Tesi: "Bacteria" – Grafiati

1

Chen, Fei [Verfasser]. "Light-controlled bacteria-surface and bacteria-bacteria adhesions / Fei Chen". Mainz : Universitätsbibliothek der Johannes Gutenberg-Universität Mainz, 2020. http://d-nb.info/1224895649/34.

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2

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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3

Maldonado, Vázquez Jesús Manuel. "Interferometric biosensors for rapid identification of nosocomial infections". Doctoral thesis, Universitat Autònoma de Barcelona, 2017. http://hdl.handle.net/10803/403761.

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Esta tesis doctoral se centra en el desarrollo de un nuevo biosensor óptico como una técnica alternativa para la identificación de infecciones nosocomiales con el fin de determinar el tratamiento más eficaz y reducir el uso inespecífico de fármacos antimicrobianos de amplio espectro. Proponemos el uso de un nuevo sensor nanofótonico basado en un dispositivo interferométrico, el biosensor de guías de onda bimodales (BiMW) para un análisis rápido, específico, directo y altamente sensible de los diferentes patógenos asociados a infecciones nosocomiales y su resistencia a múltiples fármacos. En primer lugar, se evaluaron y optimizaron diferentes estrategias de biofuncionalización para conseguir una inmovilización eficiente de los elementos de bioreconocimiento que aseguran una detección bacteriana altamente sensible con suficiente selectividad y reproducibilidad, particularmente para la detección directa en matrices complejas tales como orina y líquido ascítico. Posteriormente, las estrategias optimizadas se utilizaron para la identificación de diversos patógenos nosocomiales como Bacillus cereus, Escherichia coli y Pseudomonas aeruginosa utilizando anticuerpos como elementos de bioreconocimiento. La detección de Escherichia coli se realizó en una matriz compleja como es el líquido ascítico humano. Finalmente, el biosensor BiMW se empleó para identificar bacterias resistentes a múltiples fármacos como: i) la identificación de Staphylococcus aureus resistente a meticilina (MRSA) usando un aptámero, que es capaz de discriminar entre un Staphylococcus susceptible a antibióticos y un Staphylococcus multirresistente y (ii) la detección ultra sensible de genes de E. coli resistentes a múltiples fármacos, sin la necesidad de una previa amplificación por PCR. En general, esta tesis aprovecha los conocimientos en biosensores fotónicos y en métodos bioanalíticos de nuestro Grupo de investigación para desarrollar una poderosa herramienta que permita la identificación directa y efectiva de patógenos nosocomiales y su resistencia a antibióticos.
This doctoral Thesis is focusing on the development of a novel optical biosensor as an alternative technique for the identification of nosocomial infections in a faster way. This new tool will also facilitate the finding of the most effective treatment for each patient, reduce the nonspecific use of broad-spectrum antimicrobial drugs, and facilitate new antibiotic treatments. We propose the use of a novel nanophotonic sensor based on an interferometric transducer device, the Bimodal Waveguide device (BiMW) for the rapid, specific, highly sensitive and direct analysis of different pathogens associated to nosocomial infections and their multidrug resistant. First, we assessed and optimized different biofunctionalization strategies for an efficient immobilization of the required biorecognition receptors, which ensure a highly sensitive bacterial detection with enough selectivity and reproducibility, particularly suitable for the direct detection in complex matrices, such as urine and ascitic fluid. The optimized strategies were employed for the identification of various nosocomial pathogens such as Bacillus cereus, Escherichia coli, and Pseudomonas aeruginosa using antibodies as biorecognition elements. The detection of Escherichia coli was done in human ascitic fluid. Finally, the BiMW biosensor was employed to identify the multidrug-resistant bacteria such as: i) the identification of methicillin-resistant Staphylococcus aureus (MRSA) using a specific aptamer, which is able to discriminate among a susceptible one to antibiotic and a multidrug-resistant Staphylococcus, and (ii) the ultra-sensitive detection of multidrug-resistant E. coli genes without PCR amplification. This Thesis takes advantage of the knowledge in photonics biosensors and bioanalytical methods in our Group in order to develop a powerful tool for the direct and effective identification of nosocomial pathogens and their antibiotic-resistance in a rapid and label-free scheme.

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4

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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5

Habeeb, Fatema. "Bacteria-cytokines interactions : effect of normal bacterial flora of pathogenic bacteria on pro-inflammatory cytokines production in human blood". Thesis, University of Strathclyde, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.501921.

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6

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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7

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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8

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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9

Hughes, Roxana Bejarano. "Distribution of a Novel Gram Negative, Capsule-Forming Bacterium". Thesis, University of North Texas, 1997. https://digital.library.unt.edu/ark:/67531/metadc500729/.

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A novel Gram negative, capsule-forming bacterium was previously isolated in Dr. G. Roland Vela's laboratory. The distribution of this bacterium in soils from various locations was investigated. Soil samples from 188 locations around the world were examined. Isolates of the bacterium were obtained from 50 of these soils, with 48 of the isolates found in soils from the southwestern United States and northern Mexico. This suggests that this region is the natural habitat of the bacterium. The other two isolates were obtained from Madrid, Spain and Taipei, Taiwan. None were found in soils from South America or Australia. A lack of variation in morphology and physiological properties in the isolates suggests that a homogeneous population exists, even from widespread geographical locations.

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10

Song, Yanqing. "Microfluidic devices for bacteria study and bacteria-based sensing". Thesis, University of Glasgow, 2017. http://theses.gla.ac.uk/8577/.

