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  • Binding Sites  (62)
  • nitrogen
  • American Association for the Advancement of Science (AAAS)  (62)
  • Springer  (53)
  • American Institute of Physics (AIP)
  • 1995-1999
  • 1990-1994  (115)
  • 1975-1979
  • 1960-1964
  • 1993  (115)
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  • American Association for the Advancement of Science (AAAS)  (62)
  • Springer  (53)
  • American Institute of Physics (AIP)
  • Wiley-Blackwell  (1)
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  • 1995-1999
  • 1990-1994  (115)
  • 1975-1979
  • 1960-1964
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  • 1
    Publication Date: 1993-07-23
    Description: Transcription initiation factor TFIIB recruits RNA polymerase II to the promoter subsequent to interaction with a preformed TFIID-promoter complex. The domains of TFIIB required for binding to the TFIID-promoter complex and for transcription initiation have been determined. The carboxyl-terminal two-thirds of TFIIB, which contains two direct repeats and two basic residue repeats, is sufficient for interaction with the TFIID-promoter complex. An extra 84-residue amino-terminal region, with no obvious known structural motifs, is required for basal transcription activity. Basic residues within the second basic repeat of TFIIB are necessary for stable interaction with the TFIID-promoter complex, whereas the basic character of the first basic repeat is not. Functional roles of other potential structural motifs are discussed in light of the present study.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yamashita, S -- Hisatake, K -- Kokubo, T -- Doi, K -- Roeder, R G -- Horikoshi, M -- Nakatani, Y -- AI27397/AI/NIAID NIH HHS/ -- CA42567/CA/NCI NIH HHS/ -- GM45258/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1993 Jul 23;261(5120):463-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, MD 20892.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8332911" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; DNA-Binding Proteins/*metabolism ; Drosophila ; Molecular Sequence Data ; Mutation ; *Promoter Regions, Genetic ; Protein Binding ; Transcription Factor TFIIB ; Transcription Factor TFIID ; Transcription Factors/*chemistry/*metabolism
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  • 2
    Publication Date: 1993-04-02
    Description: The human BTF2 basic transcription factor (also called TFIIH), which is similar to the delta factor in rat and factor b in yeast, is required for class II gene transcription. A strand displacement assay was used to show that highly purified preparation of BTF2 had an adenosine triphosphate-dependent DNA helicase activity, in addition to the previously characterized carboxyl-terminal domain kinase activity. Amino acid sequence analysis of the tryptic digest generated from the 89-kilodalton subunit of BTF2 indicated that this polypeptide corresponded to the ERCC-3 gene product, a presumed helicase implicated in the human DNA excision repair disorders xeroderma pigmentosum and Cockayne's syndrome. These findings suggest that transcription and nucleotide excision repair may share common factors and hence may be considered to be functionally related.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schaeffer, L -- Roy, R -- Humbert, S -- Moncollin, V -- Vermeulen, W -- Hoeijmakers, J H -- Chambon, P -- Egly, J M -- New York, N.Y. -- Science. 1993 Apr 2;260(5104):58-63.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉UPR 6520 (CNRS), Unite 184 (INSERM), Faculte de Medecine, Strasbourg, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8465201" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/pharmacology ; Binding Sites ; Cockayne Syndrome/enzymology/genetics ; DNA/metabolism ; DNA Helicases/metabolism ; *DNA Repair ; Humans ; Immunoblotting ; Peptide Fragments ; Promoter Regions, Genetic ; Protein Kinases/metabolism ; RNA Polymerase II/metabolism ; Recombinant Proteins/metabolism ; Sequence Analysis ; Transcription Factor TFIIH ; Transcription Factors/*metabolism ; *Transcription Factors, TFII ; Transcription, Genetic ; Trypsin/metabolism ; Xeroderma Pigmentosum/enzymology/genetics
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  • 3
    Publication Date: 1993-09-10
    Description: Recent progress in regioselective and enantioselective epoxidations catalyzed by metalloporphyrins is discussed here, with an explanation of the biomimetic antecedents of this area and its relevance to synthetic applications. Classification of the catalysts that have been studied allows useful conclusions to be drawn about the development of this field. In particular, both the most promising biomimetic and practical catalysts have arisen from systems that can be systematically modified by convenient synthetic methodology.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Collman, J P -- Zhang, X -- Lee, V J -- Uffelman, E S -- Brauman, J I -- 5R37-GM 17880/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1993 Sep 10;261(5127):1404-11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Stanford University, CA 94305.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8367724" target="_blank"〉PubMed〈/a〉
    Keywords: Alkenes/chemistry ; Binding Sites ; Catalysis ; Epoxy Compounds/chemistry/*metabolism ; Ethylenediamines/chemistry ; Hydroxylation ; Ligands ; Metalloporphyrins/chemistry/*metabolism ; Molecular Structure ; Oxidation-Reduction ; Stereoisomerism
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  • 4
    Publication Date: 1993-08-27
    Description: The Escherichia coli Ada protein repairs methylphosphotriesters in DNA by direct, irreversible methyl transfer to one of its own cysteines. Upon methyl transfer, Ada acquires the ability to bind specific DNA sequences and thereby to induce genes that confer resistance to methylating agents. The amino-terminal domain of Ada, which comprises the methylphosphotriester repair and sequence-specific DNA binding elements, contains a tightly bound zinc ion. Analysis of the zinc binding site by cadmium-113 nuclear magnetic resonance and site-directed mutagenesis revealed that zinc participates in the autocatalytic activation of the active site cysteine and may also function as a conformational switch.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Myers, L C -- Terranova, M P -- Ferentz, A E -- Wagner, G -- Verdine, G L -- New York, N.Y. -- Science. 1993 Aug 27;261(5125):1164-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Program for Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8395079" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/chemistry/genetics/*metabolism ; Binding Sites ; Cadmium ; Cysteine/metabolism ; DNA/*metabolism ; *DNA Repair ; *Escherichia coli Proteins ; Isotopes ; Magnetic Resonance Spectroscopy ; Methylation ; Mutagenesis, Site-Directed ; O(6)-Methylguanine-DNA Methyltransferase ; Protons ; Transcription Factors ; Zinc/chemistry/*metabolism
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  • 5
    Publication Date: 1993-08-06
    Description: The structure of the bifunctional, pyridoxal phosphate-dependent enzyme dialkylglycine decarboxylase was determined to 2.1-angstrom resolution. Model building suggests that a single cleavage site catalyzes both decarboxylation and transamination by maximizing stereoelectronic advantages and providing electrostatic and general base catalysis. The enzyme contains two binding sites for alkali metal ions. One is located near the active site and accounts for the dependence of activity on potassium ions. The other is located at the carboxyl terminus of an alpha helix. These sites help show how proteins can specifically bind alkali metals and how these ions can exert functional effects.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Toney, M D -- Hohenester, E -- Cowan, S W -- Jansonius, J N -- GM13854/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1993 Aug 6;261(5122):756-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, University of Basel, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8342040" target="_blank"〉PubMed〈/a〉
    Keywords: Amination ; Amino Acid Sequence ; Binding Sites ; Carboxy-Lyases/*chemistry/metabolism ; Catalysis ; Computer Graphics ; Decarboxylation ; Metals, Alkali/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Secondary ; X-Ray Diffraction
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  • 6
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1993-02-12
    Description: Pyruvate oxidase from Lactobacillus plantarum is a tetrameric enzyme that decarboxylates pyruvate, producing hydrogen peroxide and the energy-storage metabolite acetylphosphate. Structure determination at 2.1 angstroms showed that the cofactors thiamine pyrophosphate (TPP) and flavin adenine dinucleotide (FAD) are bound at the carboxyl termini of six-stranded parallel beta sheets. The pyrophosphate moiety of TPP is bound to a metal ion and to a beta alpha alpha beta unit corresponding to an established sequence fingerprint. The spatial arrangement of TPP and FAD suggests that the oxidation of the oxyethyl intermediate does not occur by hydride displacement but rather by a two-step transfer of two electrons.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Muller, Y A -- Schulz, G E -- New York, N.Y. -- Science. 1993 Feb 12;259(5097):965-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Organische Chemie und Biochemie, Albert-Ludwigs-Universitat, Freiburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8438155" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Chemistry, Physical ; Crystallization ; Flavin-Adenine Dinucleotide/metabolism/*pharmacology ; Lactobacillus/*enzymology ; Macromolecular Substances ; Molecular Sequence Data ; Molecular Structure ; Physicochemical Phenomena ; Protein Structure, Secondary ; Pyruvate Oxidase/*chemistry/metabolism ; Thiamine Pyrophosphate/metabolism/*pharmacology ; X-Ray Diffraction
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  • 7
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1993-12-03
    Description: Studies in vivo and in vitro have shown that the packaging of DNA into chromatin can affect gene expression. Here, binding of the yeast transcriptional activator GAL4 to DNA in chromatin has been investigated in vivo with a yeast episome. A positioned nucleosome that is present in cells grown in glucose and contains a single GAL4 binding site is disrupted by GAL4 binding in galactose. GAL4 can also bind to DNA in chromatin when the carboxyl-terminal activation domain of GAL4 is either masked by GAL80 or is absent. These results show that a transcription factor can bind to its site in vivo in what would appear to be a repressive chromatin structure.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Morse, R H -- New York, N.Y. -- Science. 1993 Dec 3;262(5139):1563-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8248805" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites ; DNA-Binding Proteins/*metabolism ; Fungal Proteins/*metabolism ; Galactose/metabolism ; Glucose/metabolism ; Molecular Sequence Data ; Nucleosomes/*metabolism ; Plasmids ; Recombinant Fusion Proteins/metabolism ; Saccharomyces cerevisiae/*metabolism ; *Saccharomyces cerevisiae Proteins ; Transcription Factors/*metabolism
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  • 8
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1993-02-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Funder, J W -- New York, N.Y. -- Science. 1993 Feb 19;259(5098):1132-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Baker Medical Research Institute, Prahran, Victoria, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8382375" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Binding Sites ; DNA/*metabolism ; DNA-Binding Proteins/*metabolism ; Gene Expression Regulation ; Glucocorticoids/*physiology ; Mineralocorticoids/*physiology ; Models, Biological ; Molecular Sequence Data ; Receptors, Glucocorticoid/*metabolism ; Receptors, Mineralocorticoid ; Receptors, Steroid/*metabolism ; *Transcription, Genetic
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  • 9
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1993-04-16
    Description: Klenow fragment of Escherichia coli DNA polymerase I, which was cocrystallized with duplex DNA, positioned 11 base pairs of DNA in a groove that lies at right angles to the cleft that contains the polymerase active site and is adjacent to the 3' to 5' exonuclease domain. When the fragment bound DNA, a region previously referred to as the "disordered domain" became more ordered and moved along with two helices toward the 3' to 5' exonuclease domain to form the binding groove. A single-stranded, 3' extension of three nucleotides bound to the 3' to 5' exonuclease active site. Although this cocrystal structure appears to be an editing complex, it suggests that the primer strand approaches the catalytic site of the polymerase from the direction of the 3' to 5' exonuclease domain and that the duplex DNA product may bend to enter the cleft that contains the polymerase catalytic site.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Beese, L S -- Derbyshire, V -- Steitz, T A -- GM28550/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1993 Apr 16;260(5106):352-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8469987" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites ; Crystallization ; DNA/chemistry/*metabolism ; DNA Polymerase I/*chemistry/metabolism ; DNA Replication ; DNA, Single-Stranded/chemistry/metabolism ; Escherichia coli/*enzymology ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Templates, Genetic
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  • 10
    Publication Date: 1993-11-26
    Description: A DNA sequence rich in (A+T), located upstream of the -10, -35 region of the Escherichia coli ribosomal RNA promoter rrnB P1 and called the UP element, stimulates transcription by a factor of 30 in vivo, as well as in vitro in the absence of protein factors other than RNA polymerase (RNAP). When fused to other promoters, such as lacUV5, the UP element also stimulates transcription, indicating that it is a separate promoter module. Mutations in the carboxyl-terminal region of the alpha subunit of RNAP prevent stimulation of these promoters by the UP element although the mutant enzymes are effective in transcribing the "core" promoters (those lacking the UP element). Protection of UP element DNA by the mutant RNAPs is severely reduced in footprinting experiments, suggesting that the selective decrease in transcription might result from defective interactions between alpha and the UP element. Purified alpha binds specifically to the UP element, confirming that alpha acts directly in promoter recognition. Transcription of three other promoters was also reduced by the COOH-terminal alpha mutations. These results suggest that UP elements comprise a third promoter recognition region (in addition to the -10, -35 recognition hexamers, which interact with the sigma subunit) and may account for the presence of (A+T)-rich DNA upstream of many prokaryotic promoters. Since the same alpha mutations also block activation by some transcription factors, mechanisms of promoter stimulation by upstream DNA elements and positive control by certain transcription factors may be related.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ross, W -- Gosink, K K -- Salomon, J -- Igarashi, K -- Zou, C -- Ishihama, A -- Severinov, K -- Gourse, R L -- AI90035/AI/NIAID NIH HHS/ -- GM49242/GM/NIGMS NIH HHS/ -- R01 GM37048/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1993 Nov 26;262(5138):1407-13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Bacteriology, University of Wisconsin-Madison 53706.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8248780" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites ; Carrier Proteins/metabolism ; DNA, Bacterial/*metabolism ; DNA-Binding Proteins/metabolism ; DNA-Directed RNA Polymerases/*metabolism ; Escherichia coli/enzymology/*genetics ; *Escherichia coli Proteins ; Integration Host Factors ; Molecular Sequence Data ; *Promoter Regions, Genetic ; Transcription Factors/metabolism ; Transcription, Genetic ; *rRNA Operon
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  • 11
    Publication Date: 1993-01-29
    Description: The phosphocarrier protein IIIGlc is an integral component of the bacterial phosphotransferase (PTS) system. Unphosphorylated IIIGlc inhibits non-PTS carbohydrate transport systems by binding to diverse target proteins. The crystal structure at 2.6 A resolution of one of the targets, glycerol kinase (GK), in complex with unphosphorylated IIIGlc, glycerol, and adenosine diphosphate was determined. GK contains a region that is topologically identical to the adenosine triphosphate binding domains of hexokinase, the 70-kD heat shock cognate, and actin. IIIGlc binds far from the catalytic site of GK, indicating that long-range conformational changes mediate the inhibition of GK by IIIGlc. GK and IIIGlc are bound by hydrophobic and electrostatic interactions, with only one hydrogen bond involving an uncharged group. The phosphorylation site of IIIGlc, His90, is buried in a hydrophobic environment formed by the active site region of IIIGlc and a 3(10) helix of GK, suggesting that phosphorylation prevents IIIGlc binding to GK by directly disrupting protein-protein interactions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hurley, J H -- Faber, H R -- Worthylake, D -- Meadow, N D -- Roseman, S -- Pettigrew, D W -- Remington, S J -- 5-R37 GM38759/GM/NIGMS NIH HHS/ -- GM 42618-01A1/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1993 Jan 29;259(5095):673-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology, University of Oregon, Eugene 97403.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8430315" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate/metabolism ; Amino Acid Sequence ; Binding Sites ; Escherichia coli/*enzymology ; Escherichia coli Proteins ; Glycerol Kinase/*chemistry/*metabolism ; Hydrogen Bonding ; Models, Molecular ; Models, Structural ; Phosphoenolpyruvate Sugar Phosphotransferase System/*chemistry/*metabolism ; *Protein Structure, Secondary
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  • 12
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1993-06-04
    Description: Pectate lyases are secreted by pathogens and initiate soft-rot diseases in plants by cleaving polygalacturonate, a major component of the plant cell wall. The three-dimensional structure of pectate lyase C from Erwinia chrysanthemi has been solved and refined to a resolution of 2.2 angstroms. The enzyme folds into a unique motif of parallel beta strands coiled into a large helix. Within the core, the amino acids form linear stacks and include a novel asparagine ladder. The sequence similarities that pectate lyases share with pectin lyases, pollen and style proteins, and tubulins suggest that the parallel beta helix motif may occur in a broad spectrum of proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yoder, M D -- Keen, N T -- Jurnak, F -- New York, N.Y. -- Science. 1993 Jun 4;260(5113):1503-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of California, Riverside 92521.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8502994" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Calcium ; Crystallography ; Isoenzymes/*chemistry ; Models, Molecular ; Molecular Sequence Data ; Pectobacterium chrysanthemi/enzymology ; Polysaccharide-Lyases/*chemistry ; Protein Structure, Secondary ; *Protein Structure, Tertiary
