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  • Mutation  (8)
  • Engineering General  (5)
  • Organic Chemistry
  • 1995-1999  (15)
  • 1
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    The promise of comparative genomics in mammals (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-10-16
    Description: Dense genetic maps of human, mouse, and rat genomes that are based on coding genes and on microsatellite and single-nucleotide polymorphism markers have been complemented by precise gene homolog alignment with moderate-resolution maps of livestock, companion animals, and additional mammal species. Comparative genetic assessment expands the utility of these maps in gene discovery, in functional genomics, and in tracking the evolutionary forces that sculpted the genome organization of modern mammalian species.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉O'Brien, S J -- Menotti-Raymond, M -- Murphy, W J -- Nash, W G -- Wienberg, J -- Stanyon, R -- Copeland, N G -- Jenkins, N A -- Womack, J E -- Marshall Graves, J A -- New York, N.Y. -- Science. 1999 Oct 15;286(5439):458-62, 479-81.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702-1201, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10521336" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Domestic/genetics ; Base Sequence ; *Chromosome Mapping ; *Evolution, Molecular ; Genetic Markers ; *Genome ; *Genome, Human ; Humans ; Mammals/*genetics ; Mutation ; *Phylogeny ; Rodentia/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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  • 2
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    Structure of the VHL-ElonginC-ElonginB complex: implications for VHL tumor suppressor function (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-04-16
    Description: Mutation of the VHL tumor suppressor is associated with the inherited von Hippel-Lindau (VHL) cancer syndrome and the majority of kidney cancers. VHL binds the ElonginC-ElonginB complex and regulates levels of hypoxia-inducible proteins. The structure of the ternary complex at 2.7 angstrom resolution shows two interfaces, one between VHL and ElonginC and another between ElonginC and ElonginB. Tumorigenic mutations frequently occur in a 35-residue domain of VHL responsible for ElonginC binding. A mutational patch on a separate domain of VHL indicates a second macromolecular binding site. The structure extends the similarities to the SCF (Skp1-Cul1-F-box protein) complex that targets proteins for degradation, supporting the hypothesis that VHL may function in an analogous pathway.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stebbins, C E -- Kaelin, W G Jr -- Pavletich, N P -- New York, N.Y. -- Science. 1999 Apr 16;284(5413):455-61.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Structural Biology, Joan and Sanford I. Weill Graduate School of Medical Sciences, Cornell University, New York, NY 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10205047" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Cell Cycle Proteins/chemistry/metabolism ; Cloning, Molecular ; Crystallography, X-Ray ; *Genes, Tumor Suppressor ; Humans ; Hydrogen Bonding ; *Ligases ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Mutation, Missense ; Neoplasms/genetics ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Proteins/*chemistry/genetics/metabolism ; S-Phase Kinase-Associated Proteins ; Surface Properties ; Transcription Factors/*chemistry/metabolism ; *Tumor Suppressor Proteins ; *Ubiquitin-Protein Ligases ; Von Hippel-Lindau Tumor Suppressor Protein ; von Hippel-Lindau Disease/*genetics
    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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    Another p53 Doppelganger? (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-07-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kaelin, W G Jr -- New York, N.Y. -- Science. 1998 Jul 3;281(5373):57-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02115, USA. William_Kaelin@dfci.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9679018" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Apoptosis ; DNA-Binding Proteins/chemistry/genetics/*physiology ; Genes, Tumor Suppressor ; Genes, p53 ; Humans ; Mutation ; Neoplasms/*etiology/genetics/therapy ; Nuclear Proteins/chemistry/genetics/*physiology ; *Phosphoproteins ; *Trans-Activators ; Transcription Factors ; Tumor Suppressor Protein p53/chemistry/genetics/*physiology ; Tumor Suppressor Proteins
    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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    Crystal structures of human topoisomerase I in covalent and noncovalent complexes with DNA (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-03-21
    Description: Topoisomerases I promote the relaxation of DNA superhelical tension by introducing a transient single-stranded break in duplex DNA and are vital for the processes of replication, transcription, and recombination. The crystal structures at 2.1 and 2.5 angstrom resolution of reconstituted human topoisomerase I comprising the core and carboxyl-terminal domains in covalent and noncovalent complexes with 22-base pair DNA duplexes reveal an enzyme that "clamps" around essentially B-form DNA. The core domain and the first eight residues of the carboxyl-terminal domain of the enzyme, including the active-site nucleophile tyrosine-723, share significant structural similarity with the bacteriophage family of DNA integrases. A binding mode for the anticancer drug camptothecin is proposed on the basis of chemical and biochemical information combined with these three-dimensional structures of topoisomerase I-DNA complexes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Redinbo, M R -- Stewart, L -- Kuhn, P -- Champoux, J J -- Hol, W G -- CA65656/CA/NCI NIH HHS/ -- GM49156/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1998 Mar 6;279(5356):1504-13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biomolecular Structure Center and Department of Biological Structure, Box 357742, School of Medicine, University of Washington, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9488644" target="_blank"〉PubMed〈/a〉