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Environmental pollutants pose great risks and adverse effects to humans and therefore arouse global environmental concern. Bacterial sensors capable of assessing the bioavailability and toxicity of pollutants show great advantages in environmental sensing. This project aims at developing a bioluminescent bacteria-based microfluidic sensor for online monitoring of environmental contaminants and toxicity. Microfluidic devices immobilised with Acinetobacter sp. ADP1_lux cells as a model strain have been developed for quantitative bioassays. Three microfluidic devices were developed and tested in order to trap and culture a monolayer of bacterial cells. The terrace device is capable of trapping a monolayer of cells in a chamber for tracking single-cell growth and response. This device utilises a barrier channel lower than the cell diameter. Two flow channels can be used to load bacterial cells, deliver fresh media and inducers and wash away overgrown cells. The device was used to measure the bioluminescence induction of ADP1_lux cells and its capability to track individual cell growth was demonstrated with E.coli cells. Since bioluminescence signals from a monolayer of ADP1_lux cells were too weak to be detected after 2 h induction by 200 µM salicylate, a microwell device was developed to concentrate cells in individual microwells for population-based analysis. Cell loading procedures, dimensions of wells, carbon sources and on-chip cultures that affect bioluminescence light intensities were investigated. This device succeeded in detecting 200 µM salicylate within 1 h. However, long-term cell culture revealed that ADP1_lux cells tend to form biofilms. Cell populations in individual wells varied greatly, making quantification impossible. Therefore, this device is only suitable for rapid detection of high concentrations of contaminants if biofilm forming bacteria cells are used as biosensors. In contrast, in the case of non-adherent cells such as E.coli, a uniform population distribution in each well was achieved after 2-day culture, suggesting this method is applicable to perform long term, quantitative bioassays using suitable, non-adherent cells. To be able to detect low concentrations of contaminants and overcome potential biofilm formation, a new population array device was developed as a proof of concept to control and isolate cell populations. It consists of a network of microfluidic channels and an array of microchambers. The device was characterised with fluorescent dyes and its capability to perform quantitative bioluminescence assays was evaluated by detecting a range of concentrations of salicylate solutions (from 10 µM to 50 µM salicylate) using ADP1_lux cells. A linear correlation between bioluminescence intensities and salicylate concentrations was successfully established within 90 min induction. It is worth noting that the population array device is the first demonstration of bioluminescence detection at the length scale of microns. Therefore, it has potential to perform multiplex detection within a small footprint where different types of whole cell biosensors can be employed simultaneously. To this end, a logarithmic serial dilution device was also developed to enable quantitative, multiplex bioassays to be conducted in the same device. This integrated dilution and population device provides a powerful tool for rapid quantification of multiple contaminants simultaneously in a sample.

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11

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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12

Ghalsasi, Vihang Vivek [Verfasser], e 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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13

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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14

Ghalsasi, Vihang Vivek Verfasser], e 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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15

Rodriguez, Luis A. (Luis Antonio). "Adenylate Energy Charge Determinations of Soil Bacteria Grown in Soil Extract Medium". Thesis, University of North Texas, 1988. https://digital.library.unt.edu/ark:/67531/metadc500662/.

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The adenylate energy charge values of twenty bacteria isolated from soil and cultured in a medium consisting of soil and distilled water were determined by the luciferin-luciferase bioluminescense method. The purpose of this study was to examine the growth and energy charge values of these organisms in soil extract medium, and to determine what effect the addition of glucose has on their energy charge values. Three of the organisms employed in this study showed energy charge values similar to those reported for bacteria grown in enriched media. The remainder of the isolates demonstrated low energy charge values, and scant growth in the soil medium.

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16

Moyà, Anderico Laura. "Deciphering the utility of Galleria mellonella as an infection and toxicity in vivo model". Doctoral thesis, Universitat de Barcelona, 2021. http://hdl.handle.net/10803/671803.

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Galleria mellonella (greater wax moth) is a popular animal model that has been extensively used as an alternative in vivo model for investigating the virulence and pathogenicity of different bacteria. G. mellonella has also been shown to be a suitable model for studying the efficacy and toxicity of various compounds. Recently, this model has been gaining popularity as the larvae are conveniently sized for manipulation, they do not need constant feeding, they are inexpensive to purchase and to breed, they do not require much space or special infrastructure, they present a low biohazard risk, and they are more ethically accepted. More importantly, G. mellonella has an innate immune system very similar to the one found in mammals. In this thesis, G. mellonella was used to develop a standardized and reproducible animal model of infection and toxicity. Pseudomonas aeruginosa is an opportunistic pathogen that has gained great medical importance as it causes serious illnesses in humans and it can be resistant to many antibiotics. During infection, ribonucleotide reductases (RNR) play an essential role as they catalyze the reduction of ribonucleotides to deoxyribonucleotides, thus providing the precursor molecules needed for DNA synthesis. Since G. mellonella has been proven to be a suitable model for P. aeruginosa infections, we developed a promoter probe vector with bioluminescence expression to enhance the study and monitoring of a P. aeruginosa in vivo infection. This vector was used to construct different RNR gene promoter fusions as proof of concept. Additionally, we optimized a total bacterial RNA extraction protocol to facilitate the study of transcriptional gene levels during in vivo infections. Staphylococcus aureus is also considered an opportunistic pathogen. This bacterium is also capable of forming biofilms and it is considered an important cause of biofilm formation in catheters and prostheses. Due to the misuse and overuse of antimicrobials, multi-resistant bacteria are rapidly appearing so there is a critical need for new antimicrobials. The toxicity and antimicrobial efficacy against S. aureus of novel oleanolic and maslinic acid derivatives were determined using G. mellonella. Out of the 14 derivatives tested, 2 were found to have improved toxicity and efficacy in vivo when compared to the in vitro results. G. mellonella was also used to test the toxicity of other therapeutical strategies and nanoparticles (NPs). Mycolicibacterium brumae was not toxic to G. mellonella larvae, and the results correlated with the results obtained with mice. The different NPs caused a variety of acute toxicity effects that were detected by an array of indicators within the larvae, such as lethal dose calculation, hemocyte proliferation, NP distribution, behavioral changes, and histological alterations. Due to the broad applicability of the G. mellonella model, new methodologies are warranted to exploit its full potential. Besides the optimized RNA extraction protocol already mentioned, an optical clearing protocol was also optimized in this work. As a proof of concept for our larvae clearance protocol, fluorescent rhodamine NPs were injected into larvae that were then fixed with paraformaldehyde, permeabilized with increasing concentrations of methanol, and cleared with BABB (Benzyl Alcohol and Benzyl Benzoate).
Galleria mellonella es un modelo animal utilizado extensamente como alternativa para investigar la virulencia y patogenicidad bacteriana in vivo. También es apropiado para estudiar la eficacia y toxicidad de compuestos. Las larvas tienen un tamaño manejable, son económicas de adquirir y reproducir, presentan un bajo riesgo biológico, y son más aceptadas éticamente. Además, tienen un sistema inmunológico innato muy similar al de los mamíferos. Utilizamos G. mellonella para desarrollar un modelo animal de infección y toxicidad estandarizado y reproducible. Pseudomonas aeruginosa, un patógeno oportunista, que infectando emplea ribonucleótido reductasa (RNR), catalizando la reducción de ribonucleótidos a desoxirribonucleótidos y proporcionando así las moléculas precursoras necesarias para la síntesis de ADN. Desarrollamos un vector sin promotor con bioluminiscencia, el cual se utilizó para construir fusiones con los promotores de los genes RNR. Además, optimizamos un protocolo de extracción de ARN bacteriano para facilitar el estudio de los niveles transcripcionales de genes in vivo. Debido a la multiresistencia emergente de Staphylococcus aureus, se probó la toxicidad y eficacia antimicrobiana de nuevos derivados del ácido oleanólico y maslínico en G. mellonella. De los catorce derivados probados, dos tenían menos toxicidad y más eficacia in vivo que in vitro. G. mellonella se usó para determinar la toxicidad de nanopartículas y estrategias terapéuticas. Mycolicibacterium brumae no fue tóxica para las larvas y los resultados se correlacionaron con los obtenidos con ratones. Las nanopartículas causaron efectos tóxicos en las larvas detectados por la medición de la dosis letal y la proliferación de hemocitos, entre otros indicadores. Debido a la amplia aplicabilidad de G. mellonella, se necesitan nuevas metodologías para maximizar su potencial. Además del protocolo de extracción de ARN previamente mencionado, también se optimizó otro de aclaramiento. Las larvas fueron inyectadas con nanopartículas, fijadas con paraformaldehído, permeabilizadas con metanol y aclaradas con alcohol bencílico y benzoato de bencilo.

