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This thesis is about the abilities of two plant extracts to cause aggregation or “clumping” of Staphylococcus aureus. This project is in response to rising levels of antibiotic-resistant bacteria, and a lack of methods to control the dispersal of bacteria of agricultural origin. As the implementation of antibiotics in the agricultural sector has increased since the discovery of antibiotics, concerns regarding human health have arisen. The use of antibiotics acts as a selection pressure against bacteria that are susceptible to the antibiotic’s effects. This allows for those bacteria that possess antibiotic resistance to reproduce, creating strains of mainly antibiotic-resistant bacteria. The purpose of this thesis is to investigate two clump-inducing plant extracts that are a potential tool to limit the dispersal of bacteria in solution (ex. Bacteria in agricultural wastewater). By promoting clumping in the bacteria, it is thought that the bacteria’s dispersal will be limited, decreasing instances of infection, thereby indirectly reducing the need for antibiotic use. The two plant extracts studied here were selected from a library of bacterial clump-inducing plant extracts. They come from different botanical families and induce clump formation in S. aureus resulting in differing clump phenotypes. In addition to clump formation, both plant extracts cause a significant reduction in the growth of S. aureus (F (3, 72) = 4.022E+17, p < 0.001), (F (3, 58) = 185, p < 0.001). It is found that clumping molecules act in an adhesive manner and that the bacteria do not play an active role in clump formation. With this finding the first steps of affinity purification of clumping molecules were carried out for further identification of their chemical identities. This thesis outlines a procedure to study, compare and purify other clump-inducing plant extracts, many of which have not been investigated.

We study the connections among three types of objects: Residual Allocation Models (RAMs), a generalized class of stick-breaking processes which include Dirichlet processes, and the occupation laws of certain discrete space time-inhomogeneous Markov chains. These connections are established through a new clumping procedure on RAMs according to a clumping sequence. We introduce and analyze two methods of its application with respect to homogeneous Markov chains. Clumping according to the rst method results in a class of stick-breaking measures we later identify as the limit of the empirical occupation measures for particular time-inhomogeneous Markov chains. Clumping according to the second method leads to a general study of self-similarity as a characterization of random probability measures, which we apply in context. We further discuss the occupation law of an inhomogeneous Markov chain related to simulated annealing and its connections to stick-breaking measures. By introducing a reverse-chronological clumping procedure, we dene and study the local occupations up to time n of the Markov chain. As n gets large, these local occupations converge jointly to the clumped RAM structure resulting from the rst method above. We then explore additional properties of the generalized stick-breaking measure uncovered by the connection to the occupation law, and consider potential applications of results.

We study the connections among three types of objects: Residual Allocation Models (RAMs), a generalized class of stick-breaking processes which include Dirichlet processes, and the occupation laws of certain discrete space time-inhomogeneous Markov chains. These connections are established through a new clumping procedure on RAMs according to a clumping sequence. We introduce and analyze two methods of its application with respect to homogeneous Markov chains. Clumping according to the rst method results in a class of stick-breaking measures we later identify as the limit of the empirical occupation measures for particular time-inhomogeneous Markov chains. Clumping according to the second method leads to a general study of self-similarity as a characterization of random probability measures, which we apply in context. We further discuss the occupation law of an inhomogeneous Markov chain related to simulated annealing and its connections to stick-breaking measures. By introducing a reverse-chronological clumping procedure, we dene and study the local occupations up to time n of the Markov chain. As n gets large, these local occupations converge jointly to the clumped RAM structure resulting from the rst method above. We then explore additional properties of the generalized stick-breaking measure uncovered by the connection to the occupation law, and consider potential applications of results.