    Keywords: Antineoplastic Agents, Phytogenic/metabolism/pharmacology ; Binding Sites ; Camptothecin/analogs & derivatives/metabolism/pharmacology ; Crystallography, X-Ray ; DNA/chemistry/*metabolism ; DNA Topoisomerases, Type I/*chemistry/genetics/metabolism ; *DNA-Binding Proteins ; Homeodomain Proteins/chemistry ; Host Cell Factor C1 ; Humans ; Hydrogen Bonding ; Integrases/chemistry ; Models, Molecular ; Mutation ; Nucleic Acid Conformation ; Octamer Transcription Factor-1 ; Oligodeoxyribonucleotides/chemistry/metabolism ; *Protein Conformation ; Protein Structure, Secondary ; Recombinant Proteins/chemistry ; Transcription Factors/chemistry ; Tyrosine/chemistry/metabolism
    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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    A neuropeptide gene defined by the Drosophila memory mutant amnesiac (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-05-12
    Description: Mutations in genes required for associative learning and memory in Drosophila exist, but isolation of the genes has been difficult because most are defined by a single, chemically induced allele. Here, a simplified genetic screen was used to identify candidate genes involved in learning and memory. Second site suppressors of the dunce (dnc) female sterility phenotype were isolated with the use of transposon mutagenesis. One suppressor mutation that was recovered mapped in the amnesiac (amn) gene. Cloning of the locus revealed that amn encodes a previously uncharacterized neuropeptide gene. Thus, with the cloning of amn, specific neuropeptides are implicated in the memory process.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Feany, M B -- Quinn, W G -- New York, N.Y. -- Science. 1995 May 12;268(5212):869-73.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7754370" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Cloning, Molecular ; Codon ; DNA Transposable Elements ; DNA, Complementary/genetics ; Drosophila/*genetics/physiology ; *Drosophila Proteins ; Female ; *Genes, Insect ; Growth Hormone-Releasing Hormone/chemistry/genetics ; Male ; Memory/*physiology ; Molecular Sequence Data ; Mutagenesis, Insertional ; Mutation ; Neuropeptides/chemistry/*genetics ; Pituitary Adenylate Cyclase-Activating Polypeptide ; Sequence Homology, Amino Acid ; Suppression, 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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  • 6
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    Myt1: a membrane-associated inhibitory kinase that phosphorylates Cdc2 on both threonine-14 and tyrosine-15 (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-10-06
    Description: Cdc2 is the cyclin-dependent kinase that controls entry of cells into mitosis. Phosphorylation of Cdc2 on threonine-14 and tyrosine-15 inhibits the activity of the enzyme and prevents premature initiation of mitosis. Although Wee1 has been identified as the kinase that phosphorylates tyrosine-15 in various organisms, the threonine-14-specific kinase has not been isolated. A complementary DNA was cloned from Xenopus that encodes Myt1, a member of the Wee1 family that was discovered to phosphorylate Cdc2 efficiently on both threonine-14 and tyrosine-15. Myt1 is a membrane-associated protein that contains a putative transmembrane segment. Immunodepletion studies suggested that Myt1 is the predominant threonine-14-specific kinase in Xenopus egg extracts. Myt1 activity is highly regulated during the cell cycle, suggesting that this relative of Wee1 plays a role in mitotic control.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mueller, P R -- Coleman, T R -- Kumagai, A -- Dunphy, W G -- New York, N.Y. -- Science. 1995 Oct 6;270(5233):86-90.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biology 216-76, Howard Hughes Medical Institute, California Institute of Technology, Pasadena 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7569953" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; CDC2 Protein Kinase/*metabolism ; *Cell Cycle Proteins ; Cell Membrane/enzymology ; Cloning, Molecular ; Cyclins/metabolism ; Interphase ; Mitosis ; Molecular Sequence Data ; Mutation ; *Nuclear Proteins ; Oocytes/enzymology ; Phosphorylation ; Phosphothreonine/metabolism ; Phosphotyrosine/metabolism ; Protein-Serine-Threonine Kinases/chemistry/genetics/*metabolism ; Protein-Tyrosine Kinases/chemistry/genetics/*metabolism ; Recombinant Proteins/metabolism ; Xenopus ; *Xenopus Proteins
    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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    Purification and molecular cloning of Plx1, a Cdc25-regulatory kinase from Xenopus egg extracts (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-09-06
    Description: Cdc2, the cyclin-dependent kinase that controls mitosis, is negatively regulated by phosphorylation on its threonine-14 and tyrosine-15 residues. Cdc25, the phosphatase that dephosphorylates both of these residues, undergoes activation and phosphorylation by multiple kinases at mitosis. Plx1, a kinase that associates with and phosphorylates the amino-terminal domain of Cdc25, was purified extensively from Xenopus egg extracts. Cloning of its complementary DNA revealed that Plx1 is related to the Polo family of protein kinases. Recombinant Plx1 phosphorylated Cdc25 and stimulated its activity in a purified system. Cdc25 phosphorylated by Plx1 reacted strongly with MPM-2, a monoclonal antibody to mitotic phosphoproteins. These studies indicate that Plx1 may participate in control of mitotic progression.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kumagai, A -- Dunphy, W G -- New York, N.Y. -- Science. 1996 Sep 6;273(5280):1377-80.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biology, 216-76, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8703070" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; CDC2 Protein Kinase/metabolism ; Cell Cycle Proteins/chemistry/*metabolism ; Cloning, Molecular ; Cyclins/metabolism ; Enzyme Activation ; Molecular Sequence Data ; Mutation ; Oocytes/enzymology ; Peptide Mapping ; Phosphoprotein Phosphatases/chemistry/*metabolism ; Phosphorylation ; Phosphoserine/analysis ; Phosphothreonine/analysis ; Protein-Serine-Threonine Kinases/chemistry/genetics/*isolation & ; purification/metabolism ; Recombinant Proteins/metabolism ; Xenopus ; *Xenopus Proteins ; cdc25 Phosphatases
