The human gut is host to a vast consortium of microorganisms, collectively referred to as the microbiota or microflora, which play important roles in health and disease. Current applications focus only on a single type of bacteria, which are not the most dominant numerically, and without detailed knowledge of the specific functions of these bacteria. A good indicator of the function of a bacterial species involves detailed analysis of its enzymes. Bacteroides thetaiotaomicron is one of the predominant bacterial species with a great representation of the carbohydrate processing enzymes, glycoside hydrolases in its proteome. This thesis reports the production and purification of one such enzyme, BT3299, suitable for kinetic and structural studies. The enzyme displayed a broad substrate specificity with a slight preference for 1-->3 and 1-->6 glycosidic linkages and longer chain saccharides. Future work will focus on structural analysis as an aid to the understanding of the enzyme function.

The mammalian intestine contains a dense and diverse community of microorganisms. The resident microbiota makes contributions to host to promote proper immune system development and limit pathogen colonization. In this study, the effects of microbiota disruption with or without TLRs stimulation on intestinal permeability and immunity were examined in C57BL/6 mice receiving antibiotic treatment for 6 days and in antibiotics-treated mice received dead E. coli or S. aureus at day 4. The results showed that antibiotic treatment significantly decreased the total number of bacteria including specific aerobic group Enterobacteriaceae and Enterococcus, and specific anaerobic group Lactococcus/Bifidobacterium in intestinal mucosa and lumen. Although only a slight increase in the intestinal permeability and no change in caspase-3 activity of intestinal mucosa were observed after antibiotic treatment, the bacterial translocation (BT) to mesenteric lymph nodes (MLN) increased significantly. Subsequent experiments showed that antibiotic treatment decreased the mucosal killing activity and the expression of non-defensin family including RegIII£], RegIII£^, CRP-ductin and RELM£] but not the defensin family, and increased the translocation of pathogen K. pneumoniae significantly, suggesting that the increase of BT to MLN after antibiotic treatment is likely due to a reduction in gut immunity rather than an increase of intestinal permeability. Moreover, stimulation of TLR4 reversed the effect of antibiotic treatment, suggesting that the functioning of TLR4 in intestinal epithelium is required to prevent pathogenic invasion and maintain intestinal homeostasis.

Hydrilla (Hydrilla verticillata) is an invasive aquatic plant that grows quickly across shallow freshwater habitats. It is a problem for recreational users of lakes and landowners. Grass carp (Ctenopharynogodon idella) is an effective biological control agent that preferentially consumes and can control the spread of hydrilla. However, grass carp also will consume other vegetation, which influences aquatic communities via direct and indirect interactions that can change food and habitat availability and use by various species. Aquatic plants influence habitat and types of prey used by sunfish (Centrarchidae), which must also avoid their own predators. Prey use among sunfish species depends on density and taxonomic identity of both prey and vegetation. This was a one-year analysis of stomach contents from three common species of invertivorous sunfish: bluegill (Lepomis macrochirus), longear sunfish (Lepomis megalotis), and redear sunfish (Lepomis microlophus). Thirteen sampling stations were randomly selected using ArcGIS software. Percentage of water surface covered by vegetation was recorded at each station. A five-minute electrofishing sample was performed within the littoral zone early morning in late September. The stomach contents of all targeted sunfish (N=489) showed high percentages of diet overlap pre- (0.77-0.92) and post- (0.83-0.88) introduction of grass carp. Multivariate analysis showed total explained variation (15.5%) in sunfish diet composition was (P < 0.05) correlated significantly with sunfish species (6.67%), percent surface vegetation coverage (3.97%), and sampling periods pre- versus post-introduction of grass carp (2.13%). Prey-specific abundance showed that all sunfishes displayed a generalized feeding strategy in both sampling periods. Diets of each sunfish species showed differences in abundance (by volume) and occurrence (among individual fish) of prey items between sampling periods. Levin?s standardized index of diet breadth for all sunfish species decreased from pre- (0.12) to post-introduction (0.05). Results imply that vegetation control by grass carp influenced the diets and feeding strategies of three cohabitating sunfish species. These findings may help fisheries biologists to plan future management actions that influence assemblages of aquatic plants and macroinvertebrates, herbivorous fish, invertivorous prey-fish, and piscivorous game fish, to promote a healthy and balanced ecosystem for Lake Conroe stakeholders.

