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de, Klerk Nele. "Host-bacteria interactions : Host cell responses and bacterial pathogenesis". Doctoral thesis, Stockholms universitet, Institutionen för molekylär biovetenskap, Wenner-Grens institut, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-126425.
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Helicobacter pylori colonizes the human stomach, where it causes gastritis that may develop into peptic ulcer disease or cancer when left untreated. Neisseria gonorrhoeae colonizes the urogenital tract and causes the sexually transmitted disease gonorrhea. In contrast, Lactobacillus species are part of the human microbiota, which is the resident microbial community, and are considered to be beneficial for health. The first host cell types that bacteria encounter when they enter the body are epithelial cells, which form the border between the inside and the outside, and macrophages, which are immune cells that engulf unwanted material. The focus of this thesis has been the interaction between the host and bacteria, aiming to increase our knowledge of the molecular mechanisms that underlie the host responses and their effects on bacterial pathogenicity. Understanding the interactions between bacteria and the host will hopefully enable the development of new strategies for the treatment of infectious disease. In paper I, we investigated the effect of N. gonorrhoeae on the growth factor amphiregulin in cervical epithelial cells and found that the processing and release of amphiregulin changes upon infection. In paper II, we examined the expression of the transcription factor early growth response-1 (EGR1) in epithelial cells during bacterial colonization. We demonstrated that EGR1 is rapidly upregulated by many different bacteria. This upregulation is independent of the pathogenicity, Gram-staining type and level of adherence of the bacteria, but generally requires viable bacteria and contact with the host cell. The induction of EGR1 is mediated primarily by signaling through EGFR, ERK1/2 and β1-integrins. In paper III, we described the interactions of the uncharacterized protein JHP0290, which is secreted by H. pylori, with host cells. JHP0290 is able to bind to several cell types and induces apoptosis and TNF release in macrophages. For both of these responses, signaling through Src family kinases and ERK is essential. Apoptosis is partially mediated by TNF release. Finally, in paper IV, we showed that certain Lactobacillus strains can reduce the colonization of H. pylori on gastric epithelial cells. Lactobacilli decrease the gene expression of SabA and thereby inhibit the binding mediated by this adhesin.At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 4: Manuscript.
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Silva, Roberta Mafra Freitas da. "Reguladores do metabolismo bacteriano em reservatórios tropicais". Universidade Federal de São Carlos, 2017. https://repositorio.ufscar.br/handle/ufscar/9041.
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Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)
Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
Reservoirs located in tropical regions are main carbon (C) sources to the atmosphere, and bacterial metabolism is a key process that regulates those emissions. However, studies on the environmental drivers of bacterial metabolism in tropical reservoirs are scarce. By measuring metabolic rates and the limnological parameters in four cascading reservoirs that form a trophic state gradient, we determined the environmental drivers of bacterial metabolism in a tropical region, and compared them with those found in the literature (mainly from temperate regions). Our multiple regression models selected variables related to the trophic state as the main drivers of bacterial production (BP) and bacterial growth efficiency (BGE). On the other hand, bacterial respiration (BR), and consequently bacterial carbon demand (BCD), were weakly and negatively correlated to dissolved organic carbon (DOC), contrasting with the literature data. BR was always high, especially in less productive reservoirs where planktonic communities were limited by phosphorus. Nutrient limitation, high temperatures and high incident light intensity increased the environmental hostility, and cells must invest more energy in maintenance mechanisms, which directs the metabolism towards BR. This was observed in the reservoirs studied, especially in the more oligotrophic environments (Nova Avanhandava and Três Irmãos) where BR was higher and ECB lower. Our results indicate that the regulatory mechanisms of bacterial metabolism may vary according to latitude.
Reservatórios de regiões tropicais são fontes de carbono (C) para a atmosfera e o metabolismo bacteriano é um processo fundamental na regulação dessas emissões. No entanto, estudos que elucidem os fatores ambientais que determinam o metabolismo bacteriano em reservatórios tropicais são ainda escassos. Neste estudo foram medidas taxas metabólicas e parâmetros limnológicos em quatro reservatórios em cascata que formam um gradiente de estado trófico, com o intuito de determinar os reguladores do metabolismo bacteriano em uma região tropical e compará-los com dados obtidos a partir da literatura disponível (principalmente de regiões temperadas). Nossos modelos de regressão múltipla selecionaram variáveis relacionadas ao estado trófico como os principais reguladores da produção bacteriana (PB) e da eficiência de crescimento bacteriano (ECB). Foi encontrada uma relação fraca e negativa entre a respiração bacteriana (RB) e o carbono orgânico dissolvido (COD), diferente dos dados da literatura. As taxas de RB foram sempre elevadas, especialmente em reservatórios menos produtivos, nos quais as comunidades planctônicas estavam limitadas por fósforo. A escassez de nutrientes, as elevadas temperaturas e a alta intensidade de luz incidente aumentam o grau de hostilidade, e as células devem investir mais energia em mecanismos de reparação, o que direciona o metabolismo para a RB. Isso foi observado nos reservatórios estudados, especialmente, nos ambientes mais oligotróficos (Nova Avanhandava e Três Irmãos) nos quais a RB foi mais elevada e a ECB mais baixa. Nossos resultados indicam que os mecanismos reguladores do metabolismo bacteriano podem variar de acordo com a latitude.
FAPESP: 14/14139-3
FAPESP: 11/50054-4
3
Lawlor, Kirsten. "Distribution of bacteria and bacterial plasmids in lake water sediments". Thesis, University of Liverpool, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.240596.
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Vetter, Yves-Alain. "Bacterial foraging with cell-free enzymes /". Thesis, Connect to this title online; UW restricted, 1998. http://hdl.handle.net/1773/11033.
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Nilsson, Annika. "Bacterial adaptation to novel selection pressures /". Stockholm, 2005. http://diss.kib.ki.se/2005/91-7140-192-X/.
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Kim, Min Jun. "Bacterial flows : mixing and pumping in microfluidic systems using flagellated bacteria /". View online version; access limited to Brown University users, 2005. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&res_dat=xri:pqdiss&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&rft_dat=xri:pqdiss:3174627.
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Wood, Ryan. "Bacteria in Blood: Optimized Recovery of Bacterial DNA for Rapid Identification". BYU ScholarsArchive, 2020. https://scholarsarchive.byu.edu/etd/8147.
