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  • 1
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    RiceNet v2: an improved network prioritization server for rice genes (2015)
    Oxford University Press
    Details
    Publication Date: 2015-07-02
    Description: Rice is the most important staple food crop and a model grass for studies of bioenergy crops. We previously published a genome-scale functional network server called RiceNet, constructed by integrating diverse genomics data and demonstrated the use of the network in genetic dissection of rice biotic stress responses and its usefulness for other grass species. Since the initial construction of the network, there has been a significant increase in the amount of publicly available rice genomics data. Here, we present an updated network prioritization server for Oryza sativa ssp. japonica , RiceNet v2 ( http://www.inetbio.org/ricenet ), which provides a network of 25 765 genes (70.1% of the coding genome) and 1 775 000 co-functional links. Ricenet v2 also provides two complementary methods for network prioritization based on: (i) network direct neighborhood and (ii) context-associated hubs. RiceNet v2 can use genes of the related subspecies O. sativa ssp. indica and the reference plant Arabidopsis for versatility in generating hypotheses. We demonstrate that RiceNet v2 effectively identifies candidate genes involved in rice root/shoot development and defense responses, demonstrating its usefulness for the grass research community.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Tangential migration of glutamatergic neurons [Neuroscience] (2015)
    National Academy of Sciences
    Details
    Publication Date: 2015-07-29
    Description: In a classic model of mammalian brain formation, precursors of principal glutamatergic neurons migrate radially along radial glia fibers whereas GABAergic interneuron precursors migrate tangentially. These migration modes have significant implications for brain function. Here we used clonal lineage tracing of active radial glia-like neural stem cells in the adult...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 3
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    Emergence of functional microcircuits [Neuroscience] (2016)
    National Academy of Sciences
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    Publication Date: 2016-03-09
    Description: During cortical circuit development in the mammalian brain, groups of excitatory neurons that receive similar sensory information form microcircuits. However, cellular mechanisms underlying cortical microcircuit development remain poorly understood. Here we implemented combined two-photon imaging and photolysis in vivo to monitor and manipulate neuronal activities to study the processes underlying...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 4
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    Genome Sequences of Three Phytopathogenic Species of the Magnaporthaceae Family of Fungi (2015)
    Genetics Society of America (GSA)
    Details
    Publication Date: 2015-12-10
    Description: Magnaporthaceae is a family of ascomycetes that includes three fungi of great economic importance: Magnaporthe oryzae , Gaeumannomyces graminis var. tritici , and Magnaporthe poae . These three fungi cause widespread disease and loss in cereal and grass crops, including rice blast disease ( M. oryzae ), take-all disease in wheat and other grasses ( G. graminis ), and summer patch disease in turf grasses ( M. poae ). Here, we present the finished genome sequence for M. oryzae and draft sequences for M. poae and G. graminis var. tritici . We used multiple technologies to sequence and annotate the genomes of M. oryzae , M. poae , and G. graminis var. tritici . The M. oryzae genome is now finished to seven chromosomes whereas M. poae and G. graminis var. tritici are sequenced to 40.0 x and 25.0 x coverage respectively. Gene models were developed by the use of multiple computational techniques and further supported by RNAseq data. In addition, we performed preliminary analysis of genome architecture and repetitive element DNA.
