subject:(RNA riboss mico 16S)

Brno University of Technology

1. Grešová, Katarína. Klasifikace bakterií do taxonomických kategorií na základě vlastností 16s rRNA: Bacteria Classification into Taxonomic Categories Based on Properties of 16s rRNA.

Degree: 2020, Brno University of Technology

URL: http://hdl.handle.net/11012/192475

► The main goal of this thesis was to design and implement a tool that would be able to classify the sequences of the 16S rRNA… (more)

Subjects/Keywords: metagenomika; 16S rRNA; kópie génu 16S rRNA; sekundárna štruktúra RNA; taxonomická klasifikácia; Metropolis-Hastings; metagenomics; 16S rRNA; copies of 16S rRNA gene; RNA secondary structure; taxonomic classification; Metropolis-Hastings

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Grešová, K. (2020). Klasifikace bakterií do taxonomických kategorií na základě vlastností 16s rRNA: Bacteria Classification into Taxonomic Categories Based on Properties of 16s rRNA. (Thesis). Brno University of Technology. Retrieved from http://hdl.handle.net/11012/192475

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Grešová, Katarína. “Klasifikace bakterií do taxonomických kategorií na základě vlastností 16s rRNA: Bacteria Classification into Taxonomic Categories Based on Properties of 16s rRNA.” 2020. Thesis, Brno University of Technology. Accessed March 03, 2021. http://hdl.handle.net/11012/192475.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Grešová, Katarína. “Klasifikace bakterií do taxonomických kategorií na základě vlastností 16s rRNA: Bacteria Classification into Taxonomic Categories Based on Properties of 16s rRNA.” 2020. Web. 03 Mar 2021.

Vancouver:

Grešová K. Klasifikace bakterií do taxonomických kategorií na základě vlastností 16s rRNA: Bacteria Classification into Taxonomic Categories Based on Properties of 16s rRNA. [Internet] [Thesis]. Brno University of Technology; 2020. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/11012/192475.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Grešová K. Klasifikace bakterií do taxonomických kategorií na základě vlastností 16s rRNA: Bacteria Classification into Taxonomic Categories Based on Properties of 16s rRNA. [Thesis]. Brno University of Technology; 2020. Available from: http://hdl.handle.net/11012/192475

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

2. Oliveira, Fernanda Filomena de. Análise da diversidade da microbiota fecal de lactentes durante o primeiro ano de vida utilizando biblioteca 16S RNA.

Degree: Mestrado, Análises Clínicas, 2011, University of São Paulo

URL: http://www.teses.usp.br/teses/disponiveis/9/9136/tde-09122013-105457/ ;

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A microbiota intestinal humana desempenha papel essencial no organismo saudável, pois sintetiza vitaminas, influencia no desenvolvimento e maturação do sistema imune da mucosa intestinal, além… (more)

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A microbiota intestinal humana desempenha papel essencial no organismo saudável, pois sintetiza vitaminas, influencia no desenvolvimento e maturação do sistema imune da mucosa intestinal, além de exercer importante função protetora, competindo por nutrientes e receptores com bactérias patogênicas. A colonização desta microbiota se inicia na criança recém-nascida e alcança estabilidade em torno do segundo ano de vida, com consequência para a saúde da criança e do adulto. As diferenças na composição da microbiota estão relacionadas a diferentes níveis de contaminação ambiental e de diferentes fatores endógenos. O objetivo do nosso estudo foi analisar a microbiota fecal de crianças com idade entre 2 dias a 1 ano de idade, que vivem em baixas condições socioeconômicas em São Paulo, Brasil. Foram coletadas amostras de fezes de crianças saudáveis, nos seguintes pontos pós-nascimento: 2º e 7º dias, 1 mês, 3 meses, 6 meses e 1 ano de vida. O DNA bacteriano foi extraído diretamente a partir das amostras de fezes e as bibliotecas 16S rRNA foram construídas utilizando 2 iniciadores bactéria-específicos. Os clones foram selecionados aleatoriamente, parcialmente sequenciados e analisados com base em bibliotecas de gene 16S rRNA. Os principais grupos filogenéticos identificados foram Escherichia, Clostridium, Streptococcus e Bacteroides, do 1º ao 30º dia de vida. A partir do 3º mês, Streptococcus e bactérias não cultiváveis, além do gênero Escherichia, ganharam relevância na microbiota. Estes dados, em conjunto com as informações nutricionais, intercorrências clínicas e ambientais, sugerem a influência da contaminação ambiental e interpessoal no aumento da complexidade na composição da microbiota fecal. Essa abordagem molecular permitiu a análise da microbiota fecal do grupo selecionado, encontrando perfil bacteriano diferente do que é descrito nos países desenvolvidos.

The human intestinal microbiota plays essential role in healthy body since it synthesizes vitamins, influences on the development and maturation of the immune system of the intestinal mucosa. Furthermore, it also plays an important protective function competing for nutrients and receptors with pathogenic bacteria. The colonization of this microbiota starts in the newborn child and achieves stability around the second year of life, with consequence for the health of children and adults. The differences in the microbiota composition are related to different levels of environmental contamination and different endogenous factors. The aim of our study was to analyze the fecal microbiota of children ranging from 2º days to 1º year old living in low socioeconomic status in São Paulo, Brazil. We collected fecal samples of healthy children at the following points after birth: 2º e 7º days, 1 month, 3 months, 6 months and one year of life. Bacterial DNA was extracted directly from stool samples, and the 16S rRNA libraries were made using 2 bacterium-specific primers. The clones were randomly selected, and partially sequenced and analyzed based on 16S rRNA libraries. The…

Advisors/Committee Members: Martinez, Marina Baquerizo.

Subjects/Keywords: 16S rRNA libraries; Análise filogenética; Biblioteca 16S RNA; Fecal microbiota; Microbiota fecal; Phylogenetic analysis

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Oliveira, F. F. d. (2011). Análise da diversidade da microbiota fecal de lactentes durante o primeiro ano de vida utilizando biblioteca 16S RNA. (Masters Thesis). University of São Paulo. Retrieved from http://www.teses.usp.br/teses/disponiveis/9/9136/tde-09122013-105457/ ;

Chicago Manual of Style (16^th Edition):

Oliveira, Fernanda Filomena de. “Análise da diversidade da microbiota fecal de lactentes durante o primeiro ano de vida utilizando biblioteca 16S RNA.” 2011. Masters Thesis, University of São Paulo. Accessed March 03, 2021. http://www.teses.usp.br/teses/disponiveis/9/9136/tde-09122013-105457/ ;.

MLA Handbook (7^th Edition):

Oliveira, Fernanda Filomena de. “Análise da diversidade da microbiota fecal de lactentes durante o primeiro ano de vida utilizando biblioteca 16S RNA.” 2011. Web. 03 Mar 2021.

Vancouver:

Oliveira FFd. Análise da diversidade da microbiota fecal de lactentes durante o primeiro ano de vida utilizando biblioteca 16S RNA. [Internet] [Masters thesis]. University of São Paulo; 2011. [cited 2021 Mar 03]. Available from: http://www.teses.usp.br/teses/disponiveis/9/9136/tde-09122013-105457/ ;.

Council of Science Editors:

Oliveira FFd. Análise da diversidade da microbiota fecal de lactentes durante o primeiro ano de vida utilizando biblioteca 16S RNA. [Masters Thesis]. University of São Paulo; 2011. Available from: http://www.teses.usp.br/teses/disponiveis/9/9136/tde-09122013-105457/ ;

3. Malli, Ergina. Ανίχνευση και ταυτοποίηση με κλασικές και μοριακές τεχνικές του αιτιολογικού παράγοντα της αυτόματης βακτηριακής περιτονίτιδας σε ασθενείς με κίρρωση.

Degree: 2019, University of Thessaly (UTH); Πανεπιστήμιο Θεσσαλίας

URL: http://hdl.handle.net/10442/hedi/45300

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Spontaneous bacterial peritonitis (SBP) is a frequent and severe complication of cirrhotic patients with ascites. It was defined for the first time in 1971 by… (more)

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Spontaneous bacterial peritonitis (SBP) is a frequent and severe complication of cirrhotic patients with ascites. It was defined for the first time in 1971 by Conn as a bacterial infection of the ascitic fluid (AF) in the absence of a focal contiguous source. The key mechanism of the pathogenesis of SBP is bacterial translocation (BT), defined as the passage of viable gut flora through the intestinal barrier to extra-luminal sites. It is τhe most frequent infectious complication in patient with cirrhosis. SBP is diagnosed on the basis of PMN cell counts equal or greater than 250 cells/mm3 in AF, regardless the result of the ascites culture. It is known that, in a high proportion of SBP patients, cultures of AF remain negative, probably due to the relative low concentration of bacteria in ascitic fluid (1 bacteria/ml). In general practice, ascites culture is negative in approximately 60% of SBP patients, despite the inoculation of ascites directly into blood culture bottles (AF vial cultures) at the bedside. Molecular assays have been widely used for detection of microorganisms directly to clinical specimens.In this study, we assessed the value of broad range 16S rRNA PCR applied either directly to ascitic fluid or to the ascitic fluid vial cultures, compared to the standard of care that includes ascitic fluid vial culture.A total of 150 ascitic fluids (39 non portal hypertension and 111 portal hypertension) obtained from individual patients, were collected. SBP was diagnosed in 32 of them. Ten ml of each ascitic fluid were inoculated into blood culture bottles at the patients’ bedside and were inoculated for a period of 14 days. In addition, 10 ml of ascitic fluid were also obtained for molecular analysis. Broad range 16S rRNA PCR was applied directly to ascitic fluid and to the ascitic fluid vial cultures after the incubation period. PCR amplicons were sequenced in both directions and were compared with those submitted to GenBank and EMBL, using the BLAST algorithm.Four out 32 AF vial cultures (12.5%) were found to be positive for Escherichia coli. The application of 16S rRNA PCR directly to AF detected only one of the four positive samples [sensitivity 25%, specificity 100%, positive predictive value (PPV) 100%, negative predictive value (NPV) 90.32%]. However, the application of 16S rRNA PCR to AF vial cultures after 14 days of incubation correctly identified all the positive samples, including one more that was positive for Brucella mellitensis (sensitivity 100%, specificity 80%, PPV 80%, NPV 100%). The elongation of the incubation period of the AF vial cultures, combined with the use of 16S rRNA in negative vials, increases the possibility of identifying the causative agents of SBP and could be applied in the clinical laboratory.

Η αυτόματη βακτηριακή περιτονίτιδα είναι μια συχνή και σοβαρή επιπλοκή που αφορά στους ασθενείς με ασκίτη. Ορίστηκε για πρώτη φορά το 1971 ως η περιτονίτιδα που εμφανίζεται σε ασθενείς με κίρρωση του ήπατος και συνοδό ασκίτη, στην οποία δεν ανευρίσκεται ενδοκοιλιακή πηγή λοίμωξης που…

Subjects/Keywords: Αυτόματη βακτηριακή περιτονίτιδα; Ασκίτης; Μοριακές μέθοδοι; Sbp; Ascites; 16S RNA

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Malli, E. (2019). Ανίχνευση και ταυτοποίηση με κλασικές και μοριακές τεχνικές του αιτιολογικού παράγοντα της αυτόματης βακτηριακής περιτονίτιδας σε ασθενείς με κίρρωση. (Thesis). University of Thessaly (UTH); Πανεπιστήμιο Θεσσαλίας. Retrieved from http://hdl.handle.net/10442/hedi/45300

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Malli, Ergina. “Ανίχνευση και ταυτοποίηση με κλασικές και μοριακές τεχνικές του αιτιολογικού παράγοντα της αυτόματης βακτηριακής περιτονίτιδας σε ασθενείς με κίρρωση.” 2019. Thesis, University of Thessaly (UTH); Πανεπιστήμιο Θεσσαλίας. Accessed March 03, 2021. http://hdl.handle.net/10442/hedi/45300.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Malli, Ergina. “Ανίχνευση και ταυτοποίηση με κλασικές και μοριακές τεχνικές του αιτιολογικού παράγοντα της αυτόματης βακτηριακής περιτονίτιδας σε ασθενείς με κίρρωση.” 2019. Web. 03 Mar 2021.

