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  • Biochemistry  (23)
  • Drosophila  (5)
  • Theoretical, Physical and Computational Chemistry  (5)
  • 1
    Electronic Resource
    Electronic Resource
    Early development of the thoracic discs ofDrosophila (1979)
    Springer
    Development genes and evolution 187 (1979), S. 375-379 
    Details
    ISSN: 1432-041X
    Keywords: Drosophila ; Segmentation ; Primordial size ; Gynandromorphs ; Bithorax mutants
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We estimate the number of blastoderm cells which generate the thoracic imaginal discs ofDrosophila. At hatching the wing disc is twice the size of the haltere disc, but the results suggest that both discs develop from a similar number of blastoderm cells. Two homeotic mutations, which transform the haltere into wing, affect embryonic growth but not the primordial number. All the segmental primordia may be of similar size and each may be similarly subdivided into a larger anterior, and a smaller posterior polyclone.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00848471
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  • 2
    Electronic Resource
    Electronic Resource
    Sexual isolation among widely distributed populations ofDrosophila immigrans (1980)
    Springer
    Behavior genetics 10 (1980), S. 401-407 
    Details
    ISSN: 1573-3297
    Keywords: sexual isolation ; Drosophila ; geographic distance ; isolation index ; resource utilization
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Psychology
    Notes: Abstract Six strains of the cosmopolitan speciesD. immigrans from the Australian life zone plus one from the USA, show weak sexual isolation and more rarely sexual selection. Levels of sexual isolation cannot be related to geographic distances. Assortative mating may have evolved as a byproduct of ecological divergence.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01065601
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  • 3
    Electronic Resource
    Electronic Resource
    Behavior, stress, and variability (1988)
    Springer
    Behavior genetics 18 (1988), S. 293-308 
    Details
    ISSN: 1573-3297
    Keywords: stress ; domestication ; extreme environments ; human evolution ; mice ; Drosophila
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Psychology
    Notes: Abstract Genetic variability of behavioral traits under optimal and stressful environments is considered with examples fromDrosophila, rodents, and our own species. In agreement with direct fitness and life history traits, behavioral traits show a maximization of preexisting andde novo variation under stress. In order to understand evolutionary change,it appears necessary to emphasize those traits showing interactions with habitats under conditions of environmental stress; this can be shown at the behavioral level especially for domestication and adaptation to novel habitats.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01260931
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  • 4
    Electronic Resource
    Electronic Resource
    Sexual isolation among isofemale strains within a population ofDrosophila immigrans (1981)
    Springer
    Behavior genetics 11 (1981), S. 127-133 
    Details
    ISSN: 1573-3297
    Keywords: sexual isolation ; Drosophila ; isofemale strains ; isolation index ; mating propensity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Psychology
    Notes: Abstract Eight isofemale strains of the cosmopolitan speciesDrosophila immigrans derived from a single location in Melbourne, Australia, were crossed in all combinations to test for sexual isolation. Statistically significant sexual isolation occurred in 12 of 28 crosses, with one strain showing significant isolation from the other seven. There were significantly unequal male mating propensities (relative rates of mating) in 7 of the 28 crosses.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01065623
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  • 5
    Electronic Resource
    Electronic Resource
    Habitat selection and evolutionary strategies inDrosophila: An invited address (1978)
    Springer
    Behavior genetics 8 (1978), S. 511-526 
    Details
    ISSN: 1573-3297
    Keywords: habitats ; evolutionary strategies ; Drosophila ; physical environments ; lek behavior ; alcohol
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Psychology
