Дисертації з теми "Escherichia coli genome"
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Neelakanta, Girish. "Genome variations in commensal and pathogenic E.coli." [S.l. : s.n.], 2005. http://deposit.ddb.de/cgi-bin/dokserv?idn=974330329.
Повний текст джерелаSchlegel, Susan. "From protein production to genome evolution in Escherichia coli." Doctoral thesis, Stockholms universitet, Institutionen för biokemi och biofysik, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-94993.
Повний текст джерелаAt the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 3: Manuscript.
Romero, Alvarez David. "Genome wide analyses of the Escherichia coli primary and secondary transcriptomes." Thesis, University of Leeds, 2014. http://etheses.whiterose.ac.uk/6917/.
Повний текст джерелаCoss, Dennis. "Insertion of genes and operons into the Escherichia coli genome through targeted recombination." Morgantown, W. Va. : [West Virginia University Libraries], 2005. https://eidr.wvu.edu/etd/documentdata.eTD?documentid=3804.
Повний текст джерелаTitle from document title page. Document formatted into pages; contains v, 125 p. : ill. (some col.). Includes abstract. Includes bibliographical references (p. 71-87).
Mosberg, Joshua Adam Weintrob. "Studying and Improving Lambda Red Recombination for Genome Engineering in Escherichia coli." Thesis, Harvard University, 2013. http://dissertations.umi.com/gsas.harvard:10777.
Повний текст джерелаSchmidt, Dorothea. "Molekulare Analyse des probiotischen Stamms Escherichia coli Nissle 1917." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2009. http://nbn-resolving.de/urn:nbn:de:bsz:14-ds-1243973355362-88295.
Повний текст джерелаThe probiotic E. coli Nissle 1917 is a fecal isolate which is traditionally used for treatment of various gastrointestinal disorders. In clinical trials where EcN was used as therapeutic alternative for remission maintenance of ulcerative colitis compared to standard medication, promising results led to an increased interest in probiotics. Today, EcN is one of the best studied probiotics. Therefore, several mechanisms of action could be enlightened. Structural components and strain-specific products are responsible for its probiotic effects. But conclusive concepts about genes, gene products and molecular mechanisms that really contribute to the probiotic character of EcN have not been offered so far. In order to create new possibilities to elucidate the probiotic traits of EcN the genome is analysed by taking this as a basis for comparison to other E. coli genomes and identification of intestinal in vivo regulated genes using a promoter-trap-library. The sequenced EcN genome is annotated and compared to 13 other so far annotated E. coli genomes. Concerning these analyses EcN encodes 121 strain-specific genes. The genome structure including the genomic islands and prophages is highly homolog to the uropathogenic E. coli CFT073. EcN encodes most of the virulence and fitness factors that are present in E. coli CFT073. Therefore, the close relationship of these two strains is confirmed at nucleotide level. Furthermore, it is shown that in artificial systems like cell culture assays and gnotobiotic mice EcN reveals a pathogenic potential although EcN is able to decrease colonization efficiency of pathogenic bacteria. The alternative sigma factor RpoS that is responsible for global regulation and activity of several genes seems to play an important role during colonization of EcN in the intestine and its immunostimulatory effects on intestinal epithelial cells. Investigation of EcN-deletion mutants lacking genomic islands and prophages lead to the conclusion that some genomic islands may play a role for specific probiotic traits. This is the first time where a promoter-trap-library was used in conventional and gnotobiotic mice for collection of intestinal in vivo active promoters. Constructing and establishing a promoter-reporter gene assay with the bioluminescent luxCDABE operon made the investigation of selected promoters in vitro possible as well as establishing a bioluminescence assay using an In Vivo Imaging System (IVIS) for investigation of promoter activity in living mice. In this research project was shown that EcN is not a completely harmless probiotic. The genome structure and regulatory mechanisms of gene expression are the strain’s molecular traits that lead to probiotic activity and immunostimulatory effects. Therefore, the molecular analyses presented here, together with the complete genome sequence, are a basis for further investigations of mechanisms that are responsible for the probiotic effects of EcN
Coulange, Frédérique. "Isolement et caracterisation de regions specifiques du genome des escherichia coli pathogenes aviaires (doctorat : microbiologie)." Paris 11, 1999. http://www.theses.fr/1999PA114802.
Повний текст джерелаPRADEL, NATHALIE. "Escherichia coli producteurs de shiga-toxines : etude epidemiologique, recherche des caracteristiques des souches pathogenes par comparaison moleculaire et hybridation soustractive (doctorat : microbiologie)." Clermont-Ferrand 1, 2001. http://www.theses.fr/2001CLF1PP02.
Повний текст джерелаBrambilla, Elisa. "Investigation of E. coli genome complexity by means of fluorescent reporters of gene expression." Thesis, Paris 6, 2014. http://www.theses.fr/2014PA066607/document.