Vancouver:

Malli E. Ανίχνευση και ταυτοποίηση με κλασικές και μοριακές τεχνικές του αιτιολογικού παράγοντα της αυτόματης βακτηριακής περιτονίτιδας σε ασθενείς με κίρρωση. [Internet] [Thesis]. University of Thessaly (UTH); Πανεπιστήμιο Θεσσαλίας; 2019. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/10442/hedi/45300.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Malli E. Ανίχνευση και ταυτοποίηση με κλασικές και μοριακές τεχνικές του αιτιολογικού παράγοντα της αυτόματης βακτηριακής περιτονίτιδας σε ασθενείς με κίρρωση. [Thesis]. University of Thessaly (UTH); Πανεπιστήμιο Θεσσαλίας; 2019. Available from: http://hdl.handle.net/10442/hedi/45300

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Penn State University

4. Schieffer, Kathleen Marie. Integrative Analysis of the Microbiome and Human Intestinal Transcriptome: Implications for the Pathogenesis of Diverticulitis.

Degree: 2017, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/14668kms646

► The formation of diverticula, or herniations of the colonic mucosa and submucosa through the bowel wall, is prevalent in the sigmoid colon of aged individuals… (more)

▼ The formation of diverticula, or herniations of the colonic mucosa and submucosa through the bowel wall, is prevalent in the sigmoid colon of aged individuals in Western countries. Individuals with diverticula have diverticulosis, a condition which is usually asymptomatic. However, in 4-25% of individuals with diverticulosis, inflammation of the diverticula results in diverticulitis. Acute diverticulitis is commonly treated with empiric antibiotics and increased dietary fiber. Despite the high prevalence of disease in the United States, the pathophysiology of diverticulitis is largely unknown. Previous data suggests that the immune system may play a role in diverticulitis pathogenesis. A key function of the intestinal immune system is to discriminate pathogens from commensal microorganisms. Microbial dysbiosis contributes to the pathogenesis of inflammatory bowel disease; however, whether the microbiome is also involved in diverticulitis pathogenesis is unknown. Therefore, we hypothesized that deregulation of the innate immune system contributes to diverticulitis pathogenesis by promoting a dysbiotic microbial ecosystem. To test this hypothesis, we used RNA-seq, an unbiased and genome-wide approach, to globally survey the intestinal transcriptome of full-thickness sigmoid colon tissue collected adjacent to areas chronically affected by diverticulitis compared to controls. Gene Ontology pathway analysis found increased expression of genes associated with the innate immune response. Expanding on these findings, we identified an increased number of macrophages expressing the scavenger receptor CD163L1 in diverticulitis tissues. In diverticulitis patients, CD163L1+ macrophages localized at the sub-epithelium and co-expressed the chemokine CXCL10. Furthermore, heightened serum CXCL10 was found in diverticulitis patients relative to controls. As the intestinal microbiome influences immune homeostasis, bacterial 16S rRNA and fungal ITS sequencing was performed from chronically diseased tissue and adjacent tissue in diverticulitis patients. We found distinct microbial interactions segregated chronically diseased tissue from adjacent tissue within the same colonic segments. The findings from this dissertation propose that deregulation of the innate immune response to an altered microbial ecosystem results in chronic inflammation and the development of diverticulitis. There are currently no prognostic or diagnostic biomarkers or targeted therapeutic options for diverticulitis; thus this work may help drive development of such targets within molecular pathways of disease relevance. Advisors/Committee Members: Walter Alex Koltun, Dissertation Advisor/Co-Advisor, Walter Alex Koltun, Committee Chair/Co-Chair, Shannon Leanne Kelleher, Committee Member, Gregory Steven Yochum, Committee Member, Regina Lamendella, Outside Member, Matam Vijay Kumar, Committee Member.

Subjects/Keywords: RNA-seq; Microbiome; Diverticular disease; Immune system; 16S rRNA

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Schieffer, K. M. (2017). Integrative Analysis of the Microbiome and Human Intestinal Transcriptome: Implications for the Pathogenesis of Diverticulitis. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/14668kms646

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Schieffer, Kathleen Marie. “Integrative Analysis of the Microbiome and Human Intestinal Transcriptome: Implications for the Pathogenesis of Diverticulitis.” 2017. Thesis, Penn State University. Accessed March 03, 2021. https://submit-etda.libraries.psu.edu/catalog/14668kms646.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Schieffer, Kathleen Marie. “Integrative Analysis of the Microbiome and Human Intestinal Transcriptome: Implications for the Pathogenesis of Diverticulitis.” 2017. Web. 03 Mar 2021.

Vancouver:

Schieffer KM. Integrative Analysis of the Microbiome and Human Intestinal Transcriptome: Implications for the Pathogenesis of Diverticulitis. [Internet] [Thesis]. Penn State University; 2017. [cited 2021 Mar 03]. Available from: https://submit-etda.libraries.psu.edu/catalog/14668kms646.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Schieffer KM. Integrative Analysis of the Microbiome and Human Intestinal Transcriptome: Implications for the Pathogenesis of Diverticulitis. [Thesis]. Penn State University; 2017. Available from: https://submit-etda.libraries.psu.edu/catalog/14668kms646

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Texas – Austin

5. Kim, Vince. Data mining techniques for classifying RNA folding structures.

Degree: MSin Engineering, Computer science, 2016, University of Texas – Austin

URL: http://hdl.handle.net/2152/44018

► RNA is a crucial biological molecule that is critical for protein synthesis. Significant research has been done on folding algorithms for RNA, in particular the… (more)

Subjects/Keywords: RNA; 16S RNA; RNA folding; Data mining; Machine learning; SVM; Support vector machines; Logit; Logistic regression; Random forest; Classifiers

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Kim, V. (2016). Data mining techniques for classifying RNA folding structures. (Masters Thesis). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/44018

Chicago Manual of Style (16^th Edition):

Kim, Vince. “Data mining techniques for classifying RNA folding structures.” 2016. Masters Thesis, University of Texas – Austin. Accessed March 03, 2021. http://hdl.handle.net/2152/44018.

MLA Handbook (7^th Edition):

Kim, Vince. “Data mining techniques for classifying RNA folding structures.” 2016. Web. 03 Mar 2021.

Vancouver:

Kim V. Data mining techniques for classifying RNA folding structures. [Internet] [Masters thesis]. University of Texas – Austin; 2016. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/2152/44018.

Council of Science Editors:

Kim V. Data mining techniques for classifying RNA folding structures. [Masters Thesis]. University of Texas – Austin; 2016. Available from: http://hdl.handle.net/2152/44018

6. Stranieri, Inês. Desenvolvimento de um marcador molecular para o diagnóstico e monitoramento da sepse neonatal bacteriana.

Degree: PhD, Pediatria, 2014, University of São Paulo

URL: http://www.teses.usp.br/teses/disponiveis/5/5141/tde-01122014-143621/ ;

► A sepse bacteriana constitui a causa mais frequente de óbitos neonatais, e seu diagnóstico é complexo devido à inexistência de um teste laboratorial definitivo. O… (more)

▼ A sepse bacteriana constitui a causa mais frequente de óbitos neonatais, e seu diagnóstico é complexo devido à inexistência de um teste laboratorial definitivo. O presente estudo desenvolveu uma técnica de amplificação quantitativa (qPCR) do gene 16S rDNA de bactérias tanto para o diagnóstico de sepse neonatal, quanto para avaliar se a qPCR é capaz de monitorar o tratamento. Para ser recrutado o RN deveria apresentar ao menos dois sinais/sintomas sugestivos de sepse, e dois parâmetros laboratoriais alterados. Amostras de sangue foram colhidas no tempo zero (suspeita de sepse), 48 horas e sete dias após o início da antibioticoterapia. Foram analisados 73 RN (21 RNT e 52 RNPT) com suspeita de sepse neonatal. A hemocultura foi positiva em 32 RN (43,8% - sepse confirmada) e negativa em 41 (56,2% - sepse clínica), enquanto a qPCR foi positiva em 65 RN (89%) e negativa em oito casos (11%). Dentre os 32 RN com sepse confirmada (11 RNT e 21 RNPT), neutrofilia foi encontrada em 22 (68,75%), CRP elevada em 21 (65,62%), plaquetopenia em 15 (46,87%) e leucopenia em 14 (43,75%). Foram analisadas 200 amostras dos 73 casos suspeitos, considerando os três tempos de coleta, resultando em 36 hemoculturas positivas (18,0%) e 135 qPCR positivas (67,5%). Nas 36 hemoculturas positivas houve 38 isolamentos. Bactérias Gram-positivas foram encontradas em 32 amostras (84,21%) e Gram-negativas em seis (15,78%). Staphylococcus coagulase negativa predominou dentre as Gram-positivas (75,0%). No grupo de 32 RN com sepse confirmada a qPCR foi positiva em 30 (30/32 - 93,7%). Em 14 casos (47%) a qPCR antecipou o diagnóstico de sepse quando comparada à hemocultura e foi positiva no tempo zero em 22 casos (68,75%), enquanto a hemocultura foi positiva em 11. Dos 41 casos de sepse clínica, a qPCR foi positiva em 35 (85,4%); em 26 casos (74,3%) já no tempo zero. O teste de McNemar encontrou discordância entre os resultados das hemoculturas e qPCR (p<0,0001, IC de 95%), indicando superioridade da qPCR. Houve nove óbitos na casuística, todos com hemocultura e qPCR positiva. Em seis dos nove óbitos somente a terceira hemocultura foi positiva, enquanto a qPCR foi positiva em cinco casos já no tempo zero e não negativou em seis casos. A qPCR empregou a técnica de touchdown, com temperaturas de annealing decaindo de 66 a 62 °C, limiar de detecção entre 1-10 UFC/mL. As cargas bacterianas foram em geral baixas (< 50 UFC/mL) mesmo nos casos com sepse confirmada e óbitos, porém quando as medianas das cargas bacterianas no tempo zero dos grupos com sepse confirmada (37,10 UFC/mL) e sepse clínica (24,49 UFC/mL) foram comparadas, foi encontrada uma diferença estatisticamente significante (p=0,0402). O estudo concluiu que a qPCR é capaz de detectar mais casos de sepse neonatal que a hemocultura, antecipando o diagnóstico na maior parte deles. Em relação à monitorização do tratamento, a qPCR apresentou associação com o sucesso ou falha terapêutica, negativou em casos que tiveram evolução favorável, não negativou na maior parte dos óbitos, porém há necessidade de… Advisors/Committee Members: Palmeira, Patricia.

Subjects/Keywords: Bacterial infections; Infant newborn; Infecções bacterianas; Reação em cadeia da polimerase em tempo Real; Real time polymerase chain reaction; Recém-nascido; RNA ribosomal 16S; RNA ribossômico 16S; Sepse; Sepsis

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Stranieri, I. (2014). Desenvolvimento de um marcador molecular para o diagnóstico e monitoramento da sepse neonatal bacteriana. (Doctoral Dissertation). University of São Paulo. Retrieved from http://www.teses.usp.br/teses/disponiveis/5/5141/tde-01122014-143621/ ;

Chicago Manual of Style (16^th Edition):

Stranieri, Inês. “Desenvolvimento de um marcador molecular para o diagnóstico e monitoramento da sepse neonatal bacteriana.” 2014. Doctoral Dissertation, University of São Paulo. Accessed March 03, 2021. http://www.teses.usp.br/teses/disponiveis/5/5141/tde-01122014-143621/ ;.

MLA Handbook (7^th Edition):

Stranieri, Inês. “Desenvolvimento de um marcador molecular para o diagnóstico e monitoramento da sepse neonatal bacteriana.” 2014. Web. 03 Mar 2021.

Vancouver:

Stranieri I. Desenvolvimento de um marcador molecular para o diagnóstico e monitoramento da sepse neonatal bacteriana. [Internet] [Doctoral dissertation]. University of São Paulo; 2014. [cited 2021 Mar 03]. Available from: http://www.teses.usp.br/teses/disponiveis/5/5141/tde-01122014-143621/ ;.

