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Ji, Boyang. "Comparative and Functional Genome Analysis of Magnetotactic Bacteria." Thesis, Aix-Marseille, 2013. http://www.theses.fr/2013AIXM4065.
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Les bactéries magnétotactiques (MTB) appartiennent à différents phyla procaryotes et ont la capacité de synthétiser des magnetosomes (cristaux de magnétite entourés par une membrane). Durant la thèse, nous avons procédé à l’analyse génomique de 2 bactéries magnétotactiques: Magnetospira sp. QH-2 et Magnetococcus MO-1. La synthénie et la correlation génique des gènes impliqués dans la formation des magnétosomes montrent que l'insertion de cet îlot chez QH-2 a eu lieu après la divergence entre les Magnetospirillum sp et Magnetospira sp. L'analyse comparative a mis en évidence trois groupes distincts de MTB : Groupe I, comprenant les souches Magnetospirillum spp. et Magnetospira; Groupe II avec MO-1 et M. marinus MC-1 et le Groupe III, avec D. magneticus RS-1. QH-2 montre aussi une évolution adaptative distincte par comparaison aux souches marines ou d'eau douce. L'analyse comparative des réseaux métaboliques révèle une très grande similitude intra-Groupe et une importante variabilité inter-Groupe. Cela est probablement dû aux enzymes impliqués dans les voies métaboliques anoxiques, qui représentent ainsi la contrainte à une distribution taxonomique large des MTB. Ces enzymes permettent ainsi de prédire le phénotype métabolique nécessaire à la production des magnétosomes. Différentes analyses (des protéines ribosomales au genome entier) indiquent une composition taxonomique chimérique des gènes de MO-1 et MC-1, et peut représenter une nouvelle lignée taxonomique chez les Protéobactéries. J’ai aussi participé à l'analyse des génomes de deux bactéries piezophiles, d’une bactérie photosynthétique pourpre et l’analyse phylogénomique des tyrosine-Kinases bactériennesMagnetotactic bacteria (MTB) are a diverse group of aquatic prokaryotes, which synthesize membrane-Enclosed magnetic crystals known as magnetosomes. In this thesis, the genome sequences of two marine MTB strains, Magnetospira sp. QH-2 and magneto-Ovoid strain MO-1 were analyzed. The magnetosome gene cluster synteny and mam gene correlation indicate that the insertion of the magnetosome island into QH-2 chromosome occurred after divergence between freshwater and marine magnetospirilla. Comparative genomic analysis revealed three distinct groups of sequenced MTB strains: Group I with Magnetospirillum spp. strains and Magnetospira strain, Group II with MO-1 strain and M. marinus MC-1, and Group III including Desulfovibrio magneticus RS-1. In addition, it shows an adaptive evolution of two marine MTB strains to marine sediments in comparison with closely related freshwater species. Moreover, comparative metabolic network analysis reveals high level of intra-Group similarity and inter-Group variety in MTB. With anoxic network enzymes, potential “MTB” strains are predicted, and are consistent with recently isolated MTB strains. It suggested that the anoxic metabolic network might be one restricted constraint for MTB distribution in bacterial lineages. Interestingly, analyses from ribosomal proteins to the whole MTB genome strongly support a taxonomic chimeric nature of MO-1 and MC-1 genes, and may represent a novel Proteobacteria lineage. Additionally, I also participate to genome analyses of piezophilic Desulfovibrio and Phaeospirillum molischianum strains as well as genome-Wide analysis of bacterial tyrosine kinases
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Köhn, Oliver [Verfasser]. "Statistical analysis of bacteria locomotion / Oliver Köhn." Saarbrücken : Saarländische Universitäts- und Landesbibliothek, 2020. http://d-nb.info/121906873X/34.
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Hill, Susannah Margaret. "Analysis of tellurite resistance in aquatic bacteria." Thesis, University of Liverpool, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.329467.
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Hitchen, Paul Gareth. "Structural analysis of lipo-oligosaccharides from pathogenic bacteria." Thesis, Imperial College London, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.268463.
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Tran, Thi thanh tam. "Comparative and functional genome analysis of Acidithiobacillus bacteria." Thesis, Aix-Marseille, 2016. http://www.theses.fr/2016AIXM4060.
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Les bactéries acidophiles du genre Acidithiobacillus joue un rôle important dans les activités industrielles de récupération des métaux au sein des sites miniers. Dans cette thèse, la séquence du génome de la bactérie psychro-tolerante Acidithiobacillus ferrivorans CF27 a été re-séquencée. L’analyse comparative du génome de CF27 et des autres bactéries du genre Acidithiobacillus a permis de montrer: (i) une synthénie conservée entre 2 clusters de tRNAs trouvés dans les génomes de At. ferrivorans CF27 et At. ferrooxidans ATCC 23270, et qui ont contribué à la redondance génique des tRNAs chez ces 2 organismes. Notre analyse in silico à grande échelle de ces clusters de tRNAs au sein des génomes procaryotes a montré que les clusters de tRNAs sont présents dans très peu de phyla bactériens; (ii) la présence d’une importante proportion de gènes spécifiques chez CF27 et SS3, ce qui indique la très grande variabilité du contenu génique dans les génomes d’Acidithiobacillus et ainsi la nature unique de chaque groupe d’espèces. L’expression de ces gènes spécifiques a été confirmée chez CF27 cultivés en présence de Fer et soufre; et (iii) une composition taxonomique chimérique des génomes de la classe des Acidithiobacillia, confirmant ainsi que ce groupe appartient à une classe taxonomique particulière. Ces résultats apporte de nouvelles connaissances sur l’adaptation de CF27 à son environnement, ainsi que la nature chimérique des génomes de la classe taxonomique Acidithiobacillia. J’ai participé au projet ‘Thioredoxine réductase (TR)’ dont l’objectif est de définir la fonction biochimique, la structure moléculaire, ainsi que l’histoire évolutive de TRi, une réductase atypiqueThe acidophilic Acidithiobacillus bacteria play an important role in industrial biomining operations for metal recovery. In this thesis, the genome sequence of a psychrotolerant Acidithiobacillus ferrivorans CF27 were first refined. The comparative genome analysis between CF27 and the closely related Acidithiobacillus genomes revealed: (i) a syntenic conservation of two tRNA array units which are only present in At. ferrivorans CF27 and At. ferrooxidans ATCC 23270 genomes and mainly contribute to the tRNA gene redundancy in both organisms. Moreover, our large-scale genome survey of the tRNA array units in prokaryotic organisms showed that tRNA arrays appear in few phyla; (ii) a high proportion of species-specific genes in CF27 and SS3 strains indicated the high variability of gene content in Acidithiobacillus genomes and therefore the unique nature of each group of species. Given that mRNA expression of some CF27 specific genes were confirmed in Fe(II)-grown cells and sulfur attached cells in CF27, these results highlighted the functional importance of specific genes for CF27 lifestyle; and (iii) the mosaic taxonomic composition of members of the Acidithiobacillia class, and thus confirmed that this group belongs to a particular taxonomic class, distinct to other proteobacterial groups. Taken together, our results provide insights into At. ferrivorans lifestyle as well as the chimeric genome nature of the Acidithiobacillus organisms. In addition, I also participated to the ‘Thioredoxin reductase’ project which aims to define the biochemical function, molecular structure and evolution of TRi, an atypical thioredoxin reductase
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Fukuyama, Yuto. "Genomic and transcriptional studies on hydrogenogenic carboxydotrophic bacteria." Kyoto University, 2019. http://hdl.handle.net/2433/242689.
