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ItemSubcloning of calcium-dependent protein kinase related kinase homologues in arabidopsis thaliana(Georgia Institute of Technology, 1997-12) Lala, Hitesh Nagin
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ItemDNA complexes with adjacent duplex and triplex domains : thermal denaturation and gel mobility shift analysis(Georgia Institute of Technology, 1997-12) Nam, Kang Hoon
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ItemCombinations of natural and anthropogenic stressors affect populations of freshwater rotifers(Georgia Institute of Technology, 1997-12) Cecchine, Gary Anthony, III
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ItemPrediction of protein coding regions in unannotated DNA sequences using an inhomogeneous Markov model of genetic information encoding(Georgia Institute of Technology, 1997-12) McIninch, James David
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ItemNitrogen stable isotope dynamics in the central Baltic Sea: influence of deep-water renewal on the N-cycle(Georgia Institute of Technology, 1997-11-17) Voss, Maren ; Nausch, Günter ; Montoya, Joseph P.The vertical profiles of NO₃-, NH₄+, O₂, and H₂S as well as the isotopic composition of particulate nitrogen and NH4+ were sampled yearly over a 5 yr period in the Gotland Basin to follow biochemical changes in N-cycling resulting from an inflow of saltwater. The water column has a pronounced interface at 80 to 120 m depth which separates warm (13°C) brackish surface waters (salinity 7 psu) and the underlying cold winter water layer from more saline (9 to 11 psu) bottom waters originating from irregularly occurring inflow events of oxygenated, nitrate-rich North Sea water masses. Anoxic conditions usually exist in the deep stagnant waters, where nutrients only occur as ammonia, which reaches concentrations of up to 30 µmol l-1. In spring 1993 large amounts of nitrate- and oxygen-rich water were transported into the deep waters of the Gotland Basin, thus displacing the stagnant deep water body. With the inflow, oxygen and nitrate concentrations rose by 3 ml l-1 and more than 10 µmol l-1 respectively. During the following years the concentrations of oxygen in the near bottom layer decreased again. The isotope signature of the suspended particles in the layer below 120 m reflects these changes: in 1993 the mean stable nitrogen isotope value in the anoxic water was at 1.1o/oo. We assume bacterial incorporation of ammonia to be the mechanism producing isotopically light particles. A fractionation factor calculated for ammonia uptake of 11 ‰ supports this hypothesis. During the following years the particles in the oxygenated water column were around 8o/oo which is characteristic for microbially degraded material. The surface sediment of the central Gotland Sea has a low isotope signal of 3 to 4o/oo. These findings might have consequences for the interpretation of sediment δ15N data where low isotope contents are usually taken as an indicator of high nutrient concentrations in surface waters.
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ItemFunctional Significance of the Sexual Dimorphism in the Cephalic Appendages of Euchaeta Rimana Bradford(Georgia Institute of Technology, 1997-09) Boxshall, Geoffrey A. ; Yen, Jeannette ; Strickler, Rudi J.In Euchaeta rimana the cephalic appendages become profoundly sexually dimorphic at the final molt. The enlarged maxillipeds and robust maxillae, which are related to the predatory nature of this pelagic marine copepod are fully functional on the fifth copepodid (CV) males and adult females. The presumed prey detection sensory apparatus, a paired 4-point setal array on the antennules, is located within the capture volume of the feeding current of the CVs and adult females. SEMs reveal specialized basal articulations of the straight and curved setae of this array, that allow setal rotations that streamline the antennule during escape movements. In the final molt of the CV male to the adult stage, the maxillae are reduced to vestiges and the maxillipeds to half the size of the female's. The loss of functional prey capture appendages is accompanied by the loss of the prominent antennulary setal array, giving support for their postulated function as prey sensors. Instead, the male gains 19 more aesthetascs primarily in the proximal region of the antennules, where fluid velocities of the scanning current are greatest. Detection of pheromones transported within the feeding/scanning current is the hypothesized function of the chemosensory system of the adult male copepod. The parallel changes in the structure of the antennule as well as of the adjacent cephalic appendages suggest that a homeobox-like gene control system could be coordinating these morphological changes.
