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  • Light  (3)
  • Sequence Analysis, DNA
  • American Association for the Advancement of Science (AAAS)  (4)
  • Wiley
  • 2000-2004  (4)
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Keywords
Publisher
  • American Association for the Advancement of Science (AAAS)  (4)
  • Wiley
Years
Year
  • 1
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    Self-assembling amphiphilic siderophores from marine bacteria (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-02-26
    Description: Most aerobic bacteria secrete siderophores to facilitate iron acquisition. Two families of siderophores were isolated from strains belonging to two different genera of marine bacteria. The aquachelins, from Halomonas aquamarina strain DS40M3, and the marinobactins, from Marinobacter sp. strains DS40M6 and DS40M8, each contain a unique peptidic head group that coordinates iron(III) and an appendage of one of a series of fatty acid moieties. These siderophores have low critical micelle concentrations (CMCs). In the absence of iron, the marinobactins are present as micelles at concentrations exceeding their CMC; upon addition of iron(III), the micelles undergo a spontaneous phase change to form vesicles. These observations suggest that unique iron acquisition mechanisms may have evolved in marine bacteria.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Martinez, J S -- Zhang, G P -- Holt, P D -- Jung, H T -- Carrano, C J -- Haygood, M G -- Butler, A -- GM38130/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Feb 18;287(5456):1245-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106-9510, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10678827" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acids/analysis ; Chemistry, Physical ; Cryoelectron Microscopy ; Evolution, Molecular ; Fatty Acids/analysis ; Ferric Compounds/metabolism ; Gammaproteobacteria/*chemistry/isolation & purification/metabolism ; Halomonas/*chemistry/isolation & purification/metabolism ; Light ; Micelles ; Phylogeny ; Physicochemical Phenomena ; Scattering, Radiation ; Seawater/microbiology ; Siderophores/*chemistry/isolation & purification/metabolism ; Surface Properties
    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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  • 2
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    The protein kinase complement of the human genome (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-12-10
    Description: We have catalogued the protein kinase complement of the human genome (the "kinome") using public and proprietary genomic, complementary DNA, and expressed sequence tag (EST) sequences. This provides a starting point for comprehensive analysis of protein phosphorylation in normal and disease states, as well as a detailed view of the current state of human genome analysis through a focus on one large gene family. We identify 518 putative protein kinase genes, of which 71 have not previously been reported or described as kinases, and we extend or correct the protein sequences of 56 more kinases. New genes include members of well-studied families as well as previously unidentified families, some of which are conserved in model organisms. Classification and comparison with model organism kinomes identified orthologous groups and highlighted expansions specific to human and other lineages. We also identified 106 protein kinase pseudogenes. Chromosomal mapping revealed several small clusters of kinase genes and revealed that 244 kinases map to disease loci or cancer amplicons.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Manning, G -- Whyte, D B -- Martinez, R -- Hunter, T -- Sudarsanam, S -- New York, N.Y. -- Science. 2002 Dec 6;298(5600):1912-34.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉SUGEN Inc., 230 East Grand Avenue, South San Francisco, CA 94080, USA. gerard-manning@sugen.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12471243" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Catalysis ; Chromosome Mapping ; Computational Biology ; Databases, Genetic ; Genes ; *Genome, Human ; Humans ; Neoplasms/genetics ; Phylogeny ; Protein Kinases/chemistry/classification/*genetics/*metabolism ; Protein Structure, Tertiary ; Pseudogenes ; Sequence Analysis, DNA ; Signal Transduction
    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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  • 3
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    The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-10-02