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Kyoto University (京都大学)0048
新制・課程博士
博士(農学)
甲第21812号
農博第2325号
新制||農||1066(附属図書館)
学位論文||H31||N5184(農学部図書室)
京都大学大学院農学研究科応用生物科学専攻
(主査)教授 左子 芳彦, 教授 澤山 茂樹, 准教授 吉田 天士
学位規則第4条第1項該当
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Chan, Yuen-piu. "Taxonomic analysis of a haloacid degrading Burkholderia species MBA4." Click to view the E-thesis via HKUTO, 2005. http://sunzi.lib.hku.hk/hkuto/record/B36096374.
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Chan, Yuen-piu, and 陳源標. "Taxonomic analysis of a haloacid degrading Burkholderia species MBA4." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2005. http://hub.hku.hk/bib/B36096374.
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Hatziioanou, Diane. "Discovery and analysis of novel bacteriocins from gut bacteria." Thesis, University of East Anglia, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.539358.
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Adams, Curtis W. "Analysis of regulatory systems in two different gram⁻ bacteria /." Thesis, Connect to this title online; UW restricted, 1998. http://hdl.handle.net/1773/11484.
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Clark, Jonathan Bradley. "A molecular phylogenetic analysis of the intracellular bacteria rickettsiae /." The Ohio State University, 1990. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487678444257197.
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McCaig, Allison E. "16S ribosomal DNA analysis of marine ammonia-oxidising bacteria." Thesis, University of Aberdeen, 1995. http://digitool.abdn.ac.uk/R?func=search-advanced-go&find_code1=WSN&request1=AAIU543307.
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Nitrification is central to the global cycling of nitrogen and is important for primary production and other processes in marine systems, where nitrogen is generally the limiting nutrient. The majority of studies on nitrification, however, have focused on terrestrial systems, where this process can cause significant losses of N-based fertilisers from agricultural land. Comparatively little is known of nitrification in marine systems and the organisms involved. In addition, technical difficulties in isolation of pure cultures of ammonia-oxidising bacteria have severely restricted studies of species diversity and community structure of these organisms. In this study, molecular technology, based on the 16S ribosomal RNA (rRNA) molecule was applied to the characterisation of marine communities of ammonia-oxidising bacteria. PCR primers were designed for specific amplification of the rRNA gene (rDNA) from ammonia-oxidisers belonging to the beta-subdivision of the Proteobacteria. These primers were used to characterise both enrichment cultures and communities within polluted and unpolluted sediment samples. These studies indicated considerable diversity of beta-subgroup ammonia-oxidisers within marine systems which has not previously been detected. It was also shown that enrichment and isolation techniques select for strains belonging to the genus Nitrosomonas while the majority of sequences obtained by direct analysis of rDNA amplified from total genomic extracts belonged to the genus Nitrosospira. In addition, novel isolation methods were developed which considerably reduced the level of heterotrophic contamination and greatly facilitated isolation of pure cultures. In situ probing, using fluorescently labelled rRNA oligonucleotide probes, indicated that CCD microscopy is less sensitive than UV microscopy alone due to quenching of the signal.
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Douglas, Roseileen M. "Analysis of glutathione gated potassium efflux systems of bacteria." Thesis, University of Aberdeen, 1992. http://digitool.abdn.ac.uk/R?func=search-advanced-go&find_code1=WSN&request1=AAIU043410.
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The KefB and KefC systems of E. coli are two separate potassium efflux systems that are regulated by glutathione and specific glutathione metabolites. The aims of this study were to clone and sequence the E. coli kefB structural gene and to investigate the subunit stoichiometry of the E. coli KefC protein. A further objective was to determine the distribution of the KefC class of transport system in a range of bacterial species, with the ultimate aim of cloning the kefC homologue from a highly divergent organism. Attempts to clone the kefB gene by various strategies proved unsuccessful; possible explanations for this are discussed. Analysis of the suppression of a kefC leaky mutation by plasmids bearing varying lengths of the wild-type kefC gene indicated that the mutant and wild-type KefC proteins interact in the membrane to form a structure that has intermediate properties. These observations are consistent with KefC functioning as an oligomer. Using a variety of techniques, it was demonstrated that the KefC class of transport system is widely distributed among Gram-negativespecies but is absent from all the Gram-positive bacteria tested with the exception of Staph. aureus. In addition the kefC homologue from Er. carotovora was cloned and DNA sequencing initiated. The cloned Er. carotovora kefC gene product was able to suppress an E. coli kefC leaky mutation, thus providing further evidence that KefC exists as an oligomer.
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Nebe-v, Caron Gerhard. "Analysis of naturally occurring microbial populations from diverse environments." Thesis, Coventry University, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.323034.
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Stratton, Taylor Kristen. "Genomic analysis of high pressure adaptation in deep sea bacteria." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2008. http://wwwlib.umi.com/cr/ucsd/fullcit?p1453660.
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Thesis (M.S.)--University of California, San Diego, 2008.Title from first page of PDF file (viewed July 28, 2008). Available via ProQuest Digital Dissertations. Includes bibliographical references (p. 156-164).
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Liu, Oscar H. "RNAseq Analysis of Gastric Bacteria in Helicobacter pylori-Associated Carcinogenesis." Thesis, Högskolan i Skövde, Institutionen för biovetenskap, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-9937.
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Helicobacter pylori infects more than half of the world's population, and is known to be involved in several diseases including gastric cancer. Its close interactions with the stomach and host immune system serves as a good model to study the co-adaptation and co-evolution of the organisms in the stomach micro-environment. In this project, we utilized RNA-seq and data analysis tools to investigate differentially expressed genes by H. pylori in patients at different stages of early gastric cancer development. We also investigated the abundance and diversity of bacterial genera other than H. pylori, and looked for correlations with H. pylori presence and number. For differential gene expression of H. pylori, one gene was differentially expressed between samples of corpus atrophy without metaplasia vs. samples of antrum gastritis, and eight genes were found to be differentially expressed between samples of corpus atrophy with metaplasia vs. samples with pan-gastritis. When samples were clustered into different groups based on the expression data, 52 genes (shared or unique to the specific comparison groups) were found to be differentially expressed, but no apparent patterns were observed that could be explained by medical or sample collection data. For bacterial diversity and abundances, we found several genera colonizing the stomach, of which some have been previously identified. While most of these bacteria colonize regardless of the presence of H. pylori, the abundance of three genera, Wolinella, Campylobacter, and Veillonella, seem to be correlated with the presence of H. pylori.