Повний текст джерелаEscherichia coli is able to survive in many different environments. The information necessary for this adaptation is encoded in the chromosome. This circular molecule is condensed in a compact DNA-protein structure, called the nucleoid. The chromosome is not uniform, and shows uneven distributions of nucleoid-associated proteins (NAPs) binding sites, AT-rich sequences and general protein occupancy domains. It has been demonstrated that the position of important genes is highly conserved in ?-Proteobacteria. These differences along the chromosome and the conserved position of important genes suggest that the position of the gene can influence gene expression. To test this hypothesis, I studied the expression of a fluorescent reporter gene inserted in different positions around the chromosome. The expression of the reporter is driven by differently regulated promoters, one repressed by the important NAP H-NS, one non regulated and one subject to supercoiling and stringent control. We studied the dynamical expression of these promoters in different growth conditions, growth phases, upon nutritional upshift and under stress. We showed that the expression of the H-NS dependent promoter depends on the location on the chromosome, because H-NS repression is enhanced in presence of AT-rich sequences. We also studied the influence of a divergent gene on the reporter expression as a function of chromosomal position, and showed that this influence depends on the location of the gene. With our study we have been therefore able to show the impact of chromosomal position on gene expression and to give a new perspective on genome complexity
Nguyen, Huong LE. "Etude des facteurs régulateurs de la traduction chez Escherichia coli." Thesis, Toulouse, INSA, 2019. http://www.theses.fr/2019ISAT0004.
Повний текст джерелаThe analysis of gene expression regulation is necessary to better understand bacterial adaptation to environment and to be able in a context of synthetic biology to optimize the production of molecules of interest. The goal of this thesis was to study translation at the genome-wide level and its relationship to other cellular processes using a systems biology approach. First, translation activity at the -omic scale (called the traductome) was measured : for each messenger RNAs, its percentage of copies in translation and ribosome density. For the first time, a complete picture of the translational state in fast growing E. coli cells was obtained, characterized by a majority of transcripts with a very high percentage of copies in translation but a low ribosome density. Our model identified sequence-related factors as determinants of translation but, more surprisingly, the model predicted the important role of a physiological parameter: the mRNA concentration. Thus, more concentrated mRNA would have higher percentage of copies in translation and higher ribosome density. For the first time, this effect of transcription on translation has been validated at the molecular level on several genes. We showed that an increase in mRNA concentration by transcriptional induction results in increases in percentage of copies in translation and in ribosome load
Henze, Stefanie [Verfasser], and Claudia [Akademischer Betreuer] Acquisti. "The impact of nitrogen deprivation on genome evolution in Escherichia coli / Stefanie Henze ; Betreuer: Claudia Acquisti." Münster : Universitäts- und Landesbibliothek Münster, 2016. http://d-nb.info/1141682036/34.
Повний текст джерелаMa, Chih-Yu. "Occurrence and characterization of antibiotic-resistant Escherichia coli in wastewater and surface water." Kyoto University, 2020. http://hdl.handle.net/2433/259030.
Повний текст джерелаCowley, Lauren A. "Use of genome sequencing to investigate the molecular basis of bacteriaphage interaction of the Escherichia coli O157 typing phages and the elucidation of the biological and public health significance of phage type." Thesis, University of Edinburgh, 2017. http://hdl.handle.net/1842/23583.
Повний текст джерелаLember, Geivi. "Sepsis-associated Escherichia coli whole-genome sequencing analysis using in-house developed pipeline and 1928 diagnostics tool." Thesis, Högskolan i Skövde, Institutionen för biovetenskap, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-19841.
Повний текст джерелаSarica, Nazim. "Identification de contraintes locales impactant l’expression des gènes chez Escherichia coli." Thesis, université Paris-Saclay, 2020. http://www.theses.fr/2020UPASL021.
Повний текст джерелаA long list of constrains that affect gene expression have been discovered thanks to the thousands of sequenced genomes and comparative genomics. These contrains can be at the nucleotidic level, but also at the 3D scale. Studies showed that the spatial organization of bacterial genomes goes from the molecular level to the cellular level. At the molecular level, NAPs (Nuceloid Associated Proteins) are modeling the chromosome by inducing 10kb loops called microdomains, that present different supercoiling levels. At the cellular scale, it has been observed 4 different structured regions + 2 non-structured regions on E.coli's chromosome. These regions of approximatively 1Mbp are called macrodomains. The first goal of this project is to study the effects of positioning and constrains on gene expression in E.coli. With the chromosome being so large and precisely organized in time and space by several interacting elements simultaneously, it is often difficult for researchers to isolate one specific feature and to accurately correlate this to gene regulation. What becomes obvious when one begins to wade through the literature is that the field would greatly benefit from simplified model chromosomes
Raeside, Colin. "Plasticité du génome au cours d'une expérience d'évolution au long terme chez Escherichia Coli." Thesis, Grenoble, 2014. http://www.theses.fr/2014GRENV070/document.
Повний текст джерелаLarge-scale DNA rearrangements, including inversions, amplifications, duplications, deletions, insertions, and transposition of mobile genetic elements, are major drivers of evolution and strongly impact on chromosome organization and expression, thereby altering organismal phenotypes. However, their long-term evolutionary dynamics and effects on organismal fitness are often unknown. We addressed these questions by using the longest-running evolution experiment, during which twelve independent populations are propagated from a common E. coli ancestor in a glucose-limited environment for now over 60,000 generations (26 years). Most past studies have focused on point mutations and small InDels. Using evolved clones sampled over time in all 12 populations, we characterized all large-scale DNA rearrangements by using whole genome sequences and Whole Genome MappingTM (i.e optical mapping). After 40,000 generations, we identified a total of 110 rearrangements including 82 deletions, 19 inversions and 9 duplications. Many chromosomal regions were repeatedly affected by similar rearrangements and, at least in one population, they occurred early in evolution when fitness increase was strong. Therefore, many rearrangements may be under positive selection. At the very least, these rearrangements strongly affected the structure of the chromosome during evolution.At the molecular level, we showed that ~ 70% of all rearrangements occurred by recombination between Insertion Sequence (IS) elements, illustrating their importance in mediating genome plasticity. We therefore investigated the distribution and temporal dynamics of these small mobile genetic elements in all 12 populations. We showed that IS elements were strong contributors of the total mutations after 40,000 generations. In one population, they even represented about half of the total mutations and one IS type, IS150, revealed a strong 6-fold increase in copy number, accounting for the production of most of the rearrangements detected in this population. We showed that IS150 revealed a dynamic temporal behavior with a strong expansion followed by domestication by the host. By testing three evolutionary scenarios, we demonstrated that the IS150 expansion was related to a strong fitness increase conferred by the initial transposition events that occurred before 2000 generations. Later, between 20,000 and 40,000 generations, we measured a decreased transposition frequency, likely owing to a down regulation imposed by the host. Finally, and for the first time, we developed an evolution model of IS dynamics confirming that the IS expansion was related to a threshold number of initial IS beneficial insertions. All of our data showed that large-scale chromosomal rearrangements and IS elements have played an active role in the evolutionary outcomes after 40,000 generations of bacterial evolution
Noll, Lance. "Detection and quantification of the top-seven Shiga toxin-producing Escherichia coli serogroups in feces and on hides of feedlot cattle and whole genome sequence-based analysis of O103 serogroup." Diss., Kansas State University, 2017. http://hdl.handle.net/2097/36204.
