Tesis sobre el tema "RRNA gene analysis"
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Lanyon, Clare. "16S rRNA gene sequence analysis of non-methanogenic Archaea in a hypereutrophic freshwater lake". Thesis, University of Liverpool, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.402322.
Texto completoHermansson, Anna. "Ammonia-oxidising bacteria in soil : studies of diversity and abundance using 16S rRNA gene analysis /". Linköping : Univ, 2001. http://www.bibl.liu.se/liupubl/disp/disp2001/tek712s.pdf.
Texto completoWakeman, Jane A. "Human ribosomal RNA : primary structure analysis of the 28S rRNA gene and preliminary studies on the distribution of pseudouridine residues in the 18S and 28S rRNA molecules". Thesis, University of Liverpool, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.317264.
Texto completoCalus, Szymon Tomasz. "Evaluation of nanopore-based sequencing technology for gene marker based analysis of complex microbial communities : method development for accurate 16S rRNA gene amplicon sequencing". Thesis, University of Glasgow, 2018. http://theses.gla.ac.uk/41086/.
Texto completoAl, Masalma Mouhamad. "Molecular and cultural analysis of the bacterial flora associated with brain abscesses". Thesis, Aix-Marseille 2, 2011. http://www.theses.fr/2011AIX20663/document.
Texto completoBrain abscess is a life-threatening infection with frequent serious sequelae. The medical management remains empirical due to a lack of comprehensive knowledge of the microorganisms responsible for this condition. In most microbiology laboratories the diagnosis of brain abscess is based on culture from pus collected surgically. Unfortunately, this procedure has many limitations and reveals only a small portion of the true microbial population. PCR-amplified 16S rDNA sequencing has recently been used to overcome the limitations of culture-based bacterial detection in brain abscess pus, and it was demonstrated to be effective in the documentation of monomicrobial infections. Unfortunately, this procedure failed to discriminate among polymicrobial floras.Metagenomic studies of complex human floras using a combination of 16S rDNA PCR and cloning-sequencing of PCR products proved useful to evaluate the bacterial diversity of dental, vaginal and intestinal floras. Thus, we applied this technique to brain abscess samples to study the flora associated with this condition. In a first step, we performed an investigation using culture and molecular techniques. The purpose of this investigation was to analyze and evaluate the bacterial flora responsible for brain abscess by comparing standard culture technique to three techniques using 16S rDNA amplification, that is, direct sequencing, multiple sequencing following cloning, and multiple sequencing via high throughput pyrosequencing. This investigation has determined that the variety of brain abscess-associated bacterial species is much larger than previously reported, and it includes many anaerobes and uncultured bacteria from the oral cavity flora. This preliminary study identified 49 distinct brain abscess bacterial agents, and enabled the identification of 27 bacteria never detected before in brain abscess, 15 of which were uncultured.Such a high number of bacterial species involved in brain abscess prompted the study of 51 new specimens in an effort to describe further the flora associated with brain abscesses and their etiologies. Thus, we performed a 16S rDNA-based metagenomic analysis of cerebral abscesses from 51 patients. Our strategy was significantly more discriminatory and enabled the identification of greater number of bacterial taxa, than culture and conventional 16S rDNA PCR/sequencing, respectively. The combination of data from 71 patients (20 from the first study and 51 from the second study) enabled the identification of several associations using the data mining analysis. Also, these studies permitted the identification of two novel bacteria, the first being a novel Staphylococcus species (Staphylococcus massiliensis) and the second being a novel anaerobic bacterium that represents a novel species in a new genus within the phylum Bacteroidetes (Phocaeicola abscesses). In addition, we reported tow unusual cases of brain abscess, the first case was a Mycoplasma hominis brain abscess following uterus curettage and the second case was a Nocardia carnea infection in a kidney transplant recipient patient.Despite limitations inherent to the cloning procedure, our results suggest that cloning and sequencing of PCR-amplified 16S rDNA is a highly valuable method to identify bacterial agents of brain abscesses
Gustafson, Aubree Marie. "T-RFLP analysis of bacterial 16S rRNA gene sequences isolated from river otter (Lontra canadensis) scat and parasite screening for the presence of Toxoplasma gondii". Scholarly Commons, 2009. https://scholarlycommons.pacific.edu/uop_etds/732.
