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Patel, Muneeza S. "Algorithms for E. coli genome engineering". Thesis, Massachusetts Institute of Technology, 2016. http://hdl.handle.net/1721.1/106461.
Pełny tekst źródłaThis electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
"June 2016." Page 90 blank. Cataloged from student-submitted PDF version of thesis.
Includes bibliographical references (pages 70-72).
Author summary: Lamba red recombineering is one of methods of performing genome engineering. However, this method of genome editing is not very specific and efficient and is highly dependent on the genomic regions that are targeted (integration sites). In this project we explored ways of identifying what makes a site well suited for lambda red genome engineering. We wanted to explore whether we can eventually predict the "goodness" of an integration site using an algorithm. Our initial approach to the problem was to write an algorithm based on some characteristics that we felt would be key to determining the goodness of a site. Choosing to initially focus on specificity of the integrations, we used experimental approaches to evaluate whether our algorithm had any predictive powers for specificity. Upon failing, we revised our plan to generate a dataset of ~150 sites and their integration data (whether integration was successful, specific and efficient at that site). We used this dataset to explore correlations between the specificity data and characteristics we thought might affect the specificity of sites. The most promising characteristics appeared to be the uniqueness of the genomic site (as determined by BLAST) and the existence of Repetitive Extragenic Palindrome (REP) sites at the site of integration. Section I of this thesis sets up the problem, section II talks about the initial approach we took to the problem and section III discusses our modified approach -- which formed the bulk of this thesis project. Section I and III are the most relevant to understand the project, while Section II gives more content to the project in addition to detailed insight to what approaches did not work.
by Muneeza S. Patel.
M. Eng. in Computer Science & Molecular Biology
Neelakanta, Girish. "Genome variations in commensal and pathogenic E.coli". [S.l. : s.n.], 2005. http://deposit.ddb.de/cgi-bin/dokserv?idn=974330329.
Pełny tekst źródłaSchlegel, 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.
Pełny tekst źródłaAt the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 3: Manuscript.
Wlodarski, Michal. "Dynamics of E. coli genome and cytosol under antibiotics". Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/275205.
Pełny tekst źródłaRomero, Alvarez David. "Genome wide analyses of the Escherichia coli primary and secondary transcriptomes". Thesis, University of Leeds, 2014. http://etheses.whiterose.ac.uk/6917/.
Pełny tekst źródłaCoss, 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.
Pełny tekst źródłaTitle 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.
Pełny tekst źródłaEl, Sayyed Hafez. "Mapping Topoisomerase IV Binding and Activity Sites on the E. coli genome". Thesis, Université Paris-Saclay (ComUE), 2016. http://www.theses.fr/2016SACLS362/document.
Pełny tekst źródłaCatenation links between sister chromatids are formed progressively during DNA replication and are involved in the establishment of sister chromatid cohesion. Topo IV is a bacterial type II topoisomerase involved in the removal of catenation links both behind replication forks and after replication during the final separation of sister chromosomes. We have investigated the global DNA-binding and catalytic activity of Topo IV in E. coli using genomic and molecular biology approaches. ChIP-seq revealed that Topo IV interaction with the E. coli chromosome is controlled by DNA replication. During replication, Topo IV has access to most of the genome but only selects a few hundred specific sites for its activity. Local chromatin and gene expression context influence site selection. Moreover strong DNA-binding and catalytic activities are found at the chromosome dimer resolution site, dif, located opposite the origin of replication. We reveal a physical and functional interaction between Topo IV and the XerCD recombinases acting at the dif site. This interaction is modulated by MatP, a protein involved in the organization of the Ter macrodomain. These results show that Topo IV, XerCD/dif and MatP are part of a network dedicated to the final step of chromosome management during the cell cycle
Johnson, Matthew David. "Understanding the regulation of acid resistance in E. coli using whole genome techniques". Thesis, University of Birmingham, 2011. http://etheses.bham.ac.uk//id/eprint/3006/.
Pełny tekst źródłaSchmidt, 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.
Pełny tekst źródłaThe 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.
Pełny tekst źródłaBrambilla, 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.
Pełny tekst źródłaEscherichia 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
PRADEL, 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.
Pełny tekst źródłaMédigue, Claudine. "Conception et exploitation d'une base de donnees specialisee dediee a l'analyse du genome d'escherichia coli". Paris 6, 1991. http://www.theses.fr/1991PA066690.
Pełny tekst źródłaHenze, Stefanie [Verfasser], i 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.
Pełny tekst źródłaCowley, 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.
Pełny tekst źródłaLember, 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.
Pełny tekst źródłaMa, Chih-Yu. "Occurrence and characterization of antibiotic-resistant Escherichia coli in wastewater and surface water". Kyoto University, 2020. http://hdl.handle.net/2433/259030.
Pełny tekst źródłaCHEVALLIER, 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.
Pełny tekst źródłaGunasekera, 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/.
Pełny tekst źródłaNguyen, Huong LE. "Etude des facteurs régulateurs de la traduction chez Escherichia coli". Thesis, Toulouse, INSA, 2019. http://www.theses.fr/2019ISAT0004.