Повний текст джерелаDepartment of Diagnostic Medicine/Pathobiology
Tiruvoor G. Nagaraja
Cattle are a reservoir for major Shiga toxin-producing Escherichia coli (STEC), which includes STEC O157 and the top six non-O157 serogroups (STEC-6; O26, O45, O103, O111, O121, O145). Collectively known as the STEC-7, these organisms are harbored in the hindgut and shed in the feces of cattle, which can contaminate hides. The de-hiding step during beef cattle processing can introduce fecal contaminants from the hide onto the carcass surface, creating the potential for contaminated beef products. The STEC-7 have been declared by the USDA-Food Safety and Inspection Service as adulterants in ground beef and non-intact beef products, and are monitored during beef cattle processing. However, many of the culture- and PCR-based tests for detection and/or quantification of the STEC, particularly of the STEC-6, are not established or require improvement and also virulence characteristics of STEC strains from cattle have not been fully analyzed. Therefore, the following studies were conducted: 1. Immunomagnetic separation (IMS)-based culture-method for detection of STEC-6 in cattle feces was developed and compared to a PCR-based method; 2. Detection sensitivity of pooled vs. individual IMS beads for isolation STEC-6 from cattle feces was evaluated; 3. Real-time PCR assay, based on the clustered regularly interspaced short palindromic repeat sequence polymorphisms (CRISPR), was developed and validated for serotype-specific detection and quantification of STEC O157:H7 in cattle feces; 4. Virulence gene profiles of bovine enterohemorrhagic (EHEC), enteropathogenic (EPEC) and putative non-pathotype E. coli O103 strains were examined with whole genome sequence (WGS)-based comparative analysis; 5. Prevalence and concentration of STEC-7 of fed-beef, cull beef and cull dairy cattle were determined. The culture and PCR methods detected all six serogroups in samples negative by the other method. Based on noninferiority tests, detection with pooled IMS beads was not inferior to detection with individual beads. Detection limits of the CRISPR-based qPCR assay for cattle feces spiked with pure cultures were 2.1 x 10³ and 2.3 x 10⁰ colony-forming units/g before and after enrichment, respectively. WGS-based analysis of E. coli O103 strains revealed key differences in the virulomes and mobilomes of EHEC, EPEC, and putative non-pathotype strains. The prevalence study revealed that a significantly higher (P < 0.01) proportion of hide samples from fed beef cattle (4.8%) were positive for STEC O157:H7, compared to samples from cull beef (1.6%) or cull dairy (0.2%); the majority of quantifiable STEC O157:H7 from each cattle type was at concentrations between 3 to 4 log CFU/100 cm². These data contribute to a knowledge gap on prevalence and concentration of STEC-7 and surrogate bacteria on cattle hides and carcasses, respectively. Furthermore, the development and refinement of culture- and PCR-based screening assays may lead to increased surveillance of major STEC serogroups, especially if the potential of WGS-based comparative genomics in identifying novel gene targets can be harnessed.
CHEVALLIER, BRUNO. "Structure et expression du genome de lactobacillus plantarum : clonage et etude de la stabilite de l'adn chez escherichia coli." Université Louis Pasteur (Strasbourg) (1971-2008), 1994. http://www.theses.fr/1994STR13184.
Повний текст джерелаGunasekera, Samantha Thilini. "Evaluating whole-genome sequencing strategies in AMR research through characterisation of mobile genetic elements in wildlife-origin Escherichia coli." Thesis, Gunasekera, Samantha Thilini (2019) Evaluating whole-genome sequencing strategies in AMR research through characterisation of mobile genetic elements in wildlife-origin Escherichia coli. Honours thesis, Murdoch University, 2019. https://researchrepository.murdoch.edu.au/id/eprint/50510/.
Повний текст джерелаLaunay, Adrien. "Etude de l'émergence de la diversité d'Escherichia coli in vivo par séquençage de génomes complets." Thesis, Paris 6, 2016. http://www.theses.fr/2016PA066692/document.