Texto completoKanso, Sungwan y n/a. "Molecular Studies of Bacterial Communities in the Great Artesian Basin Aquifers". Griffith University. School of Biomolecular and Biomedical Science, 2004. http://www4.gu.edu.au:8080/adt-root/public/adt-QGU20040219.140509.
Texto completoKanso, Sungwan. "Molecular Studies of Bacterial Communities in the Great Artesian Basin Aquifers". Thesis, Griffith University, 2004. http://hdl.handle.net/10072/366613.
Texto completoThesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Biomolecular and Biomedical Sciences
Full Text
Kuo, Tai-chih. "The group I ribozyme from the chloroplast rRNA gene of Chlamydomonas reinhardtii : kinetic and structural analysis of the divalent metal requirement and specific interactions with manganese (II) /". Digital version accessible at:, 1998. http://wwwlib.umi.com/cr/utexas/main.
Texto completoHarvey, Robert Jr. "Using PCR Amplification and Genetic Sequence Analysis of 18S rRNA Genes to Survey the Microbial Diversity and Distribution of Eukaryotic Microbes Inhabiting Two Thermo-acidic Streams in Yellowstone National Park, Wyoming". ScholarWorks@UNO, 2009. http://scholarworks.uno.edu/td/978.
Texto completoDouglass, James F. "Biomineralization of atrazine and analysis of 16S rRNA and catabolic genes of atrazine-degraders in a former pesticide mixing and machinery washing area at a farm site and in a constructed wetland". The Ohio State University, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=osu1440373757.
Texto completoMartin, Florence. "Exploration de la biodiversité bactérienne dans un sol pollué par les hydrocarbures : analyse par marquage isotopique du potentiel métabolique et de la dynamique des communautés impliquées dans la dégradation". Phd thesis, Université de Grenoble, 2011. http://tel.archives-ouvertes.fr/tel-00637464.
Texto completoChen, Lian-Cheng y 陳連城. "Phylogenetic analysis of oncomelania hupensis subspecies by rRNA gene sequences". Thesis, 1996. http://ndltd.ncl.edu.tw/handle/52295479836688087213.
Texto completoChen, Ssu-An y 陳思安. "Airway Microbiota Analysis Using 16S rRNA Gene Sequencing Data for Childhood Asthma". Thesis, 2015. http://ndltd.ncl.edu.tw/handle/9f4f38.
Texto completo國立陽明大學
生物醫學資訊研究所
103
Asthma is a chronic inflammatory disease of the airways and the etiology of asthma is a complicated mechanism containing unknown genetic and environmental factors. Microbiota in airway is hypothesized to play an important role in the development of asthma. The aim of this study is to explore the changes of the microbiota between children with atopic diseases and controls using 16S rRNA gene sequencing data. We have applied the QIIME (the Quantitative Insights Into Microbial Ecology) unsupervised analytic method to 16S rRNA sequencing data in order to understand the composition of microbiota in the airways of children with asthma and healthy controls.
Wu, Chen-Fu y 巫振富. "Phyolgenetic analysis of pleurocerid and thiarid snails based on the rRNA gene sequence". Thesis, 1997. http://ndltd.ncl.edu.tw/handle/02814897854758236468.
Texto completoYE, GUO-ZHEN y 葉國楨. "Nucleotide sequence analysis of chloroplast 16S rRNA gene in wild-type and streptomycin-resistant Nicotiana plumbaginifolia". Thesis, 1991. http://ndltd.ncl.edu.tw/handle/10996070894498852275.