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17

Thongmee, Acharawan. "Isolation and Characterization of a New Capsule-Forming Bacterium". Thesis, University of North Texas, 1999. https://digital.library.unt.edu/ark:/67531/metadc500460/.

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A unique, previously undescribed Gram-negative bacterium was isolated from several soils in Texas and extensively characterized in this study. The cells measured 1-2 by 4-6 μm. The distinguishing characteristic of the bacterium is the extraordinary capsular material which surrounds the cells. The new isolates are aerobic, mesophilic, non motile and have the ability to utilize a variety of organic compounds as the sole source of carbon and energy. The organism grows optimally at 30° C and the optimal pH lies between 7.0-8.0. The isolates produce catalase but oxidase is not produced. They do not produce indole or hydrogen sulfide. The organism can hydrolyze gelatin and Tween 80 but not starch, esculin and casein. The major cellular fatty acid is anteiso 15:0. The guanine and cytosine content is 58-62 mole%. The organism's taxonomic position was further established by specific gene probes, 16S rRNA homology, DNA homology and "ribotyping." These data showed that it was most closely related to members of the genus Paenibacillus, although somewhat divergent from other species classified in this genus. After careful evaluation of the results obtained during this study, it is proposed that this unique bacterium be named Paenibacillus velasolus sp. nov.

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18

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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19

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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20

Budiharjo, Anto. "Plant-bacteria interactions". Doctoral thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät I, 2011. http://dx.doi.org/10.18452/16333.

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Bacillus amyloliquenaciense FZB42 ist ein bekanntes Pflanzenwachstum-stimulierendes Rhizobakterium. Es produziert neben einer Vielzahl an Sekundärmetaboliten mit antibakterieller und antifungaler Wirkung, auch das Pflanzenhormon IAA. Obwohl viele dieser Mechanismen diskutiert werden, ist wenig darüber bekannt, auf welche Weise die Bakterien das Pflanzenwachstum fördern. In dieser Arbeit wurde eine Transposonmutagenese mithilfe des ‘mariner-transposons’ durchgeführt, und so eine Transposonbibliothek erstellt. Diese wurde dann auf geeignete Phänotypen untersucht, um die Gene zu finden, welche bestimmte Phänotypen verursachen. So konnten drei Mutanten erzeugt werden, die auf Grund der gestörten Biofilmbildung und der Fähigkeit zu schwärmen die Pflanzenwurzeln nicht mehr kolonialisieren konnten. Eine solche degU-Mutante, welche in der Biofilmbildung und ‚Swarming’ defizitär war und zwei Mutanten (yusV und pabB), die eine Beeinträchtigung in der Biofilmbildung aufwiesen, konnten durch Komplementation und Retransformation bestätigt werden. Mithilfe des Lemna-Biosystems und anderer Analysen mit A. thaliana konnten drei Gene bei B. amyloliqufaciens FZB42 gefunden werden, die wichtig für die Förderung des Pflanzenwachstums sind. Koloniesierungsexperimente der Wurzeln von A. thaliana mit diesen Mutanten zeigten deutlich verändertes Wachstum, verglichen mit dem Wildtypstamm. Ein weiteres Ziel dieser Arbeit war es neue Antibiotika in Mutanten, die in ihren nicht-ribosomalen Synthesen blockiert sind, zu finden. So konnten durch die Untersuchungen der Transposonbibliothek der Mutanten zwei neue Antibiotika entdeckt werden. Genauere Analysen dieser Antibiotika bestätigten, dass es sich um ein neues Bacteriocin (Amylocyclicin A) und ein neues Thiazol/Oxazole-modifiziertes Microcin (Plantazolicin) handelt. Die abschließenden Arbeiten beschäftigten sich dann mit Untersuchungen von Genen, welche für die Produktion von Substanzen gegen Nematoden verantwortlich sind. Hierbei konnten vier Mutanten gefunden werden, die durch eine Transposoninsertion eine schlechtere.
Bacillus amyloliqufaciens FZB42 has been known as PGPR which has an impressive effect to improve plant growth. It produces not only vast array of secondary metabolites with antibacterial and antifungal activities, but also produces the plant hormone IAA. Although many mechanisms have been elucidated, our knowledge about basic molecular mechanisms responsible for its beneficial action is far from complete. In this study, transposon mutagenesis based on mariner tranposon was applied to generate tranposon library which then was screened to identify the genes involved in plant growth-promoting activity. Three mutants that were impaired in their ability to colonize plant surface due to defects in biofilm formation and swarming motility were found. One mutant (degU mutant) showed defect in biofilm formation and swarming motility, as well, two mutants (yusV mutant and pabB mutant) impaired in biofilm formation were confirmed by complementation and retransformation. Screening by the Lemna biosystem and further assays with A. thaliana revealed three genes responsible for reduction in plant growth promoting activity of B. amyloliqufaciens FZB42. Colonization studies of these mutants in A. thaliana roots revealed patterns different to the wild type. A further issue pursued in this study was to discover new antibiotics using a mutant which has been blocked in its nonribosomally pathway. Screening of tranposon librabries from this mutant led to the finding of two novel ribosomally synthesized antibiotics. Further characterization revealed that these new antibiotics belonged to a novel bacteriocin (Amylocyclicin A) and a novel thiazole/oxazole-modified microcin (Plantazolicin). Last work in this study was looking for genes responsible for nematocidal production. Four mutants which showed reduction in nematocidal activity due to transposon insertion were found.

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21

Longford, Sharon Rae Faculty of Science UNSW. "The ecology of epiphytic bacteria on the marine red alga Delisea pulchra". Awarded by:University of New South Wales, 2007. http://handle.unsw.edu.au/1959.4/36783.