    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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  • 8
    Electronic Resource
    Electronic Resource
    A second order finite element method for the solution of the transonic Euler and Navier-Stokes equations (1995)
    Chichester : Wiley-Blackwell
    International Journal for Numerical Methods in Fluids 20 (1995), S. 671-693 
    Details
    ISSN: 0271-2091
    Keywords: airfoil ; artificial viscosity ; upwinding ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: The numerical solution of the compressible Euler and Navier-Stokes equations in primitive variables form requires the use of artificial viscosity or upwinding. Methods that are first-order-accurate are too dissipative and reduce the effective Reynolds number substantially unless a very fine grid is used. A first-order finite element method for the solution of the Euler and Navier-Stokes equations can be constructed by adding Laplacians of the primitive variables to the governing equations. Second-order schemes may require a fourth-order dissipation and higher-order elements. A finite element approach is proposed in which the fourth-order dissipation is recast as the difference of two Laplacian operators, allowing the use of bilinear elements. The Laplacians of the primitive variables of the first-order scheme are thus balanced by additional terms obtained from the governing equations themselves, tensor identities or other forms of nodal averaging. To demonstrate formally the accuracy of this scheme, an exact solution is introduced which satisfies the continuity equation identically and the momentum equations through forcing functions. The solutions of several transonic and supersonic inviscid and laminar viscous test cases are also presented and compared to other available numerical data.
    Additional Material: 17 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/fld.1650200802
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  • 9
    Electronic Resource
    Electronic Resource
    BOUNDARY CONDITIONS IN SHALLOW WATER MODELS - AN ALTERNATIVE IMPLEMENTATION FOR FINITE ELEMENT CODES (1996)
    Chichester : Wiley-Blackwell
    International Journal for Numerical Methods in Fluids 22 (1996), S. 603-618 
    Details
    ISSN: 0271-2091
    Keywords: shallow water equations ; wave continuity equation ; boundary conditions ; finite elements ; generalized functions ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Finite element solution of the shallow water wave equations has found increasing use by researchers and practitioners in the modelling of oceans and coastal areas. Wave equation models, most of which use equal-orderC0 interpolants for both the velocity and the surface elevation, do not introduce spurious oscillation modes, hence avoiding the need for artificial or numerical damping. An important question for both primitive equation and wave equation models is the interpretation of boundary conditions. Analysis of the characteristics of the governing equations shows that for most geophysical flows a single condition at each boundary is sufficient, yet there is not a consensus in the literature as to what that boundary condition must be or how it should be implemented in a finite element code. Traditionally (partly because of limited data), surface elevation is specified at open ocean boundaries while the normal flux is specified as zero at land boundaries. In most finite element wave equation models both of these boundary conditions are implemented as essential conditions. Our recent work focuses on alternative ways to numerically implement normal flow boundary conditions with an eye towards improving the mass-conserving properties of wave equation models. A unique finite element formulation using generalized functions demonstrates that boundary conditions should be implemented by treating normal fluxes as natural conditions with the flux interpreted as external to the computational domain. Results from extensive numerical experiments show that the scheme does conserve mass for all parameter values. Furthermore, convergence studies demonstrate that the algorithm is consistent, as residual errors at the boundary diminish as the grid is refined.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    A DIRECTIONALLY ADAPTIVE METHODOLOGY USING AN EDGE-BASED ERROR ESTIMATE ON QUADRILATERAL GRIDS (1996)
    Chichester : Wiley-Blackwell
    International Journal for Numerical Methods in Fluids 23 (1996), S. 673-690 
    Details
    ISSN: 0271-2091
    Keywords: Euler equations ; directionally adaptive meshes ; edge-based error estimate ; structured grids ; mesh movement ; finite element method ; high-speed flows ; Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: The present paper describes a directionally adaptive finite element method for high-speed flows, using an edge-based error estimate on quadrilateral grids. The error of the numerical solution is estimated through its second derivatives and the resulting Hessian tensor is used to define a Riemannian metric. An improved mesh movement strategy, based on a spring analogy, but with no orthogonality constraints, is introduced to equidistribute the lengths of the edges of the elements in the defined metric. The grid adaptation procedure is validated on an analytical test case and the efficiency of the overall methodology is investigated on supersonic and hypersonic benchmarks.
    Additional Material: 21 Ill.
    Type of Medium: Electronic Resource
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