Council of Science Editors:

Stranieri I. Desenvolvimento de um marcador molecular para o diagnóstico e monitoramento da sepse neonatal bacteriana. [Doctoral Dissertation]. University of São Paulo; 2014. Available from: http://www.teses.usp.br/teses/disponiveis/5/5141/tde-01122014-143621/ ;

Universidade Estadual de Campinas

7. Rodrigues, Viviane Drumond, 1983-. Avaliação da biodiversidade de bactérias associadas a ambientes de mina: Biodiversity evaluation of bacteria associated with mine environments.

Degree: 2014, Universidade Estadual de Campinas

URL: http://repositorio.unicamp.br/jspui/handle/REPOSIP/316917

► Abstract: The knowledge concerning microbial diversity associated with mine environments is limited, despite the importance that some microorganisms can have on environmental bioremediation and bioleaching… (more)

▼ Abstract: The knowledge concerning microbial diversity associated with mine environments is limited, despite the importance that some microorganisms can have on environmental bioremediation and bioleaching process. Additionally, microorganisms that live in inhospitable conditions, such as different mine environments, have attracted growing interest because they could have enzymes with industrial applications. In this way, structural and functional biodiversity analysis in mine environments is an important issue to understand the structure and complexity of the microbial communities in extreme environments. The present work shows a microbial diversity analyses in some cooper mine environments of Sossego Mine localized in Canaã dos Carajás mineral province, Pará state, Brazil. The bacterial taxonomic composition associated with Sossego cooper mine: slopes (geotechnical structures) and surrounding drainage of Sossego and Sequeirinho deposits was evaluated using pyrosequencing of 16S rRNA gene. The results indicated slope bacterial community differs from surrounding drainage and organic matter content and higher water availably were the main factors of these differences. The foremost taxons accountable by those differences were Acidobacteria, Chloroflexi, Gammaproteobacteria and Firmicutes. Sixty four bacteria were isolated using culture-dependent methods from SO5, SO6, SO7 and SO9 samples. These bacteria were identified and evaluated concerning the capability of enzyme production (hydrolase, betalactamase, monooxygenase and sulphoxidases) and compounds (siderophore, biosurfactants and antimicrobials). It was identified bacteria related with the followed genera: Acidovorax, Acinetobacter, Brevundimonas, Cupriavidus, Curtobacterium, Kocuria, Lysinibacillus, Pseudomonas, Roseomonas, Ralstonia, Stenotrophomonas and Bacillus, the last one showed 43 isolates. In relation with functional screening, 95% of bacteria were capable to produce siderophores, 58% to produce biosurfactants, 69% betalactamases, 50% antimicrobials, 53% proteases, 75% sterases, 20% monooxygenases and three strains (SO5.4, SO5.9 and SO6.2) exhibited selective oxidation for organic sulphides. Iron oxidizing microorganism consortia were obtained from drainage samples and were tested according with its ability for bioleaching of chalcopyrite. The consortia obtained from SO5, SO6, and SO7 samples were more efficient than Acidithiobacillus ferrooxidans LR regarding bioleaching of copper from chalcopyrite. The identification of microorganism presented in the consortia was performed using DGGE technique and the more evident bands were classified as Bacillus sp., Delftia sp., Phenylobacterium sp. and Methylobacterium sp. The bacterial community in Sossego cooper mine was diverse and complex. These results showed a microbiota inventory in distinct mine environments and enzymes and compounds obtained from those bacteria could be used in new processes and technologies that allow to recovery metals as bioleaching, bioremediation or others industrial applications Advisors/Committee Members: UNIVERSIDADE ESTADUAL DE CAMPINAS (CRUESP), Ottoboni, Laura Maria Mariscal, 1955- (advisor), Universidade Estadual de Campinas. Instituto de Biologia (institution), Programa de Pós-Graduação em Genética e Biologia Molecular (nameofprogram), Fantinatti-Garboggini, Fabiana (committee member), Gaziola, Salete Aparecida (committee member), Gonçalves, Edmilson Ricardo (committee member), Melo, Mônica Barbosa de (committee member).

Subjects/Keywords: Comunidades bacterianas; RNA ribossômico 16S; Cobre - Minas e mineração; Análise funcional; Biomineração; Bacterial communities; RNA, Ribosomal, 16S; Copper mines and mining; Functional analysis; Biomining

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Rodrigues, Viviane Drumond, 1. (2014). Avaliação da biodiversidade de bactérias associadas a ambientes de mina: Biodiversity evaluation of bacteria associated with mine environments. (Thesis). Universidade Estadual de Campinas. Retrieved from http://repositorio.unicamp.br/jspui/handle/REPOSIP/316917

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Rodrigues, Viviane Drumond, 1983-. “Avaliação da biodiversidade de bactérias associadas a ambientes de mina: Biodiversity evaluation of bacteria associated with mine environments.” 2014. Thesis, Universidade Estadual de Campinas. Accessed March 03, 2021. http://repositorio.unicamp.br/jspui/handle/REPOSIP/316917.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Rodrigues, Viviane Drumond, 1983-. “Avaliação da biodiversidade de bactérias associadas a ambientes de mina: Biodiversity evaluation of bacteria associated with mine environments.” 2014. Web. 03 Mar 2021.

Vancouver:

Rodrigues, Viviane Drumond 1. Avaliação da biodiversidade de bactérias associadas a ambientes de mina: Biodiversity evaluation of bacteria associated with mine environments. [Internet] [Thesis]. Universidade Estadual de Campinas; 2014. [cited 2021 Mar 03]. Available from: http://repositorio.unicamp.br/jspui/handle/REPOSIP/316917.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Rodrigues, Viviane Drumond 1. Avaliação da biodiversidade de bactérias associadas a ambientes de mina: Biodiversity evaluation of bacteria associated with mine environments. [Thesis]. Universidade Estadual de Campinas; 2014. Available from: http://repositorio.unicamp.br/jspui/handle/REPOSIP/316917

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Universidade Estadual de Campinas

8. Corrêa, Daniele Bussioli Alves, 1985-. Caracterização de novas espécies de Streptomyces associadas à sarna da batata no Brasil: Characterization of new Streptomyces species associated with potato scab in Brazil.

Degree: 2015, Universidade Estadual de Campinas

URL: http://repositorio.unicamp.br/jspui/handle/REPOSIP/317294

► Abstract: Potato scab is a widespread disease in growing areas in Brazil, becoming a limiting factor in potato production. This disease affects potato quality due… (more)

▼ Abstract: Potato scab is a widespread disease in growing areas in Brazil, becoming a limiting factor in potato production. This disease affects potato quality due to injuries on the tuber surface decreasing its market value or precluding its commercialization. Several species of the genus Streptomyces causing potato scab are known and the survey of pathogenic species present in the Brazilian producing areas is the most important factor for performing management measures. This study aimed to characterize 57 strains of Streptomyces, considered possible new species associated with potato scab in Brazil, through polyphasic taxonomy. The morphological, biochemical, pathogenic (nec1, tomA and txtAB genes and in vitro pathogenicity tests on radishes and potatoes) and molecular characterization (species-specific primers for S. acidiscabies, S. scabiei and S. turgidiscabies, PCR-RFLP of atpD gene, multilocus sequence analysis of atpD, gyrB, recA, rpoB and trpB genes and 16S rRNA gene sequence analysis) of the strains were performed. Using PCR-RFLP of atpD gene technique and sequence analysis of atpD and rpoB genes, the strains were initially separated into 20 genetic groups (G1 to G20). These groups showed high heterogeneity in their spore chains morphology, pigment production and the appearance and color of the colonies and spores, as well as the utilization of different carbon sources. From a total of 57 strains evaluated, 24 (35.3%) showed presence of the three pathogenicity genes, six (8.8%) showed no amplification of the genes and 38 (55.9%) showed absence of one or more genes. All strains were pathogenic on radish causing symptoms of necrosis, radial swelling and/or stunting of shoot and roots, however, they showed differences in virulence level. The most virulent strains were evaluated in pathogenicity test on potato tubers slices and the aggressiveness of the strains, determined by the extent and depth of necrosis, was dependent on the cultivar of potato used, and all evaluated varieties were susceptible. The phylogenetic relationship of the strains has been established with respect to the main species of plant pathogenic Streptomyces and most groups were allocated in different branches and/or with low sequence similarity values. G11 group was closely related to S. scabiei and its genomospecies and G7 was allocated with S. turgidiscabies/S. reticuliscabiei, but they showed no amplification in experiments using species-specific primers and different morphological features were observed. The molecular data, associated with morphological, biochemical and pathogenic characteristics of the strains, allowed confirmation that these genetic groups represent at least 34 new species of phytopathogenic Streptomyces in Brazil. The polymorphisms in the atpD gene sequences allowed the development of species-specific primers for S. caviscabies/S. setonii (Cavis1F/Cavis4R) and S. scabiei (ScADF2/ScADR1). The specificity of these primers was confirmed by amplification experiments using DNA from other Streptomyces species causing… Advisors/Committee Members: UNIVERSIDADE ESTADUAL DE CAMPINAS (CRUESP), Destéfano, Suzete Aparecida Lanza (advisor), Universidade Estadual de Campinas. Instituto de Biologia (institution), Programa de Pós-Graduação em Genética e Biologia Molecular (nameofprogram), Fantinatti-Garboggini, Fabiana (committee member), Bedendo, Ivan Paulo (committee member), Souza, Alessandra Alves de (committee member), Araújo, Welington Luiz de (committee member).

Subjects/Keywords: Análise de sequências gênicas por multilocus; Batata; Streptomyces - Patogenicidade; Polimorfismo de fragmento de restrição; RNA ribossômico 16S; Multilocus sequence analysis; Potatoes; Streptomyces - Pathogenicity; Restriction fragment length polymorphism; RNA, Ribosomal, 16S

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Corrêa, Daniele Bussioli Alves, 1. (2015). Caracterização de novas espécies de Streptomyces associadas à sarna da batata no Brasil: Characterization of new Streptomyces species associated with potato scab in Brazil. (Thesis). Universidade Estadual de Campinas. Retrieved from http://repositorio.unicamp.br/jspui/handle/REPOSIP/317294

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Corrêa, Daniele Bussioli Alves, 1985-. “Caracterização de novas espécies de Streptomyces associadas à sarna da batata no Brasil: Characterization of new Streptomyces species associated with potato scab in Brazil.” 2015. Thesis, Universidade Estadual de Campinas. Accessed March 03, 2021. http://repositorio.unicamp.br/jspui/handle/REPOSIP/317294.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Corrêa, Daniele Bussioli Alves, 1985-. “Caracterização de novas espécies de Streptomyces associadas à sarna da batata no Brasil: Characterization of new Streptomyces species associated with potato scab in Brazil.” 2015. Web. 03 Mar 2021.