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Hull, Katherine. "Statistical analysis of the accessory and core genomes in bacteria." Thesis, University of York, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.438057.
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Garza, de León Federico. "Single-molecule fluorescence analysis of transcription factors in living bacteria." Thesis, University of Oxford, 2015. https://ora.ox.ac.uk/objects/uuid:f1d10535-915c-4295-8df8-ade0f2a52259.
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Super-resolution microscopy has become an important tool to image cells at ever increasing resolution. Specifically, localization microscopy, in which single emitters are localized with high accuracy, has allowed us to follow and track single-molecules in live cells. The technique has revealed aspects in the proteins' real-time function that were impossible to study previously. Despite their extensive use in recent years, there are still possibilities to improve and validate the technique and the resulting data. This thesis presents the first tracking photo-activation localization microscopy (tracking PALM) on three transcription factors (TFs): the lac repressor (LacI), araC protein and the cAMP receptor protein (CRP). With this work I expand the range of applicability of localization methods and increase in detail an important part of cellular function. TFs control the expression of genes so that cells can adapt to external conditions. In Escherichia coli (E. coli), previous studies have shown that more than 60% of TFs have less than 100 monomers per genome copy. For example LacI, involved in the lactose utilization control, exists in E. coli in around 40 monomers in contrast to other proteins that exist in the tens of thousands. To study such low-copy numbers we found it necessary increase the throughput of tracking PALM and this thesis summarises our efforts to increase throughput. After constructing a setup capable of tracking PALM with a 3X increased throughput, I studied the diffusion and localization of LacI and LacI relative to its operators. By studying LacI, I found that there were a number of challenges related to low copy numbers, specifically background noise that leads to localisations that can affect the results. I characterized the background tracks and tested the ability of clustering to find a number of tandem operators. This knowledge allowed us to study other TFs: araC, involved in the control of arabinose utilization which also exists in low-copy numbers but functions in multiple genes; and the CRP, which both regulates multiple sites and exists in large copy numbers. In addition I worked towards the understanding of TF binding by simulating the combination of non-specific binding and free diffusion that emulates the search process of TFs. I obtained insight into the analysis of the data generated from tracking PALM. Finally I focused on creating a strategy to use our existing data to extract blinking rates from the fluorescent protein. Our insights into TFs diffusion and binding have shown that tracking PALM can yield important insights at this regime of protein concentrations. Our work can be applied to other TFs and proteins that function in low copy numbers.
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Altabtbaei, Khaled. "METAGENOMIC ANALYSIS OF PERIODONTAL BACTERIA ASSOCIATED WITH GENERALIZED AGGRESSIVE PERIODONTITIS." The Ohio State University, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=osu1466590877.
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Peden, John F. "Analysis of codon usage." Thesis, University of Nottingham, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.311834.
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Hoe, Nancy Palme. "Analysis of Temperature Sensing in Yersinia pestis: A Dissertation." eScholarship@UMMS, 1994. https://escholarship.umassmed.edu/gsbs_diss/98.
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The lcrF gene of Yersinia pestis, the etiological agent of plague, encodes a transcription activator responsible for inducing expression of several virulence-related proteins (Yops) in response to temperature. The mechanism of this thermoregulation was investigated. Using a yopE::lacZ reporter fusion, lcrF-mediated thermal regulation was observed in Y. pestis and Escherichia coli. The lcrF gene was sequenced, the 30.8 kDa. LcrF protein identified and purified, and LcrF-dependent yopE-specific DNA binding activity was detected. A sequence similarity search revealed that LcrF exhibits 98% homology to VirF of Yersinia enterocolitica and significant homology to the carboxy termini of other members of the AraC family of transcription activators. During localization studies, a significant proportion of LcrF was found associated with the membrane fraction in E. coli. However, pulse-chase experiments indicated that this result is an artifact of fractionation. lcrF-mediated thermal induction of the yopE::lacZ reporter fusion remains intact in a Shigella flexneri virR mutant. The virR mutation is known to affect thermal induction of Shigellavirulence genes, which are also controlled by an activator in the AraC family.
As a first step toward identifying the temperature-sensitive step in the regulation of yop expression, lcrF::lacZ transcriptional fusions were constructed and analyzed in Y. pestis and E. coli. The activity of the fusions was not affected by the native pCD1 virulence plasmid, an intact lcrF gene, or temperature. Thus, induction of lcrF transcription is not essential for temperature-dependent activation of yopE transcription. To confirm these results, attempts were made to identify both the native lcrF message in Y. pestis, and a lcrF-lacZ hybrid message in Y. pestis and E. coli. These attempts were unsuccessful. Examination of LcrF protein production revealed temperature-dependent expression in Y. pestis. Surprisingly, high-level T7 polymerase-directed transcription of the lcrF gene in Escherichia coli also resulted in temperature-dependent production of the LcrF protein. Pulse-chase experiments showed that the LcrF protein was stable at both 26 and 37°C, suggesting that translation rate or message degradation is thermally controlled. Comparison of the amount of LcrF protein produced per unit of message at 26 and 37°C in E. coli indicated that the efficiency of translation of lcrF message increased with temperature. mRNA secondary structure predictions suggest that the lcrF Shine-Dalgarno sequence is sequestered in a stem-loop. A model in which decreased stability of this stem-loop with increasing temperature leads to increased efficiency of translation initiation of lcrF message is presented.
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Leung, Po-shan. "In silico analysis of 16S ribosomal RNA gene sequencing based methods for identification of medically important Gram-positive cocci /." View the Table of Contents & Abstract, 2007. http://sunzi.lib.hku.hk/hkuto/record/B38348159.
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Leung, Po-shan, and 梁寶珊. "In silico analysis of 16S ribosomal RNA gene sequencing based methods for identification of medically important Gram-positive cocci." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2007. http://hub.hku.hk/bib/B45011382.
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Porter, Kimberly Rae. "Determining Sources of Fecal Pollution in Washington D.C. Waterways." Thesis, Virginia Tech, 2003. http://hdl.handle.net/10919/36009.
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Antibiotic resistance analysis (ARA) of Enterococci was used to determine sources of fecal contamination in three District of Columbia waterways: Rock Creek, the Anacostia River, and the Potomac River. These three waterways were identified as exceeding water quality standards set for fecal coliform levels and were designated by the District of Columbia to the Environmental Protection Agency's 303 (d) impaired waters list.
