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ItemDNA conformational change in Gal repressor-operator complex: involvement of central G-C base pair(s) of dyad symmetry(Georgia Institute of Technology, 1988-12-23) Wartell, Roger M. ; Adhya, Sankar LalGal repressor dimer binds to two gal operator sites, O[subscript E] and O[subscript I], which are 16 bp long similar sequences with hyphenated dyed symmetries (11,12). Repressor occupation hinders the reactivity of the N7 atoms in the major groups of guanines, located at positions 1,3 and 8, and the rotational 1′, 3 and 8′ of the symmetries. We have shown that Gal repressor binding to O[subscript E] or O[subscript I] DNA fragments increases the circular dichroism (CD) spectral peak in the 270 to 300 nm range. The CD change is similar to that observed for Lac repressor binding to its operator site (14). It is consistent with a DNA conformational change during complex formation between Gal repressor and O[subscript E] and O[subscript I] DNA. The CD spectral change was not observed when the central 8,8′ C-C base pairs in the DNA-protein complex were replaced by A-T base pairs, whereas substitution of the 1,1′ G-C base pairs do show the accompanying increase in the spectra during repressor binding. The absence of CD change of the Gal repressor complex with DNA mutated at the 8,8′ base pairs suggest that the central G-C base pairs are required for the repressor induced conformational change.
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ItemEvaluation of caenorhabditis elegans as an acute lethality and a neurotoxicity screening model(Georgia Institute of Technology, 1988-12) Williams, Phillip Lindly
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ItemA biophysical investigation of the mechanisms of the catabolite gene activator protein(Georgia Institute of Technology, 1988-12) DeGrazia, Henry
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ItemDNA curvature and fluctuational base pair opening in the promoter regions of escherichia coli(Georgia Institute of Technology, 1988-12) Plaskon, Randolph Richard
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ItemChemical defense in the seaweed Dictyopteris delicatula: differential effects against reef fishes and amphipods(Georgia Institute of Technology, 1988-09-21) Hay, Mark E. ; Duffy, J. Emmett ; Fenical, William ; Gustafson, KirkMany seaweeds produce chemicals that deter feedlng by fishes and sea urchins. A growing body of evidence suggests that small, relatively immobile herbivores (mesograzers) such as amphpods, polychaetes, and ascoglossan gastropods are often unaffected by these compounds and may preferentially consume seaweeds that are chemically defended from fishes. We tested this hypothesis by examining the responses of reef fishes and amphipods to a mutture of 2 C,, hydrocarbons, &ctyopterenes A and B, produced by the Canbbean brown alga D~ctyopteris delicatula. This alga was intermediate in preference for reef fishes, and the dictyopterenes reduced fish grazing by a significant 40 %. In contrast, D. delicatula was highly preferred by a muted-species group of amphipods and the dlctyopterenes had no effect on their feeding Despite the tendency for mesograzers to selectively consume some seaweeds that are chemically deterrent to fishes, true specialization by these or other marine herbivores appears to be rare in companson with terrestnal systems. Plant-dwelling amphipods at our study site in the Grenadine Islands were found on, and consumed a variety of, macrophytes; they were not restrict~velys pecialized to D. delicatula. Many terrestnal insects are very specialized feeders, sequester toxins from theu food plants, and use these as duect defenses against predation. In contrast, sequestenng of seaweed toxlns by marine mesograzers appears to be relahvely rare. However, the indirect advantage of llving on seaweeds that are not eaten by fishes may be considerable. We hypothesize that mesograzers living on plants chemically defended from fishes wlll experience less predation than those living on plants preferred by fishes.
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ItemThe ecology of rubble structures of the South Atlantic bight: a community profile(Georgia Institute of Technology, 1988-09) Hay, Mark E. ; Sutherland, John P. ; Watzin, Mary C.
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ItemIdentification and partial characterization of a stage-specific surface antigen in C elegans(Georgia Institute of Technology, 1988-08) Donkin, Steven Glenn
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ItemLife histories and secondary production of mayflies in a southeastern US blackwater stream(Georgia Institute of Technology, 1988-08) Jacobi, David Ira
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ItemDNA stem-loop structures in oligopurine-oligopyrimidine triplexes(Georgia Institute of Technology, 1988-01-23) Harvey, Stephen C. ; Luo, Jia ; Lavery, RichardClosed circular DNA containing polypurine-polypyrimidine sequences can adopt a triple helical stem-loop structure under supercoiling pressure. We describe an automated procedure for building model loops and its application to the investigation of the polypyrimidine loop at the end of such a triple helical stem. All possible combinations of 3'-stacked and 5'-stacked structures have been examined for loops containing three, four, five, and six nucleotides. The lowest energy conformation is a four-membered loop with all bases stacked on the strand at the 3' end of the loop. The model predicts that sequences (GA)n, (GGGA)n and (GAAA)n should form the stem-loop structure more easily than (GGA)n and (GAA)n. It is also predicted that when a polypurine-polypyrimidine sequence converts from a double stranded structure to a triple stranded stem-loop, the most favorable conditions are those where an even number of basepairs makes the transition. Experimental tests of these predictions are also described.
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ItemPhenomenological theory of the dynamics of polymer melts. I. Analytic treatment of self-diffusion(Georgia Institute of Technology, 1988-01-15) Kolinski, Andrzej ; Skolnick, Jeffrey ; Yaris, RobertIn the context of dynamic Monte Carlo (MC) simulations on dense collections of polymer chains confined to a cubic lattice, the nature of the dynamic entanglements giving rise to the degree of polymerization n, dependence of the self-diffusion constant D~n[superscript −2] is examined. Consistent with our previous simulation results, which failed to find evidence for reptation as the dominant mechanism of polymer melt motion [J. Chem. Phys. 86, 1567, 7164, 7174 (1987)], long-lived dynamic entanglement contacts between pairs of segments belonging to different chains are extremely rare and are mobile with respect to the laboratory fixed frame. It is suggested that dynamic entanglements involve the dragging of one chain by another through the melt for times on the order of the terminal relaxation time of the end-to-end vector. Employing the physical description provided by the MC simulation, the general expression of Hess [Macromolecules 19, 1395 (1986)] for the friction constant increment experienced by a polymer due to the other polymers forms the basis of a phenomenological derivation of D~n[superscript −2] for monodisperse melts that does not require the existence of reptation. Rather, such behavior is dependent on the relatively benign assumptions that the long distance global motions of the chains are uncorrelated, that the dynamic contacts can be truncated at the pair level, and that the propagator describing the evolution between dynamic contacts contains a free Rouse chain component. The mean distance between dynamic entanglements is predicted to depend inversely on concentration, in agreement with experiment. Moreover, as the free Rouse component is frozen out, for chains greater than an entanglement length ne, a molecular weight independent glass transition is predicted. Extension to bidisperse melts predicts that the probe diffusion coefficient Dp depends on the matrix degree of polymerization, nm, as n. Finally, comparison is made between the theoretical expressions and MC results for mono- and bidisperse melts