Повний текст джерелаEscherichia coli is a commensal species living in the digestive tract of vertebrates, but can also be a harmful pathogen involved in both intra and extraintestinal diseases. As clones can behave both as commensals and pathogens, the comprehension of the mechanisms involved in the diversification of E. coli in those two habitats represents a major public health concern. In vitro experimental evolution studies using E. coli have unraveled the different faces of bacterial adaptation. However, as those experiments used artificial conditions, the relevance of these observations and more generally the contribution of adaptation to the diversification of E. coli in the wild remain questionable. To answer these questions, I analyzed the genomic profiles of diversification of E. coli during (1) adaptation to the mice digestive tract or (2) during acute extraintestinal infections. In both cases, I found a strong convergence at the gene level, i.e. observation of several impendent mutations in the same gene, suggesting a dynamic adaptation. In acute infections, mutations in global regulators were recovered, while more specific genes were recruited in the mice gut. Finally, the existence of clones with high mutation rate in the infections, allowed me to document for the first time the genomics of mutator emergence in the wild. In conclusion, my work shows that adaptation is playing an important role in the diversification of E. coli, and that this process is fairly similar to the one observed in the laboratory. Nevertheless, adaptation seems more active during infections than in the mice gut
Yesil, Mustafa. "Enhancing the inactivation of Escherichia coli O157:H7 by bacteriophage and gaseous ozone to improve postharvest fresh produce safety." The Ohio State University, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=osu1512103801957122.
Повний текст джерелаStoesser, Nicole Elinor. "Applications of whole genome sequencing to understanding the mechanisms, evolution and transmission of antibiotic resistance in Escherichia coli and Klebsiella pneumonia." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:10ed1097-b2a1-4e3e-a4b3-58318d325f89.
Повний текст джерелаMaistrenko, Oleksandr. "Variation in Core and Accessory Parts of Genome of Escherichia Coli Isolated from Soil from Riparian Areas in New York State." Thesis, North Dakota State University, 2016. https://hdl.handle.net/10365/28022.
Повний текст джерелаFederal Formula Funding (Hatch-Act)
ND-EPSCoR
Fulbright-STEP scholarship
Royer, Guilhem. "Génomique comparée à grande échelle de souches d’Escherichia coli responsables de bactériémies chez l’Homme : implications cliniques et analyse des réseaux métaboliques PlaScope: a targeted approach to assess the plasmidome from genome assemblies at the species level Mortality in Escherichia coli bloodstream infections: antibiotic resistance still does not make it." Thesis, université Paris-Saclay, 2021. https://www.biblio.univ-evry.fr/theses/2021/interne/2021UPASL012.pdf.
Повний текст джерелаEscherichia coli is the predominant aero-anaerobic bacterium of the human gut and also the leading cause of bacteremia in industrialized countries. The E. coli population presents a high but structured diversity, with certain phylogenetic groups preferentially associated with a given lifestyle (e.g. A/B1 and commensal, B2/D and extraintestinal pathogen). Many virulence factors have been described in extraintestinal pathogenic strains (ExPEC), but the prognosis of E. coli bacteremia appears to be linked mainly to host-associated factors. However, some virulent and multi-resistant clones have recently emerged and dramatically modified the epidemiology of these infections. At the same time, the democratization of sequencing methods now offers a granularity yet never reached in the analysis of bacterial genomes. The objective of this thesis is to take advantage of comparative genomic methods to improve our understanding of the physiopathology of E. coli bacteremia, while taking into account the major epidemiological changes that are observed. Carrying out such genomic comparisons required, first of all, the implementation of an analysis strategy, including in particular the development of a targeted approach for the identification of plasmid sequences within genome assemblies.This strategy, applied on 545 strains collected during the Septicoli study in 2016-2017, confirmed the minor role of bacterial determinants in the outcome of E. coli bacteremia. In addition, by comparing these strains to those of the Colibafi study, we studied the population dynamics over 12 years. While the population appears to be stable overall, further exploration of the main clones shows significant changes, sometimes associated with virulence factors typical of ExPEC. On the other hand, the antigenic diversity of these clones is variable and suggests different selective pressures according to their respective ecological niches. Finally, in a last part we reconstructed the metabolic networks of more than 1400 E. coli strains in order to study the links between metabolism and lifestyle. The results highlight the conservation of metabolism in E. coli and its strong association with phylogeny. In addition, a detailed analysis of the main clones found in bacteremia, including the ST131, highlights a metabolic pathway involved in the degradation of aromatic compounds derived from lignin. This pathway, usually absent in phylogroup B2 strains, could provide a selective advantage to this recently emerging global pandemic clone
Walz, Paul S. "Influence of pathogenic bacterial determinants on genome stability of exposed intestinal cells and of distal liver and spleen cells." Thesis, Lethbridge, Alta. : University of Lethbridge, Dept. of Biology, c2011, 2011. http://hdl.handle.net/10133/3405.
Повний текст джерелаxiv, 132 leaves : ill. (chiefly col.) ; 29 cm
Cavalcanti, Leonardo Sousa. "Papel da celulase XF-0818 na interação Xylella fastidiosa X Citros." Universidade de São Paulo, 2005. http://www.teses.usp.br/teses/disponiveis/11/11135/tde-16052005-162932/.