Pełny tekst źródłaThe 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
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.
Pełny tekst źródłaLarge-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.
Pełny tekst źródłaDepartment 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.
Ghosh, Hiren [Verfasser]. "A genome-based approach to study the ecology and epidemiology of Extended-Spectrum Beta-Lactamases (ESBLs) producing E. coli / Hiren Ghosh". Gießen : Universitätsbibliothek, 2019. http://d-nb.info/1186624604/34.
Pełny tekst źródłaStoesser, 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.
Pełny tekst źródłaMaistrenko, 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.
Pełny tekst źródłaFederal Formula Funding (Hatch-Act)
ND-EPSCoR
Fulbright-STEP scholarship
Sarica, Nazim. "Identification de contraintes locales impactant l’expression des gènes chez Escherichia coli". Thesis, université Paris-Saclay, 2020. http://www.theses.fr/2020UPASL021.
Pełny tekst źródłaA 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
Singh, Harminder. "Identification of Genes Encoding Acyl-Coa Reductases and Aldehyde Reductases in Mycobacterial Genome By Characterization of the Reductases Expressed in E. Coli". Master's thesis, University of Central Florida, 2007. http://digital.library.ucf.edu/cdm/ref/collection/ETD/id/3238.
Pełny tekst źródłaM.S.
Department of Molecular Biology and Microbiology
Burnett College of Biomedical Sciences
Molecular and Microbiology MS
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.
Pełny tekst źródłaLaunay, 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.
Pełny tekst źródłaEscherichia 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
Mainda, Geoffrey. "Molecular epidemiology of antimicrobial resistance (AMR) and Shiga toxin producing E. coli (STEC) in dairy herds of central Zambia". Thesis, University of Edinburgh, 2016. http://hdl.handle.net/1842/25416.
Pełny tekst źródłaWalz, 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.
Pełny tekst źródłaxiv, 132 leaves : ill. (chiefly col.) ; 29 cm
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.
Pełny tekst źródłaEscherichia 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
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/.
Pełny tekst źródłaFrom 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.
Bürfent, Benedikt [Verfasser]. "The immunomodulatory capacity of helminths on inflammation: Impact of eosinophils on E. coli-induced sepsis and genome-wide transcriptome profiling of human monocytes stimulated with helminth extract and LPS implicate immune functions and diseases / Benedikt Bürfent". Bonn : Universitäts- und Landesbibliothek Bonn, 2017. http://d-nb.info/1149154284/34.
Pełny tekst źródłaMendes, 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/.
Pełny tekst źródłaThe 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/.
Pełny tekst źródłaLeptospirosis 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.
Davenport, Colin [Verfasser], i Burkhard [Akademischer Betreuer] Tümmler. "Genomic and metagenomic application of microbial genome signatures / Colin Davenport. Burkhard Tümmler. Biomedical Research School (HBRS) Department of Paediatrics Hannover Medical School". Hannover : Bibliothek der Medizinischen Hochschule Hannover, 2010. http://d-nb.info/100117173X/34.
Pełny tekst źródłaWalters, 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.
Pełny tekst źródłaChan, Kamfai. "Erythromycin Susceptibility and Genomic Regions Characterization of Campylobacter coli". NCSU, 2007. http://www.lib.ncsu.edu/theses/available/etd-05162007-114033/.
Pełny tekst źródłaSun, Xueguang. "Characterization of E. coli HFQ structure and its RNA binding properties". Available online, Georgia Institute of Technology, 2006, 2006. http://etd.gatech.edu/theses/available/etd-12052005-145342/.
Pełny tekst źródłaWartell Roger, Committee Chair ; Chernoff Yury, Committee Member ; Harvey Stephen, Committee Member ; Spiro Stephen, Committee Member ; Williams Loren, Committee Member.
Price, Erin Peta. "Development of novel combinatorial methods for genotyping the common foodborne pathogen Campylobacter jejuni". Thesis, Queensland University of Technology, 2007. https://eprints.qut.edu.au/16601/1/Erin_Peta_Price_Thesis.pdf.
Pełny tekst źródłaPrice, Erin Peta. "Development of novel combinatorial methods for genotyping the common foodborne pathogen Campylobacter jejuni". Queensland University of Technology, 2007. http://eprints.qut.edu.au/16601/.
Pełny tekst źródłaMahmoud, 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.
Pełny tekst źródłaSantos, 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.
Pełny tekst źródłaBanca: 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...
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Mahfouz, Norhan, Serena Caucci, Eric Achatz, Torsten Semmler, Sebastian Guenther, Thomas U. Berendonk i Michael Schroeder. "High genomic diversity of multi-drug resistant wastewater Escherichia coli". Nature Publishing Group, 2018. https://tud.qucosa.de/id/qucosa%3A32482.
Pełny tekst źródłaSun, Xueguang. "Characterization of E coli Hfq structure and its RNA binding properties". Diss., Georgia Institute of Technology, 2005. http://hdl.handle.net/1853/10416.
Pełny tekst źródłaBin, 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.
Pełny tekst źródłaEger, 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.
Pełny tekst źródłaNelson, 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.
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