Organizational Unit:
College of Sciences
College of Sciences
Permanent Link
Research Organization Registry ID
Description
Previous Names
Parent Organization
Parent Organization
Includes Organization(s)
Organizational Unit
Organizational Unit
Organizational Unit
Organizational Unit
Organizational Unit
ArchiveSpace Name Record
Publication Search Results
Now showing
1 - 10 of 31
-
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.
-
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.
-
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.
-
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
-
ItemPhenomenological theory of the dynamics of polymer melts. II. Viscoelastic properties(Georgia Institute of Technology, 1988-01-15) Skolnick, Jeffrey ; Yaris, RobertA phenomenological theory of the nonmechanical and viscoelastic properties of polymer melts is developed. Consistent with computer simulation results [A. Kolinski, J. Skolnick, and R. Yaris, J. Chem. Phys. 86, 1567, 7164, 7174 (1987)], that fail to find evidence for reptation as the dominant mechanism of long distance motion in a melt, we assume that the long-time behavior of a chain is that of a Rouse-like chain having a number of slow moving points, each with a friction constant proportional to the degree of polymerization n. Coupled with the assumption of rubber like behavior at short times made previously by Doi and Edwards [J. Chem. Soc., Faraday Trans. 2 74, 1802 (1978)], the theory predicts that over a broad molecular weight range the shear viscosity scales with n as approximately the 3.4 power of the molecular weight, and that ~n³ in the infinite molecular weight limit. Furthermore, the theory rationalizes the origin of the different crossover molecular weights for the shear viscosity and the self-diffusion coefficient, D. It also accounts for the origin of the intermediate time coupling of the center-of-mass motion into the internal coordinates and for the time dependence of the single bead positional autocorrelation functions seen in previous simulations. Proceeding by analogy to Graessley [J. Poly. Sci. Poly. Phys. Ed. 18, 27 (1980)], in the large molecular weight limit, phenomenological expressions for D and are derived and comparison is made with experiment.
-
ItemDirectionality and Swimming Speeds in Predator-Prey and Male-Female Interactions of Euchaeta rimana, a Subtropical Marine Copepod(Georgia Institute of Technology, 1988) Yen, JeannetteThis examination showed how the sexual dichotomy in morphology and feeding was reflected in the swimming behavior of Euchaeta rimana. Nonrandom swimming was clearly exhibited by this copepod, and the evolutionary reasons for the behaviors involve the dual requirements of encountering food and mates. Mechanoreceptive females, with their enlarged feeding appendages and elongated antennal setae, must find prey to feed. Non-feeding males, with reduced mouthparts and antennal setules, must find females to inseminate before exhausting their lipid reserves which were accumulated during juvenile stages. Directional swimming by the female predatory copepod supports the predictions of models in which encounter rate was maximized by swimming orthogonally to their mates and their prey. The female swam horizontally in a turn-and-search pattern to intersect the male which swam vertically in a swim-up-and-sink pattern. Adult female copepods (~2.5 mm prosome length) generally swam smoothly and continuously at an average swimming speed of 7 mm's-I, with their antennae oriented into the flow not disturbed by their own movements. Besides mating, females also must find and capture prey. Analysis of swimming by one potential prey, Acartia fossae, showed that these smaller copepods darted up and stopped in various directions to counteract sinking due to gravity. This resulted in a strong vertical component to their directionality which increased the likelihood of encounter with the predatory copepod. The dart-and-stop swimming pattern of Acartia fossae may be an alternate mode of escape from a mechanoreceptive copepod, such as Euchaeta which can not sense prey when they are not moving.
-
ItemHead and thoracic transformations caused by ectopic expression ofAntennapedia during Drosophila development(Georgia Institute of Technology, 1988) Gibson, Greg ; Gehring, Walter J.Segmental identity in Drosophila is controlled by the activities of the homeotic genes. One such gene is Antennapedia, which is required for the proper development of the thoracic segments. Alteration of Antennapedia expression either in mutants, or artificially using an inducible promoter, can lead to alterations of segmental identity. In this report, we present the consequences of ectopic expression of the Antennapedia gene under the control of a heat-shock promoter, at distinct stages throughout Drosophila development. In young embryos, up to the stage of germ-band retraction, the ubiquitous expression of the Antennapedia protein causes a range of effects throughout the embryo, including failure of head involution, induction of extra denticles on the dorsal surface of the head and disruption of the prothoracic denticle belts. In older embryos, it results in larval lethality. Heat shocks during larval development can lead to defects in leg formation, but no alterations in leg identity have been observed. However, clear transformations of head towards second (meso-) thoracic segment can be induced in early third instar larvae. There is a distal-to-proximal temporal response to ectopic Antennapedia expression in the antennal disc, as evidenced by successive transformations of the arista, third antennal segment, second antennal segment and occiput towards their corresponding leg and dorsal thoracic structures. Overproduction of Antennapedia protein during the pupal stage is generally lethal. Comparison of the homeotic transformations in, and Western analysis of, different lines suggests that a relatively large amount of Antennapedia protein is required to cause antenna-to-leg transformations, and further argues that, in general, developmental programmes in the insect are well buffered against the effects of ectopic homeotic gene expression. Immunodetection of Scr and Antp protein also allows us to interpret the results in light of the hypothesis that the various selector genes compete with one another to control not only their own expression, but also that of downstream genes. The role of Antennapedia in imaginal disc determination is also discussed. rosophila development, segmentation.