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ItemSpacing mechanisms within light-induced copepod swarms(Georgia Institute of Technology, 1997-08-28) Leising, Andrew W. ; Yen, JeannetteMany species of copepods form dense aggregations, known as swarms. In the laboratory, we experimentally induced 5 different species of copepod to swarm in response to a point source of light. To map out the (x, y, z, t) positions of swarm members, 2 right-angle views of the 3-dimensional swarm were videotaped. Since images of individual copepods appear indistinguishable on the paired 2-dimensional projections, an algorithm was developed which matched the temporal changes of the vertical (z) positions of all images from the 2-dimensional projections of the 3-dimensional copepod movement to produce (x, y, z, t) positions of each individual. With the temporal/spatial positional data of swarm members, we tested the hypothesis that the fluid disturbance surrounding individual moving copepods, rather than the exoskeleton, maintains minimum separation distance. As the density of the swarm increased, the average nearest-neighbor distance NND decreased, as did the mean minimum NND (MNND). For 3 of the 5 species, the MNND was significantly greater than that predicted from a random distribution, and was greater than twice the antennule or prosome length. While occasional physical contact may occur, resulting in escapes or attempted mating, it appears that most swarm members remain outside the field of self-generated fluid motion in the boundary layers surrounding their neighbors.
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ItemDeterminants of secondary structure of polypeptide chains: Interplay between short range and burial interactions(Georgia Institute of Technology, 1997-07-15) Kolinski, Andrzej ; Skolnick, JeffreyThe effect of tertiary interactions on the observed secondary structure found in the native conformation of globular proteins was examined in the context of a reduced protein model. Short-range interactions are controlled by knowledge based statistical potentials that reflect local conformational regularities seen in a database of three-dimensional protein structures. Long-range interactions are approximated by mean field, single residue based, centrosymmetric hydrophobic burial potentials. Even when pairwise specific long-range interactions are ignored, the inclusion of such burial preferences noticeably modifies the equilibrium chain conformations, and the observed secondary structure is closer to that seen in the folded state. For a test set of 10 proteins (belonging to various structural classes), the accuracy of secondary structure prediction is about 66% and increases by 9% with respect to a related model based on short-range interactions alone [Kolinski et al., J. Chem. Phys. 103, 4312 (1995)]. The increased accuracy is due to the interplay between the short-range conformational propensities and the burial and compactness requirements built into the present model. While the absolute level of accuracy assessed on a per residue basis is comparable to more standard techniques, in contrast to these approaches, the conformation of the chain now has a better defined geometric context. For example, the assumed spherical domain protein model that simulates the segregation of residues between the hydrophobic core and the hydrophilic surface allows for the prediction of surface loops/turns where the polypeptide chain changes its direction. The implications of having such self-consistent secondary structure predictions for the prediction of protein tertiary structure are briefly discussed.
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ItemRibonuclease P RNA: Models of the 15/16 Bulge From Escherichia Coli and the P15 Stem Loop of Bacillus Subtilis(Georgia Institute of Technology, 1997-06) Easterwood, Thomas R. ; Harvey, Stephen C.The Escherichia coli ribonuclease P RNA 15/16 internal bulge loop and the Bacillus subtilis P15 stem loop are important substrate binding sites for the CCA-3' terminus of pre-tRNA. Models of E. coli 15/16 bulge loop and the B. subtilis P15 stem loop have been constructed using MC-SYM, a constraint satisfaction program. The models use covariation analysis data for suggesting initial base pairings, chemical probing, and protection/modification results to determine particular pairing orientations, and mutational experimental analysis data for tRNA-RNase P RNA contacts. The structures from E. coli and B. subtilis, although different _in secondary structure, have similar sequence and function. Using MC-SYM, we are able to illustrate how the 3' end of the pre-tRNA is able to interact with this segment of the catalytic RNase P RNA. In addition, we propose additional hydrogen bonding between A76 in the 3' terminus of the tRNA and the 15/16 region of E. coli and to the loop of B. subtilis.
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ItemComparative toxicity of nine freshwater rotifer species in support of probabilistic risk assessment(Georgia Institute of Technology, 1997-01) McDaniel, Margaret Lida