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  • 13
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1993-06-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lehn, J M -- New York, N.Y. -- Science. 1993 Jun 18;260(5115):1762-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉College de France, Paris, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8511582" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Chemical Phenomena ; *Chemistry ; *Macromolecular Substances
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  • 14
    Publication Date: 1993-09-17
    Description: Staphylococcal nuclease is an enzyme with enormous catalytic power, accelerating phosphodiester bond hydrolysis by a factor of 10(16) over the spontaneous rate. The mechanistic basis for this rate acceleration was investigated by substitution of the active site residues Glu43, Arg35, and Arg87 with unnatural amino acid analogs. Two Glu43 mutants, one containing the nitro analog of glutamate and the other containing homoglutamate, retained high catalytic activity at pH 9.9, but were less active than the wild-type enzyme at lower pH values. The x-ray crystal structure of the homoglutamate mutant revealed that the carboxylate side chain of this residue occupies a position and orientation similar to that of Glu43 in the wild-type enzyme. The increase in steric bulk is accommodated by a backbone shift and altered torsion angles. The nitro and the homoglutamate mutants display similar pH versus rate profiles, which differ from that of the wild-type enzyme. Taken together, these studies suggest that Glu43 may not act as a general base, as previously thought, but may play a more complex structural role during catalysis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Judice, J K -- Gamble, T R -- Murphy, E C -- de Vos, A M -- Schultz, P G -- GM 14012-02S1/GM/NIGMS NIH HHS/ -- R01 GM49220/GM/NIGMS NIH HHS/ -- T32GM-08388/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1993 Sep 17;261(5128):1578-81.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of California, Berkeley 94720.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8103944" target="_blank"〉PubMed〈/a〉
    Keywords: 2-Aminoadipic Acid/chemistry ; Amino Acids/chemistry ; Aminobutyrates/chemistry ; Arginine/*chemistry ; Binding Sites ; Catalysis ; Glutamates/*chemistry ; Glutamic Acid ; Homocysteine/analogs & derivatives/chemistry ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Kinetics ; Micrococcal Nuclease/chemistry/genetics/*metabolism ; Mutation ; Plasmids ; X-Ray Diffraction
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  • 15
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1993-11-26
    Description: Protein phosphatases play important roles in the regulation of cell growth and metabolism, yet little is known about their enzymatic mechanism. By extrapolation from data on inhibitors of other types of hydrolases, an inhibitor of prostatic acid phosphatase was designed that is likely to function as a mechanism-based phosphotyrosine phosphatase inactivator. This molecule, 4-(fluoromethyl)phenyl phosphate, represents a useful paradigm for the design of potent and specific phosphatase inhibitors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Myers, J K -- Widlanski, T S -- R01 GM47918-01/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1993 Nov 26;262(5138):1451-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Indiana University, Bloomington 47405.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8248785" target="_blank"〉PubMed〈/a〉
    Keywords: Acid Phosphatase/*antagonists & inhibitors/metabolism ; Alkylation ; Binding Sites ; Drug Design ; Humans ; Hydrolysis ; Kinetics ; Male ; Organophosphorus Compounds/metabolism/*pharmacology ; Prostate/*enzymology
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  • 16
    Publication Date: 1993-09-03
    Description: Annexins are a family of calcium- and phospholipid-binding proteins implicated in mediating membrane-related processes such as secretion, signal transduction, and ion channel activity. The crystal structure of rat annexin V was solved to 1.9 angstrom resolution by multiple isomorphous replacement. Unlike previously solved annexin V structures, all four domains bound calcium in this structure. Calcium binding in the third domain induced a large relocation of the calcium-binding loop regions, exposing the single tryptophan residue to the solvent. These alterations in annexin V suggest a role for domain 3 in calcium-triggered interaction with phospholipid membranes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Concha, N O -- Head, J F -- Kaetzel, M A -- Dedman, J R -- Seaton, B A -- R01-DK-41740/DK/NIDDK NIH HHS/ -- R01-NS-20357/NS/NINDS NIH HHS/ -- R29-GM-44554/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1993 Sep 3;261(5126):1321-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiology, Boston University School of Medicine, MA 02118.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8362244" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Annexin A5/*chemistry/metabolism ; Binding Sites ; Calcium/*metabolism ; Computer Graphics ; Crystallization ; Humans ; Hydrogen Bonding ; Molecular Sequence Data ; Protein Conformation ; Rats ; Sequence Alignment ; Tryptophan/chemistry ; X-Ray Diffraction
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  • 17
    Publication Date: 1993-07-02
    Description: The enhancer for the immunoglobulin mu heavy chain gene (IgH) activates a heterologous gene at the pre-B cell stage of B lymphocyte differentiation. A lymphoid-specific element, microB, is necessary for enhancer function in pre-B cells. A microB binding protein is encoded by the PU.1/Spi-1 proto-oncogene. Another sequence element, microA, was identified in the mu enhancer that binds the product of the ets-1 proto-oncogene. The microA motif was required for microB-dependent enhancer activity, which suggests that a minimal B cell-specific enhancer is composed of both the PU.1 and Ets-1 binding sites. Co-expression of both PU.1 and Ets-1 in nonlymphoid cells trans-activated reporter plasmids that contained the minimal mu enhancer. These results implicate two members of the Ets family in the activation of IgH gene expression.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nelsen, B -- Tian, G -- Erman, B -- Gregoire, J -- Maki, R -- Graves, B -- Sen, R -- 1K04GM00563/GM/NIGMS NIH HHS/ -- GM38663/GM/NIGMS NIH HHS/ -- GM38925/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1993 Jul 2;261(5117):82-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Rosenstiel Research Center, Brandeis University, Waltham, MA 02254.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8316859" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; B-Lymphocytes/cytology/*metabolism ; Base Sequence ; Binding Sites ; Cell Differentiation ; Cell Line ; DNA-Binding Proteins/*genetics/metabolism ; *Enhancer Elements, Genetic ; Female ; Genes, Immunoglobulin ; Humans ; Immunoglobulin mu-Chains/*genetics ; Molecular Sequence Data ; Mutation ; Proto-Oncogene Protein c-ets-1 ; Proto-Oncogene Proteins/*genetics/metabolism ; Proto-Oncogene Proteins c-ets ; Retroviridae Proteins, Oncogenic ; Transcription Factors/*genetics/metabolism
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1993-06-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schroeder, R -- Streicher, B -- Wank, H -- New York, N.Y. -- Science. 1993 Jun 4;260(5113):1443-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Microbiology and Genetics, Vienna Biocenter, Austria.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8502988" target="_blank"〉PubMed〈/a〉
    Keywords: Aminoglycosides ; Anti-Bacterial Agents/metabolism/*pharmacology ; Anticodon/genetics ; Binding Sites ; Codon/genetics ; Introns/genetics ; Models, Genetic ; RNA Splicing/*drug effects ; RNA, Catalytic/drug effects ; RNA, Ribosomal/*drug effects/genetics/metabolism ; RNA, Ribosomal, 16S/drug effects
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  • 19
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1993-04-02
    Description: Lesions in the transcribed strand block transcription and are repaired more rapidly than lesions in the nontranscribed (coding) strand which do not block RNA polymerase (RNAP). It has been shown previously that in Escherichia coli the mfd (mutation frequency decline) gene is necessary for strand-specific repair. The mfd gene was cloned and sequenced and the Mfd protein was purified and used to reconstitute strand-specific repair in a completely defined system. The mfd gene encodes a protein of 130 kilodaltons and contains the so-called "helicase motifs," a leucine zipper motif, and regions of sequence similarity to UvrB and RecG proteins. The Mfd protein was shown to (i) displace RNAP stalled at a lesion in an adenosine triphosphate-dependent reaction, (ii) bind to the damage recognition subunit (UvrA) of the excision nuclease, and (iii) stimulate the repair of the transcribed strand only when transcription is taking place. Thus, Mfd appears to target the transcribed strand for repair by recognizing a stalled RNAP and actively recruiting the repair enzyme to the transcription blocking lesion as it dissociates the stalled RNAP.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Selby, C P -- Sancar, A -- New York, N.Y. -- Science. 1993 Apr 2;260(5104):53-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill 27599.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8465200" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/chemistry/*genetics/metabolism ; Base Sequence ; Binding Sites ; Cloning, Molecular ; *DNA Helicases ; DNA Repair/*genetics ; DNA, Bacterial/metabolism ; DNA-Directed RNA Polymerases/metabolism ; Endodeoxyribonucleases/metabolism ; Escherichia coli/*genetics ; *Escherichia coli Proteins ; Leucine Zippers ; Molecular Sequence Data ; Multienzyme Complexes/chemistry/genetics ; Mutation/genetics ; Transcription Factors/chemistry/*genetics/metabolism ; *Transcription, Genetic
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  • 20
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1993-08-06
    Description: Metalloenzymes effect a variety of important chemical transformations, often involving small molecule substrates or products such as molecular oxygen, hydrogen, nitrogen, and water. A diverse array of ions or metal clusters is observed at the active-site cores, but living systems use basic recurring structures that have been modified or tuned for specific purposes. Inorganic chemists are actively involved in the elucidation of the structure, spectroscopy, and mechanism of action of these biological catalysts, in part through a synthetic modeling approach involving biomimetic studies.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Karlin, K D -- GM28962/GM/NIGMS NIH HHS/ -- GM45971/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1993 Aug 6;261(5122):701-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7688141" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Oxidoreductases/chemistry/metabolism ; Binding Sites ; Electron Transport ; Enzymes/*chemistry/metabolism ; Hydrolysis ; Iron-Sulfur Proteins/chemistry/metabolism ; Metalloproteins/*chemistry/metabolism ; *Models, Chemical ; Models, Molecular ; Nitric Oxide/metabolism ; Nitric Oxide Synthase ; Oxidation-Reduction ; Peptides/metabolism
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  • 21
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1993-02-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kassavetis, G A -- Geiduschek, E P -- New York, N.Y. -- Science. 1993 Feb 12;259(5097):944-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of California San Diego, La Jolla 92093-0634.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7679800" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Dna ; DNA Polymerase II/metabolism ; DNA-Directed RNA Polymerases/*metabolism ; Escherichia coli/enzymology ; Humans ; Hydrolysis ; RNA/biosynthesis/*metabolism ; Templates, Genetic ; Transcription Factors/metabolism/pharmacology ; *Transcription Factors, TFII ; Transcription, Genetic
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  • 22
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1993-12-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Birge, R B -- Hanafusa, H -- New York, N.Y. -- Science. 1993 Dec 3;262(5139):1522-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Oncology, Rockefeller University, New York, NY 10021.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7504323" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Molecular Sequence Data ; Phosphotyrosine ; Proto-Oncogene Proteins pp60(c-src)/*chemistry ; Receptor Protein-Tyrosine Kinases/*metabolism ; Sequence Homology, Amino Acid ; Signal Transduction/physiology ; Structure-Activity Relationship ; Tyrosine/analogs & derivatives/metabolism
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  • 23
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1993-03-26
    Description: The RAD51 protein functions in the processes of DNA repair and in mitotic and meiotic genetic recombination in the yeast Saccharomyces cerevisiae. The protein has adenosine triphosphate-dependent DNA binding activities similar to those of the Escherichia coli RecA protein, and the two proteins have 30 percent sequence homology. RAD51 polymerized on double-stranded DNA to form a helical filament nearly identical in low-resolution, three-dimensional structure to that formed by RecA. Like RecA, RAD51 also appears to force DNA into a conformation of approximately a 5.1-angstrom rise per base pair and 18.6 base pairs per turn. As in other protein families, its structural conservation appears to be stronger than its sequence conservation. Both the structure of the protein polymer formed by RecA and the DNA conformation induced by RecA appear to be general properties of a class of recombination proteins found in prokaryotes as well as eukaryotes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ogawa, T -- Yu, X -- Shinohara, A -- Egelman, E H -- GM35269/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1993 Mar 26;259(5103):1896-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Osaka University, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8456314" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/pharmacology ; Binding Sites ; DNA/chemistry/metabolism ; DNA Repair ; DNA, Single-Stranded/chemistry/metabolism ; DNA-Binding Proteins/*chemistry/metabolism ; Fourier Analysis ; Fungal Proteins/*chemistry/metabolism ; Meiosis ; Mitosis ; Molecular Structure ; Nucleic Acid Conformation ; Protein Structure, Secondary ; Rad51 Recombinase ; Rec A Recombinases/*chemistry/metabolism ; Recombinant Proteins/chemistry/metabolism ; Saccharomyces cerevisiae/*chemistry ; Saccharomyces cerevisiae Proteins
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  • 24
    Publication Date: 1993-08-20
    Description: Single-site mutants in the Cu,Zn superoxide dismutase (SOD) gene (SOD1) occur in patients with the fatal neurodegenerative disorder familial amyotrophic lateral sclerosis (FALS). Complete screening of the SOD1 coding region revealed that the mutation Ala4 to Val in exon 1 was the most frequent one; mutations were identified in exons 2, 4, and 5 but not in the active site region formed by exon 3. The 2.4 A crystal structure of human SOD, along with two other SOD structures, established that all 12 observed FALS mutant sites alter conserved interactions critical to the beta-barrel fold and dimer contact, rather than catalysis. Red cells from heterozygotes had less than 50 percent normal SOD activity, consistent with a structurally defective SOD dimer. Thus, defective SOD is linked to motor neuron death and carries implications for understanding and possible treatment of FALS.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Deng, H X -- Hentati, A -- Tainer, J A -- Iqbal, Z -- Cayabyab, A -- Hung, W Y -- Getzoff, E D -- Hu, P -- Herzfeldt, B -- Roos, R P -- New York, N.Y. -- Science. 1993 Aug 20;261(5124):1047-51.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurology, Northwestern University Medical School, Chicago, IL 60611.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8351519" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amyotrophic Lateral Sclerosis/enzymology/*genetics ; Base Sequence ; Binding Sites ; Erythrocytes/enzymology ; Exons ; Free Radicals/metabolism ; Humans ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Protein Folding ; Protein Structure, Tertiary ; Superoxide Dismutase/blood/chemistry/*genetics/metabolism ; X-Ray Diffraction
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  • 25
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1993-12-17
    Description: Myosin II, which converts the energy of adenosine triphosphate hydrolysis into the movement of actin filaments, is a hexamer of two heavy chains, two essential light chains, and two regulatory light chains (RLCs). Dictyostelium myosin II is known to be regulated in vitro by phosphorylation of the RLC. Cells in which the wild-type myosin II heavy chain was replaced with a recombinant form that lacks the binding site for RLC carried out cytokinesis and almost normal development, processes known to be dependent on functional myosin II. Characterization of the purified recombinant protein suggests that a complex of RLC and the RLC binding site of the heavy chain plays an inhibitory role for adenosine triphosphatase activity and a structural role for the movement of myosin along actin.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Uyeda, T Q -- Spudich, J A -- GM46551/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1993 Dec 17;262(5141):1867-70.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Stanford University School of Medicine, CA 94305.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8266074" target="_blank"〉PubMed〈/a〉
    Keywords: Actins/metabolism ; Amino Acid Sequence ; Animals ; Base Sequence ; Binding Sites ; Ca(2+) Mg(2+)-ATPase/metabolism ; Calcium-Transporting ATPases/metabolism ; Cell Division ; Dictyostelium/cytology/genetics/*metabolism ; Genes, Fungal ; Molecular Sequence Data ; Myosin-Light-Chain Kinase/metabolism ; Myosins/chemistry/genetics/*metabolism ; Phosphorylation ; Recombinant Proteins/chemistry/metabolism
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1993-12-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Alper, J -- New York, N.Y. -- Science. 1993 Dec 17;262(5141):1817.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8266067" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Epithelium/microbiology ; Gastric Mucosa/*microbiology ; Helicobacter Infections/microbiology ; Helicobacter pylori/*metabolism ; Humans ; Lewis Blood-Group System/*metabolism ; Sialic Acids/*metabolism ; Stomach Neoplasms/microbiology ; Stomach Ulcer/microbiology
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  • 27
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1993-09-24