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Bacteria are ubiquitous to marine living surfaces, taking on a broad spectrum of roles from mutualistic to pathogenic. Despite their universality, much remains unknown about their basic ecology and interactions with higher organisms. To address this gap, this thesis firstly examines the bacterial communities associated with three co-occurring marine eukaryote hosts from temperate Australia: the demosponge Cymbastela concentrica, the subtidal red macroalga Delisea pulchra and the intertidal green macroalga Ulva australis. Molecular characterisation of the bacterial communities was undertaken using 16S rRNA gene library analysis to compare within-host (alpha) and between-host (beta) diversity for the three microbial communities. This study highlights the potentially substantial contribution host-associated microorganisms could have on marine microbial diversity. The remaining focus for this thesis was on the bacterial community associated with D. pulchra. This alga produces a suite of biologically active secondary metabolites (furanones) that non-toxically inhibit acyl homoserine lactone (AHL)-driven quorum sensing in bacteria, affecting a range of phenotypes including colonisation and virulence traits. The ecology of D. pulchra???s epiphytic bacteria was investigated using a mechanistic approach to explain bacterial colonisation patterns. In particular, concepts and models of ecological succession founded in eukaryote ecology were investigated. The thesis concludes with a study investigating the effect of furanones and elevated temperature on bacteria-induced disease and thallus bleaching of D. pulchra. In the presence of furanones colonisation and infection of two Roseobacter isolates from D. pulchra???s epiphytic bacterial community were inhibited. Ruegeria strain R11 was demonstrated to have temperature regulated virulence, which caused thallus bleaching in furanone-free algae. The implications of elevated sea temperatures resulting from global warming for algal health are discussed.

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22

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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23

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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24

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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25

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 persistantes
Aminoglycoside (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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26

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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27

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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28

Long, Richard A. "Bacteria-bacteria antagonism on marine organic particles and its biogeochemical implications /". Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2001. http://wwwlib.umi.com/cr/ucsd/fullcit?p3035420.

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29

Silva, Avalos Juan G. (Juan Guillermo). "Isolation, Characterization and Physiological Studies of Cyanide-Utilizing Bacteria". Thesis, University of North Texas, 1991. https://digital.library.unt.edu/ark:/67531/metadc278291/.

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Ten bacteria capable of growth on the metal-cyano complex, tetracyanonickelate (II) {K2 [Ni(CN)J } (TCN), supplied as the sole nitrogen source, were isolated. Seven isolates were identified as pseudomonads while the remaining three were classified as Klebsiella species. In addition to TCN, all isolates were able to utilize KCN although it was significantly more toxic. The degradation of TCN was most complete when supplied at growth-limiting concentrations, did not occur when ammonia was present, and resulted in the formation of nickel cyanide [Ni(CN)2] as a degradation product.

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30

Gaviria, Cantín Tania Cristina. "Factores Gre de Salmonella enterica serovar Typhimurium, su papel en el control de la filosofía y patogenicidad". Doctoral thesis, Universitat de Barcelona, 2016. http://hdl.handle.net/10803/397788.

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El género Salmonella, está compuesto de bacterias Gram-negativas, no esporuladas, en forma de bacilo. Salmonella tiene importante relevancia a nivel de salud pública ya que es uno de los principales patógenos entéricos tanto en países desarrollados como en vías de desarrollo. En los casos de gastroenteritis notificados en España, Salmonella se posiciona en segundo lugar, después de Campylobacter. En este trabajo se utilizó como organismo modelo de estudio S. enterica serovar Typhimurium (S. Typhimurium), que en humanos causa salmonelosis, gastroenteritis caracterizada por diarrea inflamatoria, originada normalmente tras la ingestión de alimentos o agua contaminados. Los genes de virulencia de S. Typhimurium están localizados mayoritariamente dentro de islas de patogenicidad (SPI). Los genes codificados en la SPI-1 promueben la invasión de células eucariotas, la regulación de la expresión de los genes de la SPI-1 está mediada por HiIA codificada en el gen, hilA, presente en la misma SPI-1. HiIA activa la expresión de los genes que codifican para la síntesis de un sistema de secreción de tipo 3 (T3SS) encargado de secretar e inyectar proteínas efectoras dentro de la célula hospedadora. La expresión de hilA se encuentra bajo el control de unl bucle de regulación, comprendido por las proteínas HiID, HiIC y RtsA. HiID es el regulador predominante de este sistema, mientras que HiIC y RtsA se encargan de amplificar la señal de activación. Por su parte, los genes que contiene la SPI-2, están implicados en causar infecciones sistémicas y la proliferación intracelular de la bacteria. Los factores Gre son factores que regulan la elongación de la transcripción génica en procariotas. Son conocidos por promover la actividad endorribonucleotídica de la ARN polimerasa (ARNpol) cuando ésta se encuentra en un estado de pausa por retroceso causado durante la elongación de la transcripción. A pesar de que los factores Gre han sido bien caracterizados en otras enterobacterias como Escherichia coli, en Salmonella no existen estudios que describan el papel de los factores Gre en la fisiología celular. Así, el objetivo principal de esta tesis doctoral fue estudiar el papel de los factores Gre en la fisiología y patogenicidad de Salmonella. En este estudio describimos que los factores Gre forman parte de la compleja red reguladora de la expresión de los genes de la SPI-1 y SPI-2 de Salmonella. Los resultados obtenidos indican que los factores Gre de Salmonella son esenciales para la correcta expresión de las proteínas efectoras codificadas dentro de la SPI-1 (SipA, SipC y SipD) y fuera de ella (SopE), y que también juegan un papel importante en la motilidad de la célula bacteriana, fenotipos predominantes en la patogenicidad. Se pudo determinar que la regulación de la expresión de los genes de la SPI-1 y la SPI-2 por parte de los factores Gre, es a través de la regulación transcripcional del gen hilD. La regulación mediada por los factores Gre requiere de la región 3'UTR del gen hilD. Además demostramos que la actividad antipausa de la transcripción de los factores Gre es necesaria para la correcta expresi formación de biofilm en Salmonella. Esta regulación al parecer también es ejercida en una región UTR, en este caso en la región 5’UTR del gen csgD, y es independiente de la temperatura. En análisis transcriptómicos mediante la técnica de microarrays, se observó que los factores Gre de Salmonella estarían implicados en la correcta expresión de muchos de los genes adquiridos horizontalmente (HGT) como son los genes presentes en las islas de patogenicidad, plásmidos y fagos. También se observó que existe un elevado número de genes distribuidos en diferentes categorías funcionales, que son corregulados por los factores Gre en conjunto con la proteína DksA, proteína que incrementa la fidelidad de la transcripción al disminuir la tasa de incorporación incorrecta de nucleótidos. Estos resultados indican que el patrón general de expresión génica de Salmonella es el resultado de una compleja interacción entre los factores Gre y la proteína DksA, que implica el control mutuo, competición por la unión a la ARNpol, y la acción similar u opuesta sobre la actividad de la ARNpol. Con los resultados presentados en esta tesis doctoral se puede concluir que los factores Gre forman parte de la compleja red de regulación de los genes de virulencia de Salmonella.ón de hilD.
Gre factors regulate gene transcription elongation in prokaryotes. In Escherichia coli they promote cleavage of the nascent RNA transcript within the elongation complex when the RNA polymerase is paused by a backtracking. Although the Gre factors have been characterized in other enterobacteria, in Salmonella there are not studies about their role in cellular physiology. The main objective of this thesis was to study the role of Gre factors in physiology and pathogenicity of Salmonella. In this study we describe Gre factors that are part of the complex regulatory network of gene expression of Salmonella pathogenicity island-1 (SPI-1) and SPI-2. The results indicate that Gre factors are pivotal in the control of predominant phenotypes in pathogenicity. They are essential for the correct expression of effector proteins encoded within (SipA, SipC and SipD) and outside SPI-1 (SopE), and they also play an important role in motility of the bacterial cell. It was determined that the regulation of gene expression of SPI-1 and SPI-2 by Gre factors is through transcriptional regulation of hilD gene. Regulation mediated by Gre factors requires hilD 3'UTR region. We demonstrated that Gre antipausa activity during transcription is necessary for the correct expression of hilD. It was also observed that Gre factors play an important role in transcriptional expression of csgD, main regulator of biofilm formation in Salmonella. This regulation is also apparently exerted through the 5'UTR region of the csgD gene, and is temperature- independent. In transcriptome analysis using Microarray, it was observed that Gre factors are implicated in the correct expression of many horizontally transferred genes (HGT) such as genes present in pathogenicity islands, plasmids and phages. It was also noted that there is a large number of genes distributed into different functional categories, which are co-regulated by Gre factors together with DksA protein, a protein that increases the accuracy of the transcript to decrease the rate of nucleotide missincorporation. These results indicate that the overall pattern of gene expression of Salmonella is the result of a complex interaction between Gre factors and DksA protein, involving the mutual control, competition for binding to ARNpol, and similar or opposite action on ARNpol activity. We can conclude that Gre factors are part of complex regulatory network of virulence genes of Salmonella.