Texto completoSousa, Marta Isabel Lopes de. "Biogeography of Arctic Eukaryotic Microbiome: A comparative approach between 18S rRNA gene metabarcoding and microscopic analysis". Master's thesis, 2020. https://hdl.handle.net/10216/130232.
Texto completoSousa, Marta Isabel Lopes de. "Biogeography of Arctic Eukaryotic Microbiome: A comparative approach between 18S rRNA gene metabarcoding and microscopic analysis". Dissertação, 2020. https://hdl.handle.net/10216/130232.
Texto completoLynch, Michael. "Characterizing the phylogenetic distribution of cryptic species in the Rhodophyta using novel gene sequence analysis and molecular morphometrics". Thesis, 2011. http://hdl.handle.net/10012/5943.
Texto completoGomes, Carla Filipa Norte. "Analysis of the microbiome of human stool samples : approaching colorectal cancer diagnosis". Master's thesis, 2018. http://hdl.handle.net/10773/25411.
Texto completoDo ponto de vista histológico, o cancro coloretal (CCR) reside na proliferação anormal de células epiteliais da mucosa do cólon, progredindo de adenoma a adenocarcinoma. Este cancro continua a ser o terceiro com maior incidência e mortalidade mundialmente. É causado por um acúmulo de mutações genéticas e silenciamento epigenético, para além de outros fatores de risco intrínsecos e extrínsecos. Devido às altas taxas de incidência e mortalidade, têm vindo a ser criadas, implementadas e otimizadas ferramentas de diagnóstico e prevenção. No entanto, continua premente a necessidade de desenvolver ferramentas que forneçam um diagnóstico cada vez mais precoce, rigoroso e sensível. Neste sentido, os objetivos desta dissertação consistiram em (1) desenvolver o estado da arte acerca das ferramentas de diagnóstico de CCR, (2) resumir as aplicações “ômicas” para indentificar biomarcadores microbianos relacionados com CCR e (3) comparar o microbioma de pacientes portugueses com CCR e indivíduos saudáveis. Atualmente, o diagnóstico de CCR tem vindo a ser conduzido por procedimentos mais (e.g., colonoscopia) ou menos (e.g., técnicas de imagem, biomarcadores moleculares) invasivos. Muito recentemente, a procura de biomarcadores microbianos através de ferramentas “ómicas” tem sido uma alternativa, principalmente devido à relevância do microbioma nas homeostase metabólica e fisiológica, assim como no funcionamento do sistema imunitário do hospedeiro. Assim, ao microbioma intestinal tem sido atribuído um papel ativo na evolução do CCR, podendo influenciar ou ser influenciado pela doença. Em particular, a análise metagenómica e metabolómica do microbioma associado a CCR em amostras de fezes tem estimulado a comunidade científica na procura de biomarcadores sensíveis, fidedignos, diferenciais, estáveis e precoces na deteção não invasiva da doença. Contudo, estes avanços carecem de uma representatividade para diversas áreas geográficas, dada o impacto cultural, genético e ambiental na incidência desta doença. Neste sentido, realizou-se a análise do microbioma (com enfoque em Bacteria) em fezes de dois grupos clínicos constituídos por indivíduos Portugueses (pacientes com CCR e indivíduos saudáveis), através da sequenciação do gene 16S rRNA usando Ilumina MiSeq. Este estudo é um contributo para colmatar a lacuna de conhecimento existente sobre o microbioma associado a CCR na população Portuguesa. Apesar da estrutura do microbioma de fezes assumir padrões homogéneos entre indivíduos do mesmo grupo clínico, houve alguma variabilidade na abundância de taxa entre esses grupos e em diferentes estádios do CCR. Por exemplo, maiores abundâncias de Prevotella, Alloprevotella, Sutterella, Desulfovibrio e Olsenella observadas em amostras de CCR podem servir como biomarcadores microbianos. No futuro, o estudo será alargado a amostras populacionais maiores, assim como a outro tipo de amostras humanas e grupos clínicos, no sentido de identificar assinaturas microbianas sensíveis e específicas, que possam traduzir o desenvolvimento de CCR, reduzindo, assim, as taxas de incidência e mortalidade.