    Description: Zinc finger proteins, of the type first discovered in transcription factor IIIA (TFIIIA), are one of the largest and most important families of DNA-binding proteins. The crystal structure of a complex containing the five Zn fingers from the human GLI oncogene and a high-affinity DNA binding site has been determined at 2.6 A resolution. Finger one does not contact the DNA. Fingers two through five bind in the major groove and wrap around the DNA, but lack the simple, strictly periodic arrangement observed in the Zif268 complex. Fingers four and five of GLI make extensive base contacts in a conserved nine base-pair region, and this section of the DNA has a conformation intermediate between B-DNA and A-DNA. Analyzing the GLI complex and comparing it with Zif268 offers new perspectives on Zn finger-DNA recognition.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pavletich, N P -- Pabo, C O -- GM-31471/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1993 Sep 24;261(5129):1701-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge 02139.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8378770" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Binding Sites ; Computer Graphics ; DNA/*chemistry/metabolism ; DNA-Binding Proteins/chemistry/metabolism ; Molecular Sequence Data ; Nucleic Acid Conformation ; Oncogene Proteins/*chemistry/genetics/metabolism ; Oncogenes ; Protein Conformation ; Trans-Activators ; Transcription Factors/*chemistry/genetics/metabolism ; X-Ray Diffraction ; *Zinc Fingers
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1993-05-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brugge, J S -- New York, N.Y. -- Science. 1993 May 14;260(5110):918-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉ARIAD Pharmaceuticals, Inc., Cambridge, MA 02139-4234.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8388123" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; *Drug Design ; Growth Substances/metabolism ; Humans ; Peptides/chemistry/*metabolism/therapeutic use ; Proteins/*metabolism ; Receptors, Cell Surface/metabolism ; *Signal Transduction
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1993-08-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marx, J -- New York, N.Y. -- Science. 1993 Aug 20;261(5124):986.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8351523" target="_blank"〉PubMed〈/a〉
    Keywords: Amyotrophic Lateral Sclerosis/enzymology/*genetics ; Binding Sites ; Free Radicals/metabolism ; Genes ; Humans ; Point Mutation ; Protein Folding ; Protein Structure, Tertiary ; Superoxide Dismutase/chemistry/*genetics/metabolism
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1993-04-23
    Description: Ribozymes derived from the self-splicing pre-ribosomal RNA of Tetrahymena act as sequence-specific endonucleases. The reaction involves binding an RNA or DNA substrate by base pairing to the internal guide sequence (IGS) to form helix P1. Site-specific photo-crosslinking localized the 5' end of the IGS in helix P1 to the vicinity of conserved bases between helices P4 and P5, supporting a major feature of the Michel-Westhof three-dimensional structure model. The crosslinked ribozyme retained catalytic activity. When not base-paired, the IGS was still specifically crosslinked, but the major site was 37 A distant from the reactive site in the experimentally supported three-dimensional model. The data indicate that a substantial induced-fit conformational change accompanies P1 formation, and they provide a physical basis for understanding the transport of oligonucleotides to the catalytic core of the ribozyme. The ability of RNA to orchestrate large-scale conformational changes may help explain why the ribosome and the spliceosome are RNA-based machines.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, J F -- Downs, W D -- Cech, T R -- New York, N.Y. -- Science. 1993 Apr 23;260(5107):504-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7682726" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Composition ; Base Sequence ; Binding Sites ; Catalysis ; DNA/chemistry/metabolism ; Molecular Sequence Data ; Nucleic Acid Conformation ; Oligoribonucleotides/chemistry/metabolism ; RNA/chemistry/*metabolism ; RNA, Catalytic/chemistry/*metabolism ; RNA, Guide/chemistry/*metabolism ; RNA, Protozoan/chemistry/metabolism ; Tetrahymena/enzymology
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  • 31
    Publication Date: 1993-03-26
    Description: Heparin or heparin-like heparan sulfate proteoglycans are obligatory for activity of the heparin-binding fibroblast growth factor (FGF) family. Heparin interacts independently of FGF ligand with a specific sequence (K18K) in one of the immunoglobulin-like loops in the extracellular domain of the FGF receptor tyrosine kinase transmembrane glycoprotein. A synthetic peptide corresponding to K18K inhibited heparin and heparin-dependent FGF binding to the receptor. K18K and an antibody to K18K were antagonists of FGF-stimulated cell growth. Point mutations of lysine residues in the K18K sequence abrogated both heparin- and ligand-binding activities of the receptor kinase. The results indicate that the FGF receptor is a ternary complex of heparan sulfate proteoglycan, tyrosine kinase transmembrane glycoprotein, and ligand.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kan, M -- Wang, F -- Xu, J -- Crabb, J W -- Hou, J -- McKeehan, W L -- New York, N.Y. -- Science. 1993 Mar 26;259(5103):1918-21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉W. Alton Jones Cell Science Center, Inc. Lake Placid, NY 12946.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8456318" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Antibodies, Monoclonal ; Binding Sites ; Fibroblast Growth Factors/metabolism ; Heparan Sulfate Proteoglycans ; Heparin/*metabolism ; Heparitin Sulfate/metabolism ; Humans ; Immunohistochemistry ; Lysine/metabolism ; Metalloendopeptidases/metabolism ; Molecular Sequence Data ; Mutagenesis ; Peptide Fragments/isolation & purification/metabolism ; Protein-Tyrosine Kinases/chemistry/genetics/*metabolism ; Proteoglycans/metabolism ; Receptors, Fibroblast Growth Factor/chemistry/genetics/*metabolism ; Recombinant Proteins/metabolism ; Sodium Chloride/pharmacology ; Trypsin/metabolism
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  • 32
    Publication Date: 1993-10-15
    Description: Electrophysiology and structural studies were performed on an annexin V variant containing a mutation of glutamic acid-95 to serine in the center of the pore region. The mutation resulted in a lower single channel conductance for calcium and a strongly increased conductance for sodium and potassium, indicating that glutamic acid-95 is a crucial constituent of the ion selectivity filter. There were only minor differences in the crystal structures of mutant and wild-type annexin V around the mutation site; however, the mutant showed structural differences elsewhere, including the presence of a calcium binding site in domain III unrelated to the mutation. Analysis of the membrane-bound form of annexin V by electron microscopy revealed no differences between the wild type and mutant.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Berendes, R -- Voges, D -- Demange, P -- Huber, R -- Burger, A -- New York, N.Y. -- Science. 1993 Oct 15;262(5132):427-30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max-Planck-Institut fur Biochemie, Martinsried, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7692599" target="_blank"〉PubMed〈/a〉
    Keywords: Annexin A5/*chemistry/genetics/metabolism ; Binding Sites ; Calcium/metabolism ; Computer Graphics ; Crystallography, X-Ray ; Electric Conductivity ; Glutamates/chemistry ; Glutamic Acid ; Humans ; Ion Channels/*metabolism ; Microscopy, Electron ; Mutagenesis, Site-Directed ; Potassium/metabolism ; Protein Structure, Secondary ; Serine/chemistry ; Sodium/metabolism ; Structure-Activity Relationship
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  • 33
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1993-01-22
    Description: The bZIP motif is characterized by a leucine zipper domain that mediates dimerization and a basic domain that contacts DNA. A series of transition metal dimerization domains were used to alter systematically the relative orientation of basic domain peptides. Both the affinity and the specificity of the peptide-DNA interaction depend on domain orientation. These results indicate that the precise configuration linking the domains is important; dimerization is not always sufficient for DNA binding. This approach to studying the effect of orientation on protein function complements mutagenesis and could be used in many systems.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cuenoud, B -- Schepartz, A -- New York, N.Y. -- Science. 1993 Jan 22;259(5094):510-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Yale University, New Haven, CT 06511-8118.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8424173" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Binding Sites ; Circular Dichroism ; Cyclic AMP Response Element-Binding Protein/chemistry/metabolism ; DNA/*metabolism ; DNA-Binding Proteins/chemistry/*metabolism ; Fungal Proteins/chemistry/*metabolism ; *Leucine Zippers ; Macromolecular Substances ; Molecular Sequence Data ; Oligodeoxyribonucleotides ; Protein Kinases/chemistry/*metabolism ; Protein Structure, Secondary ; Proto-Oncogene Proteins c-jun/chemistry/metabolism ; *Saccharomyces cerevisiae Proteins ; Substrate Specificity
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  • 34
    Publication Date: 1993-07-23
    Description: The three-dimensional solution structure of a complex between the DNA binding domain of the chicken erythroid transcription factor GATA-1 and its cognate DNA site has been determined with multidimensional heteronuclear magnetic resonance spectroscopy. The DNA binding domain consists of a core which contains a zinc coordinated by four cysteines and a carboxyl-terminal tail. The core is composed of two irregular antiparallel beta sheets and an alpha helix, followed by a long loop that leads into the carboxyl-terminal tail. The amino-terminal part of the core, including the helix, is similar in structure, although not in sequence, to the amino-terminal zinc module of the glucocorticoid receptor DNA binding domain. In the other regions, the structures of these two DNA binding domains are entirely different. The DNA target site in contact with the protein spans eight base pairs. The helix and the loop connecting the two antiparallel beta sheets interact with the major groove of the DNA. The carboxyl-terminal tail, which is an essential determinant of specific binding, wraps around into the minor groove. The complex resembles a hand holding a rope with the palm and fingers representing the protein core and the thumb, the carboxyl-terminal tail. The specific interactions between GATA-1 and DNA in the major groove are mainly hydrophobic in nature, which accounts for the preponderance of thymines in the target site. A large number of interactions are observed with the phosphate backbone.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Omichinski, J G -- Clore, G M -- Schaad, O -- Felsenfeld, G -- Trainor, C -- Appella, E -- Stahl, S J -- Gronenborn, A M -- New York, N.Y. -- Science. 1993 Jul 23;261(5120):438-46.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8332909" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; Binding Sites ; Chickens ; DNA-Binding Proteins/*chemistry ; Erythroid-Specific DNA-Binding Factors ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Tertiary ; Transcription Factors/*chemistry ; Zinc Fingers
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  • 35
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1993-12-24
    Description: Five small nuclear RNAs (U1, U2, U4, U5, and U6) participate in precursor messenger RNA (pre-mRNA) splicing. To probe their interactions within the active center of the mammalian spliceosome, substrates containing a single photoactivatable 4-thiouridine residue adjacent to either splice site were synthesized, and crosslinks were induced during the course of in vitro splicing. An invariant loop sequence in U5 small nuclear RNA contacts exon 1 before and after the first step of splicing because a crosslink between U5 and the last residue of exon 1 appeared in the pre-mRNA and then in the cutoff exon 1 intermediate. Both of these crosslinked species could undergo subsequent splicing, indicating that the crosslinks reflect a functional interaction that is maintained through both reaction steps. The same U5 loop aligns the two exons for ligation since the first residue of exon 2 also became crosslinked to U5 in the lariat intermediate. An invariant sequence in U6 RNA became crosslinked to the conserved second position of the intron within both the lariat intermediate and the lariat intron product. On the basis of these results, several conformational arrangements of small nuclear RNAs within the spliceosomal active center can be distinguished, and additional mechanistic parallels between the spliceosome and self-splicing introns can be drawn.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sontheimer, E J -- Steitz, J A -- GM26514/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1993 Dec 24;262(5142):1989-96.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, Boyer Center for Molecular Medicine, New Haven, CT 06536-0812.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8266094" target="_blank"〉PubMed〈/a〉
    Keywords: Adenoviridae/genetics ; Base Sequence ; Binding Sites ; Catalysis ; Exons/genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA Precursors/metabolism ; RNA Splicing/*physiology ; RNA, Small Nuclear/*physiology ; RNA, Viral/physiology ; Spliceosomes/*physiology ; Thiouridine
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  • 36
    Publication Date: 1993-05-28
    Description: The retinoblastoma gene product (Rb) is a nuclear phosphoprotein that regulates cell cycle progression. Elf-1 is a lymphoid-specific Ets transcription factor that regulates inducible gene expression during T cell activation. In this report, it is demonstrated that Elf-1 contains a sequence motif that is highly related to the Rb binding sites of several viral oncoproteins and binds to the pocket region of Rb both in vitro and in vivo. Elf-1 binds exclusively to the underphosphorylated form of Rb and fails to bind to Rb mutants derived from patients with retinoblastoma. Co-immunoprecipitation experiments demonstrated an association between Elf-1 and Rb in resting normal human T cells. After T cell activation, the phosphorylation of Rb results in the release of Elf-1, which is correlated temporally with the activation of Elf-1-mediated transcription. Overexpression of a phosphorylation-defective form of Rb inhibited Elf-1-dependent transcription during T cell activation. These results demonstrate that Rb interacts specifically with a lineage-restricted Ets transcription factor. This regulated interaction may be important for the coordination of lineage-specific effector functions such as lymphokine production with cell cycle progression in activated T cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, C Y -- Petryniak, B -- Thompson, C B -- Kaelin, W G -- Leiden, J M -- R01 AI29673-01/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 1993 May 28;260(5112):1330-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medicine, University of Chicago, IL 60637.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8493578" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; Binding Sites ; Cell Cycle ; Cell Line ; DNA-Binding Proteins/chemistry/*metabolism ; Eye Neoplasms/genetics ; Humans ; Lymphocyte Activation ; Molecular Sequence Data ; Mutation ; Oligodeoxyribonucleotides ; Phosphorylation ; Recombinant Fusion Proteins/metabolism ; Retinoblastoma/genetics ; Retinoblastoma Protein/*metabolism ; T-Lymphocytes/immunology/*metabolism ; Transcription Factors/chemistry/*metabolism ; Transcription, Genetic
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  • 37
    Publication Date: 1993-02-19
    Description: Ligand-gated ion channels gated by glutamate constitute the major excitatory neurotransmitter system in the mammalian brain. The functional modulation of GluR6, a kainate-activated glutamate receptor, by adenosine 3',5'-monophosphate-dependent protein kinase A (PKA) was examined with receptors expressed in human embryonic kidney cells. Kainate-evoked currents underwent a rapid desensitization that was blocked by lectins. Kainate currents were potentiated by intracellular perfusion of PKA, and this potentiation was blocked by co-application of an inhibitory peptide. Site-directed mutagenesis was used to identify the site or sites of phosphorylation on GluR6. Although mutagenesis of two serine residues, Ser684 and Ser666, was required for complete abolition of the PKA-induced potentiation, Ser684 may be the preferred site of phosphorylation in native GluR6 receptor complexes. These results indicate that glutamate receptor function can be directly modulated by protein phosphorylation and suggest that a dynamic regulation of excitatory receptors could be associated with some forms of learning and memory in the mammalian brain.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, L Y -- Taverna, F A -- Huang, X P -- MacDonald, J F -- Hampson, D R -- New York, N.Y. -- Science. 1993 Feb 19;259(5098):1173-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiology, University of Toronto, Ontario, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8382377" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Binding Sites ; Brain/*physiology ; Cells, Cultured ; Concanavalin A/pharmacology ; Evoked Potentials/drug effects ; Humans ; Kainic Acid/*pharmacology ; Kidney ; Kinetics ; Membrane Potentials/drug effects ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Oligodeoxyribonucleotides ; Protein Kinases/*metabolism ; Receptors, Glutamate/drug effects/genetics/*physiology ; Receptors, Kainic Acid ; Serine ; Wheat Germ Agglutinins/pharmacology
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  • 38
    Publication Date: 1993-01-08
    Description: The human and Drosophila heat shock transcription factors (HSFs) are multi-zipper proteins with high-affinity binding to DNA that is regulated by heat shock-induced trimerization. Formation of HSF trimers is dependent on hydrophobic heptad repeats located in the amino-terminal region of the protein. Two subregions at the carboxyl-terminal end of human HSF1 were identified that maintain the monomeric form of the protein under normal conditions. One of these contains a leucine zipper motif that is conserved between vertebrate and insect HSFs. These results suggest that the carboxyl-terminal zipper may suppress formation of trimers by the amino-terminal HSF zipper elements by means of intramolecular coiled-coil interactions that are sensitive to heat shock.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rabindran, S K -- Haroun, R I -- Clos, J -- Wisniewski, J -- Wu, C -- New York, N.Y. -- Science. 1993 Jan 8;259(5092):230-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Biochemistry, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8421783" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Cell Line ; DNA/metabolism ; Drosophila/chemistry ; Heat-Shock Proteins/*chemistry/genetics/metabolism ; Hot Temperature ; Humans ; *Leucine Zippers ; Macromolecular Substances ; Molecular Sequence Data ; Mutagenesis ; Structure-Activity Relationship ; Transfection
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  • 39
    Publication Date: 1993-08-06