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Blood stream infections are challenging infections to rapidly diagnose. The current clinical diagnostic methods for blood stream infections require culturing the blood sample prior to identifying the bacteria and any resistance the bacteria may contain. Removing the culturing step from the bacterial identification process of a blood stream infection provides a significant reduction in the processing time. However, eliminating the culturing step shifts the difficulty from processing time to concentration, since clinical concentration levels can be as low as 10 CFU/mL in blood. This dissertation developed and evaluated many aspects of the process required to identify bacteria from a blood stream infection without culturing the bacteria. Two new methods of separating the bacteria from the blood cells were developed: inducing clotting using a centrifugal-sedimentation on a hollow disk, and filtering whole blood. Inducing clotting achieved 69\% bacterial recovery from 7 mLs of whole blood in 117 s. Filtering whole blood achieved 100\% bacterial removal from 5 mLs of whole blood in $\approx 90$ s, but the bacteria were difficult to remove from the filter. Bacterial removal from the filter after blood filtration was also investigated. At a very low bacterial concentration of 200 CFU/mL, a blood lysis solution of 3\% Tween 80 followed by a 3\% Pluronic F108 backflush solution achieved 60\% removal of the bacteria from the filter. In addition to developing two new methods, a previously developed technique using centrifugal-sedimentation on a hollow disk underwent a stability analysis in order to decrease the occurrence of mixing. This analysis yielded the development of the analytical solution to the Navier-Stokes equations for a two-fluid flow with a moving wall boundary and a free surface. The analysis also experimentally identified a stability boundary that was found to be in good agreement with the Kelvin-Helmholtz instability model. After exploring the methods to recover bacteria from blood, experiments were performed to identify a bacterial lysing solution that could lyse \textit{E. coli}, \textit{E. cloacae} and \textit{K. pneumoniae} bacteria. The best bacterial lysing solution consisted of incubating the bacteria with 1 mg/mL lysozyme for 10 min followed by the addition of 6 M GHCl and 1\% SDS. This solution obtained a 46\% DNA recovery. The DNA were then fragmented by ultrasound to reduce the segment length for DNA labelling. In addition to lysing and fragmenting the DNA, a microfluidic device was prototyped and tested for incorporating the lysing, capturing, releasing, and fragmenting of the DNA all on a single device. Whole experiments were performed which extracted the bacteria from the blood, removed and collected the DNA from the bacteria, and fragmented the DNA. The best overall recovery from an experiment performing the whole process was 26.8\%. The 26.8\% recovery was achieved with a 68\% recovery of the bacteria from spinning and a 54.1\% removal of bacteria from off of the filter and a 72.9\% recovery of the DNA from the bacteria.
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Adebayo, Olajumoke O. "Evaluation of bacterial polymers as protective agents for sensitive probiotic bacteria". Thesis, University of Wolverhampton, 2018. http://hdl.handle.net/2436/621096.
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Probiotics are live microorganisms which when administered in adequate amounts confer one or more health benefits on the host. Different processing conditions, the acidic condition of the stomach and exposure to hydrolytic enzymes affect the viability and efficacy of probiotic organisms. This study investigated the protective effects of two biopolymers poly-gamma-glutamic acid (γ-PGA) and bacterial cellulose (BC) on probiotics during freeze drying and during exposure to simulated intestinal juices and bile salts. The antibacterial property of Bifidobacterium strains was also investigated against four pathogenic bacteria. γ-PGA, a naturally occurring biopolymer was produced by two bacteria (Bacillus subtilis ATCC 15245 and B. licheniformis ATCC 9945a) in GS and E media, γ-PGA yields of about 14.11g/l were achieved in shake flasks and molecular weight of up to 1620 k Da was recorded, γ-PGA production was scaled up in a fermenter with B. subtilis using GS medium. BC, an edible biopolymer was produced by Gluconacetobacter xylinus ATCC 23770 in HS medium and a modified HS (MHS) medium. A yield of about 1.37g/l was recorded and BC production with MHS medium was used for probiotic application. B. longum NCIMB 8809 B. breve NCIMB 8807 and B. animalis NCIMB 702716 showed the best antimicrobial properties against the investigated pathogens. Survival of Bifidobacterium strains was improved when protected with powdered BC (PBC) although γ-PGA offered better protection than PBC. Viability of B. longum NCIMB 8809, B. breve NCIMB 8807 and B. animalis NCIMB 702716 in simulated gastric juice (SGJ) and simulated intestinal juice with bile salts was improved when protected with 5% γ-PGA and 5% γ-PGA+PBC with a reduction of < 1 Log CFU/ml while a reduction of ≤2 Log CFU/ml was recorded in PBC protected cells. Protecting Bifidobacterium strains with γ-PGA, PBC or a novel γ-PGA + PBC combination is a promising method to deliver probiotic bacteria to the target site in order to confer their health benefits on the host.
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Bergström, Niklas. "Structural studies of bacterial carbohydrate antigens with focus on oral commensal bacteria /". Stockholm : Karolinska institutets bibl, 2002. http://diss.kib.ki.se/2002/91-7349-236-1.
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Ghalsasi, Vihang Vivek [Verfasser], i Victor [Akademischer Betreuer] Sourjik. "Engineering bacteria to disperse bacterial biofilms / Vihang Vivek Ghalsasi ; Betreuer: Victor Sourjik". Heidelberg : Universitätsbibliothek Heidelberg, 2015. http://d-nb.info/1180608275/34.
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Deveci, Haci. "Bacterial leaching of complex zinc/lead sulphides using mesophilic and thermophilic bacteria". Thesis, University of Exeter, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.341175.
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Ghalsasi, Vihang Vivek Verfasser], i Victor [Akademischer Betreuer] [Sourjik. "Engineering bacteria to disperse bacterial biofilms / Vihang Vivek Ghalsasi ; Betreuer: Victor Sourjik". Heidelberg : Universitätsbibliothek Heidelberg, 2015. http://d-nb.info/1180608275/34.
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Château, Maarten de. "Functional, structural and evolutionary studies on a family of bacterial surface proteins". Lund : Dept. of Cell and Molecular Biology, Lund University, 1996. http://catalog.hathitrust.org/api/volumes/oclc/38947242.html.
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Reeves, Adam J. "Signaling and interaction of the Bacillus subtilis physical stress pathway regulators of sigma B : a dissertation /". San Antonio : UTHSC, 2007. http://proquest.umi.com/pqdweb?did=1390290691&sid=1&Fmt=2&clientId=70986&RQT=309&VName=PQD.
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Kalaskey, Lawrence J. "Bacterial adherence to orthodontic brackets an in vitro study /". Morgantown, W. Va. : [West Virginia University Libraries], 1999. http://etd.wvu.edu/templates/showETD.cfm?recnum=541.
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Thesis (M.S.)--West Virginia University, 1999.Title from document title page. Document formatted into pages; contains x, 118 p. : ill. Vita. Includes abstract. Includes bibliographical references (p. 65-72).
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Palm, Oskar. "Bacterial growth models". Thesis, KTH, Teoretisk fysik, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-44034.
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In this thesis the growth patterns of certain bacterial colonies are studied through numerical simulations of a continuous model, describing the growth of the colony. The objective was to construct a mathematical model capable of recreating observed growth patterns and thus try to gain some insight into the dynamics of bacterial growth. The model constructed in this thesis consists of a set of reaction-diffusion equations describing the evolution of the bacterial colony viewed as a continuous body rather than many individual bacteria. This approach was partially successful, in the sense that similar patterns to those observed in experiments were indeed observed in the simulations. On the other hand, the model was found inadequate in the sense that it could not satisfactory account for the initial rapid expansion of the colony in combination with the fact that the expansion is severely diminished after a few days. From the results it could be concluded that in order to get a satisfactory description of the complete evolution of the bacterial colonies studied here a more sophisticated theory for the diffusion processes is needed. The main conclusion is that the changes in the growth patterns are most likely due to genetic changes, or ’mutations’, in some bacteria causing the mutated bacteria to diffuse faster. There is an upper bound for the mutation frequency in order to get the patterns seen in experiments. The biological mechanism behind this phenomenon could be that the bacteria that mutate lose their pili enabling them to diffuse faster.
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McQuillan, Jonathan. "Bacterial-nanoparticle interactions". Thesis, University of Exeter, 2010. http://hdl.handle.net/10036/3101.