    Notes: Abstract There is an association among resource utilization divergence, habitat selection, and taxonomic divergence in the genusDrosophila. Given permissive conditions of temperature, humidity, and light intensity, an enormous variety of resources is used in a diversity of habitats. These resources are considered in the cosmopolitan and endemic Australian fauna, providing evidence for habitat selection in the laboratory and field. Lek behavior in picture-winged species of subgenusHirtodrosophila, a case of parallel evolution with lek behavior in subgenusDrosophila in Hawaii, is discussed in detail. Other examples of habitat selection discussed concern behavioral reactions of larvae to alcohol and other metabolites and the avoidance by adults of extreme physical environments. Evolutionary strategies involved in habitat selection are considered at various taxonomic levels inDrosophila. These considerations show that it is essential to relate results from laboratory studies to natural environments in order to explore the genetics of habitat selection.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01067480
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  • 6
    Electronic Resource
    Electronic Resource
    The reaction of n-butyllithium with benzoic acid: is nucleophilic addition competitive with deprotonation?Dedicated to Frederick G. Bordwell for his many and continuing contributions to physical organic chemistry (1997)
    Chichester : Wiley-Blackwell
    Journal of Physical Organic Chemistry 10 (1997), S. 537-541 
    Details
    ISSN: 0894-3230
    Keywords: n-Butyllithium ; benzoic acid ; nucleophilic addition ; deprotonation ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Physics
    Notes: ---An evaluation of a branching vs sequential mechanism for the reaction of benzoic acid with n-butyllithium favors the latter. © 1997 John Wiley & Sons, Ltd.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    Free energy perturbation calculations on models of active sites: Applications to adenosine deaminase inhibitors (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 994-1002 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Free energy perturbation calculations were performed to determine the free energy of binding associated with the presence of perhaps an unusual hydroxyl group in the transition state analog of nebularine, an inhibitor of the enzyme adenosine deaminase. The presence of a single hydroxyl group in this inhibitor has been found to contribute -9.8 kcal/mol to the free energy of binding, with a 108-fold increase in the binding affinity by the enzyme. In this work, we calculate the difference in solvation free energy for the 1,6-dihydropurine complex versus that of the 6-hydroxyl-1,6-dihydropurine complex to determine if this marked increase in binding affinity is attributed to an unusually hydrophobic hydroxyl group. The calculated ΔG associated for the solvation free energy is -11.8 kcal/mol. This large change in the solvation free energy suggests that this hydroxyl is instead unusually hydrophilic and that the difference in free energy of interaction for the two inhibitors to the enzyme must be at least ca. 20 kcal/mol. Although the crystal structure for adenosine deaminase is currently not known, we attempt to mimic the nature of the active site by constructing models which simulate the enzyme-inhibitor complex. We present a first attempt at determining the change in free energy of binding for a system in which structural data for the enzyme is incomplete. To do this, we construct what we believe is a minimal model of the binding between adenosine deaminase and an inhibitor. The active site is simulated as a single charged carboxyl group which can form a hydrogen bond with the hydroxyl group of the analog. Two different carboxyl anion models are used. In the first model, the association is modeled between an acetic acid anion and the modified inhibitor. The second model consists of a hydrophobic amino acid pocket with an interior Glu residue in the active site. From these models we calculate the change in free energy of association and the overall change in free energy of binding. We calculate the free energies of interaction both in the absence and presence of water. We conclude from this that the presence of a single suitably placed-CO-2 group probably cannot explain the binding effect of the-OH group and that additional interactions will be found in the adenosine deaminase active site.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110811
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  • 8
    Electronic Resource
    Electronic Resource
    Comparison of ab initio, semiempirical, and molecular mechanics calculations for the conformational analysis of ring systems (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 525-532 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The potential energy surfaces of four cyclic alkanes have been examined using molecular mechanics, semiempirical, and ab initio methods to determine if they produce mutually consistent results and investigate the source of any errors between the methods. The C5 — C8 cyclic alkanes were chosen since these structures present a finite set of conformations and transition-state geometries and are still within the computational time and memory limits of the quantum mechanical approaches. We also examined several conformations of 1,2-dideoxyribose to determine the effect of heteroatoms on the results for the 5-membered ring. The