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  • Wiley-Blackwell  (31)
  • 1985-1989  (31)
  • 1
    Electronic Resource
    Electronic Resource
    Loop formation in polynucleotide chains. II. Flexibility of the anticodon loop of tRNAPhePresented in part at the Biophysical Society Meeting, San Antonio, Texas, February 1984. (1987)
    New York : Wiley-Blackwell
    Biopolymers 26 (1987), S. 415-438 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The flexibility of hairpin loops containing n bases (residues) has been examined using a theoretical model [N. L. Marky and W. K. Olson (1982), Biopolymers, 21, 2329-2344] of oligonucleotide loop closure. The study is based on correlated probabilities of chain separation and terminal residue orientation as outlined previously. The probabilities are calculated using standard statistical mechanical methods as functions of local conformational changes of the chain backbone. Our results for an RNA chain of 9 residues suggest that the anticodon loop is a dynamic structure capable of assuming a variety of different spatial conformations. Free energy values related to the various conformations span a narrow range of values (2-4 kcal/mole) and compare well with experimental observations in aqueous solution. Conformational transitions between the loop conformations are within less than 0.5 kcal/mole in free energy. The different spatial loop conformations and the likely pathways between them may have potential relevance to the molecular translation of the genetic code.
    Additional Material: 16 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360260309
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  • 2
    Electronic Resource
    Electronic Resource
    Base sequence effects in double-helical DNA. II. Configurational statistics of rodlike chains (1988)
    New York : Wiley-Blackwell
    Biopolymers 27 (1988), S. 561-584 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Matrix generator techniques have been adapted to account for precise structural features of the nucleotide repeating unit and to translate the primary sequence of DNA base pairs into three-dimensional structures. Chains have been constructed to reflect the local sequence-dependent differences of bending and twisting of adjacent residues and various overall chain properties, including the average unperturbed moments of the end-to-end vector r and the mean angular orientation (〈γ〉 between base pair normals, 〈φ1〉 between long axes, and 〈φ2〉 between short axes) of terminal chain residues, have been computed. The chain backbone is treated implicitly in terms of the spatial fluctuations of successive base pairs. Motions are limited to low-energy perturbations of the standard B-DNA helix. Approximate potential energy schemes are used to represent the rules governing the patterns of local base-base morphology and flexibility. Theoretical predictions are compared with experimental observations at both the local and the macro-molecular level. Initial applications are limited to the rodlike poly(dA) · poly(dT) and poly(dG) · poly(dC) helices. The former duplex is found to be more compressed and the latter more extended than random-sequence DNA of the same chain length. The flexibility of the duplexes as a whole is described in terms of the average higher moments of the displacement vector ρ = r - 〈r〉 and the likelihood of chain cyclization is estimated from the three-dimensional Hermite series expansions of the displacement tensors. Emphasis is placed on theoretical methodology and the practical relevance of the calculated chain moments to observed physical properties.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360270403
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  • 3
    Electronic Resource
    Electronic Resource
    Base sequence effects in double-helical DNA. III. Average properties of curved dna (1988)
    New York : Wiley-Blackwell
    Biopolymers 27 (1988), S. 585-603 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The matrix-generator methods set forth in the preceding paper for treating rodlike DNA are adapted here to the calculation of average chain extension, macroscopic flexibility, and terminal residue orientation in curved duplexes. The different characteristics of curved vs rodlike chains are illustrated with the hypothetical poly[d(A5G5)] · poly[d(T5C5)] duplex. The curved helix is both more compact and macroscopically stiffer than either the poly(dA) · poly(dT) or the poly(dG) · poly(dC) chain. The calculations have also been extended to simple repetitive DNA sequences generated by synthetic ligation studies and the computed average chain properties compared with observed gel mobilities. The predicted chain extension is also checked against the measured persistence lengths of the rodlike poly[d(GC)] and poly[d(AT)] alternating copolymers, and the known cyclization tendencies of selected repeating sequences. Chains are generated from local potential energy maps describing the morphology and flexibility of adjacent base pairs. The energy maps, while approximate, are more accurate descriptors of local structure than many of the intuitive models of DNA curvature offered to date. According to the energy surfaces, the intrinsic bending of curved DNA can be traced to asymmetry in the bending of the Gs and Cs that join half-helical turn stretches of adenines in these chains. The oligo A stretches are analogous to residues of a perfectly elastic DNA that bend with equal likelihood in opposing directions. In other models of DNA curvature, the (G · C) base pairs are presumed to adopt the classical B-DNA structure, while the (A · T) base pairs are thought to be in some perturbed conformation.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360270404
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  • 4
    Electronic Resource
    Electronic Resource
    An adaptive boundary element method (1987)
    Chichester [u.a.] : Wiley-Blackwell
    International Journal for Numerical Methods in Engineering 24 (1987), S. 1187-1202 
    Details
    ISSN: 0029-5981
    Keywords: Engineering ; Engineering General
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Mathematics , Technology
    Notes: This paper explores the concept of moving singularities in the boundary element analysis. The singularities are placed on an auxiliary boundary which is located outside the domain of the problem and are allowed to move as part of the solution process. This results in a highly adaptive but non-linear method. Examples involving the two- and three-dimensional Laplace's equations are solved. Excellent agreement with exact solutions is obtained using a minimal number of singularities. Also, the trajectories of the singularity motion are plotted. The behaviour seen here is that, as the solution approaches convergence, the singularities exhibit a general trend of moving away from the domain of the problem.