Explored in this report is the essential interconnectedness of Grand Unified and String Theoretic Phenomenology. In order to extract a modeled connection to low-energy physics from the context of superstring theory, it is presently necessary to input some preferred region of parameter space in which to search. This need may be well filled by a parallel study of Grand Unification, which is by contrast in immediate proximity to a wealth of experimental data. The favored GUT so isolated may then reasonably transfer this phenomenological correlation to a string embedding, receiving back by way of trade a greater sense of primary motivation, and potentially enhanced predictability for parameters taken as input in a particle physics context. The Flipped SU(5) GUT will be our preferred framework in which to operate and first receives an extended study in a non-string derived setting. Of particularly timely interest are predictions for super-particle mass ranges and the interrelated question of proton decay lifetime. Corrections to such a picture under the lift to a string embedding are also considered. Two principal approaches to string model building are next treated in turn: the Heterotic Free Fermionic construction and Intersecting D-branes in Orientifold compactifications. In both contexts, a summary of existing constructions, extensions to known procedures, and original phenomenological contributions are described.

In vitro gut models provide several advantages over in vivo models for the study of the human gut microbiota. However, because communities developed in these models are simplified simulations of the in vivo environment it is necessary to characterize the reproducibility, repeatability and stability of cultured communities. We also need to broadly define the differences between in vitro consortia and the communities from which they are derived. In this study we characterized and validated a twin-vessel (independent, identical) single-stage chemostat model of the human distal gut. Samples were analyzed using a molecular fingerprinting technique (Denaturing Gradient Gel Electrophoresis) to compare and monitor changes in the overall structure of the communities while a phylogenetic microarray (Human Intestinal Tract Chip) was used to obtain phylogenetic information. We found that twin-vessels inoculated with feces developed and maintained diverse communities that reached stable compositions by at most 36 days post-inoculation. Communities were enriched in Bacteroidetes but not Clostridium cluster XIVa, Bacilli or other Firmicutes relative to the fecal inocula. Vessels were very reproducible when inoculated with identical fecal inocula, less similar when inoculated with consecutive fecal donations from the same donor, and maintained donor-specific identities when inoculated with feces from different donors. Norepinephrine exposure (undefined perturbation) did not appear to have a substantial effect on the structure of chemostat communities, while clindamycin treatment (defined perturbation) caused large changes in the structure of chemostat communities. Packed-column biofilm reactors incorporated a simulated mucosal environment into our chemostat system, allowing us to simultaneously culture biologically relevant planktonic and biofilm communities that were complex, reproducible, and distinct. Defined communities were comparable to fecal communities at the phylum/class-level but established stable compositions more rapidly. While it was difficult to assess the persistence of synthetic stool in a healthy fecal chemostat community (+/- antibiotic perturbation), mixing communities from two donors resulted in a mixed community that more closely resembled one donor over the other. Although future experimentation is required, the results presented here show our twin-vessel single-stage chemostat model represents a valid simulation of the human distal gut environment and can support complex, representative microbial communities ideal for experimental manipulation. / Canadian Institutes of Health Research; Ontario Ministry of Agriculture, Food and Rural Affairs; Ontario Ministry of Research and Innovation; Canada Foundation for Innovation; Ontario Ministry of Training, Colleges and Universities

No description available.

Secondary plant metabolites have recently been gaining interest in livestock production systems following the ban of in-feed antibiotics within the European Union. The rise in antimicrobial resistance found in pathogenic and non-pathogenic bacteria has lead to increased interest in the research community regarding the use of phythochemicals as an alternative to antibiotics. The purpose of this research was to evaluate the impact of including phytochemicals in a livestock production system. Specifically, a high tannin-containing forage, sainfoin (Onobrychis viciifolia), was evaluated in vitro for its antimicrobial effect on Escherichia coli. We determined that phytochemicals alone are not as inhibitory as synthetic antibiotics. Thus, the use of combination therapy to deter the development of antimicrobial resistance was evaluated. A myriad of plant compounds were screened for their synergistic interactions with ciprofloxacin. Geraniol, an essential oil, was identified to possess good antimicrobial activity and synergistic interactions with ciprofloxacin. Therefore the effect of long term exposure to both ciprofloxacin and geraniol were examined. Results demonstrated that once an antimicrobial concentration threshold was reached, resistance to ciprofloxacin increased markedly in the presence of both geraniol and ciprofloxacin. Finally, an in vivo trial was conducted in which forty steers were fed sainfoin or alfalfa over a 9-week period to evaluate its ability to reduce E. coli shedding and its impact on gut microbiota in the context of popular theoretical ecology concepts. Results from the in vivo study indicate that sainfoin was able to promote a slight decrease in generic E. coli shedding which could be maintained throughout the trial. Using high-throughput sequencing, the effect of sainfoin on the microbial ecosystem of the ruminant gut was evaluated. Sainfoin induced a significant shift in the microbial community structure of the rumen and to a lesser extent in the hindgut. Using ecology theories, a hypothesis was formulated regarding the mechanisms that mediate the development of tolerance and the fundamental ecological processes controlling microbial population shifts. Understanding how the gut ecosystem functions and predicting its behaviour in the presence of various fluctuating environmental conditions will enable more efficient manipulation of the rumen and promote best management practices in livestock production.