Vancouver:

Corrêa, Daniele Bussioli Alves 1. Caracterização de novas espécies de Streptomyces associadas à sarna da batata no Brasil: Characterization of new Streptomyces species associated with potato scab in Brazil. [Internet] [Thesis]. Universidade Estadual de Campinas; 2015. [cited 2021 Mar 03]. Available from: http://repositorio.unicamp.br/jspui/handle/REPOSIP/317294.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Corrêa, Daniele Bussioli Alves 1. Caracterização de novas espécies de Streptomyces associadas à sarna da batata no Brasil: Characterization of new Streptomyces species associated with potato scab in Brazil. [Thesis]. Universidade Estadual de Campinas; 2015. Available from: http://repositorio.unicamp.br/jspui/handle/REPOSIP/317294

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

9. Patrícia Silva Costa. Diversidade molecular de procariotos em solo de cupinzeiro e seu agente Cornitermes cumulans.

Degree: 2011, Universidade Federal de Minas Gerais

URL: http://hdl.handle.net/1843/BUOS-8W2J8K

►

Symbiosis between insects and prokaryotes are recognized as essential to the survival of these invertebrates. The bacterial community in the gastrointestinal tract of termites, social… (more)

▼

Symbiosis between insects and prokaryotes are recognized as essential to the survival of these invertebrates. The bacterial community in the gastrointestinal tract of termites, social insects, is diverse and the function of this microbiota has been characterized. This study investigated the molecular diversity of prokaryotes in soil of the mound and its agent Cornitermes cumulans using a cultivation-independent approach. Thus, samples of the termite nest soil (SC), reference soil (SR) and termite (CP) - Cornitermes cumulans - were collected. The amplicon of the 16S rRNA gene of bacteria was used for the ARDRA fingerprint analysis of the SC, SR and CP samples and the construction of libraries from SC and CP. Moreover, the construction of 16S rDNA library from archaea was obtained using SC sample. Analysis of restriction profiles of 16S rRNA gene revealed that bacterial communities in SC, SR and CP were different, although SR and CP communities were more similar. Phylogenetic analysis using 16S rRNA gene sequences revealed a high diversity of bacterial communities in SC, detecting 67 OTUs which were affiliated to ten phyla: Actinobacteria, Proteobacteria, Acidobacteria, Firmicutes, Planctomycetes, Bacteroidetes, Verrucomicrobia, Chloroflexi, Gemmatimonadetes and Bacteria_incertae_sedis. On the other hand, the community of archaea of the sample SC showed that only two OTUs affiliated to the phylum Chrenoarcheota. The bacterial community of Cornitermes cumulans presented eight OTUs which were affiliated with four phyla Proteobacteria, Firmicutes, Actinobacteria and Synergistetes. Identified bacterial phyla, Proteobacteria, Firmicutes and Actinobacteria were common to both communities in SC and CP. The Shannon-Weaver and Simpson indices and the ACE and Chao1 values showed that SC and CP had high bacterial diversity while SC had a low diversity of archaea. Thus, the results reveal bacterial diversity, yet unexplored, in the soil of termite mound and Cornitermes cumulans.

A simbiose entre insetos e procariotos é reconhecida como sendo essencial para a sobrevivência desses invertebrados. A microbiota existente no trato gastrointestinal de cupins, insetos sociais, é diversa e a sua função vem sendo caracterizada. Este estudo pesquisou a diversidade molecular de procariotos em solo do cupinzeiro e de seu agente Cornitermes cumulans, utilizando uma abordagem independente de cultivo. Assim amostras de solo do cupinzeiro (SC), do solo de referência (SR) e do cupim (CP) - Cornitermes cumulans - foram coletadas. O amplicon do gene de rRNA 16S de bactérias foi usado para a análise do fingerprint ARDRA das amostras SC, SR e CP e para a construção de bibliotecas de clones de SC e CP. Além disso, a construção da biblioteca de clones do gene de rRNA 16S de arqueias foi obtida para a amostra SC. A análise do perfil de restrição do gene de rRNA 16S revelou que as comunidades bacterianas de SC, SR e de CP foram distintas, sendo as comunidades SR e CP mais similares. A análise filogenética utilizando o gene de rRNA 16S revelou uma alta…

Advisors/Committee Members: Andrea Maria Amaral Nascimento, Edmar Chartone de Souza, Andrea Maria Amaral Nascimento, Edmar Chartone de Souza, Vera Lucia dos Santos, Alvaro Cantini Nunes.

Subjects/Keywords: Genética Teses.; Cupim Teses.; Genética bacteriana Teses.; Genetica molecular Teses.; Procariotos; RNA ribossômico 16S

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Costa, P. S. (2011). Diversidade molecular de procariotos em solo de cupinzeiro e seu agente Cornitermes cumulans. (Thesis). Universidade Federal de Minas Gerais. Retrieved from http://hdl.handle.net/1843/BUOS-8W2J8K

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Costa, Patrícia Silva. “Diversidade molecular de procariotos em solo de cupinzeiro e seu agente Cornitermes cumulans.” 2011. Thesis, Universidade Federal de Minas Gerais. Accessed March 03, 2021. http://hdl.handle.net/1843/BUOS-8W2J8K.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Costa, Patrícia Silva. “Diversidade molecular de procariotos em solo de cupinzeiro e seu agente Cornitermes cumulans.” 2011. Web. 03 Mar 2021.

Vancouver:

Costa PS. Diversidade molecular de procariotos em solo de cupinzeiro e seu agente Cornitermes cumulans. [Internet] [Thesis]. Universidade Federal de Minas Gerais; 2011. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/1843/BUOS-8W2J8K.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Costa PS. Diversidade molecular de procariotos em solo de cupinzeiro e seu agente Cornitermes cumulans. [Thesis]. Universidade Federal de Minas Gerais; 2011. Available from: http://hdl.handle.net/1843/BUOS-8W2J8K

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

10. Campbell, Alexandra Mandina. Prokaryotic Diversity of the Wastewater Outfalls, Reefs, and Inlets of Broward County.

Degree: 2014, Nova Southeastern University

URL: http://nsuworks.nova.edu/occ_stuetd/7

► We applied culture-independent, next-generation sequencing (NGS) high throughput pyrosequencing, to characterize the microbial communities associated with near shore seawater in Broward County, FL. These waters… (more)

Subjects/Keywords: 16S; Ribosomal RNA; Bacteria; Archaea; Pyrosequencing; Seawater; Outfalls; Inlets; Reefs; Marine Biology

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Campbell, A. M. (2014). Prokaryotic Diversity of the Wastewater Outfalls, Reefs, and Inlets of Broward County. (Thesis). Nova Southeastern University. Retrieved from http://nsuworks.nova.edu/occ_stuetd/7

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Campbell, Alexandra Mandina. “Prokaryotic Diversity of the Wastewater Outfalls, Reefs, and Inlets of Broward County.” 2014. Thesis, Nova Southeastern University. Accessed March 03, 2021. http://nsuworks.nova.edu/occ_stuetd/7.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Campbell, Alexandra Mandina. “Prokaryotic Diversity of the Wastewater Outfalls, Reefs, and Inlets of Broward County.” 2014. Web. 03 Mar 2021.

Vancouver:

Campbell AM. Prokaryotic Diversity of the Wastewater Outfalls, Reefs, and Inlets of Broward County. [Internet] [Thesis]. Nova Southeastern University; 2014. [cited 2021 Mar 03]. Available from: http://nsuworks.nova.edu/occ_stuetd/7.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Campbell AM. Prokaryotic Diversity of the Wastewater Outfalls, Reefs, and Inlets of Broward County. [Thesis]. Nova Southeastern University; 2014. Available from: http://nsuworks.nova.edu/occ_stuetd/7

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

11. S. Colombo. DISCLOSING THE PHAGE-MEDIATED ANTIBIOTIC RESISTANCES IN THE FOOD CHAIN.

Degree: 2017, Università degli Studi di Milano

URL: http://hdl.handle.net/2434/487927

► The aim of this PhD project is to evaluate the presence and the role of viruses in food related environment with particular attention on the… (more)

▼ The aim of this PhD project is to evaluate the presence and the role of viruses in food related environment with particular attention on the mobilization of antibiotic resistance genes (ARGs). During the last three years it has been investigated samples from different food related environments in order to fully characterize the respective microbial and viral communities with a focus on the identification of ARGs in virome and microbiomes. Water from aquaculture was the first sample analyzed (i) being a matrix that has a strong direct contact with the respective food; secondly, it has been analyzed water from Lambro river (ii) since it is used in the field’s irrigation so it directly came in contact with cereals and vegetables. Last project involved the analysis of air surrounding different moment of cheesemaking production (iii). Once again the viruses present in the air could deposit on the surface of the food and they can be ingested by humans. Shotgun metagenomic sequencing was used to study both microbes and viruses, while 16S rRNA profiling analysis completed the characterization of the bacterial community. The three different projects showed how antibiotic resistance genes are wide spread in the viromes of different environments irrespective of the presence of associated anthropic activities. In this context, we hypothesize that the release of antibiotics molecules in the environment by the microbiota is a driving force able to maintain ARGs in the microbiome and, consequently, mobilize them in the virome. In addition, we should consider the effect of the intense environmental release of antibiotics by humans activities. For these reasons this novel approach even if really useful to collect a high amount of information on the sample, is insufficient to discriminate how ARGs have mobilized to the virome and from the virome to the microbiome. In this context, the development of mesocosms can be the turning point since this system let us to work with complex environmental samples but focusing the attention only at one variable at time as, for example, the supplementation of defined amount of antibiotics. Advisors/Committee Members: tutor: D. Mora, coordinator: F. Bonomi, MORA, DIEGO, BONOMI, FRANCESCO.

Subjects/Keywords: virome; microbiome; antibiotic resistance genes; metagenomic; 16s rna profiling; Settore AGR/16 - Microbiologia Agraria

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Colombo, S. (2017). DISCLOSING THE PHAGE-MEDIATED ANTIBIOTIC RESISTANCES IN THE FOOD CHAIN. (Thesis). Università degli Studi di Milano. Retrieved from http://hdl.handle.net/2434/487927

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Colombo, S.. “DISCLOSING THE PHAGE-MEDIATED ANTIBIOTIC RESISTANCES IN THE FOOD CHAIN.” 2017. Thesis, Università degli Studi di Milano. Accessed March 03, 2021. http://hdl.handle.net/2434/487927.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Colombo, S.. “DISCLOSING THE PHAGE-MEDIATED ANTIBIOTIC RESISTANCES IN THE FOOD CHAIN.” 2017. Web. 03 Mar 2021.

Vancouver:

Colombo S. DISCLOSING THE PHAGE-MEDIATED ANTIBIOTIC RESISTANCES IN THE FOOD CHAIN. [Internet] [Thesis]. Università degli Studi di Milano; 2017. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/2434/487927.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Colombo S. DISCLOSING THE PHAGE-MEDIATED ANTIBIOTIC RESISTANCES IN THE FOOD CHAIN. [Thesis]. Università degli Studi di Milano; 2017. Available from: http://hdl.handle.net/2434/487927

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Universitat de Valencia

12. Gomar Vercher, Sonia. Estudio transversal de la microbiología salival mediante pirosecuenciación en escolares de la Comunitat Valenciana y su relación con la caries dental .

Degree: 2013, Universitat de Valencia

URL: http://hdl.handle.net/10550/26191

► La salud oral, que está fuertemente influenciada por la microbiota oral, ejerce un papel significativo en la salud general. Las comunidades bacterianas orales contienen especies… (more)

▼ La salud oral, que está fuertemente influenciada por la microbiota oral, ejerce un papel significativo en la salud general. Las comunidades bacterianas orales contienen especies que promueven estados de salud, mientras que otras contribuyen a la enfermedad. Conocer qué especies están presentes y cómo se componen las comunidades microbianas en estados de salud es el primer paso para comprender qué cambios pueden llevar a la enfermedad. El tipo de muestras a utilizar para este tipo de estudios, bien con objetivos epidemiológicos o etiológicos, es crucial. La saliva representa un medio fácil y no invasivo de obtención de muestras que contengan bacterias orales de varias localizaciones como las mucosas y la placa supra y subgingival, pero esta puede ser tomada por distintos procedimientos, como saliva estimulada con chicles estériles de parafina, saliva no estimulada con puntas de papel en suelo de boca, “spitting method”, enjuagues con solución salina estéril, etc. Los componentes salivales pueden jugar un rol en la susceptibilidad y desmineralización del esmalte, remineralización y resistencia a la caries dental, la cuál se produce al alterarse el equilibrio ecológico de los biofilms microbianos orales. Los cambios en la composición salival pueden producir alteraciones de la microflora oral en el desarrollo de la caries, y viceversa. En estudios epidemiológicos previos, se ha tomado saliva no estimulada de forma habitual como muestra representativa del ecosistema oral. El objetivo principal de la tesis fue estudiar la microbiota oral a partir de muestras de saliva no estimulada mediante pirosecuenciación de productos de PCR del gen 16S rRNA, y determinar la variabilidad interindividual entre los distintos estadíos de caries dental, y consecuentemente, de salud bucodental. Se seleccionaron 110 individuos de 12 años de edad explorados en la Encuesta de Salud Bucodental de la Comunidad Valenciana del año 2010, de forma aleatoria y siendo esta muestra representativa de la población, organizados en seis grupos según su estado de salud oral siguiendo el índice de caries ICDAS (Internacional Caries Detection and Assessment System). Se tomaron muestras de saliva no estimulada del suelo de la boca con puntas de papel depositadas en suelo de boca. Al mismo tiempo, se recogieron muestras de saliva estimulada con chicles de parafina, de las cuáles se seleccionaron 10 muestras para compararlas con las de saliva no estimulada del mismo paciente. Se realizó la extracción de ADN de las muestras; amplificaciones por PCR, con cebadores universales modificados del gen 16S RNA para bacterias (27F y 533R) a los que se les añadió previamente los adaptadores A y B del sistema Titanium del pirosecuenciador FLX de 454-Roche, permitiendo la unión de los amplicones obtenidos a las microbolas de captura así como su secuenciación. Cada muestra se amplificó mediante un cebador forward que contenía una secuencia identificativa distinta de 8 pares de bases, la cuál servía de “código de barras” para separar las distintas muestras. Ello permitió… Advisors/Committee Members: Montiel Company, José María (advisor).

