5, a newly identified gene that affects plasma triglyceride levels in humans and mice. Arteriosclerosis Thrombosis and Vascular Biology 23(4), 529-534. Doi 10.1161/01.Atv.0000054194.78240.45
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Pennacchio, L. A. et al. (2003) Comparative genomic tools and databases: providing insights into the human genome. Journal of Clinical Investigation 111(8), 1099-1106. Doi 10.1172/Jci200317842
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Pennacchio, L. A. et al. (2003) Human-mouse comparative genomics: successes and failures to reveal functional regions of the human genome. Cold Spring Harb Symp Quant Biol 68, 303-9.
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Rocap, G. et al. (2003) Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424(6952), 1042-1047. Doi 10.1038/Nature01947
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Santini, S. et al. (2003) Evolutionary conservation of regulatory elements in vertebrate Hox gene clusters. Genome Research 13(6), 1111-1122. Doi 10.1101/Gr.700503
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Satou, Y. et al. (2003) A genomewide survey of developmentally relevant genes in Ciona intestinalis - I. Genes for bHLH transcription factors. Development Genes and Evolution 213(5-6), 213-221. Doi 10.1007/S00427-003-0319-7
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Saunders, N. F. W. et al. (2003) Mechanisms of thermal adaptation revealed from the genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii. Genome Research 13(7), 1580-1588. Doi 10.1101/Gr.1180903
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Shen, X. et al. (2003) Genome-wide examination of myoblast cell cycle withdrawal during differentiation. Developmental Dynamics 226(1), 128-138. Doi 10.1002/Dvdy.10200
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Terajima, D. et al. (2003) Identification of candidate genes encoding the core components of the cell death machinery in the Ciona intestinalis genome. Cell Death and Differentiation 10(6), 749-753. Doi 10.1038/Sj.Cdd.4401223
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Vu-Dac, N. et al. (2003) Apolipoprotein A5, a crucial determinant of plasma triglyceride levels, is highly responsive to peroxisome proliferator-activated receptor alpha activators. Journal of Biological Chemistry 278(20), 17982-17985. Doi 10.1074/Jbc.M212191200
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Wada, S. et al. (2003) A genomewide survey of developmentally relevant genes in Ciona intestinalis - II. Genes for homeobox transcription factors. Development Genes and Evolution 213(5-6), 222-234. Doi 10.1007/S00427-003-0321-0
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Yagi, K. et al. (2003) A genomewide survey of developmentally relevant genes in Ciona intestinalis - III. Genes for Fox, ETS, nuclear receptors and NF kappa B. Development Genes and Evolution 213(5-6), 235-244. Doi 10.1007/S00427-003-0322-Z
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