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  • 1
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    A basal transcription factor that activates or represses transcription (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-11-04
    Description: We have identified an activity that is required for transcription of downstream promoter element (DPE)-containing core promoters in vitro. The purified factor was found to be the Drosophila homolog of the transcriptional repressor known as NC2 or Dr1-Drap1. Purified recombinant dNC2 activates DPE-driven promoters and represses TATA-driven promoters. A mutant version of dNC2 can activate DPE promoters but is unable to repress TATA promoters. Thus, the activation and repression functions are distinct. These studies reveal that NC2 (Dr1-Drap1) is a bifunctional basal transcription factor that differentially regulates gene transcription through DPE or TATA box motifs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Willy, P J -- Kobayashi, R -- Kadonaga, J T -- CA13106/CA/NCI NIH HHS/ -- GM41249/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Nov 3;290(5493):982-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Section of Molecular Biology and Center for Molecular Genetics, University of California, San Diego, La Jolla, CA 92093-0347, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11062130" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Drosophila/*genetics ; Molecular Weight ; Mutation ; Phosphoproteins/chemistry/genetics/isolation & purification/*metabolism ; *Promoter Regions, Genetic ; Protein Subunits ; Recombinant Proteins/metabolism ; TATA Box ; Transcription Factors/chemistry/genetics/isolation & purification/*metabolism ; *Transcription, Genetic ; *Transcriptional Activation
    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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    Argonaute2, a link between genetic and biochemical analyses of RNAi (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-08-11
    Description: Double-stranded RNA induces potent and specific gene silencing through a process referred to as RNA interference (RNAi) or posttranscriptional gene silencing (PTGS). RNAi is mediated by RNA-induced silencing complex (RISC), a sequence-specific, multicomponent nuclease that destroys messenger RNAs homologous to the silencing trigger. RISC is known to contain short RNAs ( approximately 22 nucleotides) derived from the double-stranded RNA trigger, but the protein components of this activity are unknown. Here, we report the biochemical purification of the RNAi effector nuclease from cultured Drosophila cells. The active fraction contains a ribonucleoprotein complex of approximately 500 kilodaltons. Protein microsequencing reveals that one constituent of this complex is a member of the Argonaute family of proteins, which are essential for gene silencing in Caenorhabditis elegans, Neurospora, and Arabidopsis. This observation begins the process of forging links between genetic analysis of RNAi from diverse organisms and the biochemical model of RNAi that is emerging from Drosophila in vitro systems.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hammond, S M -- Boettcher, S -- Caudy, A A -- Kobayashi, R -- Hannon, G J -- R01-GM62534/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Aug 10;293(5532):1146-50.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11498593" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Argonaute Proteins ; Cell Line ; Drosophila ; *Drosophila Proteins ; Endoribonucleases/metabolism ; *Gene Silencing ; Genes, Insect ; Insect Proteins/chemistry/genetics/isolation & purification/*metabolism ; Molecular Sequence Data ; Multigene Family ; Protein Structure, Tertiary ; RNA, Double-Stranded/genetics/*metabolism ; *RNA-Induced Silencing Complex ; Repetitive Sequences, Nucleic Acid ; Ribonuclease III ; Transfection
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
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    Rules for biologically inspired adaptive network design (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-01-23
    Description: Transport networks are ubiquitous in both social and biological systems. Robust network performance involves a complex trade-off involving cost, transport efficiency, and fault tolerance. Biological networks have been honed by many cycles of evolutionary selection pressure and are likely to yield reasonable solutions to such combinatorial optimization problems. Furthermore, they develop without centralized control and may represent a readily scalable solution for growing networks in general. We show that the slime mold Physarum polycephalum forms networks with comparable efficiency, fault tolerance, and cost to those of real-world infrastructure networks--in this case, the Tokyo rail system. The core mechanisms needed for adaptive network formation can be captured in a biologically inspired mathematical model that may be useful to guide network construction in other domains.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tero, Atsushi -- Takagi, Seiji -- Saigusa, Tetsu -- Ito, Kentaro -- Bebber, Dan P -- Fricker, Mark D -- Yumiki, Kenji -- Kobayashi, Ryo -- Nakagaki, Toshiyuki -- New York, N.Y. -- Science. 2010 Jan 22;327(5964):439-42. doi: 10.1126/science.1177894.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Research Institute for Electronic Science, Hokkaido University, Sapporo 060-0812, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20093467" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; *Computer Simulation ; Food ; *Models, Biological ; Physarum polycephalum/*cytology/growth & development/*physiology ; *Railroads ; Systems Biology ; Tokyo
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
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    Earthquake source fault beneath Tokyo (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-07-16