Subjects/Keywords: estudio del RNA del gen del 16S; escolares; microbiología salival; epidemiología; pirosecuenciación; caries dental

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Gomar Vercher, S. (2013). Estudio transversal de la microbiología salival mediante pirosecuenciación en escolares de la Comunitat Valenciana y su relación con la caries dental . (Doctoral Dissertation). Universitat de Valencia. Retrieved from http://hdl.handle.net/10550/26191

Chicago Manual of Style (16^th Edition):

Gomar Vercher, Sonia. “Estudio transversal de la microbiología salival mediante pirosecuenciación en escolares de la Comunitat Valenciana y su relación con la caries dental .” 2013. Doctoral Dissertation, Universitat de Valencia. Accessed March 03, 2021. http://hdl.handle.net/10550/26191.

MLA Handbook (7^th Edition):

Gomar Vercher, Sonia. “Estudio transversal de la microbiología salival mediante pirosecuenciación en escolares de la Comunitat Valenciana y su relación con la caries dental .” 2013. Web. 03 Mar 2021.

Vancouver:

Gomar Vercher S. Estudio transversal de la microbiología salival mediante pirosecuenciación en escolares de la Comunitat Valenciana y su relación con la caries dental . [Internet] [Doctoral dissertation]. Universitat de Valencia; 2013. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/10550/26191.

Council of Science Editors:

Gomar Vercher S. Estudio transversal de la microbiología salival mediante pirosecuenciación en escolares de la Comunitat Valenciana y su relación con la caries dental . [Doctoral Dissertation]. Universitat de Valencia; 2013. Available from: http://hdl.handle.net/10550/26191

University of Pretoria

13. Debeila, Thipe Jan. Characterisation of selected Culicoides (Diptera : Ceratopogonidae) populations in South Africa using genetic markers.

Degree: Veterinary Tropical Diseases, 2011, University of Pretoria

URL: http://hdl.handle.net/2263/25696

► Culicoides (Diptera: Ceratopogonidae) are small (<3mm) blood feeding flies. These flies are biological vectors of viruses, protozoa and filarial nematodes affecting birds, humans, and other… (more)

▼ Culicoides (Diptera: Ceratopogonidae) are small (<3mm) blood feeding flies. These flies are biological vectors of viruses, protozoa and filarial nematodes affecting birds, humans, and other animals. Among the viruses transmitted those causing bluetongue (BT), African horse sickness (AHS) and epizootic haemorrhagic disease (EHD) are of major veterinary significance. Culicoides (Avaritia) imicola Kieffer, a proven vector of both AHS and BT viruses, is the most abundant and wide spread livestock-associated Culicoides species in South Africa. Field isolations of virus and oral susceptibility studies, however, indicated that a second Avaritia species, C. bolitinos Meiswinkel may be a potential vector of both BT virus (BTV) and AHS virus (AHSV). Differences in oral susceptibility, which are under genetic control, of populations from different geographical areas to viruses may be an indication of genetic differences between these populations, which may be the result of limited contact between these populations. A good knowledge of the distribution, spread and genetic structure of the insect vector is essential in understanding AHS or BT disease epidemiology. In the present study, an effort was made to gather field specimens of both C. imicola and C. bolitinos from different areas within their natural distribution in South Africa. The aim was to partially sequence two mitochondrial genes from these specimens and to analyse the sequence data making use of phylogenetic trees to clarify the genetic relationships between individuals or groups collected from geographically distinct sites. The two species were collected from four geographically separated areas in South Africa viz. Gauteng Province, Eastern Cape Province, Western Cape Province as well as the Free State Province. DNA was extracted from a total of 120 individual midges of the two Culicoides species using DNA extraction kits. Extracted DNA was analysed using PCR, sequencing as well as phylogenetic methods. A total of 117 mitochondrial DNA COI and 104 mitochondrial 16S ribosomal RNA Culidoides</i. sequences were analysed. DNA sequence polymorphism and phylogenetic relationships of various groups of C. imicola and C. bolitinos midges were determined. The results of the phylogenetic analysis of Culicoides populations using mitochondrial COI gene fragment showed that, at least one subpopulation of C. imicola and two distinct genotypes of C. bolitinos species do exist in South Africa, and further analysis is necessary. This study showed that COI has the potential to separate Culicoides midges based on their geography Advisors/Committee Members: Koekemoer, J.J.O. (advisor).

Subjects/Keywords: Bluetongue (BT); Culicoides; Mitochondrial DNA (mtDNA); Sequences; Cytochrome oxidase subunit i coi; 16S ribosomal RNA (16S rRNA); C imicola; C bolitinos; South Africa (SA); African horse sickness (AHS); UCTD

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Debeila, T. J. (2011). Characterisation of selected Culicoides (Diptera : Ceratopogonidae) populations in South Africa using genetic markers. (Masters Thesis). University of Pretoria. Retrieved from http://hdl.handle.net/2263/25696

Chicago Manual of Style (16^th Edition):

Debeila, Thipe Jan. “Characterisation of selected Culicoides (Diptera : Ceratopogonidae) populations in South Africa using genetic markers.” 2011. Masters Thesis, University of Pretoria. Accessed March 03, 2021. http://hdl.handle.net/2263/25696.

MLA Handbook (7^th Edition):

Debeila, Thipe Jan. “Characterisation of selected Culicoides (Diptera : Ceratopogonidae) populations in South Africa using genetic markers.” 2011. Web. 03 Mar 2021.

Vancouver:

Debeila TJ. Characterisation of selected Culicoides (Diptera : Ceratopogonidae) populations in South Africa using genetic markers. [Internet] [Masters thesis]. University of Pretoria; 2011. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/2263/25696.

Council of Science Editors:

Debeila TJ. Characterisation of selected Culicoides (Diptera : Ceratopogonidae) populations in South Africa using genetic markers. [Masters Thesis]. University of Pretoria; 2011. Available from: http://hdl.handle.net/2263/25696

14. Alves, Marina Gumiere. Degradação da microcistina-XR por bactérias isoladas de sistema de abastecimento público de água.

Degree: PhD, Microbiologia Agrícola, 2011, University of São Paulo

URL: http://www.teses.usp.br/teses/disponiveis/11/11138/tde-24112011-160040/ ;

►

Microcistinas são potentes hepatotoxinas e promotoras de tumores encontradas em águas doces que causam riscos à saúde pública e, portanto, representam um sério problema para… (more)

▼

Microcistinas são potentes hepatotoxinas e promotoras de tumores encontradas em águas doces que causam riscos à saúde pública e, portanto, representam um sério problema para as estações de tratamento de água. O gênero de cianobactéria Microcystis é o mais conhecido produtor dessas toxinas e também o mais comumente encontrado formando florações em reservatórios de água usados para abastecimento público. Entretanto, algumas bactérias são capazes de utilizar essas toxinas como fonte de carbono o que pode contribuir para a sua remoção da água. Neste estudo foi avaliado o potencial de degradação da microcistina-XR (MCYST-XR) por bactérias heterotróficas isoladas de um sistema de abastecimento público de água da cidade de Piracicaba-SP. A cianotoxina MCYST-XR avaliada foi isolada da linhagem Microcystis aeruginosa NPLJ-4 e purificada. Culturas puras de 35 bactérias isoladas do sistema de abastecimento de água foram testadas. Para isso, cada bactéria foi inoculada em meio mínimo de sais contendo 60 g mL-1 de MCYST-XR purificada e após 144 horas a degradação da toxina foi avaliada por análise em LC-MS/MS. Os picos indicando a massa da microcistina-XR (m/z 1037) não foram detectados no meio de cultura de seis bactérias, as quais foram identificadas pelo sequenciamento quase completo do gene de RNAr 16S como pertencentes aos gêneros Pseudomonas sp., Sphingomonas sp., Microbacterium sp., Agromyces sp., Bacillus sp. e Acinetobacter sp. Este é o primeiro relato de uma linhagem de Acinetobacter capaz de degradar MCYST. A cinética de biodegradação da MCYST-XR mostrou redução de 80% em 72 horas, período em que as bactérias apresentaram o máximo crescimento. A presença do gene mlrA codificante da enzima microcistinase envolvida no metabolismo da microcistina foi avaliada nos genomas dos seis isolados bacterianos usando iniciadores de PCR específicos. Fragmentos de aproximadamente 800 pb foram amplificados em dois isolados, Bacillus sp.e Microbacterium sp. Ensaios de toxicidade utilizando o cládocero Daphnia similis foram realizados para verificar a efetiva remoção da MCYST-XR e a não formação de subprodutos tóxicos na via de biodegradacão. Os resultados negativos dos bioensaios após 48 horas indicaram a ausência de subprodutos tóxicos na via da degradação.

Microcystins are potent hepatotoxins and tumor promoters found in freshwaters that cause public health risks and thus represent a serious problem for water treatment plants. The cyanobacterium genus Microcystis is the most known toxin-producer and the most common bloom-forming in water reservoirs used for public supply. However, some bacteria are able to use these toxins as carbon source, which can contribute to its removal from water. This study assessed the potential for degradation of microcystin-XR (MCYST-XR) by heterotrophic bacteria isolated from a public water supply system of the city of Piracicaba-SP. The cyanotoxin MCYSTXR evaluated was isolated from Microcystis aeruginosa strain NPLJ-4 and purified. Pure cultures of 35 bacteria isolated from the water supply system…

Advisors/Committee Members: Fiore, Marli de Fatima.

Subjects/Keywords: 16S rRNA; Biodegradação; Cianobactérias; Cromatografia líquida de alta eficiência; Cyanobacteria; Cyanotoxin; Microbiologia da água; Microcystis aeruginosa NPLJ-4; RNA ribossômico; Toxinas

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Alves, M. G. (2011). Degradação da microcistina-XR por bactérias isoladas de sistema de abastecimento público de água. (Doctoral Dissertation). University of São Paulo. Retrieved from http://www.teses.usp.br/teses/disponiveis/11/11138/tde-24112011-160040/ ;

Chicago Manual of Style (16^th Edition):

Alves, Marina Gumiere. “Degradação da microcistina-XR por bactérias isoladas de sistema de abastecimento público de água.” 2011. Doctoral Dissertation, University of São Paulo. Accessed March 03, 2021. http://www.teses.usp.br/teses/disponiveis/11/11138/tde-24112011-160040/ ;.

MLA Handbook (7^th Edition):

Alves, Marina Gumiere. “Degradação da microcistina-XR por bactérias isoladas de sistema de abastecimento público de água.” 2011. Web. 03 Mar 2021.

Vancouver:

Alves MG. Degradação da microcistina-XR por bactérias isoladas de sistema de abastecimento público de água. [Internet] [Doctoral dissertation]. University of São Paulo; 2011. [cited 2021 Mar 03]. Available from: http://www.teses.usp.br/teses/disponiveis/11/11138/tde-24112011-160040/ ;.