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Bionanotechnology is an intersection between biology and nanotechnology, a field in which novel applications for very small materials are being realised at an alarming rate. Nanoparticles have 3 dimensions that can be measured in nanometers, their small size conferring upon them different properties from individual atoms or the bulk material. The interactions between these unique materials and microorganisms are often toxic, thus have been exploited for antimicrobial applications. However, there is a considerable paucity of data for the underlying molecular mechanisms. This study has been carried out to investigate the interactions that occur between nanoparticles and bacteria with the objective of identifying these toxicological mechanisms and novel nanoparticle effects, using the model Gram negative organism Escherichia coli K12. This study has identified metal nanoparticles that are a superior vehicle for the delivery of toxic metal ions to E. coli. The nanoparticles associate with the bacterial surface, but do not cross the cell wall. They then dissolve, releasing a concentration of metal ions that accumulate at the bacterial-nanoparticle interface, enhancing the antibacterial efficacy compared to the concentration of metal ions in the bulk solution phase. Measurement of the whole transcriptome response to silver nanoparticles in comparison to the silver ion indicates that the different modes of ion delivery may induce a differential stress response. Moreover, this data identifies molecular mechanisms that are involved in the toxicity of this metal that is now becoming increasingly prevalent in society. The dissolution based toxic effects of zinc oxide nanoparticles are augmented by an interaction with ultra-violet light, offering an alternative mode for nanoparticle toxicity.
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Noyce, Jonathan Oliver. "Electrostatic bacterial control". Thesis, University of Southampton, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.274692.
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Loman, Nicholas James. "Comparative bacterial genomics". Thesis, University of Birmingham, 2012. http://etheses.bham.ac.uk//id/eprint/2839/.
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For the most part, diagnostic clinical microbiology still relies on 19th century ideas and techniques, particularly microscopy and laboratory culture. In this thesis I investigate the utility of a new approach, whole-genome sequencing (WGS), to tackle current issues in infectious disease. I present four studies. The first demonstrates the utility of WGS in a hospital outbreak of Acinetobacter baumannii. The second study uses WGS to examine the evolution of drug resistance following antibiotic treatment. I then explore the use of WGS prospectively during an international outbreak of food-borne Escherichia coli infection, which caused over 50 deaths. The final study compares the performance of benchtop sequencers applied to the genome of this outbreak strain and touches on the issue of whether WGS is ready for routine use by clinical and public health laboratories. In conclusion, through this programme of work, I provide ample evidence that whole-genome sequencing of bacterial pathogens has great potential in clinical and public health microbiology. However, a number of technical and logistical challenges have yet to be addressed before such approaches can become routine.
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Milne, Keith Livingston. "Bacterial isoprenoid biosynthesis". Thesis, University of Edinburgh, 1990. http://hdl.handle.net/1842/11172.
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This thesis describes a possible alternative isoprenoid pathway in bacteria by considering some previously unpublished feeding studies in the context of the related background literature. Three synthetic routes to 2,4-dihydroxy-4-methyltetrahydropyran (63) and three synthetic strategies towards the synthesis of 2-carboxy-2,4-dihydroxy-4-methyltetrahydropyran (63) are discussed. These compounds are considered as potential intermediates in the proposed alternative bacterial isoprenoid pathway. Labelled synthesis of (63) and structural analysis of (63) and 4-hydroxy-2-methoxy-4-methyltetrahydropyran (99) by proton nmr are also described. Feeding studies including the 13C isotopically labelled tetrahydropyrans (63) and (99) are described and a revised interpretation of all of the feeding studies considered. HMGCoA synthase is assayed in Rh. capsulata after a description of its assay in bakers yeast.
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Aspoas, A. R. "Bacterial intracranial aneurysms". Thesis, University of Cape Town, 1990. http://hdl.handle.net/11427/25637.
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Omer, Zahra Saad. "Bacterial-plant associations with special focus on pink-pigmented facultative mehtylotrophic bacteria (PPFMs) /". Uppsala : Dept. of Plant Pathology and Biocontrol Unit, Swedish Univ. of Agricultural Sciences, 2004. http://epsilon.slu.se/a456-ab.html.
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Staley, Zachery. "Direct and Indirect Effects of Agrochemicals on Bacterial Pathogens and Fecal Indicator Bacteria". Scholar Commons, 2013. http://scholarcommons.usf.edu/etd/4584.
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The presence of agrochemical residues in both urban and agricultural water bodies has become ubiquitous, often producing deleterious effects in the impacted watershed including reductions in biodiversity, alterations in species interactions, and toxicity to non-target organisms. While these effects have been studied on metazoan consumers, the consequences of agrochemical contamination on microorganisms, such as bacteria, protozoa, and viruses, are poorly understood. Agrochemicals could act directly on microorganisms, including pathogens, by either facilitating their survival or decreasing their abundance. Further, a multitude of indirect effects of agrochemicals on microorganisms are possible, whereby agrochemicals alter predation, competition, or parasitism on or available nutrient to microbes.
The primary method by which agrochemicals enter water bodies is through stormwater and agricultural runoff, which can also introduce agriculturally-associated zoonotic pathogens. Presently, regulatory standards utilize fecal indicator bacteria (FIB) to predict the presence of pathogens in contaminated watersheds. However, if agrochemicals have different effects on FIB and bacterial pathogens, then these regulatory standards might be confounded by the presence of pesticide residues in impacted water bodies. Additionally, if agrochemicals promote the survival of zoonotic pathogens, then the presence of pesticide residues could potentially increase risks to human health.
The studies in this dissertation investigated both the direct and indirect effects of agrochemicals on the growth and survival of FIBs ( Escherichia coli and Enterococcus faecalis), zoonotic bacterial pathogens (E. coli O157:H7, and Salmonella enterica), and two virus groups (human polyomaviruses and adenoviruses). The agrochemicals utilized in these experiments are among the most prominently used in their respective pesticide classes and included the herbicide atrazine, the insecticide malathion, the fungicide chlorothalonil and inorganic fertilizer containing phosphate and fixed nitrogen. Initially, complex mesocosms containing zooplankton, phytoplankton, leaf litter, and vertebrate and invertebrate species were used to examine net (direct and indirect) effects of agrochemicals on FIB in sediments. Subsequent studies utilized experiments in simplified microcosms to detect direct or indirect effects (i.e., predation, competition or effects on nutrient resources) on FIBs and pathogens.
In complex mesocosms, atrazine and fertilizer significantly increased FIB densities in the sediment; however, because of the complexity of the mesocosms, it was not possible to determine whether these results were the product of direct or indirect agrochemical effects. Simplified microcosms, limited to predominantly direct effects, as well as in vitro growth curves, revealed no direct effects of any agrochemical treatment on either growth or survival of FIB or bacterial pathogens. When algal communities were allowed to establish, however, atrazine significantly reduced both phytoplankton and E. coli densities in the water column, but increased E. coli densities within the sediments. These effects on E. coli were indirect because they required the presence of algal species.
To investigate indirect effects of predation on FIBs and E. coli O157:H7, we manipulated the presence and absence of an obligate heterotroph, Tetrahymena pyriformis, a facultative heterotroph, Ochromonas danica, and natural protozoan populations. In both laboratory and greenhouse microcosm experiments, the fungicide chlorothalonil significantly reduced all protozoan populations, which resulted in increased densities of FIBs and E. coli O157:H7 because of reduced predation. Atrazine was not found to have any significant direct effect on the densities of T. pyriformis or natural protozoans; however, atrazine did significantly reduce O. danica densities in greenhouse experiments. In laboratory experiments with O. danica, atrazine treatments resulted in decreased densities of E. coli O157:H7. Presumably, atrazine prevented or reduced photosynthesis forcing O. danica to increase its predation on E. coli thus shifting its trophic level.