Повний текст джерелаFrom the genome sequencing of the bacteria Xylella fastidiosa, the agent responsible for the citrus variegated chlorosis (CVC), studies on the pathogenicity mechanisms expressed during the occurrence of the disease were started in genomic function projects, aiming to confirm the function of the genic sequences identified in the project X. fastidiosa Genome. Among these mechanisms, the enzymes involved in the bacterium attaching process are highlighted. The present study had, as a goal, the orf denominated Xf-0818, cloned in Escherichia coli by means of the insertion into pET 28b(+) plasmid, which codifies a cellulase of a size nearly 60 kDa, possibly involved in the degradation of cellulose fibers present in the membranes of the xylem vessels of citrus plants. The degradation of this membrane would allow for the movement of bacterial cells among the xylem vessels, which would be important for the development of CVC symptoms. The enzyme was over expressed into E. coli by means of their induction using lactose and purified using ultra-filtration associated to metal affinity chromatography. The enzyme presented high activity over 1%-carboximethyl cellulose (CMC), which was evaluated through quantification of released reduced sugars. The antibodies were obtained by injection of the purified enzyme into mice, which were evaluated by using the ELISA. The enzyme activity over CMC was reduced after previous incubation with the antibodies. These antibodies represent a tool for the researches aiming the identification of conditions that favor the expression of this enzyme in vivo. The presence of gold particles on the citrus diseased tissue samples indicate the participation of this cellulase on the disease, but other studies using immunocytochemistry and mutants of X. fastidiosa are necessary to confirm this hypothesis.
Mendes, Renata de Siqueira. "Caracterização de proteínas de membrana de Leptospira interrogans expressas em Escherichia coli." Universidade de São Paulo, 2011. http://www.teses.usp.br/teses/disponiveis/87/87131/tde-27092011-151543/.
Повний текст джерелаThe genomic sequencing of the L. interrogans serovar Copenhageni and the advances of bioinformatics analysis allowed the identification of six new vaccine candidates. These genes were subjected to genomic DNA, mRNA and native protein conservation assays in twelve serovars from Leptospira, and the gene LIC11469 was the most conserved among these serovars. The recombinant proteins rLIC11469 and rLIC11030 were purified by metal affinity chromatography, and subjected to circular dichroism. Through cellular localization assays we could observe the presence of the corresponding native proteins on the outer membrane of Leptospira. In adhesion assays, the protein rLIC11469 showed binding to laminin and plasminogen. Immunization and challenge assays showed that the protein rLIC11030 afforded protection against lethal leptospiral inoculation in hamsters. Both proteins showed reactivity against sera of patients diagnosed with leptospirosis, suggesting that these proteins are probably expressed during infection.
Souza, Natalie Michele de. "Avaliação da atividade imunogênica de três proteínas de Leptospira interrogans expressas em Escherichia coli." Universidade de São Paulo, 2013. http://www.teses.usp.br/teses/disponiveis/87/87131/tde-07062013-110750/.
Повний текст джерелаLeptospirosis is a zoonotic disease caused by pathogenic bacteria of genus Leptospira. In the world, nearly 500,000 cases are reported each year, with 10% of mortality rate. Currently, vaccines against leptospirosis are composed by inactivated cells that are ineffective in many aspects. After genome analysis, the genes LIC11121, LIC11087, LIC11228 e LIC11084 were chosen for immunogenicity characterization of their respective proteins. These genes were cloned in the pAE expression vector and the proteins encoded by LIC11087, LIC11228 and LIC11084 were purified. The results suggest the localization of these proteins in the bacterial outer membrane, are immunogenic, are possibly expressed during infection and may have involvement in mechanisms of immune system evasion and pathogenicity. Moreover, in one of two experiments, the rLIC11084 protein induced partial protective immunity of immunized hamsters against lethal challenge.
Walters, D. E. "A further nar gene in Escherichia coli." Thesis, University of Leeds, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.383761.
Повний текст джерелаSantos, Ana Carolina da Silva. "Caracterização fenotípica, sequenciamento e anotação do genoma total de uma cepa de Escherichia coli isolada de uma paciente com Doença de Crohn." Botucatu, 2015. http://hdl.handle.net/11449/144081.
Повний текст джерелаBanca: Silvio Luís de Oliveira
Banca: Rogéria Keller
Resumo: A Doença de Crohn (DC) é uma variante das doenças inflamatórias intestinais que não tem uma causa definida, porém há o envolvimento de fatores ambientais e genéticos, entre eles a microbiota. Portadores da DC apresentam desequilíbrio na composição de espécies da microbiota intestinal, incluindo o aumento da Escherichia coli. A E. coli é uma bactéria versátil em sua relação com o hospedeiro, isto é, inclui cepas comensais e várias categorias patogênicas. Estas compreendem dois grupos: linhagens causadoras de infecções intestinais e linhagens causadoras de infecção extraintestinais. As E. coli isoladas de portadores da DC em geral pertencem ao segundo grupo, e uma das principais características apresentadas por estas bactérias é a interação com células epiteliais (aderência e invasão). Estudos feitos na década de 90 levaram a identificação de um novo patótipo de E. coli, capaz de aderir e invadir células epiteliais e ainda invadir e se replicar dentro de macrófagos, produzindo granulomas, característica histopatológica da DC. Este novo patótipo, chamado de Adherent and Invasive E. coli (AIEC), têm sido usada como referência na caracterização de E. coli isoladas a partir de portadores da DC. Neste trabalho, foi feito o estudo de caracterização fenotípica e genética de E. coli isoladas a partir de 9 portadores da DC e 5 pacientes controles, as quais foram submetidas a testes de adesão e invasão celular em células epiteliais, teste de formação de biofilme e identificação de filogrupos da coleção de referência de E. coli (EcoR). Dentre o conjunto de amostras bacterianas estudado, foi encontrada uma amostra isolada de uma paciente com DC que apresentou invasibilidade superior às demais, e foi intensivamente estudada, tendo-se verificado que ela apresenta um perfil de virulência distinto de AIEC. O genoma da amostra em questão foi sequenciado e anotado. Os resultados da caracterização...