Council of Science Editors:

Alves MG. Degradação da microcistina-XR por bactérias isoladas de sistema de abastecimento público de água. [Doctoral Dissertation]. University of São Paulo; 2011. Available from: http://www.teses.usp.br/teses/disponiveis/11/11138/tde-24112011-160040/ ;

15. Armas, Rafael Dutra de. Degradação do tetracloroeteno por consórcios bacterianos em reator horizontal de leito fixo.

Degree: PhD, Microbiologia Agrícola, 2011, University of São Paulo

URL: http://www.teses.usp.br/teses/disponiveis/11/11138/tde-20122011-091035/ ;

► O tetracloroeteno (PCE), um dos principais contaminantes de águas subterrâneas, é uma molécula recalcitrante, com toxicidade elevada. Processos de biorremediação de água ou solo contaminados… (more)

▼ O tetracloroeteno (PCE), um dos principais contaminantes de águas subterrâneas, é uma molécula recalcitrante, com toxicidade elevada. Processos de biorremediação de água ou solo contaminados com PCE são normalmente limitados pela baixa eficiência de microrganismos sabidamente envolvidos em sua degradação. No entanto, a prospecção de novos microrganismos, mais eficientes na degradação do PCE é uma alternativa para otimizar esses processos. Os objetivos deste estudo foram desenvolver uma técnica de biorremediação utilizando um reator horizontal de leito fixo (RHLF) contendo consórcios de microrganismos eficientes na degradação do PCE, e caracterizar a via de degradação do PCE utilizada pelo consórcio selecionado. Para tanto, amostras de sedimento de dois poços de monitoramento de água foram coletadas de uma metalúrgica com histórico de contaminação com PCE. Os sedimentos foram imobilizados, acondicionados em RHLFs específicos e submetidos a cultivo de enriquecimento em meio mínimo suplementado com PCE. A estrutura das comunidades e a diversidade bacteriana dos RHLFs foram avaliadas e comparadas com as amostras do PM1 e PM2, por PCR-DGGE e sequenciamento de bibliotecas de clones do gene rRNA 16S. Os resultados evidenciaram a seleção de populações bacterianas no RHLF contendo o inóculo do PM1 (In1) após o cultivo de enriquecimento, enquanto no RHLF contendo o inóculo do PM2 (In2), a estrutura da comunidade bacteriana não diferiu daquela observada no PM2. Ensaios de degradação do PCE nos RHLFs, usando cromatografia gasosa associada à espectrometria de massas (CG/EM), mostraram, após 12 horas, uma eficiência de 87 % na degradação do PCE no reator com In1 e 96 % no reator com In2. Foi feito o isolamento e identificação, por sequenciamento do gene rRNA 16S, das bactérias dos RHLFs, sendo identificados 4 isolados do In1, similares a Burkholderia sp., Pseudomonas stutzeri, P. oryzihabitans e Stenotrophomonas maltophilia e 7 isolados do In2, similares a Microbacterium trichotecenenolyticum, S. maltophilia, Klebsiella sp., Exiguobacterium acetylicum, P. oryzihabitans, Acinetobacter junii e Comamonas sp. Compostos orgânicos voláteis nos reatores com In1 e In2 foram analisados por CG/EM, identificando a produção de clorofórmio (TCM) e 1,1,1-tricloroetano (TCA) como produtos da degradação do PCE. Consórcios formados por bactérias isoladas dos reatores In1 (IIn1) e In2 (IIn2) foram imobilizados e acondicionados em RHLFs distintos para avaliar o potencial dos mesmos na degradação do PCE. Após 12 horas, 92 % do PCE foi degradado nos reatores com IIn1 e IIn2, com produção de TCM e TCA. Testes de degradação usando células em suspensão foram conduzidos para avaliar a eficiência de cada isolado na degradação do PCE. O isolado I8 do In2 (I8In2), identificado como Comamonas sp., teve 68 % de eficiência na degradação do PCE. Ensaios com inibidor de monoxigenases do citocromo P-450 (1-aminobenzotriazole) mostraram que a degradação do PCE nos RHLFs, contendo IIn1, IIn2 e I8In2, foram dependentes dessa enzima. Como conclusão, nós identificamos… Advisors/Committee Members: Lambais, Marcio Rodrigues.

Subjects/Keywords: 16S rRNA; Água - Contaminação; Bacterial immobilization; Bactérias; Biofilmes; Biorremediação; Cromatografia; Gas chromatography; Monooxygenase; PCR-DGGE; RNA Ribossômico

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Armas, R. D. d. (2011). Degradação do tetracloroeteno por consórcios bacterianos em reator horizontal de leito fixo. (Doctoral Dissertation). University of São Paulo. Retrieved from http://www.teses.usp.br/teses/disponiveis/11/11138/tde-20122011-091035/ ;

Chicago Manual of Style (16^th Edition):

Armas, Rafael Dutra de. “Degradação do tetracloroeteno por consórcios bacterianos em reator horizontal de leito fixo.” 2011. Doctoral Dissertation, University of São Paulo. Accessed March 03, 2021. http://www.teses.usp.br/teses/disponiveis/11/11138/tde-20122011-091035/ ;.

MLA Handbook (7^th Edition):

Armas, Rafael Dutra de. “Degradação do tetracloroeteno por consórcios bacterianos em reator horizontal de leito fixo.” 2011. Web. 03 Mar 2021.

Vancouver:

Armas RDd. Degradação do tetracloroeteno por consórcios bacterianos em reator horizontal de leito fixo. [Internet] [Doctoral dissertation]. University of São Paulo; 2011. [cited 2021 Mar 03]. Available from: http://www.teses.usp.br/teses/disponiveis/11/11138/tde-20122011-091035/ ;.

Council of Science Editors:

Armas RDd. Degradação do tetracloroeteno por consórcios bacterianos em reator horizontal de leito fixo. [Doctoral Dissertation]. University of São Paulo; 2011. Available from: http://www.teses.usp.br/teses/disponiveis/11/11138/tde-20122011-091035/ ;

16. Cannavan, Fabiana de Souza. Diversidade das comunidades bacterianas em solos de Terra Preta Antropogênica da Amazônia Central e Oriental.

Degree: Mestrado, Ecologia Aplicada, 2007, University of São Paulo

URL: http://www.teses.usp.br/teses/disponiveis/91/91131/tde-01022008-085546/ ;

►

Terra Preta Antropogênica (TPA) é um dos tipos de solos mais \"férteisd̈o mundo. A TPA recebe esta denominação por ser encontrada em sítios arqueológicos onde… (more)

▼

Terra Preta Antropogênica (TPA) é um dos tipos de solos mais \"férteisd̈o mundo. A TPA recebe esta denominação por ser encontrada em sítios arqueológicos onde viveram grupos pré-históricos. São pequenas faixas de solos que apresentam altas concentrações de nutrientes, matéria orgânica e encontram-se distribuídas aleatoriamente pela região Amazônica. A verdadeira origem destes solos ainda não está bem esclarecida. Devido à falta de informações sobre sua diversidade bacteriana, este trabalho estudou a diversidade bacteriana em amostras de solos TPA coletadas em duas regiões: Lagoa Balbina - sítio Terra preta (Amazônia Central- Amazonas) e Floresta Nacional de Caxiuanã - sítio arqueológico Mina I (Amazônia Oriental - Pará), através de técnicas moleculares independentes de cultivo. O DNA genômico total das amostras de solo foi extraído e usado como molde em uma reação de PCR utilizando oligonucleotídeos específicos do gene 16S rRNA para o Domínio Bactéria. O produto de PCR amplificado foi clonado no vetor pGEM-T e 980 clones foram selecionados e comparados com o banco de dados de 16S rRNA do RDP II e GenBank (NCBI-EUA). Os resultados apresentaram predominância com microrganismos não-conhecidos representando 41,6 % das seqüências de solo TPA- Balbina, 68,3 % das seqüências de ADJ-Balbina, 84,8% das seqüências de solo TPAMina e 47,7 % das seqüências de ADJ-Mina. O filo mais predominante nas amostras TPABalbina foi Firmicutes, representando 37,1% do total de seqüências analisadas. Os filos em destaque foram Proteobacteria (9,6%), seguidos de Verrucomicrobia (5,6%), Acidobacteria (2,5%), Gemmatimonadetes (2,5%), Actinobacteria (0,5%) e Nitrospira (0,5%). Por outro lado, em ADJ-Balbina destacaram-se os filos Proteobacteria 15,1%, Acidobacteria (12,5%), Firmicutes (2,3%), Nitrospira (1,1%) e Verrucomicrobia (0,8%). Em TPA-Mina, os filos apresentados foram Proteobacteria (6,5%), Acidobacteria (4,7%), Firmicutes (1,4%), Nitrospira (1,1%), Planctomycetes (1,1%) e Verrucomicrobia (0,4%). Contudo, na biblioteca ADJ-Mina verificou a presença dos filos Acidobacteria (27,2%), Proteobacteria (14,2%), Firmicutes (3,8%), Verrucomicrobia (3,8%), Nitrospira (1,3%), Planctomycetes (1,3%), Actinobacteria (0,4%) e Gemmatimonadetes (0,4%). O pH do solo pode ser um dos atributos do solo que pode ter influência direta na diversidade bacteriana dos solos estudados, assim como pode ter efeito uma floresta natural sobre as populações microbianas em seu solo, fato observado na adjacência do solo Terra Preta em Caxiuanã - PA. A estimativa da riqueza de UTOs pelo Bootstrap corroborou diretamente os valores de diversidade obtidos pelos índices de Simpson e Shannon. De um modo geral, uma maior probabilidade de ocorrência de UTOs únicas empregadas pelo estimador Jackknife se correlacionou com uma maior percentagem de baixas frequências de filotipos nas quatro bibliotecas. Os métodos não-paramétricos ACE e Chao1 para a estimativa da riqueza de UTOs também corroboraram com os valores obtidos com o estimador Jackknife.

Anthropogenic Dark Earth (ADE) is…

Advisors/Committee Members: Mui, Tsai Siu.

Subjects/Keywords: 16S rRNA; Bacterial Diversity; Black Earth; Diversity Index.; Ecologia microbiana; Microbiologia do solo; RNA; Sequenciamento genético Solos.; Sequencing

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Cannavan, F. d. S. (2007). Diversidade das comunidades bacterianas em solos de Terra Preta Antropogênica da Amazônia Central e Oriental. (Masters Thesis). University of São Paulo. Retrieved from http://www.teses.usp.br/teses/disponiveis/91/91131/tde-01022008-085546/ ;

Chicago Manual of Style (16^th Edition):

Cannavan, Fabiana de Souza. “Diversidade das comunidades bacterianas em solos de Terra Preta Antropogênica da Amazônia Central e Oriental.” 2007. Masters Thesis, University of São Paulo. Accessed March 03, 2021. http://www.teses.usp.br/teses/disponiveis/91/91131/tde-01022008-085546/ ;.

MLA Handbook (7^th Edition):

Cannavan, Fabiana de Souza. “Diversidade das comunidades bacterianas em solos de Terra Preta Antropogênica da Amazônia Central e Oriental.” 2007. Web. 03 Mar 2021.

Vancouver:

Cannavan FdS. Diversidade das comunidades bacterianas em solos de Terra Preta Antropogênica da Amazônia Central e Oriental. [Internet] [Masters thesis]. University of São Paulo; 2007. [cited 2021 Mar 03]. Available from: http://www.teses.usp.br/teses/disponiveis/91/91131/tde-01022008-085546/ ;.

Council of Science Editors:

Cannavan FdS. Diversidade das comunidades bacterianas em solos de Terra Preta Antropogênica da Amazônia Central e Oriental. [Masters Thesis]. University of São Paulo; 2007. Available from: http://www.teses.usp.br/teses/disponiveis/91/91131/tde-01022008-085546/ ;

17. O'Connell, Lauren M. Fine-Grained Bacterial Compositional Analsysis of the Port Everglades Inlet (Broward County, FL) Microbiome using High Throughput DNA Sequencing.