    Description: Regions of Escherichia coli ribonuclease P (RNase P) RNA in proximity to a bound transfer RNA (tRNA) substrate were mapped by photoaffinity. A photoaffinity cross-linking reagent was introduced at specific sites in the interior of the native tRNA structure by modification of the 5' ends of circularly permuted tRNAs (cptRNAs). The polymerase chain reaction was used for the production of cptRNA templates. After the amplification of a segment of a tandemly duplicated tRNA gene, the cptRNA gene was transcribed in vitro to produce cptRNA. Modified cptRNAs were cross-linked to RNase P RNA, and the conjugation sites in RNase P RNA were determined by primer extension. These sites occur in phylogenetically conserved structures and sequences and identify regions of the ribozyme that form part of the tRNA binding site. The use of circularly permuted molecules to position specific modifications is applicable to the study of many inter- and intramolecular interactions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nolan, J M -- Burke, D H -- Pace, N R -- GM34527/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1993 Aug 6;261(5122):762-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Indiana University, Bloomington 47405.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7688143" target="_blank"〉PubMed〈/a〉
    Keywords: Affinity Labels ; Base Sequence ; Binding Sites ; Endoribonucleases/*chemistry/metabolism ; Escherichia coli/enzymology/genetics ; *Escherichia coli Proteins ; Molecular Sequence Data ; Nucleic Acid Conformation ; Polymerase Chain Reaction ; RNA/chemistry/metabolism ; RNA, Bacterial/*chemistry/genetics/metabolism ; RNA, Catalytic/*chemistry/metabolism ; RNA, Transfer/*chemistry/genetics/metabolism ; Ribonuclease P
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  • 40
    Publication Date: 1993-02-12
    Description: To investigate the mechanism of interaction of the toxin colicin E1 with membranes, three cysteine substitution mutants and the wild type of the channel-forming fragment were spin labeled at the unique thiol. Time-resolved interaction of these labeled proteins with phospholipid vesicles was investigated with stopped-flow electron paramagnetic resonance spectroscopy. The fragment interacts with neutral bilayers at low pH, indicating that the interaction is hydrophobic rather than electrostatic. The interaction occurs in at least two distinct steps: (i) rapid adsorption to the surface; and (ii) slow, rate-limiting insertion of the hydrophobic central helices into the membrane interior.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shin, Y K -- Levinthal, C -- Levinthal, F -- Hubbell, W L -- EY05216/EY/NEI NIH HHS/ -- New York, N.Y. -- Science. 1993 Feb 12;259(5097):960-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Jules Stein Eye Institute, University of California, Los Angeles 90024.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8382373" target="_blank"〉PubMed〈/a〉
    Keywords: Adsorption ; Binding Sites ; Cell Membrane/*metabolism ; Colicins/chemistry/genetics/*metabolism ; Cysteine/genetics ; Electron Spin Resonance Spectroscopy ; Hydrogen-Ion Concentration ; Kinetics ; Lipid Bilayers/metabolism ; *Mutagenesis ; Peptide Fragments/metabolism ; Protein Structure, Secondary ; *Spin Labels
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  • 41
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1993-10-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tsou, C L -- New York, N.Y. -- Science. 1993 Oct 15;262(5132):380-1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Laboratory of Biomacromolecules, Institute of Biophysics, Academia Sinica, Beijing, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8211158" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Creatine Kinase/chemistry/metabolism ; Enzyme Inhibitors ; Enzymes/chemistry/*metabolism ; Glyceraldehyde-3-Phosphate Dehydrogenases/chemistry/metabolism ; Guanidine ; Guanidines/pharmacology ; Papain/chemistry/metabolism ; Protein Conformation ; Protein Denaturation ; Protein Folding ; Ribonuclease, Pancreatic/chemistry/metabolism
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  • 42
    Publication Date: 1993-03-05
    Description: A molecular docking computer program (DOCK) was used to screen the Fine Chemical Directory, a database of commercially available compounds, for molecules that are complementary to thymidylate synthase (TS), a chemotherapeutic target. Besides retrieving the substrate and several known inhibitors, DOCK proposed putative inhibitors previously unknown to bind to the enzyme. Three of these compounds inhibited Lactobacillus casei TS at submillimolar concentrations. One of these inhibitors, sulisobenzone, crystallized with TS in two configurations that differed from the DOCK-favored geometry: a counterion was bound in the substrate site, which resulted in a 6 to 9 angstrom displacement of the inhibitor. The structure of the complexes suggested another binding region in the active site that could be exploited. This region was probed with molecules sterically similar to sulisobenzone, which led to the identification of a family of phenolphthalein analogs that inhibit TS in the 1 to 30 micromolar range. These inhibitors do not resemble the substrates of the enzyme. A crystal structure of phenolphthalein with TS shows that it binds in the target site in a configuration that resembles the one suggested by DOCK.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shoichet, B K -- Stroud, R M -- Santi, D V -- Kuntz, I D -- Perry, K M -- GM24485/GM/NIGMS NIH HHS/ -- GM31497/GM/NIGMS NIH HHS/ -- GM39553/GM/NIGMS NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1993 Mar 5;259(5100):1445-50.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmaceutical Chemistry, University of California, San Francisco 94143.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8451640" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Benzophenones/chemistry/*pharmacology ; Binding Sites ; *Computers ; Databases, Factual ; Lactobacillus casei/enzymology ; Models, Molecular ; Molecular Conformation ; Molecular Structure ; Phenolphthaleins/chemistry/*pharmacology ; Protein Structure, Secondary ; Thymidylate Synthase/*antagonists & inhibitors/chemistry ; X-Ray Diffraction
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  • 43
    Publication Date: 1993-10-15
    Description: The cell cycle regulatory protein CksHs2 binds to the catalytic subunit of the cyclin-dependent kinases (Cdk's) and is essential for their biological function. The crystal structure of the protein was determined at 2.1 A resolution. The CksHs2 structure is an unexpected hexamer formed by the symmetric assembly of three interlocked dimers into an unusual 12-stranded beta barrel fold that may represent a prototype for this class of protein structures. Sequence-conserved regions form the unusual beta strand exchange between the subunits of the dimer, and the metal and anion binding sites associated with the hexamer assembly. The two other sequence-conserved regions line a 12 A diameter tunnel through the beta barrel and form the six exposed, charged helix pairs. Six kinase subunits can be modeled to bind the assembled hexamer without collision, and therefore this CksHs2 hexamer may participate in cell cycle control by acting as the hub for Cdk multimerization in vivo.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Parge, H E -- Arvai, A S -- Murtari, D J -- Reed, S I -- Tainer, J A -- New York, N.Y. -- Science. 1993 Oct 15;262(5132):387-95.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8211159" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; CDC2-CDC28 Kinases ; Carrier Proteins/*chemistry/physiology ; *Cell Cycle ; *Cell Cycle Proteins ; Computer Graphics ; Conserved Sequence ; Crystallography, X-Ray ; Humans ; Macromolecular Substances ; Models, Molecular ; Molecular Sequence Data ; Protein Folding ; Protein Kinases/metabolism ; Protein Structure, Secondary ; Sequence Alignment
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  • 44
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1993-01-15
    Description: A transfer RNA (tRNA) binding protein present in HeLa cell nuclear extracts was purified and identified as the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH). Studies with mutant tRNAs indicated that GAPDH recognizes both sequence and structural features in the RNA. GAPDH discriminated between wild-type tRNA and two tRNA mutants that are defective in nuclear export, which suggests that the protein may participate in RNA export. The cofactor nicotinamide adenine dinucleotide disrupted complex formation between tRNA and GAPDH and thus may share a common binding site with the RNA. Indirect immunofluorescence experiments showed that GAPDH is present in the nucleus as well as in the cytoplasm.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Singh, R -- Green, M R -- GM35490/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1993 Jan 15;259(5093):365-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Program in Molecular Medicine, University of Massachusetts Medical Center, Worcester 01605.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8420004" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Binding Sites ; Binding, Competitive ; Cell Nucleus/enzymology ; Cytoplasm/enzymology ; Escherichia coli/genetics ; Glyceraldehyde-3-Phosphate Dehydrogenases/chemistry/immunology/*metabolism ; HeLa Cells ; Humans ; Molecular Sequence Data ; Mutagenesis ; RNA, Transfer, Met/chemistry/*metabolism ; RNA, Transfer, Ser/metabolism ; RNA, Transfer, Tyr/metabolism ; Saccharomyces cerevisiae/genetics ; Transcription, Genetic
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  • 45
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1993-10-29
    Description: The gamma delta resolvase protein is one of a large family of transposon-encoded site-specific recombinases. It performs recombination in a DNA-protein complex that contains 12 resolvase protomers and two copies of the 120-base pair DNA substrate, res (each with three binding sites for a resolvase dimer). A derivative of resolvase with altered DNA binding specificity was used to show that the role of resolvase at site I, which contains the crossover point, differs from its role at the other two binding sites. The resolvase dimers that initially bind to site I are the only ones that require the residue Ser10, essential for catalysis of DNA breakage. In addition, these site I-bound dimers do not use a specific interaction between dimers that is required elsewhere in the complex for synapsis of the res sites.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Grindley, N D -- New York, N.Y. -- Science. 1993 Oct 29;262(5134):738-40.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, Bass Center for Molecular and Structural Biology, New Haven, CT 06511.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8235593" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites ; Biopolymers ; Catalysis ; DNA-Binding Proteins/*chemistry ; Molecular Sequence Data ; Mutation ; Nucleoproteins/chemistry ; Nucleotidyltransferases/*chemistry ; Synaptosomes/*chemistry ; Transposases
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  • 46
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1993-06-04
    Description: Aminoglycoside inhibitors of translation have been shown previously to inhibit in vitro self-splicing by group I introns. Chemical probing of the phage T4-derived sunY intron shows that neomycin, streptomycin, and related antibiotics protected the N-7 position of G96, a universally conserved guanine in the binding site for the guanosine cofactor in the splicing reaction. The antibiotics also disrupted structural contacts that have been proposed to bring the 5' cleavage site of the intron into proximity to the catalytic core. In contrast, the strictly competitive inhibitors deoxyguanosine and arginine protected only the N-7 position of G96. Parallels between these results and previously observed protection of 16S ribosomal RNA by aminoglycosides raise the possibility that group I intron splicing and transfer RNA selection by ribosomes involve similar RNA structural motifs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉von Ahsen, U -- Noller, H F -- GM17129/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1993 Jun 4;260(5113):1500-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Sinsheimer Laboratories, University of California, Santa Cruz 95064.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8502993" target="_blank"〉PubMed〈/a〉
    Keywords: Aminoglycosides ; Animals ; Anti-Bacterial Agents/metabolism/*pharmacology ; Base Sequence ; Binding Sites ; Introns/genetics ; Molecular Sequence Data ; Mutation ; Nucleic Acid Conformation/drug effects ; RNA Splicing/drug effects ; RNA, Catalytic/chemistry/*drug effects/metabolism ; Tetrahymena/genetics
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  • 47
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1993-10-15
    Description: The Tax protein of human T cell leukemia virus type-1 (HTLV-I) transcriptionally activates the HTLV-I promoter. This activation requires binding sites for activating transcription factor (ATF) proteins, a family of cellular proteins that contain basic region-leucine zipper (bZIP) DNA binding domains. Data are presented showing that Tax increases the in vitro DNA binding activity of multiple ATF proteins. Tax also stimulated DNA binding by other bZIP proteins, but did not affect DNA binding proteins that lack a bZIP domain. The increase in DNA binding occurred because Tax promotes dimerization of the bZIP domain in the absence of DNA, and the elevated concentration of the bZIP homodimer then facilitates the DNA binding reaction. These results help explain how Tax activates viral transcription and transforms cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wagner, S -- Green, M R -- New York, N.Y. -- Science. 1993 Oct 15;262(5132):395-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Program in Molecular Medicine, University of Massachusetts Medical Center, Worcester 01605.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8211160" target="_blank"〉PubMed〈/a〉
    Keywords: Activating Transcription Factor 1 ; Activating Transcription Factor 2 ; Base Sequence ; Basic-Leucine Zipper Transcription Factors ; Binding Sites ; Cell Line ; Cell Transformation, Viral ; Cyclic AMP Response Element-Binding Protein/metabolism ; DNA/*metabolism ; DNA-Binding Proteins ; G-Box Binding Factors ; Gene Products, tax/*metabolism ; Leucine Zippers ; Molecular Sequence Data ; Oligodeoxyribonucleotides/*metabolism ; Plant Proteins ; Polymers ; Recombinant Fusion Proteins/metabolism ; Transcription Factors/*metabolism
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  • 48
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1993-08-13
    Description: The peptide alpha 4 is a designed four-helix bundle that contains a highly simplified hydrophobic core composed exclusively of leucine residues; its tertiary structure is therefore largely dictated by hydrophobic forces. This small protein adopts a structure with properties intermediate between those of the native and molten globule states of proteins: it is compact, globular, and has very stable helices, but its apolar side chains are mobile and not as well packed as in many natural proteins. To induce a more native-like state, two Zn(2+)-binding sites were introduced into the protein, thereby replacing some of the non-specific hydrophobic interactions with more geometrically restrictive metal-ligand interactions. In the metal-bound state, this protein has properties that approach those of native proteins. Thus, hydrophobic interactions alone are sufficient to drive polypeptide chain folding nearly to completion, but specific interactions are required for a unique structure.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Handel, T M -- Williams, S A -- DeGrado, W F -- New York, N.Y. -- Science. 1993 Aug 13;261(5123):879-85.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Du Pont Merck Pharmaceutical Company, Wilmington, DE 19880-0328.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8346440" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Anilino Naphthalenesulfonates/metabolism ; Binding Sites ; Histidine/chemistry/metabolism ; Magnetic Resonance Spectroscopy ; Molecular Sequence Data ; *Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Proteins/chemical synthesis/*chemistry/metabolism ; Thermodynamics ; Zinc/*chemistry
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  • 49
    Publication Date: 1993-07-09
    Description: Expression of the myogenic helix-loop-helix (HLH) protein myogenin in muscle cell precursors within somites and limb buds is among the earliest events associated with myogenic lineage determination in vertebrates. Mutations in the myogenin promoter that abolish binding sites for myogenic HLH proteins or myocyte enhancer factor-2 (MEF-2) suppressed transcription of a linked lacZ transgene in subsets of myogenic precursors in mouse embryos. These results suggest that myogenic HLH proteins and MEF-2 participate in separable regulatory circuits leading to myogenin transcription and provide evidence for positional regulation of myogenic regulators in the embryo.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cheng, T C -- Wallace, M C -- Merlie, J P -- Olson, E N -- New York, N.Y. -- Science. 1993 Jul 9;261(5118):215-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, University of Texas M.D. Anderson Cancer Center, Houston 77030.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8392225" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; DNA-Binding Proteins/genetics/metabolism ; Embryo, Mammalian/*metabolism ; Extremities/embryology ; Female ; MEF2 Transcription Factors ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Inbred CBA ; Mice, Transgenic ; Muscle Proteins/*genetics ; Muscles/*embryology/metabolism ; Mutation ; Myogenic Regulatory Factors ; Myogenin ; Promoter Regions, Genetic ; Trans-Activators/*genetics ; Transcription Factors/genetics/metabolism ; *Transcription, Genetic
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  • 50
    Publication Date: 1993-08-06
    Description: Cytochrome P450BM-3, a bacterial fatty acid monoxygenase, resembles the eukaryotic microsomal P450's and their flavoprotein reductase in primary structure and function. The three-dimensional structure of the hemoprotein domain of P450BM-3 was determined by x-ray diffraction and refined to an R factor of 16.9 percent at 2.0 angstrom resolution. The structure consists of an alph and a beta domain. The active site heme is accessible through a long hydrophobic channel formed primarily by the beta domain and the B' and F helices of the alpha domain. The two molecules in the asymmetric unit differ in conformation around the substrate binding pocket. Substantial differences between P450BM-3 and P450cam, the only other P450 structure available, are observed around the substrate binding pocket and the regions important for redox partner binding. A general mechanism for proton transfer in P450's is also proposed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ravichandran, K G -- Boddupalli, S S -- Hasermann, C A -- Peterson, J A -- Deisenhofer, J -- GM43479/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1993 Aug 6;261(5122):731-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas 75235-9050.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8342039" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; *Bacterial Proteins ; Binding Sites ; Computer Graphics ; Crystallization ; Cytochrome P-450 Enzyme System/*chemistry ; Heme/chemistry ; Mixed Function Oxygenases/*chemistry ; Models, Molecular ; Molecular Sequence Data ; NADPH-Ferrihemoprotein Reductase ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sequence Alignment ; X-Ray Diffraction
