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  • 1
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    Evolution of a transfer RNA gene through a point mutation in the anticodon (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-03-28
    Description: The transfer RNA (tRNA) multigene family comprises 20 amino acid-accepting groups, many of which contain isoacceptors. The addition of isoacceptors to the tRNA repertoire was critical to establishing the genetic code, yet the origin of isoacceptors remains largely unexplored. A model of tRNA evolution, termed "tRNA gene recruitment," was formulated. It proposes that a tRNA gene can be recruited from one isoaccepting group to another by a point mutation that concurrently changes tRNA amino acid identity and messenger RNA coupling capacity. A test of the model showed that an Escherichia coli strain, in which the essential tRNAUGUThr gene was inactivated, was rendered viable when a tRNAArg with a point mutation that changed its anticodon from UCU to UGU (threonine) was expressed. Insertion of threonine at threonine codons by the "recruited" tRNAArg was corroborated by in vitro aminoacylation assays showing that its specificity had been changed from arginine to threonine. Therefore, the recruitment model may account for the evolution of some tRNA genes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Saks, M E -- Sampson, J R -- Abelson, J -- GM 48560/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1998 Mar 13;279(5357):1665-70.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biology 147-75, California Institute of Technology, Pasadena, CA 91125, USA. peggy@seqaxp.bio.caltech.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9497276" target="_blank"〉PubMed〈/a〉
    Keywords: Anticodon/*genetics ; Arginine/metabolism ; Base Composition ; Base Sequence ; Escherichia coli/*genetics ; *Evolution, Molecular ; Genes, Bacterial ; Haemophilus influenzae/genetics ; Models, Genetic ; Molecular Sequence Data ; Multigene Family ; Nucleic Acid Conformation ; *Point Mutation ; Polymerase Chain Reaction ; RNA, Bacterial/chemistry/genetics/metabolism ; RNA, Transfer, Arg/chemistry/*genetics/metabolism ; RNA, Transfer, Thr/chemistry/*genetics/metabolism ; Recombination, Genetic ; Temperature ; Threonine/metabolism ; Transformation, Bacterial
    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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    Nicotinic receptor binding site probed with unnatural amino acid incorporation in intact cells (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-04-21
    Description: The nonsense codon suppression method for unnatural amino acid incorporation has been applied to intact cells and combined with electrophysiological analysis to probe structure-function relations in the nicotinic acetylcholine receptor. Functional receptors were expressed in Xenopus oocytes when tyrosine and phenylalanine derivatives were incorporated at positions 93, 190, and 198 in the binding site of the alpha subunit. Subtle changes in the structure of an individual side chain produced readily detectable changes in the function of this large channel protein. At each position, distinct features of side chain structure dominated the dose-response relation, probably by governing the agonist-receptor binding.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nowak, M W -- Kearney, P C -- Sampson, J R -- Saks, M E -- Labarca, C G -- Silverman, S K -- Zhong, W -- Thorson, J -- Abelson, J N -- Davidson, N -- New York, N.Y. -- Science. 1995 Apr 21;268(5209):439-42.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biology, California Institute of Technology, Pasadena 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7716551" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Binding Sites ; Codon ; Hydrogen Bonding ; Ligands ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Oocytes ; Phenylalanine/analogs & derivatives/*chemistry ; Receptors, Nicotinic/chemistry/*metabolism ; Structure-Activity Relationship ; Tyrosine/analogs & derivatives/*chemistry ; Xenopus
    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 transfer RNA identity problem: a search for rules (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-01-14