The angular profiles of canopy gap fraction curves are influenced by canopy structure, and are commonly expected to vary with stand- and crown-level variables such as tree pattern, crown shape and leaf orientation. In this study, measurements of canopy structure, gap fractions and effective LA! in 986 plots of Scots pine, Norway spruce and Silver birch stands in Finland were used to assess how similar the angular canopy gap fraction profiles are for common boreal tree species. The profiles were characterized with help of the shape function psi(theta), defined as the normalized value of the canopy light extinction coefficient at zenith angle (theta). Variation in psi(theta) would be induced not only by a non-spherical leaf orientation, but also by differences in the directional clumping indices, such as could result from species-specific differences in crown shape. Our results showed that there is wide variation in the shape of psi in the individual plots of the three different species. The species-specific mean curves psi(theta), however, showed relatively small variation with theta, except for a sudden drop at large zenith angles, and the shape of the curves was similar for the different tree species. Results indicate that differences in crown shape of the study species do not significantly affect the angular profiles of canopy gap fraction. (C) 2015 The Authors. Published by Elsevier B.V.

Brucella spp. are Gram-negative, facultative intracellular bacteria that cause brucellosis in mammals. Brucella strains containing the O-polysaccharide in their cell wall structure exhibit a smooth phenotype whereas the strains devoid of the polysaccharide show rough phenotype. B. abortus strain RB51 is a stable rough attenuated mutant which is used as a licensed live vaccine for bovine brucellosis. Previous studies have shown that the wboA gene, which encodes a glycosyltransferase required for the synthesis of O-polysaccharide, is disrupted in B. abortus RB51 by an 1711 element. Although complementation of strain RB51 with a functional wboA gene results in O-polysaccharide synthesis in the cytoplasm, it does not result in smooth phenotype. The aim of this study was to determine if overexpression of Brucella WbkA or WbkE, two additional putative glycosyltransferases essential for O-polysaccharide synthesis, in strain RB51 would result in the O-polysaccharide synthesis and smooth phenotype. Our results demonstrate that overexpression of wbkA or wbkE gene in RB51 does not result in O-polysaccharide expression as shown by Western blotting with specific antibodies. However, wbkA, but not wbkE, overexpression leads to the development of a clumping phenotype and the production of exopolysaccharide(s) containing mannose, galactose, N-acetylglucosamine, and N-acetylgalactosamine. Moreover, we found that the clumping recombinant strain displays increased adhesion to polystyrene plates. The recombinant strain was similar to strain RB51 in its attenuation characteristic and in its ability to induce protective immunity against virulent B. abortus challenge in mice.

Brucella spp. are Gram-negative, facultative intracellular bacteria that cause brucellosis in mammals. Brucella strains containing the O-polysaccharide in their cell wall structure exhibit a smooth phenotype whereas the strains devoid of the polysaccharide show rough phenotype. B. abortus strain RB51 is a stable rough attenuated mutant which is used as a licensed live vaccine for bovine brucellosis. Previous studies have shown that the wboA gene, which encodes a glycosyltransferase required for the synthesis of O-polysaccharide, is disrupted in B. abortus RB51 by an 1711 element. Although complementation of strain RB51 with a functional wboA gene results in O-polysaccharide synthesis in the cytoplasm, it does not result in smooth phenotype. The aim of this study was to determine if overexpression of Brucella WbkA or WbkE, two additional putative glycosyltransferases essential for O-polysaccharide synthesis, in strain RB51 would result in the O-polysaccharide synthesis and smooth phenotype. Our results demonstrate that overexpression of wbkA or wbkE gene in RB51 does not result in O-polysaccharide expression as shown by Western blotting with specific antibodies. However, wbkA, but not wbkE, overexpression leads to the development of a clumping phenotype and the production of exopolysaccharide(s) containing mannose, galactose, N-acetylglucosamine, and N-acetylgalactosamine. Moreover, we found that the clumping recombinant strain displays increased adhesion to polystyrene plates. The recombinant strain was similar to strain RB51 in its attenuation characteristic and in its ability to induce protective immunity against virulent B. abortus challenge in mice.