These studies reveal that agrochemicals can have a significant effect on microbial communities, but that these effects are often indirect and mediated through alterations of nutrient resources and predation. Atrazine application reduced FIB and pathogen densities in the water column via reduction of phytoplankton and increased predation by O. danica. These data suggest that the net effects of atrazine is deleterious to FIB survival in the water column and that application of this herbicide could result in an ecosystem service, reducing the abundance of zoonotic pathogens and lessening the risk to human health. However, elevation of FIB densities was observed in the sediments when atrazine was applied. The potential resuspension of increased sediment bacteria may negate or out-weigh the deleterious effects of atrazine on bacteria in the water column. Chlorothalonil application decreased protozoan densities, lessening the stress of predation on the bacterial targets and increasing FIB and E. coli O157:H7 densities. The use of chlorothalonil may therefore have negative implications for human health risks, as the reduction in predation seems to facilitate the survival of zoonotic waterborne pathogens. Understanding the net effects of agrochemicals is important for public health, as pesticide applications can act to either maintain or diminish potential bacterial and protozoan pathogens of humans. These studies show that indirect effects of agrochemicals on non-target microbes tend to be more prominent than direct effects and can significantly impact the fate of bacterial pathogens in aquatic environments.
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Sabeti, Azad Mahnaz. "Accumulation of a bactericidal antibiotic by tolerant bacteria and insights into bacterial persistence". Thesis, Université Paris-Saclay (ComUE), 2019. http://www.theses.fr/2019SACLS585.
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Les aminoglycosides (AG) sont une famille d’antibiotiques qui ciblent le ribosome bactérien. À titre d’exemple il s’agit de la néomycine, la gentamicine et la streptomycine. Quand ces antibiotiques se fixent au ribosome, ils provoquent des erreurs de lectures ou inhibent la synthèse des protéines, ce qui conduit à la mort cellulaire. Même s’ils ont été découverts il y a plus d’un demi-siècle, de nombreux aspects de leur mode d’action restent inconnus. L’accumulation des AG dans les bactéries se passe en trois étapes. La première consiste en une interaction électrostatique avec la membrane. La deuxième est une phase I énergie-dépendante (EDPI). Les antibiotiques rentrent dans le cytoplasme, atteignent les ribosomes, ce qui cause des erreurs de lecture et donc la production de protéines mal repliées. EDPI dépend du niveau énergétique de la cellule et le mécanisme d’entrée à travers les membranes reste inconnu. La troisième étape est la deuxième phase énergie-dépendante (EDPII), où l’antibiotique pénètre dans le cytoplasme en grande quantité par des membranes endommagées lors de la phase I. Le but de cette thèse était de créer de nouveaux outils afin d’étudier l’interaction des AG avec les bactéries et d’appliquer la méthodologie à des bactéries en phase rapide de croissance ou bien en état de persistance. Nous avons synthétisé des conjugués fluorescents des AG aux propriétés bactéricides. Avec ces conjugués nous avons analysé l’interaction des AG avec les bactéries à l’échelle de la cellule unique par microscopie de fluorescence. Nous avons combiné cette technique avec la cytométrie de flux (FACS) pour évaluer la cinétique d’accumulation. Cette étude démontre qu’il y a deux types d’accumulation : une à la périphérie avec interaction à la membrane et une deuxième où l’antibiotique est localisé dans le cytoplasme. Notre analyse démontre aussi que de faibles niveaux d’antibiotiques dans le cytoplasme sont tolérés et n’inhibent pas la croissance cellulaire. En utilisant un inhibiteur des phases EDPI et EDPII nous démontrons que cette technique permet de distinguer les différentes étapes de l’accumulation. Au cours d’ajustements du protocole, nous avons découvert que les AG peuvent entrer dans le cytoplasme par mechano-sensation et activation de canaux mécanosensibles (MS). Ces canaux sont connus pour avoir une affinité pour les AG. Ici pour la première fois nous montrons qu’une manipulation mécanique ouvre les canaux et stimule une entrée massive d’antibiotiques. Ce résultat inattendu pourrait permettre de mieux comprendre le mécanisme d’entrée des AG dans le cytoplasme. Après avoir étudié l’accumulation des AG dans les cellules en croissance nous avons étudié la tolérance aux AG pour les bactéries en phase de dormance : les cellules persistantes. Elles forment une sous-population parmi une population sensible. Elles sont en dormance et tolèrent de fortes doses d’antibiotiques. En absence d’antibiotique elles sortent de l’état de dormance pour reformer une population sensible à l’antibiotique. Par microscopie de fluorescence, nous montrons que les cellules persistantes ont une accumulation périphérique d’AG. Grâce à notre méthodologie, nous avons un outil performant pour identifier les différents états d’accumulation des AG. Avant cette étude il était seulement possible de connaître les niveaux d’accumulation mais la localisation de l’antibiotique demeurait inaccessible. Nous avons avec cette méthode étudié deux mutants d’E. coli, qui sont moins tolérants aux AG et identifié leurs caractéristiques d’accumulation. Enfin, nous avons développé un système de microfluidique adapté à l’étude de nos conjugués fluorescents pour étudier en temps réel l’accumulation par les cellules persistantesAminoglycoside (AG) is a family of antibiotic which target bacterial ribosome. Few examples of this family are neomycin, gentamicin and streptomycin. When these antibiotics bind to ribosomes, they cause miscoding or inhibit protein synthesis which consequently leads to cell death. Although discovery of these antibiotics was more than half a century ago, there are many facts about AGs’ action mechanism which remain unknown. AG accumulation in the bacterial cells happens in three steps. First step is cell membrane attachment. This step is driven by an electrostatic interaction with the cationic AGs. Second step is an energy dependent phase I (EDPI). In EDPI, the antibiotic enters into the cytoplasm and reaches ribosomes, causing miscoding and production of misfolded proteins. EDPI depends on cellular energy level, however to date the mechanism by which AGs pass through membranes and enter cytoplasm is unknown. The third step is energy dependent phase II (EDPII) in which the antibiotic enters into the cytoplasm in larger amount due to damages in the membrane that resulted from EDPI. The aim of this PhD was to create new tools to study the interaction of AGs with bacteria and apply the methodology to study fast growing bacteria as well as persister cells. We have made fluorescently-tagged AGs with preserved bactericidal properties. We used these conjugates to track down the interaction of AG at single cell level by fluorescence microscopy. We combined fluorescence microscopy and fluorescence-activated cell sorting (FACS) analysis to measure AGs accumulation in the cells at different time points to capture the kinetics of antibiotic penetration. This study showed that there are two accumulations patterns for the drug in cells: in the first step there is a peripheral accumulation, which corresponds to specific binging to cell membrane. Next there is a cytoplasmic accumulation in which the antibiotic in entering into the cytoplasm. According to microscopy time laps study, low levels of cytoplasmic accumulation is tolerated by cells and did not cause cell death. Using FACS analysis, we used an inhibitor of EDPI and EDPII and proved that with this technique we can distinguish different steps of AGs accumulation. During protocol adjustment steps we found that AGs can enter into the cytoplasm as a result of mechanosensation and activation of mechanosensitive (MS) channels. These channels have already been shown to have affinity to AG and here this is a first time that we observed that mechanical manipulation of cells lead to opening of MS channel causing massive cytoplasmic accumulation. This unpredictable result may lead us to a better understanding of the mechanism of AG entrance into the cytoplasm. After studying AG accumulation in fast growing cells, we studied AG tolerance for non-growing cells, which are called persisters. Persisters are antibiotic tolerant sub-population among susceptible bacterial cell population. Persisters are non-growing, dormant cells which tolerate high concentrations of antibiotic. In the absence of antibiotic, they exit this dormant state and grow into an antibiotic susceptible population. By fluorescence microscopy we showed that persister cells have peripheral accumulation of AG. Thanks to our methodology, we have a powerful tool by which we can determine the patterns of AG accumulation. Prior to this study, it was only possible to know the levels of accumulation and not the corresponding patterns. We applied the method to investigate AG accumulation in two mutants of E. coli, which are less tolerant to AG and defined their pattern of accumulation. Finally, we developed a coated microfluidic system, which is adapted to our antibiotics for studying in real time drug accumulation by persister cells
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Dixit, Sameer M. "Antagonistic activity of probiotic bacteria based on bacterial diversity in the porcine gut". Thesis, View thesis, 2004. http://handle.uws.edu.au:8081/1959.7/35614.