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  • 51
    Publication Date: 1993-03-26
    Description: RecA protein is essential in eubacteria for homologous recombination and promotes the homologous pairing and strand exchange of DNA molecules in vitro. Recombination proteins with weak sequence similarity to bacterial RecA proteins have been identified in bacteriophage T4, yeast, and other higher organisms. Analysis of the primary sequence relationships of DMC1 from Saccharomyces cerevisiae and UvsX of T4 relative to the three-dimensional structure of RecA from Escherichia coli suggests that both proteins are structural homologs of bacterial RecA proteins. This analysis argues that proteins in this group are members of a single family that diverged from a common ancestor that existed prior to the divergence of prokaryotes and eukaryotes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Story, R M -- Bishop, D K -- Kleckner, N -- Steitz, T A -- GM22778/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1993 Mar 26;259(5103):1892-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics, Yale University, New Haven, CT 06511.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8456313" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/chemistry/metabolism ; Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Binding Sites ; *Cell Cycle Proteins ; Conserved Sequence ; DNA/metabolism ; DNA-Binding Proteins/metabolism ; Escherichia coli/chemistry ; Fungal Proteins/chemistry/metabolism ; Membrane Proteins/metabolism ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; Protein Structure, Secondary ; Rec A Recombinases/*chemistry/metabolism ; Recombinant Proteins/chemistry ; Saccharomyces cerevisiae/*chemistry ; Saccharomyces cerevisiae Proteins ; Sequence Homology, Amino Acid ; T-Phages/*chemistry ; Viral Proteins/metabolism
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  • 52
    Publication Date: 1993-07-02
    Description: Muscle contraction consists of a cyclical interaction between myosin and actin driven by the concomitant hydrolysis of adenosine triphosphate (ATP). A model for the rigor complex of F actin and the myosin head was obtained by combining the molecular structures of the individual proteins with the low-resolution electron density maps of the complex derived by cryo-electron microscopy and image analysis. The spatial relation between the ATP binding pocket on myosin and the major contact area on actin suggests a working hypothesis for the crossbridge cycle that is consistent with previous independent structural and biochemical studies.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rayment, I -- Holden, H M -- Whittaker, M -- Yohn, C B -- Lorenz, M -- Holmes, K C -- Milligan, R A -- New York, N.Y. -- Science. 1993 Jul 2;261(5117):58-65.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Wisconsin, Madison 53705.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8316858" target="_blank"〉PubMed〈/a〉
    Keywords: Actins/*chemistry/metabolism ; Actomyosin/*chemistry/metabolism ; Adenosine Triphosphate/metabolism ; Binding Sites ; Image Processing, Computer-Assisted ; *Models, Molecular ; *Muscle Contraction ; Myosin Subfragments/*chemistry/metabolism ; *Protein Conformation ; Protein Structure, Secondary ; X-Ray Diffraction
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  • 53
    Publication Date: 1993-07-02
    Description: Directed movement is a characteristic of many living organisms and occurs as a result of the transformation of chemical energy into mechanical energy. Myosin is one of three families of molecular motors that are responsible for cellular motility. The three-dimensional structure of the head portion of myosin, or subfragment-1, which contains both the actin and nucleotide binding sites, is described. This structure of a molecular motor was determined by single crystal x-ray diffraction. The data provide a structural framework for understanding the molecular basis of motility.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rayment, I -- Rypniewski, W R -- Schmidt-Base, K -- Smith, R -- Tomchick, D R -- Benning, M M -- Winkelmann, D A -- Wesenberg, G -- Holden, H M -- New York, N.Y. -- Science. 1993 Jul 2;261(5117):50-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Wisconsin, Madison 53705.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8316857" target="_blank"〉PubMed〈/a〉
    Keywords: Actins/metabolism ; Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Binding Sites ; Crystallization ; Image Processing, Computer-Assisted ; Methylation ; *Models, Molecular ; Molecular Sequence Data ; Muscle Contraction ; Myosin Subfragments/*chemistry/metabolism ; *Protein Conformation ; Protein Structure, Secondary ; X-Ray Diffraction
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  • 54
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1993-08-13
    Description: Related DNA binding proteins often recognize similar DNA sites but can distinguish among them with the use of different protein-DNA contacts. Here, it is shown that members of the C6 zinc cluster family of yeast transcriptional activators distinguish related DNA sites by a different mechanism. The DNA binding site for each of these proteins contains identical nucleotide triplets (CGG ... CCG) but differs in the spacings between the triplets. It is shown that zinc clusters of these proteins work interchangeably to recognize the conserved triplets and that the region 19 amino acids to the carboxyl-terminal side of the zinc cluster, comprising the linker and the beginning of a dimerization element as inferred from the GAL4 crystal structure, directs the protein to its preferred site.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reece, R J -- Ptashne, M -- GM32308/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1993 Aug 13;261(5123):909-11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, Harvard University, Cambridge, MA 02138.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8346441" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Binding Sites ; DNA/metabolism ; DNA-Binding Proteins/*chemistry/metabolism ; Fungal Proteins/*chemistry/metabolism ; Molecular Sequence Data ; Oligodeoxyribonucleotides/metabolism ; Recombinant Fusion Proteins/chemistry/metabolism ; *Saccharomyces cerevisiae Proteins ; Trans-Activators/*chemistry/metabolism ; Transcription Factors/*chemistry/metabolism
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  • 55
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1993-11-19
    Description: Interleukin-4 (IL-4) is an immunoregulatory cytokine produced by activated T lymphocytes to promote the growth and differentiation of cells that participate in immune defense. This study demonstrates the rapid activation of a specific DNA binding factor by IL-4. The IL-4 nuclear-activated factor (IL-4 NAF) appeared within minutes of IL-4 stimulation and recognized a specific DNA sequence found in the promoters of IL-4-responsive genes. Activation of this putative transcription factor required tyrosine phosphorylation, and antibodies specific for phosphotyrosine recognize the IL-4 NAF-DNA complex. Thus, IL-4 appears to transduce a signal to the nucleus through tyrosine phosphorylation of a latent DNA binding factor.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kotanides, H -- Reich, N C -- R29CA50773/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1993 Nov 19;262(5137):1265-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Graduate Program in Molecular and Cellular Biology, State University of New York at Stony Brook 11794.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7694370" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites ; Cell Nucleus/metabolism ; DNA-Binding Proteins/*metabolism ; *Gene Expression Regulation ; Humans ; Interferon-gamma/pharmacology ; Interleukin-4/metabolism/*pharmacology ; Molecular Sequence Data ; Monocytes/metabolism ; Phosphorylation ; Phosphotyrosine ; Promoter Regions, Genetic ; Receptors, IgG/genetics ; Signal Transduction ; Transcription Factors/*metabolism ; Tyrosine/analogs & derivatives/analysis/*metabolism
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  • 56
    Publication Date: 1993-01-15
    Description: Potassium permanganate (KMnO4) footprinting in the absence and presence of magnesium (Mg2+) at the lambda PR promoter identified two different open complexes with Escherichia coli E sigma 70 RNA polymerase (designated RPo1 and RPo2). The single-stranded region in RPo1 (formed in the absence of Mg2+) was at most 12 bases long, whereas that in RPo2 (formed in the presence of Mg2+) spanned at least 14 bases. Only in RPo2 did the single-stranded region extend to the start point of transcription (+1, +2). These results provide a structural basis for the requirement for uptake of Mg2+ in the formation of RPo2 from RPo1, as deduced from kinetic studies at this promoter.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Suh, W C -- Ross, W -- Record, M T Jr -- GM23467/GM/NIGMS NIH HHS/ -- GM37048/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1993 Jan 15;259(5093):358-61.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Wisconsin, Madison 53706.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8420002" target="_blank"〉PubMed〈/a〉
    Keywords: Barium/metabolism ; Base Sequence ; Binding Sites ; Calcium/metabolism ; DNA, Bacterial/chemistry/metabolism ; DNA, Single-Stranded/*chemistry/metabolism ; DNA, Superhelical/chemistry/metabolism ; DNA-Directed RNA Polymerases/*genetics ; Escherichia coli/enzymology/genetics ; Magnesium/*metabolism ; Molecular Sequence Data ; Oxidation-Reduction ; Plasmids ; Potassium Permanganate/metabolism/pharmacology ; *Promoter Regions, Genetic ; Pyrimidines/metabolism ; Temperature ; *Transcription, Genetic
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  • 57
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1993-02-19
    Description: The Src homology 3 (SH3) region is a small protein domain present in a very large group of proteins, including cytoskeletal elements and signaling proteins. It is believed that SH3 domains serve as modules that mediate protein-protein associations and, along with Src homology 2 (SH2) domains, regulate cytoplasmic signaling. The SH3 binding sites of two SH3 binding proteins were localized to a nine- or ten-amino acid stretch very rich in proline residues. Similar SH3 binding motifs exist in the formins, proteins that function in pattern formation in embryonic limbs of the mouse, and one subtype of the muscarinic acetylcholine receptor. Identification of the SH3 binding site provides a basis for understanding the interaction between the SH3 domains and their targets.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ren, R -- Mayer, B J -- Cicchetti, P -- Baltimore, D -- CA 08875/CA/NCI NIH HHS/ -- CA 09673/CA/NCI NIH HHS/ -- CA 51462/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1993 Feb 19;259(5098):1157-61.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Rockefeller University, New York, NY 10021.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8438166" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Cytoskeletal Proteins/genetics/*metabolism ; DNA/genetics/metabolism ; Genes, abl ; Glutathione Transferase/genetics/metabolism ; Kinetics ; Mice ; Molecular Sequence Data ; *Proline ; Proto-Oncogene Proteins c-abl/genetics/*metabolism ; Rats ; Receptors, Muscarinic/metabolism ; Recombinant Fusion Proteins/metabolism ; Sequence Homology, Amino Acid ; Signal Transduction
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  • 58
    Publication Date: 1993-12-24
    Description: The glycosyl-enzyme intermediate in lysozyme action has long been considered to be an oxocarbonium ion, although precedent from other glycosidases and theoretical considerations suggest it should be a covalent enzyme-substrate adduct. The mutation of threonine 26 to glutamic acid in the active site cleft of phage T4 lysozyme (T4L) produced an enzyme that cleaved the cell wall of Escherichia coli but left the product covalently bound to the enzyme. The crystalline complex was nonisomorphous with wild-type T4L, and analysis of its structure showed a covalent linkage between the product and the newly introduced glutamic acid 26. The covalently linked sugar ring was substantially distorted, suggesting that distortion of the substrate toward the transition state is important for catalysis, as originally proposed by Phillips. It is also postulated that the adduct formed by the mutant is an intermediate, consistent with a double displacement mechanism of action in which the glycosidic linkage is cleaved with retention of configuration as originally proposed by Koshland. The peptide part of the cell wall fragment displays extensive hydrogen-bonding interactions with the carboxyl-terminal domain of the enzyme, consistent with previous studies of mutations in T4L.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kuroki, R -- Weaver, L H -- Matthews, B W -- GM21967/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1993 Dec 24;262(5142):2030-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology, Howard Hughes Medical Institute, University of Oregon, Eugene 97403.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8266098" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Bacteriophage T4/*enzymology ; Binding Sites ; Carbohydrate Conformation ; Carbohydrate Sequence ; Cell Wall/*metabolism ; Chickens ; Disaccharides/*metabolism ; Egg White ; Escherichia coli ; Molecular Sequence Data ; Muramidase/*metabolism ; Mutation ; Oligopeptides/*metabolism ; Peptidoglycan
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  • 59
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1993-09-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Miller, C -- New York, N.Y. -- Science. 1993 Sep 24;261(5129):1692-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Brandeis University, Waltham, MA 02254.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8397443" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Carboxy-Lyases/chemistry/*metabolism ; Oxygen/*metabolism ; Potassium/*metabolism ; Potassium Channels/chemistry/*metabolism ; Sodium/metabolism ; Sodium Channels/metabolism
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  • 60
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1993-12-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wise, J A -- New York, N.Y. -- Science. 1993 Dec 24;262(5142):1978-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Illinois, Roger Adams Laboratory, Urbana 61801.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8266091" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalysis ; *Models, Genetic ; RNA Splicing/*physiology ; RNA, Small Nuclear/*physiology ; Spliceosomes/*physiology
    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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  • 61
    Publication Date: 1993-03-05
    Description: Rhabdomyosarcoma cells express the myogenic helix-loop-helix proteins of the MyoD family but do not differentiate into skeletal muscle cells. Gel shift and transient transfection assays revealed that MyoD in the rhabdomyosarcoma cells was capable of binding DNA but was relatively nonfunctional as a transcriptional activator. Heterokaryon formation with fibroblasts resulted in the restoration of transcriptional activation by MyoD and the differentiation of the rhabdomyosarcoma cells into skeletal muscle cells. These results suggest that rhabdomyosarcomas are deficient in a factor required for MyoD activity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tapscott, S J -- Thayer, M J -- Weintraub, H -- New York, N.Y. -- Science. 1993 Mar 5;259(5100):1450-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Fred Hutchinson Cancer Research Center, Seattle, WA 98104.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8383879" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Cell Differentiation ; Cell Nucleus/metabolism/ultrastructure ; Chloramphenicol O-Acetyltransferase/genetics/metabolism ; Humans ; Mice ; Muscle Proteins/genetics/*metabolism ; Muscles/pathology ; MyoD Protein ; Promoter Regions, Genetic ; Recombinant Fusion Proteins/metabolism ; Rhabdomyosarcoma/genetics/*metabolism/pathology ; Transcription Factors/*metabolism ; Transcription, Genetic ; Transfection ; Tumor Cells, Cultured
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  • 62
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    Publication Date: 1993-08-20
    Description: Microtubule polarity arises from the head-to-tail orientation of alpha-beta tubulin heterodimers in the microtubule lattice. The identity of the polypeptide at each end of the microtubule is unknown, but structural models predict that the beta-tubulin end contains an exchangeable guanosine triphosphate (GTP) binding site. When GTP-coated fluorescent beads were incubated with microtubules, they bound specifically to plus ends, suggesting that tubulin is oriented in microtubules with beta-tubulin toward the plus end.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mitchison, T J -- GM-39565/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1993 Aug 20;261(5124):1044-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, University of California, San Francisco 94143-0450.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8102497" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Animals ; Binding Sites ; Binding, Competitive ; Ethylmaleimide ; Guanosine Triphosphate/*metabolism ; Microtubules/chemistry/*metabolism ; Paclitaxel ; Tetrahymena ; Tubulin/chemistry/*metabolism
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  • 63
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    Nutrient cycling in agroecosystems 35 (1993), S. 217-226 
    ISSN: 1573-0867
    Keywords: calcium ; dry matter distribution ; fertilizer ; harvest index ; magnesium ; manure ; millet ; nitrogen ; nutrient uptake ; phosphorus ; potassium ; Senegal
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract In a fertilizer and manure experiment, millet was grown under four treatments (no fertilizer or manure, farmyard manure, chemical fertilizer, and both). Grain yield and total aboveground biomass production of the unfertilized plot were relatively high. The observed differences in total dry matter production must be attributed to differences in nutrient availability, as amount of rainfall and its distribution were favourable. Results show only small differences in distribution of dry matter among the various plant organs between the best and the non-fertilized treatments. Nutrient supply from natural sources, defined as crop content of N, P, and K at maturity without fertilizer application, amounted to 104, 16 and 103 kg ha−1, respectively, which are very high values. Total uptake of calcium and magnesium is related to that of potassium, as the combined content of these three elements is linearly related to total aboveground biomass production. Minimum removal of nitrogen and phosphorus per ton grain dry matter amounts to 29 and 4kg, respectively, and 9 kg potassium per ton total aboveground dry matter. A possible double function of phosphorus as element of structural biomass and for maintenance of electro-neutrality is discussed.