    Description: Devastating earthquakes occur on a megathrust fault that underlies the Tokyo metropolitan region. We identify this fault with use of deep seismic reflection profiling to be the upper surface of the Philippine Sea plate. The depth to the top of this plate, 4 to 26 kilometers, is much shallower than previous estimates based on the distribution of seismicity. This shallower plate geometry changes the location of maximum finite slip of the 1923 Kanto earthquake and will affect estimations of strong ground motion for seismic hazards analysis within the Tokyo region.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sato, Hiroshi -- Hirata, Naoshi -- Koketsu, Kazuki -- Okaya, David -- Abe, Susumu -- Kobayashi, Reiji -- Matsubara, Makoto -- Iwasaki, Takaya -- Ito, Tanio -- Ikawa, Takeshi -- Kawanaka, Taku -- Kasahara, Keiji -- Harder, Steven -- New York, N.Y. -- Science. 2005 Jul 15;309(5733):462-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Earthquake Research Institute (ERI), University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16020734" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
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    Phosphorylation and activation of 13S condensin by Cdc2 in vitro (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-10-17
    Description: 13S condensin is a multisubunit protein complex essential for mitotic chromosome condensation in Xenopus egg extracts. Purified 13S condensin introduces positive supercoils into DNA in the presence of topoisomerase I and adenosine triphosphate in vitro. The supercoiling activity of 13Scondensin was regulated by mitosis-specific phosphorylation. Immunodepletion, in vitro phosphorylation, and peptide-mapping experiments indicated that Cdc2 is likely to be the kinase that phosphorylates and activates 13S condensin. Multiple Cdc2 phosphorylation sites are clustered in the carboxyl-terminal domain of the XCAP-D2 (Xenopus chromosome-associated polypeptide D2) subunit. These results suggest that phosphorylation of 13Scondensin by Cdc2 may trigger mitotic chromosome condensation in vitro.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kimura, K -- Hirano, M -- Kobayashi, R -- Hirano, T -- CA45508/CA/NCI NIH HHS/ -- GM53926/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1998 Oct 16;282(5388):487-90.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cold Spring Harbor Laboratory, Post Office Box 100, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9774278" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/chemistry/*metabolism ; Amino Acid Sequence ; Animals ; CDC2 Protein Kinase/*metabolism ; Chromosomes/chemistry/*metabolism ; DNA, Circular/chemistry/metabolism ; DNA, Superhelical/*chemistry ; DNA-Binding Proteins/chemistry/*metabolism ; Enzyme Activation ; Interphase ; *Mitosis ; Molecular Sequence Data ; Multiprotein Complexes ; Nucleic Acid Conformation ; Peptide Mapping ; Phosphorylation ; Xenopus
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
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    Yeast origin recognition complex functions in transcription silencing and DNA replication (1993)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1993-12-17
    Description: The genes encoding two of the subunits of the Saccharomyces cerevisiae origin recognition complex (ORC) have been isolated. Characterization of a temperature-sensitive mutation in the gene encoding the 72-kD subunit of ORC (ORC2) indicates that this protein complex functions early in the DNA replication process. Moreover, ORC derived from orc2ts cells is defective for DNA binding. Others have shown a defect in orc2ts cells in transcriptional silencing at the silent mating-type loci. Consistent with this finding, ORC specifically binds to each of the four mating-type silencers identified in yeast. These findings support the hypothesis that ORC acts as an initiator protein at yeast origins of DNA replication and suggest that ORC also functions in the determination of transcriptional domains.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bell, S P -- Kobayashi, R -- Stillman, B -- AI20460/AI/NIAID NIH HHS/ -- CA13106/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1993 Dec 17;262(5141):1844-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cold Spring Harbor Laboratory, NY 11724.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8266072" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; *DNA Replication ; DNA, Fungal/biosynthesis ; *DNA-Binding Proteins ; Fungal Proteins/chemistry/*genetics/metabolism ; *Gene Expression Regulation, Fungal ; Genes, Fungal ; Genes, Mating Type, Fungal ; Molecular Sequence Data ; Mutation ; Origin Recognition Complex ; *Replicon ; Repressor Proteins/chemistry/*genetics/metabolism ; S Phase ; Saccharomyces cerevisiae/cytology/*genetics/metabolism ; Saccharomyces cerevisiae Proteins ; Temperature ; Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
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    Crystallization and vitrification of electrons in a glass-forming charge liquid (2017)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2017-09-30
    Description: Charge ordering (CO) is a phenomenon in which electrons in solids crystallize into a periodic pattern of charge-rich and charge-poor sites owing to strong electron correlations. This usually results in long-range order. In geometrically frustrated systems, however, a glassy electronic state without long-range CO has been observed. We found that a charge-ordered organic material with an isosceles triangular lattice shows charge dynamics associated with crystallization and vitrification of electrons, which can be understood in the context of an energy landscape arising from the degeneracy of various CO patterns. The dynamics suggest that the same nucleation and growth processes that characterize conventional glass-forming liquids guide the crystallization of electrons. These similarities may provide insight into our understanding of the liquid-glass transition.
    Keywords: Physics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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