Degree: 2015, Nova Southeastern University

URL: http://nsuworks.nova.edu/occ_stuetd/391

► Port Everglades Inlet is one of the busiest ports in the country and is a point source of pollution to surrounding beaches and offshore corals… (more)

Subjects/Keywords: Microbiome; 16S; Ribosomal RNA; Bacterioplankton; Port Everglades; Inlet; Illumina; Marine Biology; Oceanography and Atmospheric Sciences and Meteorology

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

O'Connell, L. M. (2015). Fine-Grained Bacterial Compositional Analsysis of the Port Everglades Inlet (Broward County, FL) Microbiome using High Throughput DNA Sequencing. (Thesis). Nova Southeastern University. Retrieved from http://nsuworks.nova.edu/occ_stuetd/391

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

O'Connell, Lauren M. “Fine-Grained Bacterial Compositional Analsysis of the Port Everglades Inlet (Broward County, FL) Microbiome using High Throughput DNA Sequencing.” 2015. Thesis, Nova Southeastern University. Accessed March 03, 2021. http://nsuworks.nova.edu/occ_stuetd/391.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

O'Connell, Lauren M. “Fine-Grained Bacterial Compositional Analsysis of the Port Everglades Inlet (Broward County, FL) Microbiome using High Throughput DNA Sequencing.” 2015. Web. 03 Mar 2021.

Vancouver:

O'Connell LM. Fine-Grained Bacterial Compositional Analsysis of the Port Everglades Inlet (Broward County, FL) Microbiome using High Throughput DNA Sequencing. [Internet] [Thesis]. Nova Southeastern University; 2015. [cited 2021 Mar 03]. Available from: http://nsuworks.nova.edu/occ_stuetd/391.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

O'Connell LM. Fine-Grained Bacterial Compositional Analsysis of the Port Everglades Inlet (Broward County, FL) Microbiome using High Throughput DNA Sequencing. [Thesis]. Nova Southeastern University; 2015. Available from: http://nsuworks.nova.edu/occ_stuetd/391

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Colorado

18. Ross, Kimberly. Molecular Phylogenetic Analysis of Municipal Drinking Water Distribution Ecosystems.

Degree: PhD, 2013, University of Colorado

URL: https://scholar.colorado.edu/mcdb_gradetds/17

► Drinking water distribution systems (DWDSs) are dark, wet environments that provide opportunity for microbial biofilm development and long-term occupancy of infrastructure surfaces. Historically, identifications… (more)

▼ Drinking water distribution systems (DWDSs) are dark, wet environments that provide opportunity for microbial biofilm development and long-term occupancy of infrastructure surfaces. Historically, identifications of microorganisms in natural environments have relied on culture-based techniques, which can underestimate the diversity of resident microbial populations. Consequently, information regarding the microbial inhabitants of DWDSs was previously limited to those that were cultivated and observed in the laboratory. Recent technological developments in molecular biology now afford the capability to directly identify organisms in the environment based on their ribosomal RNA (rRNA) gene sequences, thus circumventing the need to isolate and culture the microbes in laboratory settings. In this study, I used rRNA sequences to identify microorganisms and investigate microbiological variation within and between samples collected from two DWDSs spatially and over time. Despite differences in the age, pipe composition, source water, and disinfectant residual type, the two DWDSs were shown to be broadly similar to each other in phylogenetic composition. For example, at the phylum level, members of the Proteobacteria, Actinobacteria, and Cyanobacteria dominated both systems. However, the DWDS using chloramine residual consistently contained more taxa, and therefore greater diversity, than the DWDS with chlorine residual. My findings further indicated the rather remarkable stability of the microbial constituents over space and time, with some variability of the abundances of microbial populations among different sample sites within each system. To expand the results and assess the microbiological similarity of additional DWDS ecosystems, I investigated six other DWDSs from separate geographical locations. All DWDSs that utilized physical water treatment processes accompanied by chemical (chlorine or chloramine) disinfection demonstrated remarkable similarity in microbiological composition. By contrast, samples from a DWDS exempt from physical processing and chemical disinfection were highly dissimilar to samples from all other DWDSs investigated. Notably, Mycobacterium spp. were identified in all disinfected DWDSs, and were notably absent in all non-chlorinated samples. This study provides the first multi-year, longitudinal, molecular microbiological examination of two DWDSs and includes a broader geographical representation of systems for comparison. These data provide a significant foundation for describing the resident microbiology of DWDSs from a culture-independent, molecular perspective. Advisors/Committee Members: Kenneth S. Krauter, Noman R. Pace, Corrella Detweiler, John Spear, Andreas Hoenger.

Subjects/Keywords: 16S rRNA; drinking water distribution systems; microbial ecology; phylogenetics; small subunit ribosomal RNA; water quality; Bioinformatics; Microbiology; Molecular Biology

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Ross, K. (2013). Molecular Phylogenetic Analysis of Municipal Drinking Water Distribution Ecosystems. (Doctoral Dissertation). University of Colorado. Retrieved from https://scholar.colorado.edu/mcdb_gradetds/17

Chicago Manual of Style (16^th Edition):

Ross, Kimberly. “Molecular Phylogenetic Analysis of Municipal Drinking Water Distribution Ecosystems.” 2013. Doctoral Dissertation, University of Colorado. Accessed March 03, 2021. https://scholar.colorado.edu/mcdb_gradetds/17.

MLA Handbook (7^th Edition):

Ross, Kimberly. “Molecular Phylogenetic Analysis of Municipal Drinking Water Distribution Ecosystems.” 2013. Web. 03 Mar 2021.

Vancouver:

Ross K. Molecular Phylogenetic Analysis of Municipal Drinking Water Distribution Ecosystems. [Internet] [Doctoral dissertation]. University of Colorado; 2013. [cited 2021 Mar 03]. Available from: https://scholar.colorado.edu/mcdb_gradetds/17.

Council of Science Editors:

Ross K. Molecular Phylogenetic Analysis of Municipal Drinking Water Distribution Ecosystems. [Doctoral Dissertation]. University of Colorado; 2013. Available from: https://scholar.colorado.edu/mcdb_gradetds/17

19. Silke, Jordan. Characterization of 16S rRNA 3’ Termini Using RNA-Seq Data .

Degree: 2019, University of Ottawa

URL: http://hdl.handle.net/10393/39044

► Optimizing the production of useful macromolecules from transgenic microorganisms is crucial to biopharmaceutical companies. Improving bacterial growth and replication depends largely on the efficiency of… (more)

Subjects/Keywords: Translation efficiency; 16S rRNA; Initation; RNA-Seq

…16S rRNA 3’ tail using RNA-Seq data We identify the 3’ TAIL in E. coli and B. subtilis… …52 3.3.1 Processing genomic and RNA-Seq data… …52 3.3.2 Aligning RNA-Seq reads to annotated rRNA sequences… …57 3.4.1 Characterizing the 3’ TAIL in bacteria using an improved RNA-Seq-based approach… …81 viii List of Tables Table 3.1. The RNA-Seq corrected 3′ TAIL in 13 bacterial species…

10 more images…

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APA (6^th Edition):

Silke, J. (2019). Characterization of 16S rRNA 3’ Termini Using RNA-Seq Data . (Thesis). University of Ottawa. Retrieved from http://hdl.handle.net/10393/39044

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Silke, Jordan. “Characterization of 16S rRNA 3’ Termini Using RNA-Seq Data .” 2019. Thesis, University of Ottawa. Accessed March 03, 2021. http://hdl.handle.net/10393/39044.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Silke, Jordan. “Characterization of 16S rRNA 3’ Termini Using RNA-Seq Data .” 2019. Web. 03 Mar 2021.

Vancouver:

Silke J. Characterization of 16S rRNA 3’ Termini Using RNA-Seq Data . [Internet] [Thesis]. University of Ottawa; 2019. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/10393/39044.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Silke J. Characterization of 16S rRNA 3’ Termini Using RNA-Seq Data . [Thesis]. University of Ottawa; 2019. Available from: http://hdl.handle.net/10393/39044

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

20. Lopes, Patrícia Ferreira. Diversidade taxonômica e potencial de biodegradação de bactérias isoladas de reservatórios de petróleo da Bacia de Campos (RJ).

Degree: Mestrado, Biotecnologia, 2010, University of São Paulo

URL: http://www.teses.usp.br/teses/disponiveis/87/87131/tde-22122010-095359/ ;

►

O presente trabalho teve como objetivos caracterizar uma coleção de 98 bactérias isoladas de amostras de petróleo e água de formação de reservatórios da Bacia… (more)

▼

O presente trabalho teve como objetivos caracterizar uma coleção de 98 bactérias isoladas de amostras de petróleo e água de formação de reservatórios da Bacia de Campos (RJ) utilizando técnicas de taxonomia molecular e avaliar o potencial de degradação de biomarcadores do petróleo. O sequenciamento e análise filogenética do gene RNAr 16S revelaram Bacillus firmus, megaterium, pumilus, sphaericus, simplex, cereus/B. thuringiensis Marinobacter lutaoensis, Halomonas shengliensis/H. alimentaria/ H.campisalis, Citreicella thiooxidans, Stenotrophomonas maltophilia, Achromobacter xylosoxidans, Micrococcus luteus, Kocuria rosea, Streptomyces alboniger/S. chartreusis /S. moderatus, Staphylococcus hominis e Staphylococcus pasteuri/S. warneri. Os resultados evidenciaram a preferência pela biotransformação do ácido nonadecanóico e esqualano. A caracterização da microbiota presente nos reservatórios e avaliação do potencial de biodegradação pode contribuir para fornecer subsídios para estudos futuros sobre os mecanismos biológicos responsáveis pela biodegradação do petróleo.

This study is aimed to characterize a collection of 98 bacteria isolated from oil and formation water samples derived from reservoirs of the Campos Basin (RJ) using molecular biology-based techniques and to evaluate the degradation potential of petroleum biomarkers. Further sequencing and phylogenetic analysis of 16S rRNA genes revealed species of Bacillus firmus, megaterium, pumilus, sphaericus, simplex, cereus/thuringiensis, Marinobacter lutaoensis, Halomonas shengliensis/H. alimentaria/H. campisalis, Citreicella thiooxidans, Stenotrophomonas maltophilia, Achromobacter xylosoxidans, Micrococcus luteus, Kocuria rosea, Streptomyces alboniger/S. chartreusis/S. moderatus, Staphylococcus hominis and Staphylococcus pasteuri/S. warneri. The results showed the preference of bacteria for the biotransformation of nonadecanoic acid and squalane. The characterization of the microbiota associated to reservoirs and the evaluation of their biodegradation potential may provide subsidies for future studies about the biological mechanisms responsible for petroleum biodegradation.

Advisors/Committee Members: Oliveira, Valéria Maia de.

Subjects/Keywords: 16S rRNA genes; Bacteria (Rank); Bactérias (Classificação); Biodegradação; Biodegradation; Biomarcadores do petróleo; Fingerprint genético; Genes RNAr 16S; Genetic fingerprint; Genetic sequencing; Oil -Campos (RJ); Petróleo - Campos (RJ); Petroleum biomarkers; Petroleum reservoirs; Reservatórios de petróleo; RNA (Genética); RNA (Genetics); Seqüenciamento genético

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APA (6^th Edition):

Lopes, P. F. (2010). Diversidade taxonômica e potencial de biodegradação de bactérias isoladas de reservatórios de petróleo da Bacia de Campos (RJ). (Masters Thesis). University of São Paulo. Retrieved from http://www.teses.usp.br/teses/disponiveis/87/87131/tde-22122010-095359/ ;

Chicago Manual of Style (16^th Edition):

Lopes, Patrícia Ferreira. “Diversidade taxonômica e potencial de biodegradação de bactérias isoladas de reservatórios de petróleo da Bacia de Campos (RJ).” 2010. Masters Thesis, University of São Paulo. Accessed March 03, 2021. http://www.teses.usp.br/teses/disponiveis/87/87131/tde-22122010-095359/ ;.

MLA Handbook (7^th Edition):

Lopes, Patrícia Ferreira. “Diversidade taxonômica e potencial de biodegradação de bactérias isoladas de reservatórios de petróleo da Bacia de Campos (RJ).” 2010. Web. 03 Mar 2021.