A library profile of 1,806 enterococcus isolates from known sources was built based on antibiotic resistance patterns from thirty concentrations of nine antibiotics. These sources included human, cattle, chicken, horse, goat, sheep, deer, raccoon, muskrat, goose, seagull, coyote, duck, wild turkey, dog, and cat.
Antibiotic profiles were characterized for 24 unknown enterococci isolates on each of 198 samples (38 samples from the Potomac River, 79 samples from the Anacostia River, and 81 samples from Rock Creek) collected periodically from July 2002 through April 2003. Two major storm events were also sampled during this period. These isolate profiles were compared to the known source library using logistic regression. Three dominant sources of fecal pollution were detected in the Potomac River: livestock (30%), human (29%), and wildlife (22%). Three dominant signatures were also detected in Rock Creek: horse (26%), human (26%), and wildlife (24%). Human was the only dominant source detected in the Anacostia River, averaging 43% over the sampling period.
The results of this study indicate that human is a substantial contributor to the fecal contamination problems, especially in the Anacostia River, but there are significant agricultural and wildlife contributions as well. Significant and predictable seasonal variations were also detected, indicating the influence of precipitation on source distributions. The results of this study will aid the Metropolitan Washington D.C. Council of Governments in making important management decisions to help improve the water quality in and around the Washington D.C. area.
Expanding the limits of ARA was also an integral part of this research. Three new and even controversial analytical techniques were run on the data collected from this project in an attempt to improve confidence and provide direction to the results of this study. The first was a comparison of the more commonly used statistical analysis model discriminate analysis (DA) with logistic regression (LR). No significant difference was found between the output of the two models for the known source libraries, therefore no suggestion could be made in favor of one model over the other. Another analytical test of the data was the introduction of a standard requiring isolates to meet a minimum of 80% similarity to the known source profiles where it was classified. With the 80% cutoff, between 41% and 44% of the isolates could not be classified to any source and were placed in an unknown category. Based on the remaining isolates, source distributions were recalculated and were not statistically different than those calculated with no restriction for isolate similarity for matching. The last major test of the data was the analysis of the library for representativeness via pulled sample cross validation and the exclusion of all duplicate patterns from the known source library. These analyses did not confirm the representativeness of the databases, but results were further analyzed based on the implications these analyses have on library based methods.Master of Science
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Khan, H. "Mutational analysis of the Klebsiella pneumoniae nifLA promoter." Thesis, University of Sussex, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.372054.
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Xia, Yu. "Phlogenetic analysis of the genus Azospirillum." Thesis, University of Newcastle Upon Tyne, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.363541.
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Pinchuk, Tommy. "Optimization of pre-processing variables for hyperspectral analysis of focal plane array Fourier transform infrared images." Thesis, McGill University, 2006. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=98769.
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A genetic algorithm was employed to select the optimal combination of preprocessing variables, including data pretreatment, data manipulation and feature extraction procedures, for eventual clustering of a data set consisting of hyperspectral images acquired by a focal plane array Fourier transform infrared (FPA-FTIR) spectrometer. The data set consisted of infrared images of bacterial films, and the classification task investigated was the discrimination between Gram-positive and Gram-negative bacteria. The genetic algorithm evaluated combinations of variables pertaining to bacterial film thickness tolerances, baseline correction, pixel co-addition, outlier removal, smoothing, mean centering, normalization, derivatization, integration and principal component selection. Following numerous iterations of unsupervised processing, the genetic algorithm arrived at a sub-optimal solution yielding a clustering accuracy of 97.8% and a data utilization of 28.6%. The results provided insight into the co-dependencies of the pre-processing variables and their consequential effect on the selected data. The robustness of the classification model was evaluated and reinforced by the successful classification of two distinct validation sets. The overall success of the genetic algorithm suggests that it is an effective time saving resource for the optimization of pre-processing variables that does not require operator intervention.
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Leigh, Spencer A. "Functional analysis of the mycoplasma fermentans P29 adhesin." free to MU campus, to others for purchase, 2000. http://wwwlib.umi.com/cr/mo/fullcit?p9999300.
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Kieser, Helen M. "Analysis of the genome of Streptomyces coelicolor A3(2)." Thesis, University of East Anglia, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.302209.
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Kumar, Purnima. "Molecular analysis of bacteria associated with chronic periodontitis and periodontal health." Connect to resource, 2005. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1124221576.
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Thesis (Ph. D.)--Ohio State University, 2005.Title from first page of PDF file. Document formatted into pages; contains x, 104 p.; also includes graphics (some col.). Includes bibliographical references (p. 92-104). Available online via OhioLINK's ETD Center
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Simon, Svenja [Verfasser]. "Visual Analysis of RNAseq Data : Discovering Genes in Bacteria / Svenja Simon." Konstanz : Bibliothek der Universität Konstanz, 2015. http://d-nb.info/1114886580/34.
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Turner, Robert David. "Development of atomic force microscopy for surface analysis of vital bacteria." Thesis, University of Leeds, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.509877.
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Stokes, Neil Robert. "Analysis of the function and regulation of mechanosensitive channels in bacteria." Thesis, University of Aberdeen, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.325233.
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Dohlich, Kim-Stephanie. "Analysis of Type Three System transport mechanism in gram-negative bacteria." Doctoral thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät I, 2014. http://dx.doi.org/10.18452/16914.