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  • 64
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    Nutrient cycling in agroecosystems 34 (1993), S. 121-126 
    ISSN: 1573-0867
    Keywords: Controlled release fertilizers ; electroultrafiltration ; nitrogen ; ryegrass
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract The efficiency of different nitrogenous fertilizers under forced leaching conditions was determined in pot experiments using ryegrass as an indicator plant in a sandy loam soil. Treatments were: ON (unfertilized), AN (ammonium nitrate), U (urea), DAP (diammonium phosphate), T (Triabon), FK (Floranid Komplett) and CDU (crotonylidendiurea). N source effects on N uptake, and N leached (as % of N applied) were evaluated. Results show that the fertilizers which behaved best with regard to N uptake were FK followed by Triabon and AN. The most soluble fertilizers, AN and urea, gave the highest N leaching losses. Significant correlations between EUF-NI (rapidly soluble fraction) and leaching, as well as between EUF-N (I + II) and N uptake by the plant (where EUF-N II relates to the slowly soluble fraction) were obtained.
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  • 65
    ISSN: 1572-9680
    Keywords: alley cropping ; maize ; nitrogen ; organic matter ; soil fertility ; Leucaena leucocephala ; Flemingia congesta
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract A detailed study of the soil chemical and physical properties in seven-year-old alley cropping trial containingLeucaena leucocephala andFlemingia congesta in Northern Zambia is described. There was a strong correlation between the maize yield and the total amount of nitrogen applied, both from prunings and fertiliser, suggesting that a major reason for the observed benefit from alley cropping, particularly withLeucaena, was due to an improvement in nitrogen supply.Leucaena produced significantly more biomass, and its leaves had higher concentrations of nitrogen, phosphorous and potassium and lower C/N and C/P ratios than did those ofFlemingia. There was also evidence that the trees had a beneficial effect on other soil chemical properties; under the hedgerows, particularly those ofLeucaena, there were higher levels of organic carbon, Mg, K and ECEC, and pH values were also highest. It is suggested that higher levels of organic carbon in the alley crop treatments were responsible for the improvements observed in soil physical properties. Lower bulk density, lower penetration resistance, and a higher infiltration rate and pore volume fraction were measured in the alley crops, although there was no significant change in the soil water release parameters. A deteriorating effect of constant applications of nitrogen fertiliser on soil fertility was observed; as the level of urea application increased, there were significant decreases in Mg, K and pH, increases in Al and soil acidity, and higher penetrometer resistance. These results highlight the urgent need for further research on biological methods of maintaining soil fertility.
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  • 66
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    Aquatic sciences 55 (1993), S. 132-142 
    ISSN: 1420-9055
    Keywords: nitrogen ; phosphorus ; uptake ; regeneration
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Dissolved inorganic nutrient pools are small relative to particulate pools, and dissolved pools turnover rapidly. It has been observed that pools change little from day to day on the sampling scales usually employed. A simple model is presented where uptake and regeneration rates balance to cause a local steady state concentration for dissolved inorganic nutrients. Enrichment and dilution perturbation experiments with lake water support the idea of steady state nutrient concentrations. Although inorganic nutrient concentrations are often controlled by biota, the absolute concentrations present tell little about the activity of that biota.
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  • 67
    ISSN: 1423-0445
    Keywords: carbon/nutrient balance hypothesis ; carbon allocation ; fertilization ; phenolics ; nitrogen ; terpene ; Abies grandis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Nitrogen fertilization resulted in a linear increase in the growth ofAbies grandis seedlings, but linear decrease in foliage concentrations of phenolic compounds. These data are consistent with the inverse relationship between growth and production of carbonbased secondary chemicals predicted by the carbon/nutrient balance (CNB) hypothesis. However, in contrast to predictions of the CNB hypothesis, nitrogen fertilization had no effect on foliage terpene concentrations. The results suggest that not all carbon-based chemicals respond in the same manner to environmental variation, and that the carbon/nutrient balance hypothesis does not adequately explain all patterns of environmentally-induced variation in secondary metabolism.
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  • 68
    ISSN: 1573-1561
    Keywords: Artificial diet ; herbivory ; nitrogen ; Lymantria dispar ; Lepidoptera ; Lymantriidae ; monoterpenes ; nutritional ecology ; phenolics ; Pseudotsuga menziesii
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract Two experiments were conducted to examine the influence of foliar nitrogen, terpenes, and phenolics of Douglas-fir on the development of gypsy moth larvae. In the first experiment, foliar concentrations of nitrogen and allelochemicals were manipulated by fertilizing 3-year-old potted seedlings with 0 or 200 ppm nitrogen. Concentrations of foliar nitrogen (0.33–2.38%) were negatively correlated with the phenolics (15.8–24.4 mg/g). Sixth-instar larvae previously reared on current-year Douglas-fir needles were allowed to feed on these seedlings. Pupal weights (312.8–995.6 mg) were positively correlated with levels of foliar nitrogen, negatively correlated with amounts of foliar phenolics, and uncorrelated with terpene concentrations. In the second experiment, terpene and phenolic extracts from Douglas-fir foliage were incorporated at natural levels into artificial diets with high and low levels of protein nitrogen. Neonate larvae grew faster and were larger on the high nitrogen control diet (4.1–4.5%), however, fourth instars performed better on the control diet with low nitrogen levels (2.5–2.7%). Foliar terpenes incorporated into diet had little effect on neonate fitness, but may induce subtle physiological changes in later instar larvae. Phenolics, alone or in combination with terpenes, excessively suppressed growth and survival, with no individuals living through the fourth instar, regardless of the nitrogen level. Incorporating foliar phenolic extracts into artificial diet caused unnatural levels of toxicity and failed to clarify the effects of Douglas-fir phenolics on gypsy moth fitness. Foliar nitrogen is a key factor influencing gypsy moth development on Douglas fir, but may be mitigated to some degree by phenolics.
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  • 69
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    Journal of applied phycology 5 (1993), S. 175-181 
    ISSN: 1573-5176
    Keywords: decomposition ; Gracilaria ; nitrogen ; nutrients ; temperature ; Ulva
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract This study determined the rate at which nitrogen accumulated in seaweeds is released during decomposition and the effect of temperature on their rates of decomposition and nitrogen release. Gracilaria verrucosa and Ulva lactuca decomposed rapidly in outdoor mesocosms. Ulva, but not Gracilaria, became nitrogen-enriched during decomposition. Maximal weekly rates of nitrogen release were 5.91 ± 2.23 and 6.37 ± 2.59 g N m−2 d−1, respectively for Gracilaria and Ulva. Temperature had a significant effect on the decomposition rate of Gracilaria in a laboratory experiment: decomposition was greater at 30 °C than at 25 °C. No net decomposition was observed at 16 °C. Gracilaria became nitrogen enriched at 30 °C, but not at 16° or 25°. The release of stored nutrients from decaying seaweeds should be included in nutrient budgets and models when seaweed standing stocks are significant. Seaweed source-sink relationships are important ecologically and can be applied to attempts at using seaweeds as environmental monitors of anthropogenic eutrophication and to efforts of cultivating seaweeds for the improvement of water quality.
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  • 70
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    Journal of applied phycology 5 (1993), S. 547-549 
    ISSN: 1573-5176
    Keywords: Trentepohlia odorata ; Dunaliella bardawil ; light intensity ; nitrogen ; growth ; carotenogenesis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract AxenicTrentepohlia odorata was cultured at three different NH4Cl levels (3.5 × 10−2, 3.5 × 10−3, 3.5 × 10−4 M) and three different light intensities (48, 76, 122 µmol m−2 s−1). Chloride had no effect on growth over this range of concentration. High light intensity and high NH4Cl concentration enhanced the specific growth rate. The carotenoid content increased under a combination of high light intensity and low N concentration. WhenD. bardawil was exposed to the same combination of growth conditions, there was an increase in its carotenoid content. The light saturation and the light inhibition constants (K s andK i, respectively) for growth, and the saturation constant (K m) for NH4Cl were determined. TheK s andK i values were higher inT. odorata (66.7 and〉 122 σmol m−2 s−1, respectively) than inD. bardawil (5.1 and 14.7 µmol m−2 s−1, respectively). TheK m value determined at 122 µmol m−2 s−1, however, was lower inT. odorata (0.048 µM) than inD. bardawil (0.062 µM).
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  • 71
    ISSN: 1573-5176
    Keywords: agar ; C:N ratio ; chemostat ; Gelidium ; nitrogen ; phycobiliproteins
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Gelidium sesquipedale is the most important raw material used for extraction of agar in Spain. Based on chemostats, a system of culture for macroalgae with a continuous flow of culture medium has been developed. A stressed morphotype from the South of Spain was cultured, and the effects of different rates of NO 3 − flow on growth and internal constituents were investigated in the laboratory. Cultivation was successful after optimizing factors affecting growth, such as irradiance level, renewal rate and water movement. Mass production was dependent on N supply. With a flow of 35 μmol NO3 − g−1 DW d−1, optimal values of growth (2.1% d−1) and biomass yield were obtained. In these conditions, biomass yield resembled the values observed in natural populations (about 500 g DW m−2 y−1). When the flow of N was reduced to 15 μmol NO 3 − g−1 DW d−1, growth rate and biomass yield were reduced three-fold, and were null when N was supplied as 7 μmol NO 3 − g−1 DW d−1. C:N ratio was an index of the physiological status of the tissue, remaining low when N was sufficient and raised to critical values when N supply was limited. Phycobiliproteins, kept at a constant irradiance level, were affected by N supply, acting as an internal nitrogen reserve, unlike chlorophylla. An effective phycobiliprotein synthesis took place when the flow of N was sufficient. Agar yield, on dry weight basis, was similar as a function of N flow, whereas agar yield of the culture was higher when N was sufficient as a result of growth not being limited by N. This system of culture, commonly used in microalgal studies, may have an important use in macroalgae as a system to obtain biomass of high quality as well as a good tool for physiological studies in conditions of continuous and controlled flow of nutrients.
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  • 72
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    Plant and soil 152 (1993), S. 19-23 
    ISSN: 1573-5036
    Keywords: acetylene reduction ; difference method ; legumes ; 15N isotope method ; nitrogen ; nitrogen fixation ; Rhizobium
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract To assure proper management and fully realize the benefits of the legume-Rhizobium symbiosis it is necessary to be able to quantify the amount of nitrogen fixed. Having measured the effectiveness of atmospheric N2 fixation the macro- or micro-symbionts as well as agronomic factors can be manipulated with the objective to maximize biological nitrogen fixation. A suitable method to quantify nitrogen fixation is therefore necessary in any programme aiming at increasing N2 fixation, like the one being reported in this volume. There are several methods available to quantify nitrogen fixation and most of the commonly used ones are described in the present paper listing their advantages and disadvantages.
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  • 73
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    Plant and soil 155-156 (1993), S. 57-66 
    ISSN: 1573-5036
    Keywords: nitrogen ; wheat ; simulation ; yield-response curve
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Models of the yield responses of crops to applied nutrients are a recent addition to the methods available for making fertilizer recommendations. They have a place in integrating nutrient information with information on other factors which affect yield and its response to added nutrients. This review deals with nitrogen models classified into three groups: those which predict yield-response curves based on empirical factors; those which simulate the yield response from complex simulation models of many processes regulating crop growth and the soil environment; and those which aim to simulate yield and selected processes based on simplified functional relationships which apply to a target region or industry. Three case studies representing the three classes of model are drawn from research on dryland wheat in different parts of Australia. They show examples in which models provide information which is unobtainable from experimental procedures and which provide information useful to farmers in making decisions about fertilizers. Suggestions are made for future developments in crop-nutrient modelling including further comparisons of models, linkage of models with tissue tests, modelling co-limiting nutrients, deciding on the appropriate level of detail within a model and the need for methods for calibrating and testing models on attributes other than yield alone.
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  • 74
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    Plant and soil 157 (1993), S. 167-174 
    ISSN: 1573-5036
    Keywords: extraction ; mineralisation ; nitrogen ; potassium chloride ; uptake
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract The mineral nitrogen extractable from 12 Scottish arable soils by boiling for 1 hour with 1 M KCl solution was compared with the quantities taken up by ryegrass, barley and oats in pot tests. High correlations were obtained for ryegrass and oats (r2=0.85 and 0.79, respectively), with a slightly lower correlation (r2=0.64) for barley. When the results for one anomalous soil were eliminated from the analysis, all r2 values were 0.81 or higher. The results confirmed earlier work indicating that this method may prove useful for predicting crop uptake of soil-derived nitrogen.
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  • 75
    ISSN: 1573-5036
    Keywords: fructans ; NIR ; nitrogen ; non-structural carbohydrates ; rice ; starch ; stress ; wheat
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Plant shoot samples are frequently analysed to assess if crops require additional nitrogen or mineral elements to maintain satisfactory growth. If plant growth is limited by temperature, water stress, disease, lodging or a mineral deficiency, non-structural carbohydrates (NSC) may be accumulated in, or depleted from, tissues especially those in the lower stems. Plant testing laboratories do not routinely analyse NSC to assist in the identification of plant stress probably because skilled technicians and time are required for the wet chemical determination. In this paper we report that routine determination of NSC is possible using near-infrared reflectance spectroscopy; the errors of determination are comparable with traditional chemical methods. The concentration of NSC in the shoots of rice grown in south eastern Australia ranges from 1.6 to 22.8%, as starch. In the shoots of wheat grown in eastern Australia the range is from 2.4 to 35.2%, as fructans. In both crops the NSC content is highly inversely correlated with the shoot nitrogen content. Based on data from commercial wheat and rice crops we suggest that the ratio between nitrogen and NSC can be used to identify crops in which growth has been limited by a stress other than nitrogen and so are unlikely to show the predicted response to an application of nitrogen fertilizer.