    Description: Correct recognition of transfer RNAs (tRNAs) by aminoacyl-tRNA synthetases is central to the maintenance of translational fidelity. The hypothesis that synthetases recognize anticodon nucleotides was proposed in 1964 and had considerable experimental support by the mid-1970s. Nevertheless, the idea was not widely accepted until relatively recently in part because the methodologies initially available for examining tRNA recognition proved hampering for adequately testing alternative hypotheses. Implementation of new technologies has led to a reasonably complete picture of how tRNAs are recognized. The anticodon is indeed important for 17 of the 20 Escherichia coli isoaccepting groups. For many of the isoaccepting groups, the acceptor stem or position 73 (or both) is important as well.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Saks, M E -- Sampson, J R -- Abelson, J N -- GM 48560/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Jan 14;263(5144):191-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biology, California Institute of Technology, Pasadena 91125.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7506844" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acyl-tRNA Synthetases/*metabolism ; Anticodon/chemistry/*genetics/metabolism ; Base Sequence ; Escherichia coli/genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA, Bacterial/chemistry/genetics/metabolism ; RNA, Transfer, Amino Acid-Specific/chemistry/*genetics/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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    Making sense out of nonsense (2001)
    National Academy of Sciences
    Details
    Publication Date: 2001-02-27
    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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  • 5
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    Variant minihelix RNAs reveal sequence-specific recognition of the helical tRNA(Ser) acceptor stem by E.coli seryl-tRNA synthetase. (1996)
    EMBO Press
    Details
    Publication Date: 1996-06-01
    Print ISSN: 0261-4189
    Electronic ISSN: 1460-2075
    Topics: Biology , Medicine
    Published by EMBO Press on behalf of European Molecular Biology Organization.
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  • 6
    Electronic Resource
    Electronic Resource
    Sharpening the LYM inequality (1992)
    Springer
    Combinatorica 12 (1992), S. 287-293 
    Details
    ISSN: 1439-6912
    Keywords: 05 D 05
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mathematics
    Notes: Abstract The level sequence of a Sperner familyF is the sequencef(F)={f i (F)}, wheref i (F) is the number ofi element sets ofF . TheLYM inequality gives a necessary condition for an integer sequence to be the level sequence of a Sperner family on ann element set. Here we present an indexed family of inequalities that sharpen theLYM inequality.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01285817
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  • 7
    Electronic Resource
    Electronic Resource
    A Dynamic location problem for graphs (1989)
    Springer
    Combinatorica 9 (1989), S. 111-131 
    Details
    ISSN: 1439-6912
    Keywords: 05 C 75
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mathematics
    Notes: Abstract We introduce a class of optimization problems, calleddynamic location problems, involving the processing of requests that occur sequentially at the nodes of a graphG. This leads to the definition of a new parameter of graphs, called the window indexWX(G), that measures how large a “window” into the future is needed to solve every instance of the dynamic location problem onG optimally on-line. We completely characterize this parameter:WX(G)≦k if and only ifG is a weak retract of a product of complete graphs of size at mostk. As a byproduct, we obtain two (polynomially recognizable) structural characterizations of such graphs, extending a result of Bandelt.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02124674
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  • 8
    Electronic Resource
    Electronic Resource
    Exponential lower bounds for depth three Boolean circuits (2000)
    Springer
    Computational complexity 9 (2000), S. 1-15 
    Details
    ISSN: 1420-8954
    Keywords: Keywords. Circuit complexity, nonlinear lower bounds, constant depth circuits.
    Source: Springer Online Journal Archives 1860-2000
    Topics: Computer Science
    Notes: Abstract. We consider the class $ \sum^{k}_{3} $ of unbounded fan-in depth three Boolean circuits, for which the bottom fan-in is limited by k and the top gate is an OR. It is known that the smallest such circuit computing the parity function has $ \Omega(2^{\varepsilon n/k}) $ gates (for k = O(n 1/2)) for some $ \varepsilon 〉 0 $ , and this was the best lower bound known for explicit (P-time computable) functions. In this paper, for k = 2, we exhibit functions in uniform NC 1 that require $ 2^{n-o(n)} $ size depth 3 circuits. The main tool is a theorem that shows that any $ \sum {2\over3} $ circuit on n variables that accepts a inputs and has size s must be constant on a projection (subset defined by equations of the form x i = 0, x i = 1, x i = x j or x i = $ \bar{x}_i $ ) of dimension at least log(a/s)log n.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00001598
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