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Das Typ III Sekretionssystem (T3SS) ist ein Proteinkomplex den Gramnegative Bakterien nutzen um in einem Schritt Effektorproteine (Effektoren) aus dem Zytosol über die Doppelmembran zu sekretieren. Für viele Bakterien ist das T3SS ein essenzieller Virulenzfaktor, der es ihnen erlaubt mit ihrem Wirt zu interagieren und diesen zu manipulieren. Charakteristisch für das T3SS ist die strukturelle Komponente, der Nadelkomplex. Dieser ähnelt strukturell einer Spritze, deren Basalkörper die bakteriellen Membranen und das Periplasma durchspannt und einer Nadel, die vom Basalkörper aus dem Bakterium ragt. Basierend auf dem Modell einer Spritze wird angenommen, dass Effektoren entfaltet und anschließend durch Basalkörper und Nadelkanal sekretiert werden. Trotz der kontinuierlichen Forschung an T3SS entbehrt dieses Modell einer experimentellen Grundlage und der Mechanismus ist nicht vollständig erklärt. Ziel der Arbeit war es, eine experimentelle Basis für den Sekretionsmechanismus des T3SS zu schaffen. Um zu verstehen, wie das T3SS Effektoren sekretiert, wurden zunächst Fusionsproteine konstruiert, welche aus einem Effektor und einem stabil gefalteten Knotenprotein bestehen. Aufgrund des Knotens in der Fusion ist davon auszugehen, dass dieser während der Sekretion nicht entfalten kann. Die Effektordomäne wird sekretiert während der Knoten im Kanal verbleibt und diesen verstopft. Nach unseremWissen ist diese Arbeit die erste Visualisierung von Effektorfusionen an isolierten Nadelkomplexen. Die Effektorfusion wird N-terminal voran durch den Kanal sekretiert, wobei der Kanal das Substrat umschließt und gegen Proteasen und chemische Modifikationen abschirmt. Die Ergebnisse dieser Arbeit untermauern eine Grundidee der Funktionsweise des T3SS und liefern eine vielversprechende Strategie für in situ-Strukturanalysen. Dieser Ansatz lässt sich auch auf andere Proteinsekretionssysteme übertragen, bei welchen Substrate vor dem Transport entfaltet werden müssen.The Type III Secretion System (T3SS) is a complex used by Gram-negative bacteria to secrete effector proteins from the cytoplasm across the bacterial envelope in a single step. For many pathogens, the T3SS is an essential virulence factor that enables the bacteria to interact with and manipulate their respective host. A characteristic structural feature of the T3SS is the needle complex (NC). The NC resembles a syringe with a basal body spanning both bacterial membranes and a long needle-like structure that protrudes from the bacterium. Based on the paradigm of a syringe-like mechanism, it is generally assumed that effectors are unfolded and secreted from the bacterial cytoplasm through the basal body and needle channel. Despite extensive research on T3SS, this hypothesis lacks experimental evidence and the mechanism of secretion is not fully understood. This work aimed to provide an experimental basis for the model of the T3SS mechanism. In order to elucidate details of the effector secretion mechanism, fusion proteins consisting of an effector and a bulky protein containing a knotted motif were generated. It is assumed that the knot cannot be unfolded during secretion of the chimera. Consequently, these fusions are accepted as T3SS substrates but remain inside the NC channel and obstruct the T3SS. This is, to our best knowledge, the first time effector fusions have been visualized together with isolated NCs and it demonstrates that effector proteins are secreted directly through the channel with their N-terminus first. The channel encloses the substrate and shields it from a protease and chemical modifications. These results corroborate an elementary understanding of how the T3SS works and provide a powerful tool for in situ-structural investigations. This approach might also be applicable to other protein secretion systems that require unfolding of their substrates prior to secretion.
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Poon, Vincent. "Analysis and exploitation of AHFCA-dependent signalling systems in Streptomyces bacteria." Thesis, University of Warwick, 2015. http://wrap.warwick.ac.uk/79957/.
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From genome sequencing and analyses, Streptomyces bacteria are predicted to produce hundreds of bioactive metabolite compounds; however, the products of some of these cryptic biosynthetic gene clusters are most often silent or produced in very small quantities in laboratory conditions. The AHFCA-dependent signalling system is an example of a regulatory systems that tightly control expression of cryptic biosynthetic gene clusters in Streptomyces bacteria. Bioinformatic analyses, using MEME and FIMO, were able to successfully reveal TetR repressor binding sites to gain insights into complex regulatory networks. The S. avermitilis cryptic biosynthetic gene cluster, which is proposed to be under the control of an AHFCA-dependent signalling system, has not been investigated before and genome mining predictions suggest the biosynthetic gene cluster could be involved in the biosynthesis of novel azoxy compounds. The 50 kb predicted azoxy biosynthetic gene cluster was captured using pESAC13A PAC technologies and introduced into S. coelicolor M1152 and S. lividans TK24 heterologous hosts. Comparative metabolic profiling successfully identified the predicted azoxy compounds in S. coelicolor M1152 by LC-MS and identification of the azoxy compounds were supported by UHPLC-ESI-TOF-MS analysis and incorporation of isotope-labelled L-serine. Consistent with the model of transcriptional regulation, exploitation of the S. avermitilis AHFCA-dependent signalling system through the inactivation of sav_2268 transcriptional repressor in S. lividans TK24 heterologous hosts unlocked the production of azoxy compounds and AHFCA signalling molecules.
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Bradley, Paul B. "Multi-system analysis of nitrogen use by phytoplankton and heterotrophic bacteria." W&M ScholarWorks, 2009. https://scholarworks.wm.edu/etd/1539616580.
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Traditional measurements of phytoplankton N uptake have been confounded by bacterial retention on filters used in 15N uptake studies, and such methodological obstacles have limited our understanding of phytoplankton-bacterial interactions regarding N cycling. In this research, uptake of various inorganic and organic N substrates by phytoplankton and bacteria was measured in several marine ecosystems using two distinct approaches: size fractionation into phytoplankton and bacterial size classes, and flow cytometric (FCM) sorting of autotrophic cells. Comprehensive assessments of N uptake dynamics were conducted in Chesapeake Bay, the Mid-Atlantic Bight, and Raunefjord, Norway, with supplementary data collected from the York River, Virginia and the Gulf of Mexico. In Chesapeake Bay, the composition of the dissolved N pool shifted from being dominated by dissolved inorganic N (DIN) in the upper bay to mostly dissolved organic N (DON) in the lower bay. Accordingly, phytoplankton nitrate uptake was highest near the head, whereas uptake of urea and dissolved free amino acids generally increased southward. Nonetheless, ammonium was the dominant form of N used by phytoplankton and bacteria throughout the bay. In the Mid-Atlantic Bight, the surface layer was devoid of DIN but ambient urea concentrations were relatively high and this organic substrate supported a large majority of total measured N uptake. The dissolved N pool in the bottom water consisted of about two-thirds DIN, with ammonium contributing most to total uptake. Bacteria were especially active in the bottom water and contributed over half of the total DIN uptake, and there was evidence of bacterial urea uptake in the surface water. In Raunefjord, a mesocosm approach was used to examine N uptake by a bloom of colonial Phaeocystis as well as the competition between phytoplankton and bacteria for limited N resources. Despite amending with nitrate, ammonium was the primary N form supporting the bloom. In the unfertilized mesocosm, bacteria were responsible for about half the urea uptake, most of the DFAA uptake, and at least a third of DIN uptake. Overall, total dissolved N concentrations and total N uptake decreased from estuarine to oceanic waters, although uptake rates were highly variable within each ecosystem. The reduced N forms, ammonium and urea, were most important to phytoplankton N nutrition, and contrary to traditional belief, urea at times played an important role in bacterial N uptake. With respect to methodological approaches, traditional filtration resulted in significant overestimation of phytoplankton N uptake due to the inclusion of, and 15N enrichment in, bacterial biomass retained on filters. This research represents the first comprehensive assessment of phytoplankton-specific N uptake across various ecosystems. It highlights not only the need for careful qualification of uptake rates measured using traditional approaches, but also the potential application of FCM sorting to more detailed examination of N uptake by phytoplankton in general, but also by specific taxa in various marine ecosystems.