Abstract: Not available
Mestre
Mahmoud, Nada. "Next-generation diagnostics of escherichia coli from community-onset sepsis patients in sweden : Studying the biodiversity of escherichia coli genomes." Thesis, Högskolan i Skövde, Institutionen för biovetenskap, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-19893.
Повний текст джерелаMahfouz, Norhan, Serena Caucci, Eric Achatz, Torsten Semmler, Sebastian Guenther, Thomas U. Berendonk, and Michael Schroeder. "High genomic diversity of multi-drug resistant wastewater Escherichia coli." Nature Publishing Group, 2018. https://tud.qucosa.de/id/qucosa%3A32482.
Повний текст джерелаBin, Thani Ali Salman. "Genomic diversity of ten Escherichia coli strains associated with bloodstream infections." Thesis, University of Leicester, 2009. http://hdl.handle.net/2381/4246.
Повний текст джерелаEger, Nicole. "Advanced Detection Methods of Genomic Barcodes for Genotyping Escherichia coli Libraries." Thesis, Uppsala universitet, Institutionen för cell- och molekylärbiologi, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-439038.
Повний текст джерелаAlbrecht, Huguette. "Les produits des genes i et iv du virus de la mosaique du chou-fleur (camv)." Université Louis Pasteur (Strasbourg) (1971-2008), 1988. http://www.theses.fr/1988STR13178.
Повний текст джерелаNelson, Adam Michael. "Genomic analysis of pathogen evolution virulence gene acquisition and genetic erosion in Escherichia coli /." Diss., Connect to online resource - MSU authorized users, 2008.
Знайти повний текст джерелаDufour, Delphine. "Recherche de déterminants génétiques permettant l'adaptation d'une souche Escherichia coli à la mamelle bovine." Thesis, Vandoeuvre-les-Nancy, INPL, 2008. http://www.theses.fr/2008INPL050N/document.
Повний текст джерелаThe objective of this work was to characterize the MPEC Escherichia coli P4 strain. A phylogenetic study showed that it belongs to the phylogenetic group A of the E. coli species and that its core genome is similar to the one of the commensal non-pathogenic E. coli K12 MG1655 strain which also belongs to the group A. A search in its genome of different genes encoding virulence factors known among other pathotypes of the E. coli species was done and only the traT gene, encoding a serum resistance factor, was detected. A screening of fifteen tRNA loci known for frequently hosting genomic islands, made in its genome, revealed for seven of them the presence of such structures. The partial or complete sequencing of the regions downstream from these seven loci showed the systematic presence of nucleotide sequences different from those present in E. coli K12 MG1655. If the content analysis of these islands does not yet explain the virulence of E. coli P4, their highlighting is the first of this kind in the pathotype MPEC and suggests the discovery of other genomic regions specific to this pathotype, which may explain its tropism and its nature. In addition, to assessing the role of E. coli P4 in milk caseinolysis observed during bovine mastitis, a constitutive secretion of four extracellular proteases was highlighted by casein zymography. However, the caseinolytic activity of these enzymes does not seem significant. This fact may suggest a role in virulence of the strain
Santos, Ana Carolina da Silva [UNESP]. "Caracterização fenotípica, sequenciamento e anotação do genoma total de uma cepa de Escherichia coli isolada de uma paciente com Doença de Crohn." Universidade Estadual Paulista (UNESP), 2015. http://hdl.handle.net/11449/144081.
Повний текст джерелаCoordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)
Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
A Doença de Crohn (DC) é uma variante das doenças inflamatórias intestinais que não tem uma causa definida, porém há o envolvimento de fatores ambientais e genéticos, entre eles a microbiota. Portadores da DC apresentam desequilíbrio na composição de espécies da microbiota intestinal, incluindo o aumento da Escherichia coli. A E. coli é uma bactéria versátil em sua relação com o hospedeiro, isto é, inclui cepas comensais e várias categorias patogênicas. Estas compreendem dois grupos: linhagens causadoras de infecções intestinais e linhagens causadoras de infecção extraintestinais. As E. coli isoladas de portadores da DC em geral pertencem ao segundo grupo, e uma das principais características apresentadas por estas bactérias é a interação com células epiteliais (aderência e invasão). Estudos feitos na década de 90 levaram a identificação de um novo patótipo de E. coli, capaz de aderir e invadir células epiteliais e ainda invadir e se replicar dentro de macrófagos, produzindo granulomas, característica histopatológica da DC. Este novo patótipo, chamado de Adherent and Invasive E. coli (AIEC), têm sido usada como referência na caracterização de E. coli isoladas a partir de portadores da DC. Neste trabalho, foi feito o estudo de caracterização fenotípica e genética de E. coli isoladas a partir de 9 portadores da DC e 5 pacientes controles, as quais foram submetidas a testes de adesão e invasão celular em células epiteliais, teste de formação de biofilme e identificação de filogrupos da coleção de referência de E. coli (EcoR). Dentre o conjunto de amostras bacterianas estudado, foi encontrada uma amostra isolada de uma paciente com DC que apresentou invasibilidade superior às demais, e foi intensivamente estudada, tendo-se verificado que ela apresenta um perfil de virulência distinto de AIEC. O genoma da amostra em questão foi sequenciado e anotado. Os resultados da caracterização...
FAPESP: 13/04475-3
Cockram, Charlotte Anne. "Genomic analysis of RecA-DNA interactions during double-strand break repair in Escherichia coli." Thesis, University of Edinburgh, 2014. http://hdl.handle.net/1842/17284.
Повний текст джерелаRogers, Ahumada Andrés Eduardo. "Predicción computacional de genes de ARN no codificante pequeño en genomas bacterianos." Tesis, Universidad de Chile, 2012. http://www.repositorio.uchile.cl/handle/2250/111355.
