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School of Biological Sciences

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College of Sciences

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Center for the Study of Systems Biology

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Publication Search Results

Now showing 1 - 10 of 12

The catabolite activator protein stabilizes its binding site in the E. coli lactose promoter

(Georgia Institute of Technology, 1985-10-25) DeGrazia, Henry ; Abhiraman, Saraswathy ; Wartell, Roger M.

The effect of catabolite activator protein, CAP, on the thermal stability of DNA was examined. Site specific binding was studied with a 62 bp DNA restriction fragment containing the primary CAP site of the E. coli lactose (lac) promoter. A 144 bp DNA containing the lac promoter region and a 234 bp DNA from the pBR322 plasmid provided other DNA sites. Thermal denaturation of protein-DNA complexes was carried out in a low ionic strength solvent with 40% dimethyl sulfoxide, DMSO. In this solvent free DNA denatured below the denaturation temperature of CAP. The temperature stability of CAP for site specific binding was monitored using an acrylamide gel electrophoresis assay. Results show that both specific and non-specific CAP binding stabilize duplex DNA. Site specific binding to the 62 bp DNA produced a 13.3 degrees C increase in the transition under conditions where non-specific binding stabilized this DNA by 2-3 degrees C.
Functional morphology of intertidal seaweeds: adaptive significance of aggregate vs. solitary forms

(Georgia Institute of Technology, 1984-08-15) Taylor, Phillip R. ; Hay, Mark E.

Many intertidal seaweeds show a tremendous gradient of morphological form ranging from spatially separated thalli, to thalli that are aggregated into dense turfs. Aggregation of seaweeds into turfs decreases productivity per g organic weight due to crowding of thalli but increases resistance to desiccation. The intertidal distribution of the turf growth form is correlated with the intensity of desiccation stress. Also turfs transplanted into tide pools developed the non-turf morphology, while non-turfs transplanted to emergent substrate either developed the turf form or died. The turf growth form is energetically expensive; apparent productivity of turfs was 23 to 48 % less than that of individuals. Increasing light and nutrients available to turfs by separating the thalli increased apparent productivity by 36 to 113 %. We tested the hypothesis that these turfs minimize energetic costs of this aggregated growth form through the spatial partitioning of photosynthetic and respirative activity. The lower portions of turfs showed less apparent photosynthesis than the upper portions (reductions of 37 to 85 %); however, this spatial partitioning was also found in the individual forms (37 to 63 % reductions) of these relatively simple seaweeds. Spatial differentiation of respiration was similar in turfs and nonturfs. The seaweeds, examined are able to alter the extent of thalli compaction in accordance with varying levels of environmental stress. This phenotypic plasticity allows seaweeds to adopt morphological features that maximize fitness in a wide variety of habitats without being developmentally committed.
Coral Reef Ecology: Have We Been Putting All of Our Herbivores in One Basket?

(Georgia Institute of Technology, 1984-05-01) Hay, Mark E.
Patterns of fish and urchin grazing on Caribbean coral reefs: are previous results typical?

(Georgia Institute of Technology, 1984-04) Hay, Mark E.

Strips of the seagrass Thalassia testudinum were used in a field bioassay to assess herbivory on 11 coral reefs scattered throughout the Caribbean. Patterns of herbivory on overfished reefs in Haiti and the United States Virgin Islands were compared to patterns on seven less fished reefs (United States Virgin Islands, Panama, Honduras, Belize, and the Bahamas). On the overfished reefs, the rate of Thalassia removal increased significantly with depth, urchin densities were high, and urchin grazing was equal to, or greater than, fish grazing in shallow (<10 m deep) habitats. On reefs subject to little fishing pressure, the rate of Thalassia removal decreased with depth, urchin densities were low, and herbivorous fishes were responsible for almost all Thalassia removal. Previous studies assessing the importance of urchin grazing in the Caribbean have been conducted on overfished reefs where urchin densities were unusually high and the density of grazing fish unusually low. It is doubtful that the intensity of urchin—algal and urchin—coral interactions observed on these heavily fished reefs occurs on reefs unaffected by humans.
Is glue production by seeds of Salvia columbariae a deterrent to desert granivores?

(Georgia Institute of Technology, 1983-08) Fuller, Patricia J. ; Hay, Mark E.

With a few notable exceptions (Borchert and Jain 1978, Inouye et at. 1980, O'Dowd and Hay 1980, Hay and Fuller 1981), most ecological studies on seed-granivore interactions in arid communities have concentrated on the adaptations and ecology of the granivores and not on characteristics of the seeds that may deter granivory. Since a large portion of the annual seed crop of many desert ephemerals is lost to seed predators (Chew and Chew 1970, French et al. 1974, Nelson and Chew 1977, Brown et al. 1979), characteristics that significantly reduce losses to granivores should be strongly selected. In this paper we show that under natural conditions seeds of the desert annual Salvia columhariae produce a glue-like substance when wetted that strongly binds sand grains to the seeds, and that seeds thus covered by sand suffer significantly less loss to desert granivores.
Effects of topological solitons on autocorrelation functions for chains of coupled torsional oscillators

(Georgia Institute of Technology, 1983-06-01) Perchak, Dennis ; Yaris, Robert ; Skolnick, Jeffrey

Brownian dynamics computer simulations were performed on chains of coupled torsional oscillators. The purpose was to observe the changes in autocorrelation functions, related to typical experimental measurements, caused by the introduction of topological solitons or kinks into the system. We considered three model systems: a chain of coupled torsional oscillators, a chain of coupled torsional oscillators with additional onefold rotational potentials acting on each oscillator, and a chain of coupled torsional oscillators with additional threefold rotational potentials. These models are of interest because of their application to torsional motions in polymeric systems, and, in particular, the system with onefold rotational potentials has been studied extensively as the sine–Gordon chain. We present simulation results for three autocorrelation functions of these three systems both with and without topological solitons.
Mechanism and rates of conformational transitions in heterogeneous polymers