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Leuthner, Moritz. "Improving cell secretome analysis and bacteria evolution by means of acoustophoresis." Thesis, KTH, Skolan för kemi, bioteknologi och hälsa (CBH), 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-285985.
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In both, cell secretome analysis and bacteria evolution, controlled handling of particles with a few to sub-micrometers in size and media exchange are inevitable in order to investigate body fluid’s proteins or change the surrounding culture conditions for pivoted evolution. Typically, nanofiltration and ultra-centrifugation are employed which can lead to cell damage, need large sample volumes and have a high sample loss. Using contactless and label-free acoustic cell manipulation, disadvantages of other magnetic, dielectric or hydrodynamic methods can be avoided. Here, a novel design using acoustic forces for small particle trapping and media exchange is thoroughly numerically investigated including first- and second-order acoustic effects. The device comprises parallel aligned medium and air channels separated by a thin wall. Particle trapping occurs at this thin wall. The medium channel dimensions (height and width) and thin wall thickness are optimized with respect to trapping forces. Thinnest walls are preferable and an aspect ratio of 0.8. First preliminary experimental variation with polystyrene particles showed good agreement with the simulations. Thereby the particle trapping efficiency is evaluated under quiescent flow conditions. For particle trapping, a device with a channel height of 290μm and an aspect ratio of 0.7 is superior which supports the numerical results. Finally, medium exchange of E. coli bacteria is demonstrated with best results for a device with a channel height of 450μm and an aspect ratio of 0.8 showing that 13.4% of the initial bacteria were released after medium exchange which can be used for further processing.
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Sharma, Poonam. "Genome analysis of multidrug resistant bacteria from patients with cystic fibrosis." Thesis, Aix-Marseille, 2013. http://www.theses.fr/2013AIXM5096.
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La mucoviscidose est une maladie génétique autosomique causée par une mutation dans le gène CFTR (Cystic Fibrosis Transmembrane Conductance Regulator). Mon travail s’est décomposé en deux parties principales : d’une part j’ai réalisé une revue de la littérature sur l’analyse des génomes bactériens isolés de patients mucoviscidosiques comparativement aux génomes des mêmes espèces isolées dans d’autrescontextes et d’autre part j’ai analysé les génomes de trois espèces bactériennes (Microbacterium yannicii, Chryseobacterium oranimense et Haemophilus parahaemolyticus). L’analyse exhaustive des génomes bactériens issus de patients atteints de mucoviscidose a révélé une extraordinaire évolution de ces génomes en fonction du temps et des traitements reçus par ces patients qui témoigne de la capacité qu’ont ces bactéries à s’adapter à leur écosystème notamment par l’acquisition de nouveaux gènes par transfert latéral de gènes. Ce travail montre l’extraordinaire plasticité des génomes bactériens dans un milieu donné et à ce titre le poumon de patients atteints de mucoviscidose représente un modèle unique pour comprendre l’évolution des génomes bactériens. De plus, notre travail a permis d’identifier leurs mécanismes moléculaires de résistance aux antibiotiques. Les travaux à venir sur l’étude des métagénomes de prélèvements chez ces patients pourrait permettre de répondre à ces questions dans le futur. La découverte de nouvelles espèces et / ou émergentes va nous permettre d’avoir une image plus complète de la mucoviscidose qui pourrait conduire à une meilleure connaissance de la maladie et donc à une meilleure prise en charge thérapeutiqueCystic fibrosis is an autosomal genetic disorder caused by a mutation in the CFTR (Cystic Fibrosis Transmembrane Conductance Regulator) gene. Pulmonary infection is the major problem faced by patients with cystic fibrosis. My work is divided into two main parts: first I made a review of the literature on the analysis of bacterial genomes isolated from CF patients compared to the genomes of the same species isolated in autrescontextes and other part I analyzed the genomes of three species of bacteria (Microbacterium yannicii, Chryseobacterium oranimense and Haemophilus parahaemolyticus). The comprehensive analysis of bacterial genomes from cystic fibrosis patients revealed an extraordinary evolution of these genomes with time and treatment received by these patients reflects the ability of these bacteria to adapt to their particular ecosystem the acquisition of new genes by lateral gene transfer. This work shows the extraordinary plasticity of bacterial genomes in a given environment and as the lungs of patients with cystic fibrosis represents a unique model for understanding the evolution of bacterial genomes. In addition, our work has identified their molecular mechanisms of resistance to antibiotics. Future work on the study of metagenomes sampling in these patients could help to answer these questions in the future. The discovery of new species and / or emerging will allow us to have a more complete picture of cystic fibrosis which could lead to a better understanding of the disease and thus a better therapeutic management
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Leangapichart, Thongpan. "Phenotypic and genomic analysis of multi-drug resistant bacteria in travelers." Thesis, Aix-Marseille, 2017. http://www.theses.fr/2017AIXM0183.
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La résistance aux antibiotiques chez les bactéries est un problème majeur mondial du fait de son augmentation. Récemment, la transmission des bactéries résistantes aux humains, aux animaux et à l’environnement sont de plus en plus décrits dans la littérature. Ces dernières années, les voyages internationaux ont augmenté massivement ce qui a permis aux bactéries résistantes de se propager d’un lieu à un autre. Les voyageurs internationaux sont les principaux acteurs de l’acquisition et de la propagation des gènes de résistance aux antibiotiques. Le plus grand rassemblement annuel de personnes comme le pèlerinage à la Mecque est connu pour être un réservoir pour la transmission des maladies infectieuses telles que la grippe, les épidémies méningococciques ou la tuberculose. Par conséquent, les voyageurs en particulier les pèlerins représentent une source importante de propagation de bactéries multi-résistantes. Les études sur la transmission et l'acquisition de gènes de résistance pendant le Hajj sont rares. Par conséquent, ce projet de thèse a trois objectifs principaux permettant de mieux comprendre la prévalence des gènes de résistance et des bactéries multi-résistantes au cours du Hajj:(i)l’étude de la surveillance épidémiologique des gènes de résistance chez les pèlerins avant et après le Hajj,(ii)l’étude des facteurs de risque d'acquisition de gènes de résistance aux antibiotiques chez les pèlerins,(iii)les études épidémiologiques moléculaires des bactéries résistantes chez les pèlerins et d'autres sources, tels que les patients, les animaux et l’environnement en utilisant des techniques comme le typage des séquences multi-locus et le séquençage du génome completAntibiotic resistance in bacteria is increasing and become a worldwide problem. Newresistance bacteria or mechanisms are emerging and spreading rapidly. Recently, thetransmission of antibiotic-resistant (AR) bacteria among humans, animals, and the variousenvironments are vastly recognized. With the growth of international travels over the pastdecades, this provides opportunities for AR bacteria to be spread rapidly from one geographiclocation to another. During trips, travelers changed diets, lifestyles, and their environmentsresulting in the alteration of AR patterns of bacteria residing in the gut. Thus, internationaltravelers are one of the most important modes for the acquisition and spread of AR genes.The largest annual mass gathering, the Hajj (pilgrimage to Mecca) is well known as a sourcefor infectious diseases transmission such as influenza, meningococcal outbreaks ortuberculosis. Thus, travelers, especially pilgrims, are one of the most significant sources forspreading AR bacteria. However, studies of the transmission and acquisition of AR genesduring Hajj in pilgrims are scarce. Therefore, this research thesis was carried out with threemain objectives to better understanding the prevalence of AR genes and bacteria during Hajj:(i) epidemiological surveillance of AR genes in pilgrims before and after Hajj, (ii) risk factorsanalysis concerning AR genes acquisition in pilgrims, (iii) molecular epidemiological studiesof AR bacteria in pilgrims, including patients, animals, and environment with the use ofmulti-locus sequence typing and whole genome sequencing
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Jeong, Sooyoung. "A custom oligonucleotide microarray analysis as a tool for dissecting soybean-bradyrhizobium japonicum nodule senescence." Diss., Columbia, Mo. : University of Missouri-Columbia, 2007. http://hdl.handle.net/10355/6266.