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31

Kassotaki, Elissavet. "Elimination of micropollutants in conventional and novel nitrogen removal processes. A comparative assessment of diverse microbial communities capabilities". Doctoral thesis, Universitat de Girona, 2018. http://hdl.handle.net/10803/664342.

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Pharmaceutically active compounds (PhACs) and endocrine disrupting compounds (EDCs) can pose a significant risk to the environment and human health, undermining prosperity. Current wastewater treatment plants (WWTPs) cannot efficiently act as barriers to their release and have been identified as main points of discharge and contamination. The present thesis aimed to investigate the fate of five PhACs (ibuprofen, sulfamethoxazole, metoprolol, carbamazepine and venlafaxine) and five EDCs (estrone, 17β-estradiol, estriol, 17α-ethinylestradiol and bisphenol A) in different systems simulating wastewater treatment scenarios and to identify factors triggering their elimination. A comparative assessment was carried out to determine the contribution of the microbial groups (either autotrophic or heterotrophic) present in different lab, pilot and full-scale treatment systems performing different processes in the removal of the selected compounds. The results indicated that the overall efficiency of wastewater treatment systems can be broadened by combining different aerobic and anaerobic conditions and different types of biomass
Els compostos farmacèuticament actius (PhACs) i els pertorbadors endocrins(EDC) poden suposar un risc considerable per al medi ambient i la salut humana. Les estacions depuradores d'aigües residuals (EDAR) no poden actuar de manera eficient com a barreres per al seu alliberament i s'han identificat com a punts principals de descàrrega. La present tesi pretén determinar el destí de cinc PhACs (ibuprofèn, sulfametoxazol, metoprolol, carbamazepina i venlafaxina) i cinc EDCs (estrona, 17β-estradiol, estriol, 17α-etinilestradiol i bisfenol A), en sistemes que simulen escenaris de tractament d'aigües residuals, per identificar els factors claus en la seva eliminació. Es va realitzar una avaluació comparativa per determinar la contribució dels diferents grups bacterians (autòtrofs o heteròtrofs) presents en diferents sistemes a escala de laboratori, pilot i a gran escala. Els resultats indiquen que l'eficiència global dels sistemes de tractament d'aigües residuals es pot ampliar combinant diferents condicions aeròbiques i anaeròbies i tipus de biomassa

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32

Singh, Umadatt. "The adherence properties of Bacteroides gingivalis". Thesis, University of British Columbia, 1990. http://hdl.handle.net/2429/31013.

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A Bacteroides gingivalis adhesin mediating attachment to red blood cells and buccal epithelial cells was isolated, cloned and characterized. The isolation procedure involved gentle stirring of the cells followed by ammonium sulphate precipitation, ion-exchange and gel chromatography. The native molecule had a Mr in excess of 10⁶ kDa and was made up of subunits with an Mr of 43 kDa. Antisera raised to the adhesin and its subunits reacted with antigens on the surface of B. gingivalis cells. No reaction with fimbriae was seen. The IgG fractions from these antisera inhibited the adherence of B. gingivalis to host tissue. Proteolytic enzymes destroyed binding capability of whole cells and of the purified adhesin but the molecular weight of the haemagglutinin was not altered. A genomic library of B. gingivalis DNA was created in E. coli JM83. 5500 colonies were screened by a colony immunoassay with anti-S. gingivalis serum and by a direct haemagglutinating assay. 337 clones tested positive by the immunoassay and two clones, 1-3,and 1-49 tested positive for haemagglutinating activity. Both haemagglutinating positive recombinants had inserts of 3.2 kb. One clone, 1-49 was chosen for further characterization. E. coli 1-49 expressed a protein of 43 kDa that was not present in E. coli JM 83 control as seen by SDS-PAGE and Western blot analysis. Anti-1-49 serum inhibited the haemagglutinating activity of B. gingivalis and E. coli 1-49. This serum reacted with surface molecules on B. gingivalis and E. coli 1-49 as seen by immunogold electron microscopy and immunofluorescence, and to the purified haemagglutinin by Western blot analysis. Like the haemagglutinin on B. gingivalis, the haemagglutinating activity of E. coli 1-49 was destroyed by heating and proteolytic enzymes but the apparent size of the molecule as determined by SDS-PAGE was not affected. A bacterial coaggregating adhesin from B. gingivalis was isolated and characterized. The isolation procedure involved adsorption of the solubilized adhesin on S. mitis followed by elution with glycine buffer. SDS-PAGE of the boiled adhesin revealed a protein with an Mr of 46 kDa. Proteolytic digestion destroyed all bacterial aggregating activity and hydrolysed the 46 kd protein. Antisera raised to the 46 kDa protein reacted with surface molecules on all strains of B. gingivalis tested. This antiserum inhibited the coaggregation reaction between B. gingivalis and other bacteria. Vesicles produced by B. gingivalis were found to enhance the binding of S. sanguis to serum coated hydroxy apatite (SeHA). Maximum vesicle mediated binding took place at 37°C and was destroyed by heating. The lipopolysaccharide from several black pigmented bacteroides were isolated and characterized physically, chemically and immunologically. All of the LPS were of the smooth type and contained the sugars rhamnose, glucose, galactose, glucosamine and galactosamine; no KDO or heptose were found.
Science, Faculty of
Microbiology and Immunology, Department of
Graduate