(Georgia Institute of Technology, 1982-12-01) Helfand, Eugene ; Skolnick, Jeffrey

A general expression is presented for the rate of a trans to gauche conformational transition of a bond in a polymer backbone. The polymer is composed of nonidentical atoms, i.e., centers of differing friction constants and masses. The rate is obtained from a multidimensional extension of Kramers' steady state solution to the Fokker–Planck equation for flux over a reaction barrier of a system in a frictional medium. Langer's formulation is used. Results are appropriate for all but extremely small friction, with simplification occurring in the high friction limit. One also determines the reaction coordinate, an examination of which gives insight into the kinetic mechanism. Explicit results are obtained for six and 32 vertex chains, and the influence of chain conformation and relative friction constants are discussed.
The kinetics of conformational transitions: Effect of variation of bond angle bending and bond stretching force constants

(Georgia Institute of Technology, 1981-11-01) Helfand, Eugene ; Wasserman, Z. R. ; Weber, Thomas A. ; Skolnick, Jeffrey ; Runnels, John H.

Conformational transitions in chain molecules have been shown to proceed via a reaction coordinate which is a localized mode involving rotations about bonds, and also bond angle bending and bond stretching. By investigating the kinetics as a function of the force constants (flexibility) for bond angle bending and bond stretching, the role of the localized mode is probed. The study reported here consists of computer simulations of the Brownian dynamics of chain motions, and of kinetic calculations of rates and reaction modes. The theory accurately predicts the relative effects of force constant variations on transition rates determined by simulation.
Herbivory, algal distribution, and the maintenance of between-habitat diversity on a tropical fringing reef

(Georgia Institute of Technology, 1981-10) Hay, Mark E.

The bases of coral reefs in the Caribbean often abut sandy plains covered by sea grasses (Randall 1965; Ogden et al. 1973b) or algae (Earle 1972; Dahl 1973). Interactions occurring at the border of reefs and sea grass beds have been studied on several occasions (Randall 1965; Ogden et al. 1973b; Ogden 1976; Parrish and Zimmerman 1977; Ogden and Lobel 1978), but little is known about those which occur between reefs and sandy plains dominated by algae. Unlike sea grasses, which root into the sand, many of the algal species that occur on sand plains require hard substrates (Dahl 1973) such as shells and coral fragments. Suitable attachment sites are uncommon on the sand plain at Galeta Point, Panama, and many are periodically buried or turned over during heavy seas. Paradoxically algal species that predominate on the sand plain tend to be rare or absent from the shallower reef slope where stable, hard substrate is abundant. The maintenance of such distinct distributional boundaries is often attributed to differential competitive abilities (Connell 1961; Holmes 1961) or to restrictive specialization to particular physical regimes (Doty 1946; Terborgh 1971). These factors have been hypothesized to be especially important (Dobzhansky 1950; Janzen 1967; Ashton 1969; Diamond 1975) in diverse tropical communities where specialization to narrow niches is thought to promote resource partitioning and allow increased coexistence. While such explanations are often consistent with observed patterns, they are seldom tested using controlled field experiments. Without such field manipulations it is impossible to adequately assess the relative importance of competition, predation, and physical stress in determining the distribution and abundance of species or the intensity of interactions that occur between them. In this paper I examine experimentally the factors maintaining these separate algal assemblages and contend that the sand-plain species (algae that are almost never found on the reef) would competitively exclude other species from the reef slope if they were not selectively removed by reef-associated grazers. Competition and physiological specialization appear to have no effect on excluding sandplain species from the reef slope. In the remainder of the paper I test the following hypotheses. (1) Low light and scarcity of attachment sites severely limit the growth of algae on the sand plain. (2) Sand-plain algae are not physiologically restricted to deep waters; they are most fit in the physical regime typical of shallower reef-slope habitats. (3) Reef-associated grazers are responsible for excluding sand-plain species from the reef slope. (4) In the absence of herbivores, sand-plain species competitively dominate reef-slope species. (5) Because of differential competitive ability, sand-plain genera are better adapted for temperate areas than are reef-slope genera.
The functional morphology of turf-forming seaweeds: persistence in stressful marine habitats

(Georgia Institute of Technology, 1981-06) Hay, Mark E.

Many seaweeds that occur in physically stressful habitats or habitats subject to moderate herbivory grow as colonial turfs rather than as spatially separated individuals. The turf growth form is energetically expensive (the net production per gram ash free dry mass of turfs being 33—61% lower than that of individuals), but turfs suffer less physiological damage during desiccating low tides and lose less biomass to herbivores. The upper portions of turf—forming species show significantly greater rates of apparent photosynthesis and dark respiration than do the lower portions. This spatial partitioning of photosynthetic activity decreases the energetic cost of the turf arrangement and may allow basal portions to function as persistent resting stages during periods of adverse conditions when uprights cannot be maintained. Turf—forming species are specialized for areas that are subject to moderate grazing pressure and physical stresses. They are dependent upon these factors to prevent their competitive exclusion by more productive, but less resistant, seaweeds. Damage to apical portions causes increased branching that results in a more tightly compacted turf. Algae that regenerate in this way can adjust their growth form in accordance with varying levels of disturbance encountered in different habitats and thus incur the minimal cost consistent with survival in that area. For seaweeds occurring in stressful habitats, selection has favored characteristics that increase persistence in space and time even though these involve considerable losses in competitive ability and productivity.