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  • 76
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    Plant and soil 155-156 (1993), S. 45-55 
    ISSN: 1573-5036
    Keywords: compartmentation ; cytoplasm ; 39K NMR ; maize ; nitrogen ; 14N NMR ; 15N NMR ; pea ; phosphorus ; potassium ; 31P NMR ; vacuole
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract The cytoplasmic and vacuolar pools of ammonium, inorganic phosphate and potassium can be studied non-invasively in plant tissues using high resolution nuclear magnetic resonance spectroscopy. The techniques that allow these pools to be discriminated in vivo are described and their application to plants is reviewed with reference to the phosphorus, nitrogen and potassium nutrition of root tissues.
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  • 77
    ISSN: 1573-5036
    Keywords: amino acid ; nitrogen ; phloem sap ; phosphorylation ; protein ; rice (Oryza sativa L.)
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Pure phloem sap was collected from insects feeding on rice (Oryza sativa L.) leaves by a laser technique similar to the aphid stylet technique. Rapid circulation of nitrogen in the sieve tubes was demonstrated directly using 15N as a tracer. Application to the roots of the metabolic inhibitors of amino acids, aminooxyacetate and methioninesulfoximine, changed the amino acid composition in the sieve tubes. Feeding methionine to leaf tips resulted in its bulk transfer into the sieve tubes. In vitro experiments confirmed the existence of protein kinases in the pure rice phloem sap. The phosphorylation status of the sieve tube sap proteins was affected by the light regime. The possibility that changes in chemical composition or protein modification such as phosphorylation in the sieve tubes might affect plant growth are discussed. Analysis of pure phloem sap collected from rice plants by insect laser technique has shown dynamic changes in the chemical composition and the quality of proteins in the sap.
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  • 78
    ISSN: 1573-5036
    Keywords: critical concentration ; magnesium ; manganese ; nitrogen ; phosphorus ; potassium ; solution culture ; zinc
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Solution culture was used to characterise deficiencies or toxicities of several essential elements in Ipomoea batatas cv. Wanmun, and to define the critical concentrations of these elements in young mature leaves during vegetative growth. Tentative critical concentrations for deficiency, expressed on the basis of dry weight of leaf blade, were: nitrogen 3.8%, phosphorus 0.17%, potassium 2.4%, magnesium 0.12%, manganese 20μg/g and zinc 10μg/g. For manganese and zinc toxicities it was possible only to designate the range within which the critical concentration occurred. Visible symptoms are briefly described.
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  • 79
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    Plant and soil 155-156 (1993), S. 21-31 
    ISSN: 1573-5036
    Keywords: nitrogen ; sulphur-nutrition ; gene cloning ; gene expression ; regulation ; crop improvement
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract In the last decade, understanding of ion transport has grown sufficiently to pose sensible questions about the molecular nature of the processes and their regulation. Techniques for identifying and cloning genes and for genetic transformation provide the means for answering these questions. Transport of ions across membranes is obviously a major aspect of mineral nutrition since it occurs during initial absorption, compartmentation and mobilisation of nutrients. Here, we will briefly review the types of transport protein involved and show how molecular biology and recombinant DNA technology have revealed something of their structure. Strategies used to identify the genes for transporters are discussed and reference is made to areas in which the availability of cloned genes will facilitate future studies. Mineral nutrition involves, however, more than membrane transport. The absorption rates of major nutrients are quite strictly regulated by biochemical factors which vary with the rate at which nutrients are used in growth. Nitrogen, sulphur and phosphate nutrition in micro-organisms are regulated by the interaction of various DNA-binding proteins with the promoter regions of genes for key enzymes in the assimilatory pathways and the specific ion permeases. The expression of the regulatory protein or its activity can be modified by metabolites, such as glutamine. Some evidence supports the idea that higher plants also have groups of genes with a common regulation of expression. An attempt is made to identify some reasonable objectives, which should increase understanding of the regulation of nutrient transport.
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    Plant and soil 152 (1993), S. 255-260 
    ISSN: 1573-5036
    Keywords: crimson clover ; field labeling ; legume ; nitrogen ; 15N ; variability
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Plant material labeled with 15N is often used to determine recovery of N from green manure crops by subsequent crops. In this study, 15N enriched crimson clover (Trifolium incarnatum L.) was grown at a field site where it was to be utilized in a subsequent experiment. A foliar spray of (NH4)2SO4 (99 atom % excess 15N) was applied to a 1.2 m × 8.8 m plot of crimson clover at a rate of 10 kg N ha−1 in early March 1990, immediately prior to the period of rapid vegetative growth. Clover shoots harvested in April contained 1.72 atom % excess 15N. Total N concentration of enriched clover was similar to that in adjacent untreated clover. Clover shoots contained 20% of the applied 15N, and an additional 27% was recovered from the surface soil horizon (0 to 15 cm). A gradient was observed across the plot, with clover enrichment increasing from 1.3 to 2.2 atom % excess 15N. Recovery of applied 15N in soil was highest in the subplots with lowest clover enrichment. Variability in 15N enrichment was also observed among plant parts: leaves from the basal half of shoots had 2.2 atom % excess 15N; while leaves from the terminal half of shoots, terminal stems, and basal stems had between 1.1 and 1.4 atom % excess 15N.
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  • 81
    ISSN: 1573-5036
    Keywords: allocation ; carbon ; nitrogen
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract In this paper we model allocation of carbon and nitrogen to roots and leaves as a function of the nitrogen status of a plant. Under steady-state conditions, allocation of carbon and nitrogen to leaves is exponentially (positively) correlated with plant nitrogen concentration, whereas allocation to roots is correlated negatively, also in an exponential manner. Allocation functions derived under steady-state conditions are used to simulate biomass partitioning under non-steady-state nutrient conditions. Upon nitrogen deprivation, measured and simulated values are rather similar with time, suggesting that allocation functions derived under steady-state conditions also hold under non-steady-state conditions.
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    Plant and soil 155-156 (1993), S. 387-390 
    ISSN: 1573-5036
    Keywords: Brassica napus L. ; canola ; critical concentrations ; nitrate ; nitrogen ; sowing time
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Critical concentrations of NO3-N in fresh petiole tissue and total N in the dried lamina were determined for the youngest mature leaf (YML) of field-grown canola. For dry matter yield of canola sown on 4 May, critical NO3-N concentration in the YML petiole at the rosette stage (RS) was 1.46 mg/g fresh wt. At the flower-buds-visible stage (BV) it was 0.45 mg/g fresh wt. For seed yield the values were 1.72 and 0.53 mg/g fresh wt. Critical total N concentration in the YML lamina for dry matter yield were 69 mg/g dry wt. at RS and 57 at BV. For seed yield they were 71 and 59 mg/g dry wt. Critical NO3-N concentrations in the YML petiole of canola sown on 30 May were reduced by 50%; critical total-N concentrations in the YML lamina were not reduced to the same extent. Despite the reductions in critical N concentrations in the YML, critical N fertilizer rates for vegetative growth and seed yield were unaffected by sowing date or plant growth stage.
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  • 83
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    Plant and soil 153 (1993), S. 255-263 
    ISSN: 1573-5036
    Keywords: acid soil ; chlorosis ; iron deficiency ; nitrogen ; Pinus sylvestris
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Scots pine (Pinus sylvestris L.) trees growing on acidic soils may show a special type of chlorosis. The current needles are yellowish and the discolouration is most pronounced at the needle base. The disease bears resemblance to iron chlorosis in trees on calcareous soils. In order to investigate the cause of the chlorosis, needle and soil samples were collected in 41 stands in the southern, central and eastern parts of the Netherlands. Needles of the chlorotic trees had low levels of chlorophylls and carotenoids and high ratios of carotenoids to chlorophylls and of chlorophyll a to chlorophyll b. These symptoms occur in plants suffering from iron deficiency. The current needles of chlorotic trees contained on average 14 mg kg−1 Fe, whereas unaffected trees from the same stands contained 24 mg kg−1. Healthy trees from stands without chlorotic trees had needle iron levels of 29 mg kg−1. Spraying the needles of chlorotic trees with ferric-EDTA containing solutions resulted in partly regreening within a few weeks. Chlorotic needles showed also high nitrogen and cadmium levels. Soils of chlorotic stands contained large amounts of extractable inorganic nitrogen and phosphorus. The possible causal relationships between the observed iron deficiency and the differences in elemental composition of needles and soils are discussed.
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  • 84
    ISSN: 1573-5036
    Keywords: farming system ; fertilization ; magnesium ; nitrogen ; potassium ; potato ; proteolytic enzymes ; senescence ; Solanum tuberosum L.
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract The influence of fertilization on senescence and nutrient remobilization in potato leaves was investigated in two farming systems on a soil with a poor potassium availability. The ‘Conventional’ farming system followed good local practices including industrial products, while in the ‘Bio-Dynamic’ farming system industrial fertilizers and synthetic pesticides were avoided. Potassium concentrations in the dry matter of mature leaves varied over a wide range. Nitrogen compounds (protein, chlorophyll) were less affected, and phosphorus concentrations in the dry matter were similar. Magnesium and potassium concentrations in the leaves were negatively correlated. In both farming systems senescence was advanced in plants with a low nutrient supply. Alkaline pyrophosphatase and aminopeptidase activities (in general highest in expanding and mature leaves) were lower and endopeptidase activities peaked earlier on plots with low fertilizer levels. A high percentage of potassium was remobilized from senescing leaves on unfertilized plots, but the phosphorus concentration remained high at the end of the season. The results suggest that the differential net remobilization of nitrogen, phosphorus and potassium depended on actual source/sink relations in the plants.
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  • 85
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    Plant and soil 157 (1993), S. 175-184 
    ISSN: 1573-5036
    Keywords: barley ; extraction ; malting quality ; mineralisation ; nitrogen ; 15N-labelling ; potassium chloride ; uptake
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract The potentially mineralisable nitrogen extracted from 10 soils by two methods involving boiling with dilute KCl were compared with the actual uptake of soil N by spring barley in the field, as determined with the use of 15N-labelled fertiliser. Generally good correlations were found for those soils which had previously been cropped with cereals (defined in Great Britain as either ‘N-Index zero’, or ‘low nitrogen status’ soils, for fertiliser recommendations), with the results obtained by the more severe of the two methods being somewhat better than by the other method. When organic matter content was also taken into account, correlations were improved. Mineral nitrogen in the soil at sowing was highly correlated with potentially mineralisable nitrogen, and with uptake, but this relationship did not hold for soil samples taken in January, well before the likely sowing date. This suggested that early measurement of soil mineral nitrogen (when decisions on cropping are normally made) was not a practicable method for determinining spring fertiliser applications, and that the measure of potentially mineralisable nitrogen appeared more promising in this regard.
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  • 86
    ISSN: 1573-5036
    Keywords: decomposition ; fine roots ; lignin ; litterbags ; nitrogen ; polyphenols ; substrate quality ; trees ; tropical montane rain forest
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Decomposition rates, initial chemical composition, and the relationship between initial chemistry and mass loss of fine roots and foliage were determined for two woody tropical species, Prestoea montana and Dacryodes excelsa, over a gradient of sites in two watersheds in the Luquillo Experimental Forest, Puerto Rico. At all locations, fine roots decayed significantly more slowly than foliage during the initial 6 months. Substrate quality of the initial tissue showed marked differences between roots and foliage when using cell wall chemistry, secondary chemistry and total elemental analysis as indices. Quantity of acid detergent fiber (ADF) (non-digestible cell wall fiber) and lignin content were higher for roots than leaves: D. excelsa roots had 55.3% ADF and 28.7% lignin while leaves had 36.2% ADF and 11.8% lignin; P. montana roots had 68.0% ADF and 26.8% lignin while leaves had 48.5% ADF and 16.1% lignin. Aluminum concentrations were higher in fine roots (843 mg kg−1 in D. excelsa, 1500 mg kg−1 in P. montana) than leaves (244 mg kg−1 in D. excelsa, 422 mg kg−1 in P. montana), while calcium concentrations were higher in foliage (5.5 mg g−1 in D. excelsa, 7.8 mg g−1 in P. montana) than roots (3.4 mg g−1 in D. excelsa, 3.1 mg g−1 in P. montana). Nitrogen did not show any trend with tissue or species type. A linear model between mass remaining after 6 months and initial tissue chemistry could be developed only for calcium (r2=0.64).
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  • 87
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    Plant and soil 149 (1993), S. 175-184 
    ISSN: 1573-5036
    Keywords: compaction ; Helianthus annuus L. ; leaf expansion ; nitrogen ; osmotic potential ; photosynthesis ; root growth ; soil strength ; turgor ; water potential
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Leaf expansion and growth response of sunflower (Helianthus annuus, L.) to soil compaction were investigated in relation to compaction effects on water relations, nitrogen nutrition, and photosynthesis. A series of field experiments were conducted with plants grown in 20 cm-diameter cylinders with soil bulk densities ranging from 1.2 to 1.7 g cm−3 at the 0–20 cm depth (equivalent to 0.8 to 2.4 MPa soil strength measured with a soil penetrometer). Relative leaf expansion rate (RLER) decreased linearly with increasing soil strength. Smaller plant size in compacted treatments was due not only to slower expansion rates, but also smaller maximum size of individual leaves. Sensitivity of leaf expansion to soil strength was best illustrated by a reduction in RLER and maximum size of the first leaf to emerge in a treatment with only the lower 10–20 cm of the profile compacted (bulk density of 1.7 g cm−3). Root growth was less affected than shoot growth by compaction and root:shoot ratios of compacted treatments were significantly higher than the control. Soil compaction had no significant effect on pre-dawn or midday leaf water potential, osmotic potential or leaf turgor. Specific leaf weight was usually higher in plants grown on compacted soil, and leaf nitrogen and photosynthesis per unit leaf area were either unaffected by treatment or significantly higher in compacted treatments. The results suggest that early growth reduction of sunflower plants grown on compacted soil was more sink- than source-limited with regard to water, nitrogen, and carbon supply. Further evaluation of this hypothesis will require verification that these whole-leaf measurements provided a sufficiently accurate approximation of treatment effects on the dynamic equilibria of expanding cells.
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  • 88
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    Plant and soil 153 (1993), S. 287-293 
    ISSN: 1573-5036
    Keywords: grain protein concentration ; grain yield ; nitrogen ; tritordeum ; triticale ; wheat
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract The new species of cereal × Tritordeum Ascherson et Graebner (Hordeum chilense Roem. et Shultz × Triticum ssp.) has a grain protein concentration (GPC) of up to 25%. The relationship between GPC and yield, and the factors responsible for the high GPC of tritordeum were examined and compared in field experiments. Three experimental tritordeum lines, two early and a later released (recombined and secondary tritordeums) were compared to wheat (cv. Cajeme) and triticale cultivars (cv. Trujillo). GPC's were 19%–22% for recombined tritordeums, 16% for the secondary tritordeum, 12–15% for wheats and 11% for triticale. Grain yields of the recombined and secondary tridordeum were 17–33% and 45–57% that of the wheats and triticale, respectively. Reducing grain sink size by spikelet removal resulted in an increased GPC of remaining grains. Considering all species together there were a strong inverse relationship between GPC and grain yield (GY) per main ear (GPC=26−4.76 ln GY; r2=0.82). In another experiment, frost damage to an early sown treatment of wheat reduced sink size. Harvest index (HI) of early sown wheat was reduced from 0.45 to 0.19, values comparable to that of tritordeum. Having similar HI, the GPC of the early sown wheat was the same as an early sown tritordeum (around 18%). Data for total N uptake and the N concentration of plant tissue during the growing season indicated that enhanced N uptake and remobilisation were not responsible for tritordeum's high GPC. These results suggest that the high GPC of the early lines of tritordeum is a consequence of the small grain yield concentrating the grain protein.