    Electronic ISSN: 2160-1836
    Topics: Biology
    Published by Genetics Society of America (GSA)
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  • 5
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    Arrest defective 1 regulates the oxidative stress response in human cells and mice by acetylating methionine sulfoxide reductase A (2014)
    Springer Nature
    Details
    Publication Date: 2014-10-24
    Description: Arrest defective 1 regulates the oxidative stress response in human cells and mice by acetylating methionine sulfoxide reductase A Cell Death and Disease 5, e1490 (October 2014). doi:10.1038/cddis.2014.456 Authors: S-H Shin, H Yoon, Y-S Chun, H-W Shin, M-N Lee, G T Oh & J-W Park
    Electronic ISSN: 2041-4889
    Topics: Biology , Medicine
    Published by Springer Nature
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  • 6
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    Miro1 protects against neurological disease [Cell Biology] (2014)
    National Academy of Sciences
    Details
    Publication Date: 2014-09-03
    Description: Defective mitochondrial distribution in neurons is proposed to cause ATP depletion and calcium-buffering deficiencies that compromise cell function. However, it is unclear whether aberrant mitochondrial motility and distribution alone are sufficient to cause neurological disease. Calcium-binding mitochondrial Rho (Miro) GTPases attach mitochondria to motor proteins for anterograde and retrograde transport...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 7
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    General mode of action of macrolide antibiotics [Biochemistry] (2014)
    National Academy of Sciences
    Details
    Publication Date: 2014-11-12
    Description: Macrolides are clinically important antibiotics thought to inhibit bacterial growth by impeding the passage of newly synthesized polypeptides through the nascent peptide exit tunnel of the bacterial ribosome. Recent data challenged this view by showing that macrolide antibiotics can differentially affect synthesis of individual proteins. To understand the general mechanism...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 8
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    Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-07-27
    Description: The compact genome of Fugu rubripes has been sequenced to over 95% coverage, and more than 80% of the assembly is in multigene-sized scaffolds. In this 365-megabase vertebrate genome, repetitive DNA accounts for less than one-sixth of the sequence, and gene loci occupy about one-third of the genome. As with the human genome, gene loci are not evenly distributed, but are clustered into sparse and dense regions. Some "giant" genes were observed that had average coding sequence sizes but were spread over genomic lengths significantly larger than those of their human orthologs. Although three-quarters of predicted human proteins have a strong match to Fugu, approximately a quarter of the human proteins had highly diverged from or had no pufferfish homologs, highlighting the extent of protein evolution in the 450 million years since teleosts and mammals diverged. Conserved linkages between Fugu and human genes indicate the preservation of chromosomal segments from the common vertebrate ancestor, but with considerable scrambling of gene order.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Aparicio, Samuel -- Chapman, Jarrod -- Stupka, Elia -- Putnam, Nik -- Chia, Jer-Ming -- Dehal, Paramvir -- Christoffels, Alan -- Rash, Sam -- Hoon, Shawn -- Smit, Arian -- Gelpke, Maarten D Sollewijn -- Roach, Jared -- Oh, Tania -- Ho, Isaac Y -- Wong, Marie -- Detter, Chris -- Verhoef, Frans -- Predki, Paul -- Tay, Alice -- Lucas, Susan -- Richardson, Paul -- Smith, Sarah F -- Clark, Melody S -- Edwards, Yvonne J K -- Doggett, Norman -- Zharkikh, Andrey -- Tavtigian, Sean V -- Pruss, Dmitry -- Barnstead, Mary -- Evans, Cheryl -- Baden, Holly -- Powell, Justin -- Glusman, Gustavo -- Rowen, Lee -- Hood, Leroy -- Tan, Y H -- Elgar, Greg -- Hawkins, Trevor -- Venkatesh, Byrappa -- Rokhsar, Daniel -- Brenner, Sydney -- New York, N.Y. -- Science. 2002 Aug 23;297(5585):1301-10. Epub 2002 Jul 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular and Cell Biology, 30 Medical Drive, Singapore 117609. saa1000@cam.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12142439" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biological Evolution ; Computational Biology ; Conserved Sequence ; DNA Transposable Elements ; Evolution, Molecular ; Exons ; Fish Proteins/chemistry/genetics ; Gene Duplication ; Gene Order ; *Genome ; *Genome, Human ; Genomics ; Humans ; Introns ; Physical Chromosome Mapping ; Proteins/chemistry/genetics ; Proteome ; Repetitive Sequences, Nucleic Acid ; *Sequence Analysis, DNA ; Synteny ; Takifugu/*genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 9