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33

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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34

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, 2005
Keywords: Lactococcus lactis ssp. lactis, chromosome profiling, pulsed field gel electrophoresis, plasmid profiling, plasmid stability. Includes bibliographical references (leaves 58-63)

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35

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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36

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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37

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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38

Ansari, M. Azim. "Inference of recombination properties in bacteria from whole genomes". Thesis, University of Oxford, 2014. https://ora.ox.ac.uk/objects/uuid:b830a37a-fa7e-4b68-9868-fc5c629d45f5.

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The concept of species in bacteria is a matter of contention. The current definition is based on DNA-DNA hybridisation and does not account for evolutionary forces that are important in demarcating species. In this thesis we investigate two evolutionary forces that are important in speciation in bacteria, propose novel statistical models for them and infer parameters of interest. We present the first attempt at inferring the bias in the recombination process from whole bacterial genomes. Despite empirical evidence that recombination is biased and theoretical results that this bias is important in speciation, it is usually ignored. We propose a coalescent based model that accounts for the bias in the recombination process. We use approximate Bayesian computation for inference and describe an efficient method for simulating from the model. We show that our method performs well on simulated datasets and is robust to slight misspecification of the history of the samples. Application of our method to a Bacillus cereus dataset shows that it contain evidence that the recombination process depends on the evolutionary distance between donors and recipients. We demonstrate that the rate of bias in the recombination process for this dataset is far lower than what theoretical studies require for the spontaneous generation of populations that can be called species under neutral model. Next we propose a model for occurrence of adaptive events on a phylogenetic tree. We use the model to infer the boundaries of clusters on a phylogenetic tree that correspond to ecologically distinct lineages. we characterise our method using simulated datasets and show that it is conservative in estimating the number of adaptive events. Finally we apply our method to two bacterial datasets of Salmonella enterica and Vibrionaceae. We show that there is decisive evidence that isolates in these datasets partition into numerous ecologically distinct lineages and use our method to delineate the boundaries of these lineages.

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39

Genís, Pagès Sandra. "Use of lactic acid bacteria as a preventive strategy against metritis in dairy cows". Doctoral thesis, Universitat Autònoma de Barcelona, 2016. http://hdl.handle.net/10803/399509.

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Aproximadament el 40% de les vaques lleteres desenvolupen una malaltia uterina durant el post-part que acaba provocant infertilitat. Alguns estudis indiquen que la infecció uterina, causada principalment per Escherichia coli durant la primera setmana post-part, està associada amb la metritis, caracteritzada per la inflamació de l’úter on la vaca és incapaç d’eliminar els bacteris patògens. El tractament antibacterià tradicional que s’utilitza per contrarestar la metritis pot no ser efectiu en tots els casos, sobretot quan hi ha una inflamació prolongada. El primer estudi està enfocat en avaluar l’efecte de 4 possibles probiòtics del grup de bacteris de l’àcid làctic (BAL): Lactobacillus rhamnosus, Pediococcus acidilactici, Lactobacillus sakei i Lactobacillus reuteri, en un cultiu primari d’endometri amb infecció bacteriana i/o inflamació. Els principals resultats obtinguts van ser que P. acidilactici disminuïa la infecció d’E. coli, que L. rhamnosus reduïa significativament la inflamació cel·lular i que L. reuteri era capaç de disminuir la infecció d’E. coli quan les cèl·lules epitelials estaven prèviament inflamades. Durant el segon estudi es van provar 4 combinacions diferents de BAL a partir dels resultats obtinguts en el primer estudi. Es va avaluar la capacitat d’aquestes combinacions de disminuir la infecció d’E. coli i reduir la inflamació en el mateix cultiu primari. La combinació composta per L. rhamnous/ P. acidilactici/ L. reuteri amb una ràtio de 12/12/1 va ser la seleccionada. Llavors es va decidir comprovar que aquesta combinació continués sent eficaç en un model ex vivo (explants d’endometri). Els resultats obtinguts confirmaven la capacitat de la combinació de BAL de reduir la inflamació tissular. Per altra banda els assajos amb microscòpia electrònica mostraven un efecte protector de BAL en les cèl·lules epitelials. Hi havia menys necrosis, menys dany mitocondrial i més moc en les cèl·lules tractades amb BAL que en les no tractades. En el tercer estudi es va aplicar la combinació de BAL intravaginalment a vaques i al cap de 3 setmanes es va recol·lectar els seus endometris per obtenir-ne explants i infectar-los amb E. coli ex vivo. No es van observar diferències en els marcadors d’inflamació entre les vaques tractades amb BAL o les vaques control, ni en el número de Lactobacillus que hi havia a l’endometri de les vaques. Per altra banda, les vaques tractades amb BAL tendien a tenir menys presència d’E. coli a la vagina que les vaques control, i a més, expressaven menys B-defensins i MUC1, considerats marcadors d’infecció. Finalment, en el quart estudi, es van analitzar els efectes in vivo de la combinació de BAL sobre la incidència de metritis i inflamació de l’endometri en vaques de llet quan s’administrava intravaginalment durant 3 setmanes pre-part i o a l’úter un dia post-part. Els principals resultats obtinguts van ser que el tractament vaginal reduïa un 58% la prevalença de metritis comparada amb el grup control mentre que el tractament endometrial no la variava. No es va observar cap diferència amb els marcadors d’inflamació però els dos tractaments disminuïen l’activitatneutrofílica.
Approximately 40% of dairy cows develop a uterine disease during the post-partum leading to infertility. Several studies indicate that uterine infection, mainly caused by Escherichia coli during the first week post-partum, is associated with metritis, characterized by inflammation in the endometrium where the cow is not able to clear pathogenic bacteria. The traditional antimicrobial treatment may lack efficacy, especially in cases of sustained inflammation. The first study is focused in the evaluation of 4 possible probiotics belonging to the lactic acid bacteria (LAB): Lactobacillus rhamnosus, Pediococcus acidilactici, Lactobacillus sakei, and Lactobacillus reuteri, in an endometrial primary culture against bacterial infection and inflammation. The main results were that P. acidilactici was able to reduce E. coli infection, L. rhamnosus diminished cellular inflammation, and L. reuteri reduced E. coli infection when the epithelial cells were inflammated. On the second study, 4 different LAB combinations based on the results of the first study, were tested using the same primary culture. The combination composed by L. rhamnosus/ P. acidilactici/ L. reuteri with a ratio of 12/12/1 was selected. Then, this combination was tested in an ex vivo model (endometrial explants). The obtained results confirmed the capacity of this LAB combination to reduce tissular inflammation. On the other hand, electron microscopy assays showed a protective effect of LAB in endometrial epithelial cells. There was less necrosis, mitochondrial damage, and more mucus in the surface of LAB-treated cells than not-treated cells. In the third study, LAB combination was applied in vivo in the vagina of several cows, and 3 weeks later, the endometrium of those animals were collected. Explants were made from the endometrium and then infected with E. coli. No differences were observed in the inflammation markers between LAB-treated and control cows, or in the final quantification of Lactobacillus in the endometrium. On the other hand, LAB-treated cows tended to have less presence of E. coli in the vagina than control cows and, moreover, they expressed less B-defensins and MUC1, considerate markers of infection. Finally, on the fourth study, the effects of LAB combination were analyzed in vivo quantifying metritis prevalence and endometrial inflammation in dairy cows when the LAB combination was applied intravaginally during 3 weeks pre-partum or intra-uterine, 1 day after calving. The main results were that the vaginal treatment reduced metritis prevalence up to 58% compared with the control cows while no differences were observed with the endometrial treatment. No differences were found in the inflammation markers whereas both treatments (vaginal and endometrial) were able to modulate neutrophilic activity