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  • 89
    ISSN: 1573-5036
    Keywords: clover ; grass ; leaching ; lysimeter ; nitrogen ; 15N ; nutrient balances ; nutrient uptake ; pasture ; subsoiling ; sulphur ; 35S
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Synthetic cow urine labelled with 35S and 15N was applied to large, undisturbed, monolith lysimeters sampled from subsoiled and non-subsoiled areas of a grass/clover pasture. For one year following the urine application, the lysimeters were subjected to a combination of natural rainfall, simulated rainfall and simulated flood irrigations. Drainage from the lysimeters was sampled regularly and monthly (approx.) pasture cuts taken. At the end of the year, the lysimeters were destructively sampled in 50 mm depth increments for soil analysis. Leachates, plant samples and soil samples were analysed for 35S and 15N. There were no significant differences in plant uptake of 35S and 15N between the subsoiled and nonsubsoiled lysimeters. Initially grass showed a higher degree of labelling than clover. Total amounts of 35S and 15N leached from the subsoiled lysimeters were approximately twice that leached from the nonsubsoiled ones. Leaching patterns differed substantially between the two nutrients. Total recoveries of 35S (in plants, leachates and soil extracts) accounted for 82% of the applied 35S for the subsoiled lysimeters and 72% for non-subsoiled ones. The unrecovered 35S is considered to have been incorporated into soil organic matter. Total recoveries of 15N (in plants, soil and leachates) were similar to those for 35S, but unrecovered 15N is attributed to loss by denitrification.
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  • 90
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    Hydrobiologia 251 (1993), S. 49-58 
    ISSN: 1573-5117
    Keywords: lake littoral ; detritus ; macrophytes ; decomposition ; nitrogen ; phosphorus
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The importance of detritus varies greatly among shore zones of lakes, but in a large majority of these regions detrital pathways prevail. Aside from a great spatial and seasonal variability, macrophytes and bottom sediments appear to be dominant stores of nutrients in these habitats. Macrophytes hold a central position in nutrient cycling in the shore-littoral lake zones. They are the main source of autochthonous detritus as they prevail in the total biomass of littoral organisms, and they are only rarely available as direct food of consumers. Various processes and interactions determine the role of macrophytes in nutrients dynamics. These are: the intensity of nutrient uptake and translocation, release of nutrients by healthy plants and from decomposing plants, exchange of elements between macrophytes and their periphyton, as well as interception of seston by macrophyte stands. Particular plant species differ in their time of dying and susceptibility to decomposition. The changes in decomposing material (size structure of particles and nutrient content) mean that detritus in various stages of decomposition differs in its role in trophic dynamics of shore-littoral lake zones. Several types of shore regions as regards detritus sources and retention level are discussed.
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  • 91
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    Hydrobiologia 251 (1993), S. 65-72 
    ISSN: 1573-5117
    Keywords: Frozen littoral ; frost heave ; nutrient release ; nitrogen ; phosphorus ; calcium
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract In winter, the littoral substrate of ecotonal zones along north Swedish rivers and lakes freezes. Even if the littoral is flooded at freeze-up, the ice freezes solid to the shore substrate due to low temperature combined with a gradual decrease in water level during winter. Frost conditions were studied during an 8-year period along eight littoral transects in the River Vindelälven and adjacent riverside lagoons. Heavy frost heave with formation of needle ice was observed in several places. Nutrient release was suggested to take place due to the frost process. Sediment was taken to a laboratory experiment where samples with sediment and water were kept under unfrozen and frozen conditions during six months. N (total-N) and Ca were significantly released to the water, while P (total-P) did not show any clear movement from the frozen sediment. The results indicate that frost processes in ecotonal zones are involved in the movement of nutrients between sediment and water.
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  • 92
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    Hydrobiologia 251 (1993), S. 95-101 
    ISSN: 1573-5117
    Keywords: Land/stream ecotones ; bank runoff ; aerial drift ; retention ; carbon ; nitrogen ; phosphorus
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The ‘stream’ ecosystem is described as a three-layered system, vertically as well as horizontally. The land/stream ecotone is defined as the area where lotic and edaphic characters overlap at the time of observation. The study site — ‘Oberer Seebach’, near the Biological Station Lunz — and the methods employed are described. Only a surprisingly small fraction (less than 10 %) of total imports is transported across the surface ecotones. The driving variables determining bank runoff and aerial drift are described and discussed. The importance of channel areas which are periodically flooded is stressed.
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  • 93
    ISSN: 1573-5095
    Keywords: eucalypt ; regrowth forest ; litter ; litterfall ; fertilizer ; nitrogen ; nutrient cycling ; phosphorus
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract The effects of fertilizer treatment on nutrient transfers to the forest floor were examined in regrowth Eucalyptus diversicolor F. Muell. forest. Dry weight and nutrient content of leaf litterfall and total litterfall were measured for 3 years in a stand to which two levels of N (0, 200 kg ha-1 year-1) were applied each year at each of three levels of a single initial application of P (0, 30, 200 kg ha-1). Annual accessions of litter to the forest floor were significantly increased by additions of both N (by 17%, 18% and 21% in the 3 years) and 200 kg P ha-1 (by 8%, 8% and 4% in the 3 years) but there was no interaction between effects of N and P treatments. Fertilizer application also had a significant effect on the nutrient content of leaf litterfall and total litterfall. Concentration of N in leaf litterfall was 9% to 23% greater on plots treated with N fertilizer compared to untreated plots. The amounts of N in litterfall were about 30% greater on N-treated compared to untreated plots. On plots treated with 200 kg P ha-1, P concentrations in leaf litter were 50% to 100% greater than in litter from plots receiving no P. Application of 200 kg P ha-1 increased the amounts of P in annual litterfall by 32% to 87%. The greatest increase in P accessions occurred soon after fertilizer treatment. The amounts of Ca, K, and Na in litterfall were also significantly increased by fertilizer application. For Ca and K this was due partly to increases in element concentrations in litterfall following application of treatments. The effect of fertilizers on internal recycling of plant nutrients and on litter accumulation and nutrient dynamics in forest floor litter is discussed.
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  • 94
    ISSN: 1573-5117
    Keywords: retention ; core-sampling ; phosphorus ; nitrogen ; resuspension ; export
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract In a Danish lowland river system intensive measurements were made, in four 80 m reaches, of the nitrogen (N) and phosphorus (P) stored in the stream sediment. The results were used for calculation of the total retention in the river system during two summers (June to August). In addition, the mobilization of nutrients from the stream bottom in autumn 1987 was compared with the export from the watershed. During the study period (June 1987 to September 1988) the amounts of N and P stored in stream reaches were determined fortnightly using a core-sample technique. In reaches dominated by submersed macrophytes, 25–40 g N m−2 and 20–30 g P m−2 were stored during two summers, against only 10–15g N and P m−2 for sandy and gravely reaches. In riparian zones with emergent macrophytes the retention was even higher than in the submersed macrophytes. Gross retention exceeded net retention by a factor of two to three. Net retention of P in the river system during the summer of 1987 was equal to the summer export from the watershed. On an annual basis, retention in the summer constituted 20% of the P export. In contrast, retention in the summer of 1988 amounted to 60% of the total P export during the same period (38% reduction) and 22% in comparison with the annual export. The corresponding figures for N were lower, showing reductions of 16% and 12% of the export of total N in the two summer periods, and about 1% of the annual exports. In September 1987 6.4% of the total N export and 65% of the total P export from the watershed consisted of resuspended material. In 1987 the N and P retained during the summer was almost completely resuspended during storm events during September to November.
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  • 95
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    Hydrobiologia 271 (1993), S. 97-108 
    ISSN: 1573-5117
    Keywords: Myriophyllum aquaticum ; parrotfeather ; nitrogen ; phosphorus ; mass flow
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The contribution of sediment interstitial water and the water column to the transpiration stream of Myriophyllum aquaticum (Vellozo) Verdcourt was determined to estimate the significance of mass flow in supply of sediment nutrients for plant growth. Sediment interstitial water accounted for about 2% of the water transpired over a 37 day period. Because of the small volume of water that originated in the sediment we concluded that mass flow did not significantly enhance nutrient supply to the roots of M. aquaticum. Relative growth rate (RGR) of adventitious, water roots was greater than whole plant RGR, and RGR of sediment roots was not significantly different from zero, indicating a shift in the biomass allocation after emergence of the apical meristem into the air. Water use, measured by the transpiration coefficient, averaged 260 ml H2O mg DW-1, which is similar to C-4 terrestrial plants. M. aquaticum has leaf characteristics commonly associated with xerophytic habitats. These characteristics may be necessary if a high transpiration rate and a mechanical requirement for high cell turgor pressure, required by a reliance upon hydrostatic pressure for support of the aerial stems, are mutually exclusive because of morphological constraints on hydraulic conductivity.
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  • 96
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    Hydrobiologia 251 (1993), S. 143-148 
    ISSN: 1573-5117
    Keywords: Danube Delta ; flood zones ; phosphorus ; nitrogen ; eutrophication
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The change of concentration of total reactive phosphorus (TRP) and dissolved inorganic nitrogen (DIN) was studied in the lower Danube river and in selected lakes situated in the wetland area of the Danube Delta. The differences Danube Delta in nutrient concentration in the river waters entering the delta and the delta in different sites (especially lakes) of the wetland area are considered to reflect retention in the system. The highest retention was found in periods of moderate and low water level when the surface-to-volume ratio of the lakes was high. In these periods the in-lake concentration of TRP and DIN could be as low as 11 and 23% of the values found in the inflowing river.
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  • 97
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    Biogeochemistry 22 (1993), S. 157-178 
    ISSN: 1573-515X
    Keywords: Serengeti ; productivity ; precipitation ; nitrogen ; grazing
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology , Geosciences
    Notes: Abstract In the Serengeti National Park, Tanzania, precipitation and soil nitrogen vary greatly between northwestern tallgrass areas and southeastern shortgrass areas, with the tallgrass having higher total precipitation and lower soil fertility. We used a model of grassland productivity, carbon/nitrogen cycling, and abiotic factors to test the hypothesis that tallgrass productivity is limited primarily by nitrogen availability while shortgrass productivity is limited by water. Under observed grazing intensities and ungrazed conditions, precipitation exerted primary control over grassland productivity for both regions, with differences in soil texture mediating soil water availability to the grasses. Mineral nitrogen availability interacted with water availability to influence productivity at precipitation levels ⩾ 130% of the mean. Nitrogen mineralization and precipitation were positively related for each grassland type, however, nitrification varied both between grassland types and between grazed and ungrazed conditions. Combined mineralization and nitrification could not maintain soil mineral nitrogen levels in the face of plant nitrogen uptake stimulated by increased precipitation, thus providing the mechanism by which nitrogen becomes a secondary limiting factor for both grasslands. Model experiments indicated that the pattern of primary limitation by precipitation and secondary limitation by nitrogen was robust to model assumptions concerning ungulate deposition of urine and dung nitrogen to the soil.
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  • 98
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    Nutrient cycling in agroecosystems 36 (1993), S. 79-90 
    ISSN: 1573-0867
    Keywords: agriculture ; Sahel ; Sudan ; Mali ; cotton ; fertilization ; nutrient ; soil ; soil degradation ; depletion ; nutrient ; nutrient balance ; nitrogen ; phosphorus ; potassium ; calcium ; magnesium ; acidification ; sustainability
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract The degree of soil mining by agricultural production in Southern Mali is assessed by calculating nutrient balances: differences between the amount of plant nutrients exported from the cultivated fields, and those added to the fields. Export processes include extraction by crops, losses due to leaching, to erosion, and to volatilization and denitrification. Inputs include applications of fertilizer and manure, restitution of crop residues, nitrogen fixation, atmospheric deposition of nutrients in rain and dust, and enrichment by weathering of soil minerals. Nutrient balances are calculated for N, P, K, Ca, and Mg. Both pessimistic and optimistic estimates are given. The resulting figures indicate, even when the most optimistic estimates are used, large deficits for nitrogen, potassium and magnesium. For the region as a whole, the calculated deficits are -25 kg N/ha,-20 kg K/ha, and -5 kg Mg/ha. Further, acidification is to be expected, in particular in areas where cotton is grown. The deficits are caused by traditional cereal crops, but also by cotton and especially by groundnut. The latter two crops are fertilized, but insufficiently. It is important to note, that the negative figures are not automatic recommendations for application of a specific amount of additional fertilizer. For phosphorus and calcium the balance of the region as a whole appears to be about in equilibrium, but locally large variations may occur. Erosion and denitrification are important causes of nutrient loss, accounting respectively for 17 and 22% of total nitrogen exports. Atmospheric deposition and weathering of minerals in the soil are still important nutrient inputs that contribute as much as nutrients as organic and mineral fertilizer combined. Nutrient depletion is very large in comparison to the amount of fertilizer applied. Drastic options, such as doubling the application of fertilizer or manure, or halving erosion losses, even if feasible, would still not be enough to make up for the calculated deficits. The annual value of withdrawn nutrients, if related to prices of fertilizers, varies between 10,000 and 15,000 FCFA/ha (40-60 US $/ha). Since the estimated average gross margin from farming in this area is 34,000 FCFA/ha (123 US $/ha), soil mining appears to provide an amount equal to 40% of farmers' total income from agricultural activities.
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    Nutrient cycling in agroecosystems 34 (1993), S. 59-65 
    ISSN: 1573-0867
    Keywords: Barley ; environment ; nitrogen ; seeding rate ; yield ; yield components
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract This study was conducted to determine the effects of rainfall and temperature during the growing season, seed rate, and N rate on grain yield and yield components of winter barley (Hordeum vulgare L.) on a Typic Haploxeralf soil in Santa Olalla (Toledo), Spain in 1986/7, 1987/8, and 1988/9. Two experiments were conducted each year using the 6-rowed variety ‘Barbarrosa’ and the 2-rowed variety ‘Reinette’. Both experiments used seed rates of 80, 160, and 240 kg ha−1 as whole plot treatments, and N rates of 0, 40, 80, 120, and 160 kg ha−1 as subplots. Responses to N depended on both the quantity and distribution of rainfall during the growing season, and temperature during grain fill. In the high rainfall, moderate grain-fill temperature year, increasing the N rate from 0 to 160 kg ha−1 increased grain yields (by 2.3 t ha−1), straw yields and the harvest index while maintaining the kernel weight for both varieties. In the low rainfall, high grain-fill temperature year, N rate had little influence on grain yield, but increased the straw yield, which reduced the harvest index, and also decreased kernel weight. Seed rate had no influence on grain yields even though wide variation in N rates, rainfall and temperatures occurred in the three-year study. Results from this study indicated that strategies to reduce (or avoid) water/high temperature stress during grain fill are necessary to assure more uniform yield responses to N application across years. However, decisions about seed rate can be made independently for conditions similar to those in this study.
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  • 100
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    Agroforestry systems 21 (1993), S. 1-10 
    ISSN: 1572-9680
    Keywords: silvo-pasture ; compaction ; cattle traffic ; penetrometer ; bulk density ; nitrogen ; seedlings
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract This paper reports on the extent of soil compaction due to cattle traffic around hardwood and softwood tree seedlings established in existing pasture, and subject to cattle pressure. A higher soil penetrometer resistance in the grazed areas pointed to a significant change in soil structure (i.e. dry bulk density) as a result of cattle traffic in the area. In a related experiment comparing the effect of three different levels of soil compaction on tree seedling growth and nitrogen cycling it was found that water infiltration and nitrogen uptake were reduced in soils treated with a medium and high level of compactive effort. This resulted in a slower rate of growth of the tree seedlings. The addition of an additional nitrogen source improved seedling growth in both the medium and high density compactive treatments.
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