    Additional Material: 12 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/nme.1620240610
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  • 5
    Electronic Resource
    Electronic Resource
    Gas chromatographic/mass spectrometric studies of the urinary metabolites of male rats given indan (1987)
    Chichester : Wiley-Blackwell
    Biological Mass Spectrometry 14 (1987), S. 649-651 
    Details
    ISSN: 0887-6134
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The identified urinary metabolites of male rats exposed to indan are: 1- and 2-indanone; 1-, 2- and 5-indanol; 2-and 3-hydroxyl-1-indanone; and cis- and trans-indan-1,2-diol. Indan causes kidney damage in male rats in a manner similar to the cyclic hydrocarbons cis- and trans-decalin and JP-10. Lesions produced by indan occur only in male rats and not in female or control rats.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bms.1200141114
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  • 6
    Electronic Resource
    Electronic Resource
    Identification of urinary metabolites in rats exposed to the nephrotoxic agent 2,3,4-trimethylpentane (1987)
    Chichester : Wiley-Blackwell
    Biological Mass Spectrometry 14 (1987), S. 639-641 
    Details
    ISSN: 0887-6134
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Branched-chain hydrocarbon-induced nephropathy in male rats was examined using 2,3,4-trimethylpentane. Lesions are elected only in male rats, not in females or in controls. Mechanisms of nephropathy may be the interaction of metabolites with the male rat-specific protein alpha 2u globulin. The identified urinary metabolites of 2,3,4-trimethylpentane in male rats given the hydrocarbon by gavage are 2,3,4-trimethyl-1-pentanol, 2,3,4-trimethyl-2-pentanol and 2,3,4-trimethyl-1-pentanoic acid. Of the C8-isomers, 2,3,4-trimethylpentane dosing leads to the highest incidence of kidney damage in male rats.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bms.1200141112
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  • 7
    Electronic Resource
    Electronic Resource
    Kinetics of milk coagulation: II. Kinetics of the secondary phase: Micelle flocculation (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 29 (1987), S. 590-600 
    Details
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: A kinetic model for the agglomeration of milk micelles following κ-casein hydrolysis is described. The key features of the model are: (1) the surface potential of casein micelles is sufficient to explain the colloidal stability of the milk system; (2) the reduction in surface potential following κ-casein hydrolysis explains the loss of stability; (3) partial hydrolysis leads to limited agglomeration; and (4) the kinetics of agglomeration are compatible with the theory that completely hydrolyzed micelles have only a limited number of interaction sites. The model accurately predicts solution turbidity increase assuming that micelles have only circa 1.2 interaction sites on the average under the experimental conditions of this study.
    Additional Material: 13 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bit.260290508
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  • 8
    Electronic Resource
    Electronic Resource
    Kinetics and mechanism of dissimilative Fe(III) reduction by Pseudomonas sp. 200 (1986)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 28 (1986), S. 1657-1671 
    Details
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The kinetics and mechanism of Fe(III) reduction to Fe(II) were studied in pure batch cultures of Pseudomonas sp. 200. The rate of iron reduction has been mechanistically related to aqueous phase iron speciation. In the absence of microbial activity the iron reduction rate was negligible. Initial rates of microbial iron reduction were accelerated more than 20-fold by the addition of equimolar quantities of nitrilotriacetic acid (NTA) to media initially containing 1.86 × 10-3M total Fe(III). Numerical techniques were utilized to quantify relationships between the observed rate of Fe(II) production and the calculated (equilibrium) aqueous phase speciation. These results indicate that soluble ferric iron species are not equivalent in terms of their susceptibility to bacterial (dissimilative) iron reduction. The concentration of Fe(NTA)(OH)22- correlated strongly with observed iron reduction rates. Ferrous iron species appeared to inhibit the reduction process.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bit.260281110
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  • 9
    Electronic Resource
    Electronic Resource
    Kinetics of milk coagulation: I. The kinetics of kappa casein hydrolysis in the presence of enzyme deactivation (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 29 (1987), S. 582-589 
    Details
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The kinetics of the primary phase of the enzymatic coagulation of milk, i.e., κ-casein hydrolysis, was investigated in the presence and in the absence of concurrent enzyme deactivation processes. For conditions under which the enzyme is stable, the rate of hydrolysis can be described by Michaelis-Menten kinetics, as has been reported by previous investigators. A mathematical model, experimental data, and parameter estimates are provided for κ-casein hydrolysis in the presence of concurrent deactivation of enzyme. The model accurately describes the experimental results when porcine pepsin was used as the renneting enzyme. The model and the experimental results indicate that samples of milk treated under conditions where deactivation of enzyme is significant can have fractional conversions of κ-casein ranging from zero to unity and yet contain no active enzyme at the termination of the treatment.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bit.260290507
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  • 10
    Electronic Resource
    Electronic Resource
    Kinetics of milk coagulation: III. Mathematical modeling of the kinetics of curd formation following enzymatic hydrolysis of κ-casein - parameter estimation (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 29 (1987), S. 601-611 
    Details
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: A step function model of milk micelle agglomeration is proposed to explain the observed kinetics of milk clotting following rennet addition. The model ties together the primary and secondary phases of coagulation. The basis of the model is that no micelle flocculation takes place until ca. 75% of the κ-casein in the milk is hydrolyzed, at which time flocculation occurs rapidly and the rate limiting step for the clotting process shifts to the κ-casein hydrolysis reaction. Using such a model, it is possible to explain the clotting kinetics for both rapidly denaturing enzymes and stable enzyme systems. The average rate of the flocculation reaction can be obtained from clotting time-versus-reciprocal-enzyme-concentration data by extrapolating the data to infinite enzyme concentration. The critical conversion required for imminent flocculation can be found by extrapolating the enzyme concentration to zero. This approach indicates that the critical conversion necessary for gelation is temperature dependent changing from a limiting value of essentially 100% hydrolysis at temperatures below 15°C to only 60% conversion at temperatures above 30°C.
    Additional Material: 14 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bit.260290509
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