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Diversity analysis of Escherichia coli have routinely utilised isolates obtained by culture of faeces on MacConkey selective media, under the assumption that the diversity identified in faecal isolates are representative of similar diversity in E. coli in the gastrointestinal tract (GIT). This study has addressed this important issue by specifically isolating E. coli from different regions of the gut in pigs and subjecting them to enzymatic multilocus enzyme electrophoresis (MLEE) and molecular virulence factor (VF) analysis to ascertain whether E. coli populations inhabiting different regions of the gut are different from each other. Combination of these results showed that on average, E. coli strains isolated from the upper GIT region (small intestine) of the pig are distinctly different from the E. coli strains isolated from the lower GIT region (large intestine). An important aspect of the finding that faecal E. coli are not truly representative of the diversity in the GIT is the mechanism used by specific clonotypes that have adapted to different geographical habitats to survive challenge from incoming strains.
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Dixit, Sameer M. "Antagonistic activity of probiotic bacteria based on bacterial diversity in the porcine gut". View thesis, 2004. http://handle.uws.edu.au:8081/1959.7/35614.
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Thesis (Ph.D.)--University of Western Sydney, Hawkesbury, 2004.A thesis presented to the University of Western Sydney, Hawkesbury, Centre for Advanced Food Research, in fulfilment of the requirements for the degree of Doctor of Philosophy. Includes bibliographies.
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Ortwine, Michelle L. "The impacts of rainfall runoff on tidal creek algal and bacterial production /". Electronic version (PDF), 2007. http://dl.uncw.edu/etd/2007-1/ortwinem/michelleortwine.pdf.
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Martins, Thaísa Zanetoni. "Mutagênese sítio-dirigida da ORF XAC0024 de Xanthomonas citri subsp. citri e suas implicações no desenvolvimento do cancro cítrico /". Jaboticabal, 2016. http://hdl.handle.net/11449/138238.
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Orientador: Jesus Aparecido FerroCoorientador: Helen Alves Penha
Banca: Fabrício José Jaciani
Banca: Flávia Maria de Souza Carvalho
Resumo: O cancro cítrico tem como agente causal a bactéria Xanthomonas citri subsp. citri (Xac), que afeta diferentes espécies de citros economicamente importantes. É uma doença ainda sem método curativo, e pela sua relevância e dano econômico, faz-se necessário o entendimento em termos moleculares da interação Xac-citros para o desenvolvimento de estratégias que controlem a doença. O objetivo do presente trabalho foi investigar os efeitos da deleção da ORF XAC0024 presente no genoma da Xac isolado 306, que codifica uma proteína hipotética conservada e que apresenta vários domínios putativos, entre eles o domínio peptidase M23. A hipótese é que esta proteína pode estar envolvida com a patogenicidade e/ou virulência da bactéria. Para obter o mutante ΔXAC0024 foi utilizada a técnica de mutagênese sítio-dirigida, seguida de recombinação homóloga com o vetor suicida pOK1. O mutante ΔXAC0024 foi analisado em relação às características de patogenicidade, crescimento in vivo e in vitro, capacidade de autoagregação, produção de biofilme e produção de goma xantana. O teste de patogenicidade e a curva de crescimento in vivo foram realizados em limão cravo utilizando o método de infiltração por seringa para a inoculação da bactéria. Os sintomas do desenvolvimento da doença foram registrados por fotografia digital até o 25º dia após a inoculação (dai) e a curva de crescimento in vivo também foi determinada até o 25º dai. A curva de crescimento in vitro e a agregação célula-a-célula foram analisa... (Resumo completo, clicar acesso eletrônico abaixo)
Abstract: The bacteria Xanthomonas citri subsp. citri (Xac) is the causal agent of citrus canker, a disease that affects different species of economically important citrus. There is no a curative method for this disease, and do to its relevance and economic damage, it is necessary to understand at molecular level the Xac-citrus interaction in order to develop strategies to control the disease. The objective of this study was to investigate the effects of the deletion of the ORF XAC0024 present in the genome of Xac strain 306, which encodes a conserved hypothetical protein and has several putative domains, including peptidase M23 domain. It is hypothesized that this protein may be involved in the pathogenicity and / or virulence of the bacterium. For the ΔXAC0024 mutant was used for site-directed mutagenesis technique, followed by homologous recombination with the suicide vector pOK1. The ΔXAC0024 mutant was analyzed in relation to pathogenicity characteristics, growth in vivo and in vitro, self-aggregation capacity, biofilm production and production of xanthan gum. The pathogenicity test and in vivo growth curves were performed on Rangpur lime using syringe-infiltration method for the inoculation of bacteria. Symptoms of the disease development were recorded by digital photography to the 25° day after inoculation (dai) and in vivo growth curve was also determined to give the 25°. The growth curve in vitro and cell-to-cell aggregation were analyzed in liquid culture medium NB. Biofilm p... (Complete abstract click electronic access below)
Mestre
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Cooper, Callum J. "Controlled delivery of bacterial viruses for the eradication of bacterial infection". Thesis, Cardiff University, 2011. http://orca.cf.ac.uk/54520/.
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A rise in antibiotic resistance has prompted renewed interest in the use of phages to treat bacterial infections. This project explored the use of phages to treat
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Hwang, Chiachi. "Assessment of bacterial communities and an iron-reducing bacterium in relation to an engineered bioremediation system designed for the treatment of uranium-nitric acid contaminated groundwater". Oxford, Ohio : Miami University, 2009. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=miami1241117969.
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Jones, Nicole Jean. "NITRIFYING BACTERIAL ABUNDANCE IN RELATION TO NITROGEN AND PHOSPHORUS COMPOUNDS IN WETLANDS". OpenSIUC, 2012. https://opensiuc.lib.siu.edu/theses/829.