molecular mechanics and ab initio calculations are consistent in the relative energies and geometries determined for the conformers of all ring systems. While the semiempirical calculations yielded geometries consistent with the other methods (except for 5-membered rings), the relative energies often deviated substantially. A decomposition analysis of the semiempirical and molecular mechanics energies revealed that the disparities are mainly due to errors in the 1-center energies of the semiempirical calculations. The 2-center bonding and nonbonding energies followed reasonable trends for the conformers. The core-repulsion function, however, is suspected of producing anomalies. A minimum in the attractive Gaussian of this term at 2.1 Å for H—H interactions partly explains the propensity of the 5-membered rings to optimize to near planarity (decreasing 1,2-diaxial hydrogen distances to 2.3 Å) and the underestimation of the relative energy of the boat structure of cyclohexane.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540130413
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  • 9
    Electronic Resource
    Electronic Resource
    AMBERCUBE MD, parallelization of Amber's molecular dynamics module for distributed-memory hypercube computers (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 312-329 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A fully functional parallel version of the molecular dynamics (MD) module of AMBER3a has been implemented. Procedures parallelized include the calculation of the long-range nonbonded Coulomb and Lennard-Jones interactions, generation of the pairlist, intramolecular bond, angle, dihedral, 1-4 nonbonded interaction terms, coordinate restraints, and the SHAKE bond constraint algorithm. As far as we can determine, this is the first published description where a distributed-memory MIMD parallel implementation of the SHAKE algorithm has been designed to treat not only hydrogen-containing bonds but also all heavy-atom bonds, and where “shaken” crosslinks are supported as well. We discuss the subtasking and partitioning of an MD time-step, load balancing the nonbonded evaluations, describe in algorithmic detail how parallelization of SHAKE was accomplished, and present speedup, efficiency, and benchmarking results achieved when this hypercube adaptation of the MD module AMBER was applied to several variant molecular systems. Results are presented for speedup and efficiency obtained on the nCUBE machine, using up to 128 processors, as well as benchmarks for performance comparisons with the CRAY YMP and FPS522 vector machines. © 1993 John Wiley & Sons, Inc.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540140307
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  • 10
    Electronic Resource
    Electronic Resource
    Free energy perturbation calculations on parallel computers: Demonstrations of scalable linear speedup (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 351-373 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A coarse-grain parallel implementation of the free energy perturbation (FEP) module of the AMBER molecular dynamics program is described and then demonstrated using five different molecular systems. The difference in the free energy of (aqueous) solvation is calculated for two monovalent cations ΔΔGaq(Li+ Δ Cs+), and for the zero-sum ethane-to-ethane′ perturbation ΔΔGaq(CH3—methyl—X → X—methyl—CH3), where X is a ghost methyl. The difference in binding free energy for a docked HIV-1 protease inhibitor into its ethylene mimetic is examined by mutating its fifth peptide bond, ΔG(CO—NH → CH=CH). A potassium ion (K+) is driven outward from the center of mass of ionophore salinomycin (SAL-) in a potential of mean force calculation ΔGMeOH(SAL- · K+) carried out in methanol solvent. Parallel speedup obtained is linearly proportional to the number of parallel processors applied. Finally, the difference in free energy of solvation of phenol versus benzene, ΔΔGoct(phenol → benzene), is determined in water-saturated octanol and then expressed in terms of relative partition coefficients, Δ log(Po/w). Because no interprocessor communication is required, this approach is scalable and applicable in general for any parallel architecture or network of machines. FEP calculations run on the nCUBE/2 using 50 or 100 parallel processors were completed in clock times equivalent to or twice as fast as a Cray Y-MP. The difficulty of ensuring adequate system equilibrium when agradual configurational reorientation follows the mutation of the Hamiltonian is discussed and analyzed. The results of a successful protocol for overcoming this equilibration problem are presented. The types of molecular perturbations for which this method is expected to perform most efficiently are described. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 11 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150310
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