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40

Viklund, Johan. "Phylogenomics of Oceanic Bacteria". Doctoral thesis, Uppsala universitet, Molekylär evolution, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-208441.

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The focus of this thesis has been the phylogenomics and evolution of the Alphaproteobacteria. This is a very diverse group which encompasses bacteria from intraceullar parasites, such as the Rickettsiales, to freeliving bacteria such as the most abundant bacteria on earth, the SAR11. The genome sizes of the Alphaproteobacteria range between 1 Mb and 10 Mb. This group is also connected to the origin of the mitochondria. Several studies have placed the SAR11 clade together with the Rickettsiales and mitochon- dria. Here I have shown that this placement is an artifact of compositional heterogeneity. When choosing genes or sites less affected by heterogeneity we find that the SAR11-clade instead groups with free-living alphaproteobacteria. Gene-content analysis showed that SAR11 was missing several genes for recombination and DNA-repair. The relationships within the SAR11- clade has also been examined and questioned. Specifically, we found no support for placing the taxon referred to as HIMB59 within the SAR11. Ocean metagenomes have been investigated to determine whether the SAR11-clade is a potential relative of the mitochondria. No such relationship was found. Further I have shown how important it is to take the phylogenetic relationships into account when doing statistical analyzes of genomes. The evolution of LD12, the freshwater representative of SAR11, was investigated. Phyloge- nies and synonymous substitution frequencies showed the presence of three distinct subclades within LD12. The recombination to mutation rate was found to be extremely low. This is re- markable in light of the very high rate in the oceanic SAR11. This is may be due to adaptation to a more specialized niche. Finally we have compared structure-based and sequence-based methods for orthology pre- diction. A high fraction of the orfan proteins were predicted to code for intrinsically disordered proteins. Many phylogenetic methods are sensitive to heterogeneity and this needs to be taken into ac- count when doing phylogenies. There have been at least three independent genome reductions in the Alphaproteobacteria. The frequency of recombination differ greatly between freshwater and oceanic SAR11. Forces affecting the size of bacterial genomes and mechanisms of evolu- tionary change depend on the environmental context.

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41

Li, Qing. "BACTERIA IN BIOETHANOL FERMENTATIONS". UKnowledge, 2014. http://uknowledge.uky.edu/pss_etds/52.

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To gain a better understanding of contaminating bacteria in bioethanol industry, we profiled the bacterial community structure in corn-based bioethanol fermentations and evaluated its correlation to environmental variables. Twenty-three batches of corn-mash sample were collected from six bioethanol facilities. The V4 region of the collective bacterial 16S rRNA genes was analyzed by Illumina Miseq sequencing to investigate the bacterial community structure. Non-metric multidimensional scaling (NMDS) ordination plots were constructed to visualize bacterial community structure groupings among different samples, as well as the effects of multiple environmental variables on community structure variation. Our results suggest that bacterial community structure is facility-specific, although there are two core bacterial phyla, Firmicutes and Proteobacteria. Feedstock, facility, and fermentation technology may explain the difference in community structure between different facilities. Lactic acid, the most important environmental variable that influences bacterial community structure grouping, could be utilized as an indicator of bacterial contamination. We also identified genes responsible for the multiple antibiotic-resistance phenotype of an Enterobacter cloacae strain isolated from a bioethanol fermentation facility. We performed PCR assays and revealed the presence of canonical genes encoding resistance to penicillin and erythromycin. However, a gene encoding resistance to virginiamycin was not detected.

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42

Mao, Xuegang. "Magnetotactic bacteria in sediment". Diss., Ludwig-Maximilians-Universität München, 2013. http://nbn-resolving.de/urn:nbn:de:bvb:19-169912.

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43

Goddard, P. A. "Metal accumulation in bacteria". Thesis, Cardiff University, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.373881.

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44

Browne, M. "Carotenoid biosynthesis in bacteria". Thesis, University of Liverpool, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.372685.

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45

Moosvi, Syeda Azra. "Methylotrophic bacteria from Antarctica". Thesis, King's College London (University of London), 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.406055.

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46

Hong, Vu Anh. "Bacteria mediated heat sinks". Thesis, Massachusetts Institute of Technology, 2010. http://hdl.handle.net/1721.1/59931.