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Floodplain lakes are wetlands which receive flood waters from nearby rivers or other sources. Water samples were taken from floodplain lakes near the Illinois River, the Mississippi River, and the Cache River in Southern Illinois. Fluorescence in situ hybridization (FISH), spectrophotometry, and gene probes were used to investigate the effect of nutrient and chemical concentrations on the abundance of nitrifying bacteria; specifically ammonia-oxidizing Nitrosococcus and Nitrosomonadales and nitrite-oxidizing Nitrospira and Nitrobacter. Nitrosococcus was the dominant ammonia-oxidizing bacteria at each river system. Nitrospira and Nitrobacter had similar average abundances. Nitrosococcus abundances showed a significant positive correlation with nitrate (NO3-) (R2= 0.247, P=0.05, 95% confidence R2≥0.199) and a positive trend with nitrite (NO2-) (R2= 0.194, P=0.10, 90% confidence R2≥0.125). Nitrosomonadales abundance positively correlated with temperature (R2= 0.530, P=0.05, 95% confidence R2≥0.510). Nitrospira abundances positively correlated with ammonium (NH4+) (R2= 0.265, P=0.05, 95% confidence R2≥0.199), NO2- (R2= 0.372, P=0.05, 95% confidence R2≥0.199), and NO3- (R2= 0.482, P=0.05, 95% confidence R2≥0.199). None of the target bacterial abundances significantly correlated with pH or dissolved inorganic phosphate.
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Camesano, Terri Anne. "An investigation of bacterial interaction forces and bacterial adhesion to porous media". Adobe Acrobat reader required to view the full dissertation, 2000. http://www.etda.libraries.psu.edu/theses/approved/PSUonlyIndex/ETD-19/index.html.
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Leszcynski, Robert A. "Determination of the Relationship Between Bacterial Coculturing, Antibiotic Resistance and Bacterial Growth". University of Dayton / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=dayton1591787505690696.
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Okuklu, Burcu Güneş Hatice. "Investigation of chromosomal and plasmid dna profiles of lactococcus lactics ssp. lactis/". [s.l.]: [s.n.], 2005. http://library.iyte.edu.tr/tezler/master/biyoloji/T000396.pdf.
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Thesis (Master)--İzmir Institute of Technology, İzmir, 2005Keywords: Lactococcus lactis ssp. lactis, chromosome profiling, pulsed field gel electrophoresis, plasmid profiling, plasmid stability. Includes bibliographical references (leaves 58-63)
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Davidson, Seana Kelyn. "Biology of the bryostatins in the marine bryozoan Bugula neritina : symbiosis, cryptic speciation and chemical defense /". Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 1999. http://wwwlib.umi.com/cr/ucsd/fullcit?p3035405.
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Sadeghi, Abbas. "Development of a Semi-synthetic Medium Supporting Adherent Growth in Coagulase-Negative Staphylococci". PDXScholar, 1992. https://pdxscholar.library.pdx.edu/open_access_etds/13.
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A semi-synthetic medium for use in determining adherent growth with Staphylococcus epidermidis and Staphylococcus saprophyticus was developed. Production of an adherent biofilm was dependent upon the presence of hematin in the growth medium. Clinical strains of Staphylococcus epidermidis were tested for production of an adherent biofilm in trypticase soy broth, the semi-synthetic medium and the hyperalimentary nutrient solution used in the neonatal hospital unit. An adherent biofilm was obtained when Staphylococcus epidermidis was cultured m hematin supplemented hyperalimentary solution. Growth in the hyperalimentary nutrient solution diluted with fetal calf serum showed the same growth rate as when the nutrient solution was diluted with water. The final growth yield was always higher in serum diluted nutrients. There was no effect of hematin on the growth rate of the organisms.
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Walkden, Heidi. "Bacterial infection of the brain: how bacteria penetrate the CNS by invading peripheral nerves". Thesis, Griffith University, 2020. http://hdl.handle.net/10072/395110.
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Bacterial infections of the central nervous system (CNS), though uncommon, are associated with very high rates of morbidity and mortality. Recent research has also highlighted the correlation between pathogens and chronic diseases of the CNS, such as neurodegenerative disorders, particularly Alzheimer’s disease. Whilst some bacteria can cross the blood-brain/blood-cerebrospinal fluid barriers, to date, other pathways by which bacteria enter the CNS remain largely unknown. Identifying alternative paths by which pathogens can enter the CNS is thus important for developing novel strategies preventing CNS infection and potential long-term sequelae.
Novel evidence suggests some bacterial species (as well as certain viruses and amoebae) can enter the brain via the cranial nerves innervating the nasal cavity, particularly the olfactory nerve that mediates the sense of smell and connects the nasal cavity with the olfactory bulb in the forebrain. The trigeminal nerve also innervates the nasal cavity and constitutes another invasion path. Only a handful of pathogens are thought to use cranial nerves to reach the brain; certain Chlamydia species (spp.) being amongst these.
Chlamydia pneumoniae is to date the bacterium with the strongest established link to Alzheimer’s disease. Previous research by our laboratory has also demonstrated that the bacterium causing the tropical disease melioidosis, Burkholderia pseudomallei, can invade both the olfactory and trigeminal nerves, travel along these nerves, to then infect the CNS (the olfactory bulb and brainstem, respectively). We have also previously shown that in outbred mice, the olfactory nerve is resistant to B. pseudomallei infection. The nasal mucosa contains both innate and adaptive immune components and prevents many infections. If pathogens penetrate the mucosal barrier and reach nerves, glial cells of the nerves can also combat the infection. Whilst only a few macrophages are present inside the olfactory nerve fascicles, olfactory nerve glial cells, termed olfactory ensheathing cells (OECs), are powerful phagocytes with innate immune functions. Thus, in addition to the immune cells and other components of the immune system in the nasal mucosa, cranial nerve glia are thus thought to be key for preventing CNS infection, explaining why such infections are relatively rare. Some pathogens, however, can evade destruction by these cells and invade the nerves, however, it remains largely unknown which pathogens are capable of doing so. Furthermore, injuries to the nasal epithelium are common, and if the mucosal barrier is removed by injury, perhaps it is easier for pathogens to infect the underlying nerves (in particular the olfactory nerve) and then reach the CNS. With the exception of one bacterium (Staphylococcus aureus) for which injury has been shown to allow infection of the olfactory nerve, it also remains unknown whether epithelial injury increases the risk of pathogens invading the CNS via these paths. Thus, we need to determine which pathogens are capable of invading the CNS via nerves connecting the nasal cavity and the brain, and whether epithelial injury increases the risk of infection. Furthermore, determining the cellular mechanisms that protect against microbial invasion of the CNS via nerves, as well as why certain pathogens can evade destruction of the immune system may pave the way for the development of novel therapies preventing and treating CNS infections.
The key aims of this thesis were to determine (1) whether prior injury to the nasal epithelium could allow B. pseudomallei to invade the olfactory nerve and bulb in the mouse strain where this nerve is usually resistant to this infection, (2) whether the bacterium Chlamydia muridarum (which infects mice and is commonly used to study Chlamydia spp. infection in rodents) can utilise cranial nerves that innervate the nasal cavity to invade the CNS and, if C. muridarum can invade the CNS, to then determine whether the bacteria remained viable and (3) whether C. muridarum can infect OECs, and how OECs respond to C. muridarum in vitro.
This thesis demonstrated that injury to the olfactory epithelium allowed the invasion of the olfactory nerve and bulb by B. pseudomallei in S100β-DsRed Quackenbush mice, in which the olfactory nerve is otherwise typically resistant to infection. This work also showed that C. muridarum can rapidly (within 48 h) reach the CNS (olfactory bulb and cerebral cortex) via the olfactory nerve, as well as infect the trigeminal nerve, in mice. Immunohistochemistry showed the presence of C. muridarum inclusion bodies (membrane-bound components inside which the bacteria replicate intracellularly) and viable C. muridarum bacteria were also isolated from these regions. C. muridarum was shown to readily infect OECs in vitro, which led to the upregulation of a range of cytokines.