Mestrado em Biologia Molecular e Celular
Timke, Markus. "Analysis of Biofilm Communities in Breweries". Doctoral thesis, 2005. https://repositorium.ub.uni-osnabrueck.de/handle/urn:nbn:de:gbv:700-2005012011.
Texto completoSchmitz, Jessica Estelle. "Isolierung von DNA und Konstruktion einer Metagenombank aus dem Sediment des Flusses Leine: partielle Sequenzierung und Annotation des Metagenoms sowie Analyse der mikrobiellen Diversität". Doctoral thesis, 2005. http://hdl.handle.net/11858/00-1735-0000-0006-ABAD-7.
Texto completoHewett, Melissa Kim. "Characterisation of bacterial symbionts in amoebae". 2006. http://arrow.unisa.edu.au:8081/1959.8/30130.
Texto completoMoyer, Craig Lee. "Microbial diversity and community structure determinations through analyses of SSU rRNA gene distributions and phylogeny". Thesis, 1995. http://hdl.handle.net/10125/10041.
Texto completoChan, Yi-Hsin y 陳宜欣. "Phylogenetic analyses of the 16S rRNA gene and Arg-gingipain A of Porphyromonas gingivalis clinical isolates". Thesis, 2015. http://ndltd.ncl.edu.tw/handle/35377341251011792264.
Texto completo中山醫學大學
醫學檢驗暨生物技術學系碩士班
103
Background and aim: Periodontitis has a high prevalent rate in Taiwan and Porphyromonas gingivalis is a major pathogen in destructive periodontal disease in humans. Porphyromonas gingivalis produces a unique class of cysteine proteinases termed gingipains that comprises Arg-gingipain A (RgpA). Gingipains have been implicated in the pathogenicity of Porphyromonas gingivalis, a major etiologic agent of chronic periodontitis. The purpose of our studies is to determine the phylogenies of 16S RNA gene and Arg-gingipain (RgpA) gene of clinical P. gingivalis strains among different years. Methods: Samples were collected from gingival pockets of periodontitis patients. All samples were treated with genomic DNA extraction, and PCR was used to amplify 16S RNA and RgpA genes for DNA sequencing. DNA sequences of all amplicons were subjected to phylogenetic analysis by using MEGA 6.01. In addition, the DNA sequences of 16S RNA genes were also deposited and submitted to National Center for Biotechnology Information Genbank database to acquire accession numbers. Results: Fifty four samples were collected from gingival pockets of periodontitis patients. The positive rates of P. gingivalis were 38.9% and 18.5% by PCR and by culture, respectively. 16S RNA and RgpA gene fragments from ten samples were amplified and sequencing. Phylogenetic analysis of 16S RNA genes indicated that P. gingivalis strains were divided into two clusters and our isolates from each other were similar to two clusters. Similarly, phylogenetic analysis of RgpA genes showed that compared with the other strains, the P.g_CSMU24、P.g_CSMU33、P.g_CSMU38、P.g_CSMU41 and P.g_CSMU51 of our clinical isolates were significantly different. Conclusion: P. gingivalis was steadily evolved on both 16S RNA gene and RgpA gene. The correlation between gene variations, fitness on human being and disease severity is requires further studies.
Tsai, Meng-Lu y 蔡孟旅. "Phylogenetic Analyses of Periwinkle Leaf Yellowing Phytoplasma Based on Combined Analyses of rRNA, rplV-rpsC, secY and tuf gene sequences". Thesis, 2009. http://ndltd.ncl.edu.tw/handle/81766488495402591801.