Повний текст джерелаEl objetivo de este estudio es desarrollar un método computacional capaz de predecir con alta especificidad y sensibilidad los genes pequeños de ARN no codificante en genomas bacterianos, identificando las variables involucradas de mayor importancia que deben ser consideradas para su correcta clasificación. El trabajo aquí presentado consistió en investigar y analizar el estado del arte en métodos de predicción computacional de genes pequeños de ARN no codificante en bacterias, recopilar un listado de las variables involucradas y determinar estadísticamente aquellas que diferencian con mayor precisión los genes pequeños de ARN no codificante de secuencias genéticas al azar, comparar distintos métodos de predicción e identificar el que otorgue mejores resultados. Finalmente, se compararon los resultados del método con otros preexistentes y se aplicó el método al genoma completo de Escherichia coli. Los principales resultados obtenidos en este estudio son la identificación de 4 variables que influyen significativamente en la detección correcta de genes pequeños de ARN no codificante. Estas son: Valor z, Valor de partición, EMPI y Porcentaje de bultos, las cuales corresponden al subconjunto de variables con mayor capacidad discriminatoria. Por este motivo se recomienda que futuros métodos predictivos consideren la inclusión de estas 4 variables. Las variables seleccionadas muestran que existe una presión selectiva en la evolución de los genes pequeños de ARN no codificante, la que apunta a aumentar la estabilidad de la molécula al modificar su estructura para disminuir la energía de plegamiento y eliminar subestructuras desestabilizantes no funcionales. El mejor método de clasificación corresponde al Perceptrón Multicapa basado en redes neuronales, con una alta sensibilidad (88,8%) y alta especificidad (85,5%), teniendo una tasa de falsos positivos relativamente baja (14,5%). Con este subconjunto de variables y el método de clasificación, se realizó una predicción sobre el genoma de la bacteria Escherichia coli, generando 1192 predicciones, con un valor de sensibilidad de 30,5% y un valor predictivo positivo de 1,51 % respecto a los genes pequeños de ARN no codificante conocidos. Seleccionando las predicciones cercanas a promotores σ70 o terminadores intrínsecos (independientes del factor ρ), se obtiene un desempeño predictivo similar al logrado por otros autores en la literatura, con el beneficio adicional de requerir la medición de sólo 4 variables y sin la necesidad de información sobre genes homólogos en organismos cercanos filogenéticamente. La contribución de este trabajo consiste en profundizar el conocimiento acerca de las características de los genes de ARN no codificante, al haber estudiado las variables utilizadas previamente en la literatura y definir las 4 más relevantes, las cuales se relacionan directamente con la estructura secundaria y su energía mínima de plegamiento. En segundo lugar se propone un listado de 1192 secuencias del genoma de Escherichia coli y un listado más corto con las 5 más probables de ser genes sARN, estas secuencias pueden ser comprobadas experimentalmente. Estos resultados inciden positivamente en mejorar la calidad de las anotaciones de estos genes en genomas bacterianos, permitiendo mayores avances en estudios de genómica funcional y regulación en redes metabólicas.
Tomko, Timothy. "Bioprospecting For Genes That Confer Biofuel Tolerance To Escherichia Coli Using A Genomic Library Approach." ScholarWorks @ UVM, 2015. http://scholarworks.uvm.edu/graddis/487.
Повний текст джерелаTomko, Timothy. "Bioprospecting For Genes That Confer Biofuel Tolerance To Escherichia Coli Using A Genomic Library Approach." ScholarWorks @ UVM, 2017. http://scholarworks.uvm.edu/graddis/798.
Повний текст джерелаKhan, Mirzaei Mohammadali. "The efficacy of bacterial viruses against multi-resistant Escherichia coli: from isolation to pharmacology." Doctoral thesis, Stockholms universitet, Institutionen för molekylär biovetenskap, Wenner-Grens institut, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-126328.
Повний текст джерелаAt the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript. Paper 4: Manuscript.
Plucain, Jessica. "Bases génétiques et écologiques de la diversification adaptative chez Escherichia coli." Phd thesis, Université de Grenoble, 2012. http://tel.archives-ouvertes.fr/tel-00947803.
Повний текст джерелаAal, Owaif Hasan. "Regulation of transcription of the Escherichia coli Group 2 capsule gene clusters." Thesis, University of Manchester, 2017. https://www.research.manchester.ac.uk/portal/en/theses/regulation-of-transcription-of-the-escherichia-coli-group-2-capsule-gene-clusters(70a8508a-9b50-49bb-ba3f-418ab4b485e0).html.
Повний текст джерелаAlghoribi, Majed. "Molecular epidemiology, virulence potential and antibiotic susceptibility of the major lineages of uropathogenic Escherichia coli." Thesis, University of Manchester, 2015. https://www.research.manchester.ac.uk/portal/en/theses/molecular-epidemiology-virulence-potential-and-antibiotic-susceptibility-of-the-major-lineages-of-uropathogenic-escherichia-coli(f1feac7d-0d26-4b6a-b240-f7da26fb1afa).html.
Повний текст джерелаUpdegrove, Taylor Blanton. "Binding properties of Hfq to RNA and genomic DNA and the functional implications." Diss., Georgia Institute of Technology, 2011. http://hdl.handle.net/1853/41075.
Повний текст джерелаTsilibaris, Virginie. "A la recherche de la fonction des systèmes toxine-antitoxine chromosomiques d'E. coli K12." Doctoral thesis, Universite Libre de Bruxelles, 2008. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/210519.