The outcomes from this project will contribute to an increased understanding of how bacteria can reach the CNS and has revealed that injury to the nasal epithelium may increase the risk of CNS bacterial invasion via the olfactory nerve. The outcomes also include an increased understanding of how olfactory nerve glia become infected by and respond to bacteria. This work may also contribute towards the growing body of knowledge regarding the link between pathogens and certain diseases of the CNS, such as Alzheimer’s disease. Furthermore, with an increased understanding of how glial cells respond to bacteria, new therapies may be developed that stimulate bacterial degradation by the glia. Such therapies may provide valid future alternatives to antibiotics, also combating the growing problem of antibiotic resistance. Thus, this work may contribute to the foundation required to develop therapies to treat diseases that are currently not curable, as well as to better diagnose and identify susceptibilities to certain conditions.Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Medical Science
Griffith Health
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Leivers, Shaun. "Characterisation of bacterial exopolysaccharides". Thesis, University of Huddersfield, 2011. http://eprints.hud.ac.uk/id/eprint/12014/.
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In this project, the structures of exopolysaccharides (EPS) produced by bacterial strains were characterised. The current techniques utilised for structural elucidation were also investigated. The structure of the novel EPS isolated from the fermentation of the lactic acid bacteria(LAB) strain, Lactobacillus helveticus Rosyjski, has been characterised. The strain of LAB was grown on skimmed milk supplemented with glucose; the subsequent EPS produced was isolated using established protocols. The 1H NMR spectrum identified the presence of five anomeric monosaccharide signals corresponding to the existence of a pentasaccharide repeating unit oligosaccharide. HP-SEC-MALLS analysis revealed the EPS has a weight average molecular weight of less than 1.4 x106 g mol-1. A combination of GC-MS and HPAEC-PAD analysis confirmed that the structure was composed of D-glucose, D-galactose and D-N-acetyl mannosamine in a molar ratio of 2:2:1. Linkage analysis of the EPS, by GCMS and 2D-NMR experiments showed that the repeating unit contains two terminal, one dilinked and two tri-linked monosaccharides. All of the data obtained allowed for the elucidation of the structure of the EPS produced by Lactobacillus helveticus Rosyjski. The current techniques used for the determination of the monomers and linkages present in EPS structures were investigated. Monomer analysis was studied by using the previously characterised EPS, Lactobacillus acidophilus 5e2 as a model. A variety of acids were used to catalyse the hydrolysis of the polysaccharide. The monosaccharides liberated from the EPS were analysed by HPAEC-PAD. It was determined that hydrolysis with TFA was the simplest technique to employ whilst also providing reliable results. Linkage analysis was investigated by the production of a number of disaccharide-derived model linkage standard compounds. This resulted in the creation of a number of terminally and di-linked linkage standards which can be used as model reference compounds when characterising previously unidentified EPS. The bacterial strain Bifidobacterium animalis subsp. lactis A1dOxR produces EPS. Initial inspection of the 1H NMR spectrum however displayed a complex anomeric region with many overlapping signals. Analysis by HP-SEC-MALLS revealed multiple peaks, further adding to the evidence of the presence of more than one EPS in the recovered ‘crude’ sample. The crude sample was subjected to dialysis and a fraction (over 100,000 Da) was recovered and denoted as high molecular weight (HMW) EPS. Examination of the 1H NMR spectrum from HMW EPS indicated a hexasaccharide repeating unit oligosaccharide, whilst HPEAC-PAD and GC-MS analysis confirmed that the structure was composed of Lrhamnose, D-galactose and D-glucose in a molar ratio of 3:2:1. Further analysis determined that one of the galactose monosaccharides was present in the furanose form as appose to the more commonly observed pyranose configuration. Linkage analysis of the EPS, by GCMS and 2D-NMR experiments, showed that the repeating unit contains one terminal, four dilinked and one tri-linked monosaccharide. All of the data obtained allowed for the elucidation of the structure of the HMW EPS from by Bifidobacterium animalis subsp. lactis A1dOxR. Solubilising EPSs has been a constant challenge, however, it was hoped with the advent of ionic liquids (IL) this issue could be solved. Ultimately, dissolution of EPS in ionic liquids though proved to be unsuccessful, so attention was turned to combining derivatisation and dissolution, as a method for solubilising polysaccharides. Derivatisation of a number of model systems of di- and polysaccharides were explored. By studying both 1D- and 2D-NMR coupled with GC-MS analysis it has demonstrated that polysaccharides such as cellulose along with a number of common disaccharides can be successfully dissolved and modified in ionic liquids.
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Sadiq, Sohaib. "Characterization of bacterial exopolysaccharides". Thesis, University of Huddersfield, 2015. http://eprints.hud.ac.uk/id/eprint/23888/.
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The present study investigated the structural characterization of exopolysaccharides (EPS) produced by Campylobacter jejuni, Bifidobacterium animalis subsp. lactis and a number of Bifidobacterium breve strains. Nuclear magnetic resonance (NMR) spectroscopy, size exclusion chromatography coupled with multiangle laser light scattering (SEC-MALLS), anion exchange chromatography, HPAEC-PAD analysis, monomer and linkage analysis employing GC-MS have been used to characterise the EPS structures. Monomer analysis of the EPS produced by Campylobacter jejuni showed the presence of glucose, linkage analysis showed the presence of an α-(1→6) glycosidic linked repeating monomer unit and NMR (1D- and 2D- experiments) showed that the EPS is an α-dextran. NMR and size exclusion chromatography analysis for B. animalis subsp. lactis shows the presence of a complex mixture of EPS. Monomer analysis for different batches suggests that each contains variable amounts of rhamnose, glucose and galactose along with trace levels of mannose. The results of the linkage analysis indicate that a complex mixture of differently linked sugars is present including : terminal rhamnose, 1,2-linked rhamnose, 1,3-linked rhamnose, terminal hexoses, 1,2,3-linked rhamnose, 1,4-linked hexose, 1,3-linked hexose, 1,6-linked hexose, Nacetyl sugars and 1,3,4-linked hexoses. SEC-MALLS showed the presence of different molecular weight EPSs. Uronic acid analysis showed that in 5.0 mg of EPS sample, only 0.28 mg of uronic acid is present. 1D- and 2D-NMR experiments were performed on the EPS samples produced by B. breve strains including UCC2003, JCM7017, JCM7019 and NCFB2258. Analysis of EPS extracted from cells using sodium hydroxide (NaOH) showed that complex mixtures of polysaccharides were being recovered. However, a common set of NMR signals was present in all the EPS samples from B. breve. Analysis of this set of signals suggests that, on treatment of cells with NaOH, a β-(1→6)-linked glucan is released from a variety of bifidobacterial strains.
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Pönisch, Wolfram. "Dynamics of bacterial aggregates". Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2018. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-235120.