-
ItemMonte Carlo studies on the long time dynamic properties of dense cubic lattice multichain systems. II. Probe polymer in a matrix of different degrees of polymerization(Georgia Institute of Technology, 1987-06-15) Kolinski, Andrzej ; Skolnick, Jeffrey ; Yaris, RobertThe dynamics of a probe chain consisting of n[subscript P]=100 segments in a matrix of chains of length of n[subscript M]=50 up to nM=800 at a total volume fraction of polymer φ =0.5 have been simulated by means of cubic lattice Monte Carlo dynamics. The diffusion coefficient of the probe chain over the range of n[subscript M]=under consideration decreases by about 30%, a behavior rather similar to that seen in real melts of very long chains. Furthermore, the analysis of the probe chain motion shows that the mechanism of motion is not reptation-like and that the cage effect of the matrix is negligible. That is, the local fluctuations of the topological constraints imposed by the long matrix chains (even for n[subscript M]=800) are sufficiently large to provide for essentially isotropic, but somewhat slowed down, motion of the probe, n[subscript P] =100, chains relative to the homopolymer melt. The results of these MC experiments are discussed in the context of theoretical predictions and experimental findings for related systems.
-
ItemMonte Carlo studies on the long time dynamic properties of dense cubic lattice multichain systems. I. The homopolymeric melt(Georgia Institute of Technology, 1987-06-15) Kolinski, Andrzej ; Skolnick, Jeffrey ; Yaris, RobertDynamic Monte Carlo simulations of long chains confined to a cubic lattice system at a polymer volume fraction of φ =0.5 were employed to investigate the dynamics of polymer melts. It is shown that in the range of chain lengths n, from n=64 to n=800 there is a crossover from a weaker dependence of the diffusion coefficient on chain length to a much stronger one, consistent with D~n⁻². Since the n⁻² scaling relation signals the onset of highly constrained dynamics, an analysis of the character of the chain contour motion was performed. We found no evidence for the well-defined tube required by the reptation model of polymer melt dynamics. The lateral motions of the chain contour are still large even in the case when n=800, and the motion of the chain is essentially isotropic in the local coordinates. Hence, the crossover to the D~ n⁻² regime with increasing chain length of this monodisperse model melt is not accompanied by the onset of reptation dynamics.
-
ItemDoes reptation describe the dynamics of entangled, finite length polymer systems? A model simulation(Georgia Institute of Technology, 1987-02-01) Kolinski, Andrzej ; Skolnick, Jeffrey ; Yaris, RobertIn order to examine the validity of the reptation model of motion in a dense collection of polymers, dynamic Monte Carlo (MC) simulations of polymer chains composed of n beads confined to a diamond lattice were undertaken as a function of polymer concentration and degree of polymerization n. We demonstrate that over a wide density range these systems exhibit the experimentally required molecular weight dependence of the center-of-mass self-diffusion coefficient D~n−[superscript 2.1] and the terminal relaxation time of the end-to-end vector R~n[superscript 3.4]. Thus, these systems should represent a highly entangled collection of polymers appropriate to look for the existence of reptation. The time dependence of the average single bead mean-square displacement, as well as the dependence of the single bead displacement on position in the chain were examined, along with the time dependence of the center-of-mass displacement. Furthermore, to determine where in fact a well-defined tube exists, the mean-square displacements of a polymer chain down and perpendicular to its primitive path defined at zero time were calculated, and snapshots of the primitive path as a function of time are presented. For an environment where all the chains move, no evidence of a tube, whose existence is central to the validity of the reptation model, was found. However, if a single chain is allowed to move in a partially frozen matrix of chains (where all chains but one are pinned every ne beads, and where between pin points the other chains are free to move), reptation with tube leakage is recovered for the single mobile chain. The dynamics of these chains possesses aspects of Rouse-like motion; however, unlike a Rouse chain, these chains undergo highly cooperative motion that appears to involve a backflow between chains to conserve constant average density. While these simulations cannot preclude the onset of reptation at higher molecular weight, they strongly argue at a minimum for the existence with increasing n of a crossover regime from simple Rouse dynamics in which reptation plays a minor role at best.