    Description: Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are responsible for approximately 20% of global carbon fixation. We report the 34 million-base pair draft nuclear genome of the marine diatom Thalassiosira pseudonana and its 129 thousand-base pair plastid and 44 thousand-base pair mitochondrial genomes. Sequence and optical restriction mapping revealed 24 diploid nuclear chromosomes. We identified novel genes for silicic acid transport and formation of silica-based cell walls, high-affinity iron uptake, biosynthetic enzymes for several types of polyunsaturated fatty acids, use of a range of nitrogenous compounds, and a complete urea cycle, all attributes that allow diatoms to prosper in aquatic environments.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Armbrust, E Virginia -- Berges, John A -- Bowler, Chris -- Green, Beverley R -- Martinez, Diego -- Putnam, Nicholas H -- Zhou, Shiguo -- Allen, Andrew E -- Apt, Kirk E -- Bechner, Michael -- Brzezinski, Mark A -- Chaal, Balbir K -- Chiovitti, Anthony -- Davis, Aubrey K -- Demarest, Mark S -- Detter, J Chris -- Glavina, Tijana -- Goodstein, David -- Hadi, Masood Z -- Hellsten, Uffe -- Hildebrand, Mark -- Jenkins, Bethany D -- Jurka, Jerzy -- Kapitonov, Vladimir V -- Kroger, Nils -- Lau, Winnie W Y -- Lane, Todd W -- Larimer, Frank W -- Lippmeier, J Casey -- Lucas, Susan -- Medina, Monica -- Montsant, Anton -- Obornik, Miroslav -- Parker, Micaela Schnitzler -- Palenik, Brian -- Pazour, Gregory J -- Richardson, Paul M -- Rynearson, Tatiana A -- Saito, Mak A -- Schwartz, David C -- Thamatrakoln, Kimberlee -- Valentin, Klaus -- Vardi, Assaf -- Wilkerson, Frances P -- Rokhsar, Daniel S -- New York, N.Y. -- Science. 2004 Oct 1;306(5693):79-86.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Oceanography, University of Washington, Seattle, WA 98195, USA. armbrust@ocean.washington.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15459382" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Algal Proteins/chemistry/genetics/physiology ; Animals ; *Biological Evolution ; Cell Nucleus/genetics ; Chromosomes ; DNA/genetics ; Diatoms/chemistry/cytology/*genetics/metabolism ; *Ecosystem ; Energy Metabolism ; *Genome ; Iron/metabolism ; Light ; Light-Harvesting Protein Complexes/chemistry/genetics/metabolism ; Mitochondria/genetics ; Molecular Sequence Data ; Nitrogen/metabolism ; Photosynthesis ; Plastids/genetics ; Restriction Mapping ; Sequence Alignment ; *Sequence Analysis, DNA ; Silicic Acid/metabolism ; Symbiosis ; Urea/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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  • 4
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    A protein sensor for siRNA asymmetry (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-11-20
    Description: To act as guides in the RNA interference (RNAi) pathway, small interfering RNAs (siRNAs) must be unwound into their component strands, then assembled with proteins to form the RNA-induced silencing complex (RISC), which catalyzes target messenger RNA cleavage. Thermodynamic differences in the base-pairing stabilities of the 5' ends of the two approximately 21-nucleotide siRNA strands determine which siRNA strand is assembled into the RISC. We show that in Drosophila, the orientation of the Dicer-2/R2D2 protein heterodimer on the siRNA duplex determines which siRNA strand associates with the core RISC protein Argonaute 2. R2D2 binds the siRNA end with the greatest double-stranded character, thereby orienting the heterodimer on the siRNA duplex. Strong R2D2 binding requires a 5'-phosphate on the siRNA strand that is excluded from the RISC. Thus, R2D2 is both a protein sensor for siRNA thermodynamic asymmetry and a licensing factor for entry of authentic siRNAs into the RNAi pathway.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tomari, Yukihide -- Matranga, Christian -- Haley, Benjamin -- Martinez, Natalia -- Zamore, Phillip D -- GM62862-01/GM/NIGMS NIH HHS/ -- GM65236-01/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Nov 19;306(5700):1377-80.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15550672" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Argonaute Proteins ; Dimerization ; Drosophila/embryology/metabolism ; Drosophila Proteins/*metabolism ; Light ; Luciferases/genetics ; Nucleic Acid Conformation ; RNA Helicases/*metabolism ; *RNA Interference ; RNA, Double-Stranded/chemistry/metabolism ; RNA, Small Interfering/*chemistry/*metabolism ; RNA-Binding Proteins/*metabolism ; RNA-Induced Silencing Complex/*metabolism ; Ribonuclease III ; Superoxide Dismutase/genetics ; Thermodynamics ; Uracil/*analogs & derivatives/analysis
    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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