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    A direct role for dual oxidase in Drosophila gut immunity (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-11-08
    Description: Because the mucosal epithelia are in constant contact with large numbers of microorganisms, these surfaces must be armed with efficient microbial control systems. Here, we show that the Drosophila nicotinamide adenine dinucleotide phosphate (NADPH) oxidase enzyme, dual oxidase (dDuox), is indispensable for gut antimicrobial activities. Adult flies in which dDuox expression is silenced showed a marked increase in mortality rate even after a minor infection through ingestion of microbe-contaminated food. This could be restored by the specific reintroduction of dDuox, demonstrating that this oxidase generates a unique epithelial oxidative burst that limits microbial proliferation in the gut. Thus, oxidant-mediated antimicrobial responses are not restricted to the phagocytes, but rather are used more broadly, including in mucosal barrier epithelia.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ha, Eun-Mi -- Oh, Chun-Taek -- Bae, Yun Soo -- Lee, Won-Jae -- New York, N.Y. -- Science. 2005 Nov 4;310(5749):847-50.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Molecular Life Science and Center for Cell Signaling Research, Ewha Woman's University, Seoul 120-750, South Korea.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16272120" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Genetically Modified ; Bacteria/*growth & development/immunology ; Catalase/genetics/metabolism ; Chlorides/metabolism ; Colony Count, Microbial ; Digestive System/enzymology/immunology/microbiology ; Drosophila/*enzymology/*immunology/microbiology ; *Immunity, Innate ; In Vitro Techniques ; Intestinal Mucosa/enzymology/immunology/microbiology ; NADPH Oxidase/genetics/*metabolism ; RNA Interference ; Reactive Oxygen Species/metabolism ; Respiratory Burst ; Saccharomyces cerevisiae/*growth & development/immunology ; Superoxides/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 10
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    Quantum annealing with manufactured spins (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-05-13
    Description: Many interesting but practically intractable problems can be reduced to that of finding the ground state of a system of interacting spins; however, finding such a ground state remains computationally difficult. It is believed that the ground state of some naturally occurring spin systems can be effectively attained through a process called quantum annealing. If it could be harnessed, quantum annealing might improve on known methods for solving certain types of problem. However, physical investigation of quantum annealing has been largely confined to microscopic spins in condensed-matter systems. Here we use quantum annealing to find the ground state of an artificial Ising spin system comprising an array of eight superconducting flux quantum bits with programmable spin-spin couplings. We observe a clear signature of quantum annealing, distinguishable from classical thermal annealing through the temperature dependence of the time at which the system dynamics freezes. Our implementation can be configured in situ to realize a wide variety of different spin networks, each of which can be monitored as it moves towards a low-energy configuration. This programmable artificial spin network bridges the gap between the theoretical study of ideal isolated spin networks and the experimental investigation of bulk magnetic samples. Moreover, with an increased number of spins, such a system may provide a practical physical means to implement a quantum algorithm, possibly allowing more-effective approaches to solving certain classes of hard combinatorial optimization problems.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Johnson, M W -- Amin, M H S -- Gildert, S -- Lanting, T -- Hamze, F -- Dickson, N -- Harris, R -- Berkley, A J -- Johansson, J -- Bunyk, P -- Chapple, E M -- Enderud, C -- Hilton, J P -- Karimi, K -- Ladizinsky, E -- Ladizinsky, N -- Oh, T -- Perminov, I -- Rich, C -- Thom, M C -- Tolkacheva, E -- Truncik, C J S -- Uchaikin, S -- Wang, J -- Wilson, B -- Rose, G -- England -- Nature. 2011 May 12;473(7346):194-8. doi: 10.1038/nature10012.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉D-Wave Systems Inc., 100-4401 Still Creek Drive, Burnaby, British Columbia V5C 6G9, Canada. mwjohnson@dwavesys.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21562559" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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