Texto completo臺灣大學
植物病理與微生物學研究所
98
A new disease named as periwinkle leaf yellowing (PLY) was first observed in a flower production farm in Dayuan Township (Taoyuan county, Taiwan) in August 2005. Sequence analysis of 16S rDNA, 16S-23S rDNA ISR, and partial 23S rDNA sequence revealed that the causative agent of PLY was closely related to the phytoplasmas of the aster yellows (AY) group (16SrI group) which cause diseases in many horticultural and vegetable crops worldwide, and can be delineated into 10 subgroups. Six cultivated plants including periwinkle plant, chrysanthemum, cosmos, torenia, Persian violet, goosegrass and cucumber, were determined to be the host plants of PLY phytolasma. Monthly PCR detection indicated that PLY phytoplasma was detected in host plants from June to October in 2007, and from July to October in 2007. However, it can be detected earlier since April in 2009. To further clarify the phylogenetic relationship of strain PLY among 16SrI phytoplasmas, six phylogenetic trees were constructed in this study. Beside the phylogenetic trees based on the independent analysis of 16S rRNA, rplV-rpsC, secY and tuf gene sequences, two other trees based on the analysis of the comprising gene sequence of 16S rRNA, rplV-rpsC and secY, and the comprising gene sequence of rplV-rpsC and secY were also constructed. The results indicate that the strain PLY was closely related to 16SrI-B and 16SrI-D subgroup, and could be a new subgroup based on the phylogenetic tree constructed by rplV-rpsC gene sequences. In addition, the phylogenetic analysis of the comprised gene sequences showed similar tree topology when compared with sequence analysis of the rplV/ rpsC gene or of the secY gene alone. The main difference is that the branch lengths were elongated in the comprised gene tree. To further confirm the subgroup affiliation of PLY phytoplasma, the 16S rRNA gene sequences of 10 closely related phytoplasma strains were digested in silico, and the similarity coefficients were then calculated. The results also support the conclusion that PLY phytoplasma might belongs to a new 16SrI subgroup. The putative restriction site analysis can also distinguish PLY phytoplasma from other close related phytoplasma strains in phylogenetic analysis.
Dutta, Partha. "Soil community analysis along a salt gradient using denaturing gradient gel electrophoresis of PCR-amplified 16s rRNA genes". Thesis, 2006. http://hdl.handle.net/10057/369.
Texto completoThesis (M.S.)--Wichita State University, College of Liberal Arts and Sciences, Dept. of Biological Sciences.
"May 2006."
Reed, Andrew Jay. "Molecular analysis of microbial 16S rRNA, mcrA, dsrAB and pmoA genes from deep-sea hydrothermal vent and cold seep sites". 2008. http://hdl.rutgers.edu/1782.2/rucore10001600001.ETD.17554.
Texto completoTung, Shung-Kai y 童聖凱. "Identification of Streptococci, Enterococci, and Nutritionally Variant Streptococci by Sequence Analysis of the Intergenic Spacer Region of rRNA Genes and by an Oligonucleotide Array". Thesis, 2005. http://ndltd.ncl.edu.tw/handle/91470574993708491119.