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The majority of bacteria are organized in surface-associated communities, the so called biofilms. Crucial processes that drive the formation of such biofilms are the motility of bacteria on a substrate, enabling cells to reach each others vicinity, and attractive cell-cell-interactions, driving the formation of microcolonies. These colonies, aggregates consisting of thousands of cells, are the precursors of biofilms. In this thesis we investigate the role of cell appendages, called type IV pili, in the substrate motion of bacteria and the formation of bacterial microcolonies. Therefore, we study the bacterial dynamics with the help of experiments and theoretical models. We introduce a novel simulation tool in the tradition of Brownian dynamics simulations. In this computational model, that was developed alongside experimental observations, we study how explicit pili dynamics, pili-substrate and pili–pili interactions drive the cell dynamics. First, we apply our model to investigate how individual cells move on a substrate due to cycles of protrusion and retraction of type IV pili. We show that the characteristic features, in particular persistent motion, can solely originate from collective interactions of pili. Next, we perform experiments to study the coalescence of bacterial microcolonies. With the help of experiments and our computational model, we identify a spatially-dependent gradient of motility of cells within the colony as the origin of a separation of time scale, a feature which is in disagreement with the coalescence dynamics of fluid droplets. Additionally, we show that altering the force generation of pili can cause demixing of cells within bacterial aggregates. Finally, we combine our knowledge of the substrate motion of cells and of the pili-mediated interactions of colonies to identify the main processes (aggregation, fragmentation and cell divisions) that drive assembly of colonies. Starting from experiments, we develop a mathematical model and observe excellent qualitative and quantitative agreement to experimental data of the density of colonies of different sizes. In summary, hand in hand with experiments, we develop theoretical frameworks to unravel the role of type IV pili in bacterial surface motility, microcolony dynamics and colony formation.
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Beek, Diederik van de. "Bacterial meningitis in adults". [S.l. : Amsterdam : s.n.] ; Universiteit van Amsterdam [Host], 2004. http://dare.uva.nl/document/72440.
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Mason, Francis Gerard. "Bacterial degradation of thiocyanate". Thesis, Queen's University Belfast, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.282235.
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Leigh, J. A. "Studies on bacterial dehalogenases". Thesis, Nottingham Trent University, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.376092.
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Cock, J. M. "Bacterial nitrate reductase genes". Thesis, University of Leeds, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.355501.
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Al-Mushrif, Shawqi A. "Pathogenicity of bacterial vaginosis". Thesis, University of Sheffield, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.310757.
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Caswell, R. C. "Bacterial degradation of alginates". Thesis, Bucks New University, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.234705.
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Zhang, Jiancheng. "Characterisation of bacterial NOS". Thesis, University College London (University of London), 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.270425.
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Borodina, Elena. "Bacterial metabolism of dimethylsulfone". Thesis, King's College London (University of London), 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.251998.
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Ahmed, Tanvir Ph D. Massachusetts Institute of Technology. "Microfluidics for bacterial chemotaxis". Thesis, Massachusetts Institute of Technology, 2011. http://hdl.handle.net/1721.1/66851.
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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 2011.Cataloged from PDF version of thesis.
Includes bibliographical references (p. 136-151).
Bacterial chemotaxis, a remarkable behavioral trait which allows bacteria to sense and respond to chemical gradients in the environment, has implications in a broad range of fields including but not limited to disease pathogenesis, in-situ bioremediation and marine biogeochemistry. And therefore, studying bacterial chemotaxis is of significant importance to scientists and engineers alike. Microfluidics has revolutionized the way we study the motile behavior of cells by enabling observations at high spatial and temporal resolution in carefully controlled microenvironments. This thesis aims to explore the potential of microfluidic technology in studying bacterial behavior by investigating different aspects of bacterial chemotaxis on a microfluidic platform. We quantified population-scale transport parameters of bacteria using videomicroscopy and cell tracking in controlled chemoattractant gradients. Previously, transport parameters have been derived theoretically from single-cell swimming behavior using probabilistic models, but the mechanistic foundations of this up-scaling process have not been proven experimentally. The parameter estimates computed directly from single-cell swimming information showed good agreement with literature values providing the experimental verification of the upscaling from single cells to population-scale models. Furthermore, we also developed a diffusion-based microfluidic device to generate steady, arbitrarily shaped chemical gradients. Steady gradients, linear or nonlinear, are often a useful model of the bacterial microenvironment to study chemotaxis in the limit of slow patch diffusion or fast motility of free swimming bacterial cells. Observed cell distribution along the gradients showed good agreement with predictions from the bacterial transport equation, providing the first quantification of chemotaxis in steady nonlinear gradients. Also, by observing the time series of the bacterial distributions in different scaled gradients (both steady and unsteady) generated using microfluidic devices, the bacterial response was found to be invariant up to an 87-fold change in ambient chemoattractant concentration. These observations provide an explanation for the ability of bacteria to cope with a broad range of chemical concentrations and gradients in the environment, by means of a flexible sensing network that allows them to rescale their response to take maximum advantage of signals, while discounting less-informative background information. Finally, a microfluidic lattice habitat was developed to study the fate of a chemotactic bacterial population under the pressure of predation. It was observed that the demographic and spatial organization of the bacterial prey population depended on the predator-to-prey ratio as well as on the degree of heterogeneity of the habitat structure. These results represent a first step towards predator-prey microcosms and pave the way for future predator-prey metapopulation studies.
by Tanvir Ahmed.
Ph.D.
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Dell'Arciprete, Dario. "Physics of bacterial microcolonies". Thesis, University of Edinburgh, 2016. http://hdl.handle.net/1842/23418.
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The growth of bacterial colonies is a very ubiquitous phenomenon occurring in nature and observed in the laboratories. However, there is a limited knowledge on how at the microscopic level these colonies develop and the individual cells spatially organize. In this thesis, we experimentally investigate the physics of growing microcolonies at the level of the individual Escherichia coli (E. coli ) cells, focussing on the order-disorder evolution and the understanding of it in the context of active matter. Bacterial cells are indeed constantly transducing energy from the environment to move and grow, therefore they behave as active microscopic units, defining an inherently far from equilibrium system. In Part I, we present a brief summary of passive liquid crystals that provide us with some basic concepts and tools for investigating the bacterial microcolony evolution. Then an overview of the biology of E. coli cell is given, both as part of multicellular structures (biofilm) and as individuals. Active matter is then discussed along with some examples of active nematics. This first part ends with the materials and methods used in the experiments and analysis. In Part II, we provide our experimental results on the study of growing bacterial microcolonies as active nematics. We describe the way a bacterial microcolony evolves from the first mother cell into a layer of hundreds of cells, and we study the global and local orientational order. We find that a transition from an anisotropic to an isotropic phase occurs as the colony increases and that instabilities and topological defects develop, in analogy to the case of an active nematic. We also compare the real system with simulated ones by investigating (i ) the case of equilibrated configurations with respect to experimental nonequilibrium ones, and (ii ) long-time behaviour of nonequilibrium analogues. In Part III, we discuss the buckling of bacterial microcolonies, that is, the transition from a 2D layer of cells to a 3D structure. We investigate the link between the buckling event and the presence of topological defects in the nematic map of the bacterial microcolony, finding that the buckling sites tend to be closer to topological defects with a negative charge. Later, we present some results of buckling in microcolonies composed of mutants lacking some appendages that play a role in the motion in and attachment to the surrounding environment, finding that buckling occurs at earlier times in the case of these mutants than the wild type. The aim of this work is to show that a growing bacterial microcolony is an interesting model of active matter to experiment on, and that the investigation tools developed for the study of liquid crystals can be useful for describing the evolution of these living systems in mechanistic terms, and for improving the current understanding of nonequilibrium phenomena.