The spatial pattern was characterized in five experimental plots of 0.5 ha established in Scots pine stands located in the Central Mountain Range of Spain with different ecological conditions and in which different silvicultural practises are employed. A new method is proposed to asses the spatial pattern from hemispherical photographs, based on the variance between the gap fractions in sky sectors, which was calculated as a function of the angular distance. The results were compared with the spatial pattern analysis based on the second moment measure, and with the analysis of the structure of the tree number semivariogram. The three methods give a very similar scale of the pattern for most of the plots. The mature plot with more intensive silviculture showed a regular pattern at scales below 6 m. The mature plot in which the silviculture was less intensive showed a cluster pattern at scales around 10 m, and clustering at similar scales was detected during regeneration. Cluster patterns at scales around 5 m were found at the upper limit of the altitudinal range of Scots pine as well as at the lower limit, where Pyrenean oak stands merge with the pinewood. The method proposed allows the scale of the pattern of the canopy to be determined from hemispherical photographs, and can be easily implemented in forest inventories. © 2007 Elsevier B.V. All rights reserved.

A typical feature of the long time behavior of continuous super-Brownian motion in a stable catalytic medium is the development of large mass clumps (or clusters) at spatially rare sites. We describe this phenomenon by means of a functional limit theorem under renormalization. The limiting process is a Poisson point field of mass clumps with no spatial motion component and with infinite variance. The mass of each cluster evolves independently according to a non-Markovian continuous process trapped at mass zero, which we describe explicitly by means of a Brownian snake construction in a random medium. We also determine the survival probability and asymptotic size of the clumps.

VLA observations at 20 and 90 cm of five distant Galactic H II regions in an area including the Sharpless S53 complex have been used to measure their effective sizes and optically thick continuum flux densities. These data have been combined with shorter wavelength, optically thin flux density measurements and electron temperature estimates to determine accurate emission measures where previous results gave only lower limits. Our analysis indicates that existing lower limits to the emission measures often underestimate the true values by more than an order of magnitude. Filling factors for the ionized gas in these H II regions have also been determined and values ranging from 0.03 to 0.50 indicate significant clumping. If these clumps are embedded in a lower density but more widely distributed ionized component, even our much higher emission measures are still lower limits to the true values for the clumps., Published in The Astrophysical Journal, v338 p152-161, 1 Mar 1989. Prepared in collaboration with University of Maryland, and with Max-Planck-Institut fuer Radio Astronomie.

For critical spatially homogeneous branching processes of finite intensity the following dichotomy is well-known: convergence to non-trivial steady states, or local extinction. In the latter case the underlying phenomenon is the growth of large clumps at spatially rare sites. For this situation a precise description is given in terms of a scaling limit theorem provided that the dimension of the ambient space is small enough. In fact, a space-time-mass scaling limit exists and is a critical measure-valued branching process without a motion component. The clumps are located at Poissonian points and their sizes evolve according to critical continuous-state Galton-Watson processes. The spatial irregularities (intermittency) will grow in the sense that clumps will disappear as time increases in spite of the fact that the overall density remains constant in time.

Sediment samples were taken from Gulf of Mexico cores. From these samples smaller ones were cut, freeze-dried and impregnated with Maraglas, an epoxy resin. Ultrathin sections of the impregnated samples were cut, and viewed in an electron microscope. Micrographs of the ultrathin sections revealed that the microstructures of most of the samples had a loose, open, random arrangement of particles. Differences in appearance of some of the microstructures are attributed to grain size variation, desiccation, remolding, and shearing of the sediment. Associated with this last factor is the formation of oriented domain structures. Variations among the samples in depth of burial, rate of deposition, and, particularly, clay mineralogy were generally small and resulted in no obvious differences in their microstructures. Cohesion, water content, and consolidation characteristics of samples were found to be generally indicative of the type of microstructure observed. Laboratory consolidation and desiccation of samples caused a 'collapse' of the microstructure and preferred, as well as non-preferred, orientation among the particles. Remolding of a sediment resulted in clumping of the particles, parallelism among the particles, and large voids. No evidence was observed in the micrographs which would substantiate the existence of a precipitated chemical cement. (Author)