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Thesis (M.S.)--University of Missouri-Columbia, 2007.The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Title from title screen of research.pdf file (viewed on May 27, 2009) Includes bibliographical references.
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Jandhyam, Haritha Lakshmi. "Molecular phylogenetic analysis of novel spiroplasma isolates." Click here to access thesis, 2009. http://www.georgiasouthern.edu/etd/archive/spring2009/haritha_l_jandhyam/jandhyam_haritha_l_200901_ms.pdf.
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Thesis (M.S.)--Georgia Southern University, 2009."A thesis submitted to the Graduate Faculty of Georgia Southern University in partial fulfillment of the requirements for the degree Master of Science." Directed by Laura B. Regassa. ETD. Includes bibliographical references (p. 64-69) and appendices.
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Burns, David Alexander. "Analysis of the spore germination mechanisms of Clostridium difficile." Thesis, University of Nottingham, 2011. http://eprints.nottingham.ac.uk/11852/.
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Clostridium difficile is the leading cause of hospital acquired diarrhoea and a major burden to healthcare services worldwide. Endospore production plays a pivotal role in infection and disease transmission, but in order to cause disease these spores must germinate and return to vegetative cell growth. Therefore, knowledge of spore germination is important and may have direct applications in future disease prevention. Germination has been well studied in Bacillus and in some clostridia, but the mechanisms of C. difficile spore germination remain unclear. Apparent homologues of genes important for germination in other spore formers have been identified in the C. difficile genome and ClosTron technology was used to inactivate homologues of sleC, cspA, cspB and cspC (Clostridium perfringens) and cwlJ, sleB and cwlD (Bacillus subtilis) in both C. difficile 630Δerm and a BI/NAP1/027 isolate (a ‘hypervirulent’ type associated with outbreaks of increased disease severity). Using a combination of several different assays to study these mutants in detail, a number of the identified target genes appear to be essential for germination and outgrowth of C. difficile spores. This is the first report of using reverse genetics to study the germination of C. difficile spores and the first gene characterisation by mutagenesis in a BI/NAP1/027 isolate of C. difficile. Furthermore, this study uncovered evidence of significant variation in the sporulation and germination characteristics of different C. difficile strains, but this variation did not appear to be type-associated.
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Wood, Claire M. "A molecular analysis of the potassium efflux system KefC." Thesis, University of Aberdeen, 1996. http://digitool.abdn.ac.uk/R?func=search-advanced-go&find_code1=WSN&request1=AAIU530038.
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KefB and KefC are glutathione-gated potassium channels that play a protective role during the detoxification of electrophiles in Gram negative bacteria. The KefC channel from Klebsiella aerogenes has been characterised and the gene cloned and sequenced. The KefC channel from K. aerogenes is analogous to KefC from Escherichia coli. The electrophile compounds NEM and CDNB are strong activators of potassium loss via the channel, whereas, methylglyoxal is a weak activator of potassium loss. At the amino acid level the putative protein shows a high degree of similarity with KefC from E. coli. While sequencing the kefC gene from K. aerogenes a difference in the genome organisation of K. aerogenes and E. coli was observed, highlighting the presence of an unassigned ORF, yabF, that overlaps the kefC by 8 bp. Clones of the K. aerogenes kefC gene that lack the first 129 bp of yabF exhibit reduced KefC activity. Analysis of the sequence surrounding the kefB gene from E. coli revealed an ORF, yhaH, that encodes a homologue of the putative YabF protein. The amino acid distribution of YabF and YhaH predict soluble proteins with significant similarity to the NAD(P)H dehydrogenase quinone oxidoreductase, DHQV. To investigate the function of YabF, a strain lacking the yabF-kefC region in E. coli was constructed. The strain was transduced into a kefB background and when transformed with a plasmid expressing only KefC channel activity was greatly reduced. The data suggest that the YabF protein is required in trans for the activity of KefC and preliminary evidence from in vitro-galactosidase fusion studies suggest that yabF and kefC genes may form an operon.
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Kornacker, Michael Gilbert. "Analysis of pullulanase secretion from Klebsiella pneumoniae strain K21." Thesis, University of Leicester, 1988. http://hdl.handle.net/2381/34437.
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Strains of the Gram-negative bacterium Klebsiella pneumoniae secrete pullulanase, a maltose-inducible starch debranching enzyme that exists as a cell surface bound intermediate. Three classes of secretion mutants were obtained by transposon In 10 mutagenesis. Class I and class III mutants carry Tn10 insertions in pullulanase secretion genes. Class II mutants carry insertions in regulatory loci that are required for the high level expression of pullulanase and other maltose-inducible genes (the maltose regulon). One such locus appears to correspond to a previously unknown locus. The phenotypes of the secretion mutants and the analysis of E.coli expressing pullulanase and/or cloned pullulanase secretion genes suggest that pullulanase secretion functions are involved in translocating pullulanase across the outer membrane and in releasing it from the cell surface. Most if not all pullulanase secretion genes are located to both sides of the structural gene for pullulanase (pu1A). Pullulanase was found to be a lipoprotein. Surprisingly, secreted pullulanase also carried lipid. However, strain K21 differed from other strains of Klebsiella pneumoniae by its ability to secrete not only acylated pullulanase but also a second, unacylated form of pullulanase. Strain K21 is also unusual because of its ability to secrete most pullulanase during logarithmic growth. This pullulanase corresponds to the unacylated pullulanase, with the remaining secreted pullulanase being acylated and secreted during stationary phase, as is the case for most or all pullulanase of other strains of Klebsiella pneumoniae. Strain K21 is also unusual because of the high level expression of the maltose regulon, including pulA, in the absence of maltose. This property, including the unusual features described above, may be a consequence of the selection of strain K21 for high level commercial production of pullulanase. Models for pullulanase secretion are discussed and approaches towards increasing the efficiency of commercial pullulanase production by strain K21 are outlined.