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Thesis (S.B.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2010.
Cataloged from PDF version of thesis.
Includes bibliographical references (p. 55).
Many applications, such as laser diode technology, utilize components (eg. resistors) which have performance characteristics heavily dependent on temperature, and therefore, maintaining constant temperature is essential in order to eliminate drift in device efficiency. Constant temperature controllers, however, can often be complicated and only stay within a certain range of a set temperature. If temperature needs to be maintained, this thesis suggests a model instead to use ice as an isothermal heat sink. The model proposes to make use of thermodynamics and stabilize an isothermal solid-liquid interface created during ice formation, which will lead to having an isothermal free surface in the liquid phase. The model was validated using a Peltier device to freeze water by applying a constant DC current, and because the inefficiency of the module decreases with decreasing temperature, the heat dissipating power of the thermoelectric eventually equalizes with the ambient losses, stabilizing a solid-liquid interface. This stabilized interface was able to be maintained in experiments using deionized (DI) water, DI water with polystyrene (PS) micro-beads, and DI water with Pseudomonas syringae, a gram-negative bacteria. Pseudomonas syringae is known as an ice-nucleating agent that can reduce the amount of supercooling needed to nucleate ice. Experiments using the bacteria were observed to stabilize a solid-liquid interface faster than the control experiments, and this phenomenon was modeled as a two-fold reason: (1) by increasing nucleation temperature using the bacteria, a reduced input Peltier power is needed to nucleate ice, thereby making the Peltier device reach the steady-state heat losses faster; and (2) a possible decreased enthalpy of fusion caused by the bacteria leads to less latent heat released during the freezing process, putting less heat load on the Peltier device and allowing it to reach steady-state faster. This prediction regarding decreased enthalpy of fusion was validated using a heat flux sensor, as the preliminary results for a mixture of DI water with bacteria yielded an enthalpy of fusion of (199.1±20.2) kJ/kg, whereas the values for DI water and DI water with PS beads were (345.1±15.6) kJ/kg and (328.3±31.2) kJ/kg respectively.
by Vu Anh Hong.
S.B.

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47

Marcos, Ph D. Massachusetts Institute of Technology. "Bacteria in shear flow". Thesis, Massachusetts Institute of Technology, 2011. http://hdl.handle.net/1721.1/65278.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2011.
Cataloged from PDF version of thesis.
Includes bibliographical references (p. 68-74).
Bacteria are ubiquitous and play a critical role in many contexts. Their environment is nearly always dynamic due to the prevalence of fluid flow: creeping flow in soil, highly sheared flow in bodily conduits, and turbulent flow in rivers, streams, lakes, and oceans, as well as anthropogenic habitats such as bioreactors, heat exchangers and water supply systems. The presence of flow not only affects how bacteria are transported and dispersed at the macroscale, but also their ability to interact with their local habitat through motility and chemotaxis (the ability to sense and follow chemical gradients), in particular their foraging. Despite the ubiquitous interaction between motility, foraging and flow, almost all studies of bacterial motility have been confined to still fluids. At the small scales of a bacterium, any natural flow field (e.g. turbulence) is experienced as a linear velocity profile, or 'simple shear'. Therefore, understanding the interaction between a simple shear flow and motility is a critical step towards gaining insight on how the ambient flow favors or hinders microorganisms in their quest for food. In this thesis, I address this important gap by studying the effect of shear on bacteria, using a combination of microfluidic experiments and mathematical modeling. In chapter 2, a method is presented to create microscale vortices using a microfluidic setup specifically designed to investigate the response of swimming microorganisms. Stable, small-scale vortices were generated in the side-cavity of a microchannel by the shear stress in the main flow. The generation of a vortex was found to depend on the cavity's geometry, in particular its depth, aspect ratio, and opening width. Using video-microscopy, the position and orientation of individual microorganisms swimming in vortices of various intensities were tracked. We applied this setup to the marine bacterium Pseudoalteromonas haloplanktis. Under weak flows (shear rates < 0.1 s 1), P. haloplanktis exhibited a random swimming pattern. As the shear rate increased, P. haloplanktis became more aligned with the flow. In order to study the detailed hydrodynamic interaction between shear and bacteria, we developed a mathematical model employing resistive force theory. In general, the modeling of a bacterium requires consideration of two factors: the rotating flagellar bundle and the cell body to which the flagella are attached. To make the problem analytically tractable, we study the hydrodynamics around the head and the flagellum separately. In chapter 3, we present a combined theoretical and experimental investigation of the fluid mechanics of a helix exposed to a shear flow. In addition to classic Jeffery orbits, resistive force theory predicts a drift of the helix across streamlines, perpendicular to the shear plane. The direction of the drift is determined by the direction of the shear and the chirality of the helix. We verify this prediction experimentally using microfluidics, by exposing Leptospira biflexa flaB mutant, a non-motile strain of helix-shaped bacteria, to a plane parabolic flow. As the shear in the top and bottom halves of the microchannel has opposite sign, we predict and observe the bacteria in these two regions to drift in opposite directions. The magnitude of the drift is in good quantitative agreement with theory. We show that this setup can be used to separate microscale chiral objects. In chapter 4, a theoretical and experimental investigation of a swimming bacterium in a shear flow is presented. The presence of the cell body results in a novel phenomenon: chiral forces induce not only a lateral drift, but also a reorienting torque on swimming bacteria. For typical flagellated bacteria, the magnitude of this drift velocity is much smaller (-0.7 gm s-1) than typical swimming speeds of bacteria (-50 [mu]m s-1). However, with the addition of a head, the chirality-dependent forces that lead to a lateral drift also lead to a reorienting torque. The model based on resistive force theory predicts that the drift velocity of swimming bacteria is in the same order of magnitude as the swimming speed. Experimental observations of the motile bacteria Bacillus subtilis exposed to shear flows show good agreement with the theoretical prediction. This process is a purely passive hydrodynamic effect, as demonstrated by further experiments showing that bacteria do not behaviorally (i.e. actively) respond to shear. This newly discovered hydrodynamic reorientation can significantly affect any process that involves changes of swimming direction, so that bacterial 'steering' in a flow cannot be understood unless the effects of chiral reorientation are quantified. Because swimming and reorientation are central to the chemotaxis used by many bacteria for foraging, we expect this coupling of motility and flow to play an important role in the ecology of many bacterial species.
by Marcos.
Ph.D.

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48

Lyutenko, M., e M. V. Miroshnichenko. "Bacteria in our lives". Thesis, Sumy State University, 2014. http://essuir.sumdu.edu.ua/handle/123456789/45351.

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Bacteria are an integral part of our lives. They don’t only surround us externally, but also live inside us. Most people think that the bacteria are harmful micro-organisms, but they are wrong. Along with the pathogenicity, they play an important role in ensuring the normal functioning of our body. Microbial colonies found on or in the body are normally benign or beneficial. Bacteria are the basis of the normal microflora of many systems, especially of the digestive tract. These microbial colonies carry out a series of helpful and necessary functions, such as aiding in digestion. They also protect the body from the penetration of pathogenic microbes. These beneficial microbial colonies compete with each other for space and resources.

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Cooley, Natalie Ann. "Organophosphonate metabolism in bacteria". Thesis, Queen's University Belfast, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.517259.

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50

Palmer, Stephen. "Cadmium biosorption by bacteria". Thesis, University of Bath, 1988. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.233027.

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