Secondary plant metabolites have recently been gaining interest in livestock production systems following the ban of in-feed antibiotics within the European Union. The rise in antimicrobial resistance found in pathogenic and non-pathogenic bacteria has lead to increased interest in the research community regarding the use of phythochemicals as an alternative to antibiotics. The purpose of this research was to evaluate the impact of including phytochemicals in a livestock production system. Specifically, a high tannin-containing forage, sainfoin (Onobrychis viciifolia), was evaluated in vitro for its antimicrobial effect on Escherichia coli. We determined that phytochemicals alone are not as inhibitory as synthetic antibiotics. Thus, the use of combination therapy to deter the development of antimicrobial resistance was evaluated. A myriad of plant compounds were screened for their synergistic interactions with ciprofloxacin. Geraniol, an essential oil, was identified to possess good antimicrobial activity and synergistic interactions with ciprofloxacin. Therefore the effect of long term exposure to both ciprofloxacin and geraniol were examined. Results demonstrated that once an antimicrobial concentration threshold was reached, resistance to ciprofloxacin increased markedly in the presence of both geraniol and ciprofloxacin. Finally, an in vivo trial was conducted in which forty steers were fed sainfoin or alfalfa over a 9-week period to evaluate its ability to reduce E. coli shedding and its impact on gut microbiota in the context of popular theoretical ecology concepts. Results from the in vivo study indicate that sainfoin was able to promote a slight decrease in generic E. coli shedding which could be maintained throughout the trial. Using high-throughput sequencing, the effect of sainfoin on the microbial ecosystem of the ruminant gut was evaluated. Sainfoin induced a significant shift in the microbial community structure of the rumen and to a lesser extent in the hindgut. Using ecology theories, a hypothesis was formulated regarding the mechanisms that mediate the development of tolerance and the fundamental ecological processes controlling microbial population shifts. Understanding how the gut ecosystem functions and predicting its behaviour in the presence of various fluctuating environmental conditions will enable more efficient manipulation of the rumen and promote best management practices in livestock production.

Orobanche ramosa L. is an annual, parasitic weed present in the western Murray-Mallee region of South Australia. A quarantine zone was established to encompass all known infestations, and has been adjusted over time as new infestations have been discovered. The movement of fodder, machinery, grain and straw, horticultural crops, livestock, and soil is controlled by strict quarantine procedures, to prevent further spread across the landscape. O. ramosa presents a unique situation for weed managers: plants are obligate parasites, relying entirely on broadleaved hosts for their water and nutrition; and seeds are tiny (0.3 mm), produced in large numbers (up to 100 000 seeds per plant), and are long-lived, persisting in the soil seed bank for up to 13 years. The dispersal vectors for O. ramosa in South Australia are the focus of this Master’s thesis. Two dispersal vectors were chosen for investigation: sheep and wind. Sheep were examined as possible vector for seeds, both via the gut (internal transport, or endozoochory) and via adhesion on the external surface of the animal (external transport, or epizoochory). Internal transport via sheep was investigated with a classic gut-passage experiment, which showed a peak in excretion of weed seeds at day 2, reducing to zero seeds excreted at day 8, and a half-life of 2 days. Two phases of external transport on sheep was studied: attachment and retention. Attachment was confirmed by finding seeds on the body wool and feet of sheep that had been kept for 7 days on soil with an O. ramosa seedbank. Seed retention was confirmed by placing seeds onto the body and still finding them in wool samples after 7 days. Wind was the other dispersal vector investigated for O. ramosa. A survey of natural wind dispersal was conducted, which confirmed wind as a vector and allowed trap design to be tested. Then a portable field-based wind tunnel was used to investigate the effects of ground cover (bare ground and cereal stubble) and wind speed (low, medium and high) on wind dispersal of O. ramosa seeds. For the stubble treatments, more seeds were trapped within the tunnel, and on bare ground more seeds were trapped exiting the tunnel. Importantly, the data showed that low wind speeds readily move O. ramosa seeds, and that the seeds are capable of aerodynamic lift in the wind profile. Results are discussed in the context of dispersal biology, quarantine procedures, and future work that would further refine knowledge of likely dispersal vectors for O. ramosa. / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1459246 / Thesis (M.Sc.) -- University of Adelaide, School of Earth and Environmental Sciences, 2009

Universiẗat, Diss., 2005--Hamburg.