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Oh, Se-Hoon. "Development of efficient systems for integrative transformation of Streptomyces coelocolor A3(2) and their use in molecular analysis of whiB." Thesis, University of East Anglia, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.267528.
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Farrell-Poe, Kitt. "Obtaining a Water Sample for Bacterial Analysis." College of Agriculture and Life Sciences, University of Arizona (Tucson, AZ), 2010. http://hdl.handle.net/10150/156924.
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2 pp.1. Drinking Water Wells; 2. Private Water Well Components; 3. Do Deeper Wells Mean Better Water; 4. Maintaining Your Private Well Water System; 5. Private Well Protection; 6. Well Water Testing and Understanding the Results; 7. Obtaining a Water Sample for Bacterial Analysis; 8. Microorganisms in Private Water Wells; 9. Lead in Private Water Wells; 10. Nitrate in Private Water Wells; 11.Arsenic in Private Water Wells; 12. Matching Drinking Water Quality Problems to Treatment Methods; 13. Commonly Available Home Water Treatment Systems; 14. Hard Water: To Soften or Not to Soften; 15. Shock Chlorination of Private Water Wells
This fact sheet is one in a series of fifteen for private water well owners. The one- to four-page fact sheets will be assembled into a two-pocket folder entitled Private Well Owners Guide. The titles will also be a part of the Changing Rural Landscapes project whose goal is to educate exurban, small acreage residents. The authors have made every effort to align the fact sheets with the proposed Arizona Cooperative Extension booklet An Arizona Well Owners Guide to Water Sources, Quality, Testing, Treatment, and Well Maintenance by Artiola and Uhlman. The private well owner project was funded by both the University of Arizonas Water Sustainability Program-Technology and Research Initiative Fund and the USDA-CSREES Region 9 Water Quality Program.
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Ramos, Patrícia Locosque. "Taxonomia do gênero Stenotrophomonas através de Multi Locus Sequence Analysis (MLSA)." Universidade de São Paulo, 2007. http://www.teses.usp.br/teses/disponiveis/87/87131/tde-26012012-170618/.
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As Stenotrophomonas são comumente encontradas no trato respiratório de pacientes com doenças pulmonares crônicas e também na rizosfera de plantas. Esse gênero apresenta resistência a diversos antibióticos, promove o crescimento de plantas e algumas espécies apresentam a capacidade de fixar o nitrogênio atmosférico. O Multi Locus Sequence Analysis (MLSA) é uma metodologia baseada em genes constitutivos para definição e alocação taxonômica de novas espécies. O objetivo geral do presente trabalho foi caracterizar taxonomicamente uma coleção ampla de Stenotrophomonas composta por isolados endófitos, linhagens-tipo e de referência. Para tanto, foi estabelecido um sistema de classificação e identificação de Stenotrophomonas por meio de MLSA. Foi possível através da metodologia de MLSA definir 9 novas espécies, detectar a presença de um novo gênero e estabelecer um sistema online de taxonomia para Stenotrophomonas.The genus Stenotrophomonas is found in the respiratory treatment of patients with chronic pulmonary and also in the rizhosfera of plants. It presents resistance to several antibiotics, promotes the growth of plants and some species present the ability to fix atmospheric nitrogen. The Multi Locus Sequence Analysis (MLSA) is a methodology based on constitutive genes for definition and taxonomic allocation of new species. The general objective of the present work was to characterize a wide collection constituted by Stenotrophomonas from isolated endophytic, type and reference strains. In such a way, a system of classification and identification of Stenotrophomonas by means of MLSA was established. It was possible through the MLSA methodology to define 9 new species, to detect the presence of a new genus and to establish an online system for Stenotrophomonas taxonomy.
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Meade, Rosemary Anne. "Analysis of ammonia oxidiser community structure in a hypereutrophic lake." Thesis, University of Liverpool, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.343612.
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Dullaghan, Edith Mary. "Analysis of gene regulation by mycobacterium tuberculosis LexA." Thesis, University College London (University of London), 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.311969.
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Reardon, Catherine Leona. "Molecular Analysis of Diversity, Gene Expression and Activity of Mineral-Associated Bacteria." Thesis, Montana State University, 2005. http://etd.lib.montana.edu/etd/2005/reardon/ReardonC1205.pdf.
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This dissertation investigated the diversity and hydrogenase activity and gene expression of mineral-associated microorganisms. Surface-associated microbes have been shown to dominate diversity and activity in the environment, however molecular analysis of sediment-associated communities is hindered by both inaccessibility to the subsurface and co-extraction of inhibitory compounds. In order to analyze microbial communities in which the environmental conditions previously had precluded the use of traditional sediment extraction techniques, biofilm coupons (metal, mesh cylinders containing surrogate substrata) were used to recover microorganisms able to attach and compete in a biofilm. The community recovered from the contaminated site using hematite as a surrogate substratum was dominated by microbes most closely related to Alcaligenes sp. (metal-tolerant), Frateuria sp. (acidophilic), and Methylobacterium radiotolerans (radionuclide-tolerant) which together reflect the acidic, metal-, and radionuclide-contaminated environment. Hematite, as compared to other substrata, was shown to recover communities most closely representative of sediment communities inhabiting the saturated zone. Surface-associated cells have been shown to express greater activity than suspended populations and mineral-associated sulfate-reducing bacteria (SRB) mediate the formation of different secondary minerals as compared to suspended cells. In order to investigate the affect of surface-association on enzyme activity, hydrogenase enzyme activity was compared in hematite-associated and suspended populations of the SRB Desulfovibrio desulfuricans Essex 6. Hydrogenase activity of surface-associated populations was higher than that displayed by suspended cells. Hydrogenase likely affects the pH and pE of the conditions immediately surrounding the cell. The greater rate of activity may be one factor which contributes to the formation of a mineral phase not observed in the presence of suspended populations of this bacterium. In order to determine the portion of cells expressing hydrogenase in the surface-associated populations, in situ reverse-transcription PCR was applied to the hematite-associated cells and all cells were expressing the [NiFe] hydrogenase gene. This thesis demonstrates that environmental conditions of contaminated subsurface environments select for microorganisms able to tolerate or utilize the contaminants. Also, the hydrogenase activity of surface-associated populations is not representative of the suspended cells thus indicating the importance of studying attached populations where enzyme activity likely influences the conditions at the mineral-microbe interface.