Texto completo國立成功大學
醫學檢驗生物技術學系
93
Many species belonging to Enterococcus, Streptococcus, and nutritionally variant streptococci (NVS) including Abiotrophia and Granulicatella, are human pathogens. The feasibility of sequence analysis of the 16S-23S ribosomal DNA intergenic spacer (ITS) for identification of strains belonging to the four genera was evaluated. In this study, ITS sequences of 62 type strains (55 species) and 12 ITS sequences obtained from the GenBank database were used to construct an ITS database for identicication of strains belonging to Enterococcus, Streptococcus, and NVS. The ITS lengths of different species varied from 189 to 602 bp, with interspecies sequence similarities ranging from 0.31 to 0.996. ITS sequences were highly conserved among strains within the same species, with intraspecies similarity ranged from 0.98 to 1.0, except for strains of Granulicatella elegans. A total of 227 strains, including 89 reference strains and 138 clinical isolates, were identified by ITS sequencing. Cinical isolates producing discrepant species names by ITS sequencingwere reconfirmed by the Rapid ID 32 STREP system (bioMe’rieux Vitek, Marcy l’Etoile, France). A total of 27 strains (11.9%, 27/227), including reference strains and clinical isolates, were found to produce discrepant identification results between by ITS sequencing and. The sequences of 16S rRNA genes were further determined for species confirmation of strains producing discrepant identification. The sensitivity of ITS sequence analysis for species identification was 98.2% (226/230). Four strains were not identified by ITS sequencing because their corresponding ITS sequences were not available in the ITS sequence database. Based on ITS sequence, an oligonucleotide array was designed to identify these bacteria. A total of 391 strains, including 336 target strains (160 reference strains and 176 clinical isolates) and 55 nontarget strains were identified by the array. The sensitivity and specificity of the array were 100% (336/336) and 96.4% (53/55), respectively. In conclusion, both ITS sequence analysis and the array hybridization method could be used as accurate alternatives for species identification of Abiotrophia, Enterococcus, Granulicatella, and Streptococcus.
Tran, Hoang-Dung [Verfasser]. "Sequencing fragments of cryptophyte plastomes from 16S rRNA to rbcL genes and phylogenetic analyses based on the protein-encoding genes located in these fragments / vorgelegt von Hoang-Dung Tran". 2009. http://d-nb.info/999683381/34.
Texto completoSu, Jui y 蘇銳. "Prevalence of the primary resistance to metronidazole, clarithromycin, and amoxicillin of Helicobacter pylori clinical isolates from Taiwan and the genetic analysis of rdxA and 23s rRNA genes in different isolates". Thesis, 2001. http://ndltd.ncl.edu.tw/handle/33646222081339576791.
Texto completo國立清華大學
生命科學系
89
Helicobacter pylori is a Gram-negative microaerophilic bacterium which colonizes the gastric mucosa of the human stomach. Infection with H. pylori is associated with gastritis, gastric ulcer, duodenal ulcer. The common treatment of H. pylori infection includes antibiotics and a combination of a proton pump inhibitor. Because of an increased use of antibiotic agents, resistance to antibiotics is the major cause of the therapy failure. The aim of this study is to investigate the efficacy of the triple therapy and the prevalence of the resistance of the three antibiotics used in eradication therapy, which are metronidazole, clarithromycin, and amoxicillin. 151 patients who took the triple therapies containing lansoprazole, clarithromycin, and metronidazole/amoxicillin in Taichung Veterans General Hospital were enrolled in this study and 137 patients completed the course of treatment. The resistance of fifty-one strains collected from patients in 2000 were determined by its minimal inhibitory concentration (MIC) values of the three antibiotics, which were determined by E-test. Two regimens were used in this study: the eradication rate of the LAC regimen total is 88.41% and it is 85.29% in LMC regimen. In LAC regimen, the prevalence of resistance of metronidazole and clarithromycin is 39.29% and 7.14% respectively. In LMC regimen, the prevalence of these two antibiotics are 43.48% and 4.35%. No amoxicillin-resistant strains are found in this study. Eighteen different strains from fifteen patients were analyzed for the reason of therapy failure. The strains were examined by polymerase chain reaction (PCR) and PCR-based restriction fragment length polymorphism (RFLP) of the vacA and ureA-ureB genes to examine whether the strains obtained before and after treatment are the same. Their MIC values were also determined by E-test. The rdxA and 23s rRNA genes from both antibiotic resistant and sensitive strains were sequenced to investigate the difference between those strains. We find that there are two re-infection cases in LAC regimen and six different strains six patients are resistant to metronidazole or clarithromycin and four different strains from four patients are resistant to both metronidazole and clarithromycin. In the gene analysis, most our data correspond with published data. We also find one interesting strain has the three amino acids deletion in its rdxA gene, which is not seen in other data.