Повний текст джерелаAu début de notre travail, cinq systèmes TA étaient identifiés dans le chromosome d’E. coli. Il avait été montré par notre laboratoire que parmi ces systèmes, seul yefM-yoeB était activé en condition de surproduction de la protéase ATP-dépendante Lon. Ce résultat était surprenant puisque Lon était connue pour dégrader également l’antitoxine RelB du système chromosomique relBE. Un des objectifs de notre travail était de comprendre les mécanismes sous-jacents à cette spécificité. Nous avons montré que l’antitoxine YefM était dégradée à la fois par Lon et les protéases ClpAP et ClpXP. Nous avons également montré qu’en condition de surproduction de Lon, YefM était fortement instable (t1/2~ 10 min. vs 60 min en condition normale). Cette instabilité accrue permet donc l’activation du système yefM-yoeB, c’est-à-dire la libération de la toxine YoeB du complexe qu’elle forme avec YefM. Nous avons également avons montré que le t1/2 de RelB n’était pas affecté par la surproduction de Lon, ce qui explique pourquoi le système relBE n’est pas activé dans ces conditions. Notre hypothèse était qu’un cofacteur soit nécessaire à la dégradation de RelB par Lon et que celui-ci serait limitant dans nos conditions expérimentales. Le crible génétique que nous avons réalisé n’a cependant pas permis d’identifier de cofacteur de dégradation ni de régulateur transcriptionnel en trans du système relBE.
Un deuxième volet de notre travail de thèse a consisté en l’étude de la fonction des systèmes TA chromosomiques. L’hypothèse prévalente au début de notre travail était que les systèmes TA soient intégrés dans les voies adaptatives de réponses au stress. Cependant, le résultat de leur activation était controversé. L’hypothèse du groupe de Gerdes était que leur activation mène à un état bactériostatique réversible alors que le groupe d’Engelberg-Kulka montrait que le système mazEF était un système de mort programmée. Afin d’éclaircir le rôle des cinq systèmes TA dans la physiologie d’E. coli, nous avons testé l’effet de nombreux stress sur la croissance et la viabilité de souches sauvages et de souches délétées de ces systèmes. Aucune des conditions que nous avons testées n’a entraîné une diminution de la viabilité excluant de manière définitive l’hypothèse de la mort programmée. De plus, l’inhibition de croissance causée par ces différents stress s’est avérée être indépendante des cinq systèmes, de même que la phase de récupération suivant les différents stress. Enfin, nos expériences de compétition ont clairement démontré que les cinq systèmes ne procuraient aucun avantage sélectif aux bactéries dans des conditions de compétition en carence nutritive. Les systèmes TA étudiés dans ce travail ne jouent donc aucun rôle dans l’adaptation aux stress que nous avons testé puisqu’ils n’améliorent ni l’aptitude (fitness), ni la compétitivité des bactéries dans ces conditions.
Doctorat en Sciences
info:eu-repo/semantics/nonPublished
Muthukumarasamy, Uthayakumar Verfasser], Karsten Peter Steffen [Akademischer Betreuer] [Hiller, and Susanne [Akademischer Betreuer] Häussler. "The genomic and transcriptomic landscape of clinical Escherichia coli and Pseudomonas aeruginosa isolates / Uthayakumar Muthukumarasamy ; Karsten Hiller, Susanne Häussler." Braunschweig : Technische Universität Braunschweig, 2019. http://d-nb.info/1186251476/34.
Повний текст джерелаSegura, Audrey. "Portage animal des Escherichia coli entérohémorragiques : colonisation et interaction avec le microbiote digestif animal." Thesis, Université Clermont Auvergne (2017-2020), 2018. http://www.theses.fr/2018CLFAC002/document.
Повний текст джерелаEnterohaemorrhagic Escherichia coli (EHEC) are Shiga-toxin producing E. coli (STEC) which represent the fourth pathogen leading to foodborne illness in Europe. Contamination by these pathogens results mainly from the ingestion of food contaminated by feces of bovine, for which the digestive tract appears as the main natural reservoir of EHEC. These pathogens survive in the digestive tract of ruminants, which is healthy carriers, and seem well-adapted to this complex ecosystem. Reducing animal carriage is a strategy of choice to limit EHEC human infections. The aim of this thesis was to increase our knowledge on the physiology and ecology of EHEC in the digestive tract of bovine, a key step to propose, ultimately, different strategies to limit the carriage. Transcriptome analysis of the EHEC O157:H7 reference strain EDL933 allowed the identification of metabolic pathways used by EHEC in different compartments of the digestive tract of the animal. Some carbohydrates, including those from the intestinal mucus layer, and amino acids as well as ethanolamine appear to be important substrates for the survival of EHEC throughout the bovine digestive tract. This transcriptomic study also revealed the activation, by the EHEC strain, of several stress resistance systems encountered in the bovine digestive tract, including toxin/anti-toxin systems. The activation of these systems and the ability to form biofilms have also been observed in a bovine STEC O157:H7 strain, MC2 strain, under conditions mimicking persistence in the environment. Genomic and phenotypic characterization allows this strain to be considered as pathogenic and in vitro and in vivo studies indicated that the MC2 strain was able to persist in the bovine digestive tract but also in the farm environment. The experimental inoculation of bovines with the MC2 strain led to the development, for the first time in France, of a reproducible animal model of carriage and excretion of STEC O157:H7. This model could be used to test in vivo the effect of food additives, such as probiotics, in order to reduce the carriage and excretion of EHEC strains by bovines, and thus limit the contamination of humans