Vancouver:

Lopes PF. Diversidade taxonômica e potencial de biodegradação de bactérias isoladas de reservatórios de petróleo da Bacia de Campos (RJ). [Internet] [Masters thesis]. University of São Paulo; 2010. [cited 2021 Mar 03]. Available from: http://www.teses.usp.br/teses/disponiveis/87/87131/tde-22122010-095359/ ;.

Council of Science Editors:

Lopes PF. Diversidade taxonômica e potencial de biodegradação de bactérias isoladas de reservatórios de petróleo da Bacia de Campos (RJ). [Masters Thesis]. University of São Paulo; 2010. Available from: http://www.teses.usp.br/teses/disponiveis/87/87131/tde-22122010-095359/ ;

Universidade Estadual de Campinas

21. Stoppe, Nancy de Castro, 1963-. Prospecção de marcadores para o rastreamento de fontes de contaminação fecal em águas superficiais do Estado de São Paulo: Markers prospection for fecal contamination source tracking on superficial waters in São Paulo State, Brazil.

Degree: 2014, Universidade Estadual de Campinas

URL: http://repositorio.unicamp.br/jspui/handle/REPOSIP/316933

► Abstract: The fecal contamination of water resources is the main cause of enteric waterborne diseases all over the world. Traditional indicator methods used in the… (more)

▼ Abstract: The fecal contamination of water resources is the main cause of enteric waterborne diseases all over the world. Traditional indicator methods used in the water microbiological quality assessment are not able to identify fecal contamination source. This work intended to prospect molecular markers in hosts and track them in water samples to identify pollution sources in surface waters in the São Paulo State, Brazil. Two library-dependent methods with E. coli strains isolated from different hosts and water samples were used, a genotypic typing method (E. coli phylogenetic groups) and a phenotypic typing method (MALDI-TOF/MS). A library-independent method using 454 pyrosequencing of hypervariable16S rRNA gene V3 region was used in DNA from feces and water samples. Phylogenetic groups were used as a tool in host classification and correspondence analysis showed feeding habits clusters. The classification of environmental samples revealed higher frequencies of subgroups A1 and B23 in rivers impacted by human pollution sources, while subgroups D1 and D2 were associated with pristine sites, and subgroup B1 with domestic animal sources, indicating their use as a first screening for pollution source identification. A simple classification is proposed based on phylogenetic subgroup distribution using the w-clique metric, enabling differentiation of polluted and unpolluted sites. Protein profiles of E. coli strains isolated from host and water samples were analyzed by MALDI-TOF/MS. Specific host biomarkers were identified and their use was indicated as a potential tool for the source tracking. Validation with E. coli strains isolated from rivers and reservoirs showed that water samples presented markers from different hosts, suggesting these rivers have mixed sources of fecal contamination. Sequencing of the 16S rRNA V3 region in stool samples (human and bovine) and water showed 4296 operational taxonomic units (OTUs). The greatest diversity was observed in samples of cattle feces and the smallest one in the pristine water sample. Firmicutes was the predominant group in samples of human feces, while in the most common bovine feces are the Firmicutes and Bacteroidetes. The interaction network showed that the stool samples had the greatest diversity and, among them, the water sample with human pollution source showed the highest diversity. The LEfSe method was used to identify host biomarkers. As human biomarkers, Actinobacteria, Betaproteobacteria and Firmicutes were identified and for cattle the potential markers are Bacteroidetes, Tenericutes and Spirochaetes. Host-specific markers were identified, but they were not found in water samples suggesting that the used tools either do not have the resolution to identify markers in environmental samples or contamination in water bodies is mixed. Additionally, as the host-specific markers were isolated from non-autochthonous micro-organisms, they could be affected by the environmental adverse effects such as physical-chemical factors and competition with native organisms Advisors/Committee Members: UNIVERSIDADE ESTADUAL DE CAMPINAS (CRUESP), Ottoboni, Laura Maria Mariscal, 1955- (advisor), Torres, Tatiana Teixeira (coadvisor), Universidade Estadual de Campinas. Instituto de Biologia (institution), Programa de Pós-Graduação em Genética e Biologia Molecular (nameofprogram), Vasconcelos, Suzan Pantarotto de (committee member), Razzolini, Maria Tereza Pepe (committee member), Oliveira, Valeria Maia de (committee member), Paulino, Luciana Campos (committee member).

Subjects/Keywords: Água - Poluição; Escherichia coli; Espectrometria de massas por ionização e dessorção a laser assistida por matriz; RNA ribossômico 16S; Sequenciamento de nucleotídeos em larga escala; Water - Pollution; Escherichia coli; Matrix-assisted laser desorption-ionization mass spectrometry; RNA, Ribosomal, 16S; High-throughput nucleotide sequencing

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APA (6^th Edition):

Stoppe, Nancy de Castro, 1. (2014). Prospecção de marcadores para o rastreamento de fontes de contaminação fecal em águas superficiais do Estado de São Paulo: Markers prospection for fecal contamination source tracking on superficial waters in São Paulo State, Brazil. (Thesis). Universidade Estadual de Campinas. Retrieved from http://repositorio.unicamp.br/jspui/handle/REPOSIP/316933

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Stoppe, Nancy de Castro, 1963-. “Prospecção de marcadores para o rastreamento de fontes de contaminação fecal em águas superficiais do Estado de São Paulo: Markers prospection for fecal contamination source tracking on superficial waters in São Paulo State, Brazil.” 2014. Thesis, Universidade Estadual de Campinas. Accessed March 03, 2021. http://repositorio.unicamp.br/jspui/handle/REPOSIP/316933.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Stoppe, Nancy de Castro, 1963-. “Prospecção de marcadores para o rastreamento de fontes de contaminação fecal em águas superficiais do Estado de São Paulo: Markers prospection for fecal contamination source tracking on superficial waters in São Paulo State, Brazil.” 2014. Web. 03 Mar 2021.

Vancouver:

Stoppe, Nancy de Castro 1. Prospecção de marcadores para o rastreamento de fontes de contaminação fecal em águas superficiais do Estado de São Paulo: Markers prospection for fecal contamination source tracking on superficial waters in São Paulo State, Brazil. [Internet] [Thesis]. Universidade Estadual de Campinas; 2014. [cited 2021 Mar 03]. Available from: http://repositorio.unicamp.br/jspui/handle/REPOSIP/316933.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Stoppe, Nancy de Castro 1. Prospecção de marcadores para o rastreamento de fontes de contaminação fecal em águas superficiais do Estado de São Paulo: Markers prospection for fecal contamination source tracking on superficial waters in São Paulo State, Brazil. [Thesis]. Universidade Estadual de Campinas; 2014. Available from: http://repositorio.unicamp.br/jspui/handle/REPOSIP/316933

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

22. Mowatt, Garnet Christopher Lloyd. Secondary Level Music Teacher Training Institution In Jamaica.

Degree: PhD, Music, 2013, University of Mississippi

URL: https://egrove.olemiss.edu/etd/705

► Jamaica, one of the many countries of the Commonwealth Caribbean, is known for its rich musical heritage that has made its impact on the international… (more)

Subjects/Keywords: Education; Jamaica; Mico; Music; Secondary; Music

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APA (6^th Edition):

Mowatt, G. C. L. (2013). Secondary Level Music Teacher Training Institution In Jamaica. (Doctoral Dissertation). University of Mississippi. Retrieved from https://egrove.olemiss.edu/etd/705

Chicago Manual of Style (16^th Edition):

Mowatt, Garnet Christopher Lloyd. “Secondary Level Music Teacher Training Institution In Jamaica.” 2013. Doctoral Dissertation, University of Mississippi. Accessed March 03, 2021. https://egrove.olemiss.edu/etd/705.

MLA Handbook (7^th Edition):

Mowatt, Garnet Christopher Lloyd. “Secondary Level Music Teacher Training Institution In Jamaica.” 2013. Web. 03 Mar 2021.

Vancouver:

Mowatt GCL. Secondary Level Music Teacher Training Institution In Jamaica. [Internet] [Doctoral dissertation]. University of Mississippi; 2013. [cited 2021 Mar 03]. Available from: https://egrove.olemiss.edu/etd/705.

Council of Science Editors:

Mowatt GCL. Secondary Level Music Teacher Training Institution In Jamaica. [Doctoral Dissertation]. University of Mississippi; 2013. Available from: https://egrove.olemiss.edu/etd/705

Virginia Tech

23. Hao, Wei. A potential energy-saving heat treatment for re-circulated irrigation water and its biological mechanisms.

Degree: PhD, Plant Pathology, Physiology, and Weed Science, 2013, Virginia Tech

URL: http://hdl.handle.net/10919/49596

► Heat pasteurization is an effective water treatment to address the emerging plant pathogen issue associated with increased water recycling practices in the ornamental horticulture industry.… (more)

▼ Heat pasteurization is an effective water treatment to address the emerging plant pathogen issue associated with increased water recycling practices in the ornamental horticulture industry. The current protocol that recommends treating water at 95"C for 30 s, however, faces two major challenges: its energy cost and environmental footprint. We hypothesized that temperature required to inactivate major pathogens in re-circulated water may be substantially lowered from 95"C with extended exposure time. The goal of this study was to test this hypothesis and make this water decontamination technology economically more attractive while reducing its environmental impact. Specific objectives were to (1) examine the effect of water temperature on the survival of Phytophthora and bacterial species, two major groups of plant pathogens in water recycling systems, and (2) elucidate the underlying biological mechanisms by which plant pathogens are killed at those temperatures. Lab assays were performed to determine the survival of zoospores and chlamydospores of P. nicotianae, and oospores of P. pini as well as seven bacterial species after heat treatments at given periods of time. Greenhouse experiments were conducted to determine the applicability of the lab assay data to the real world using annual vinca (Catharanthus roseus) and P. nicotianae as a model system. The results of these studies indicated that the water temperature required to eliminate Phytophthora and bacterial species can be lowered to 48"C from 95"C if treatment time extends to 24 h. Two major steps were taken to elucidate the underlying biological mechanisms. Firstly, a scheme based on the DNA fingerprint and sequence analysis was developed for characterizing bacterial species in irrigation water, after comparing two typing strategies, three sample concentration methods, and evaluating conditions in denaturing gradient gel electrophoresis (DGGE) profiling. Bacterial species detected by culture-dependent and -independent strategies were rather different. The greater bacterial diversity was detected when water samples were concentrated by using both methods than centrifugation or filtration alone. As for DGGE profiling, 40 to 60% denaturant concentrations at 70 V for 16 h revealed the highest bacterial diversity. Secondly, water samples were taken from an irrigation reservoir in a local nursery and analyzed for bacterial diversity following heat treatments at 42 and 48"C. After these heat treatments "-proteobacteria, "-proteobacteria, and Firmicutes became dominant which presents a substantial shift of bacterial community structure compared to those in the control water at 25"C. Among the dominant in treated water were Bacillus, Pseudomonas, Paenibacillus, Brevibacillus, and Lysobacter species, which may have potential biocontrol activities against plant pathogens. This study provided the scientific basis for developing a more energy-efficient and environmentally sound heat pasteurization protocol for water decontamination. Advisors/Committee Members: Hong, Chuanxue (committeechair), Vinatzer, Boris A. (committee member), Benson, D. Michael (committee member), Baudoin, Antonius B. (committee member), Stromberg, Erik L. (committee member).

Subjects/Keywords: 16S rRNA

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Hao, W. (2013). A potential energy-saving heat treatment for re-circulated irrigation water and its biological mechanisms. (Doctoral Dissertation). Virginia Tech. Retrieved from http://hdl.handle.net/10919/49596

Chicago Manual of Style (16^th Edition):

Hao, Wei. “A potential energy-saving heat treatment for re-circulated irrigation water and its biological mechanisms.” 2013. Doctoral Dissertation, Virginia Tech. Accessed March 03, 2021. http://hdl.handle.net/10919/49596.

MLA Handbook (7^th Edition):

Hao, Wei. “A potential energy-saving heat treatment for re-circulated irrigation water and its biological mechanisms.” 2013. Web. 03 Mar 2021.

Vancouver:

Hao W. A potential energy-saving heat treatment for re-circulated irrigation water and its biological mechanisms. [Internet] [Doctoral dissertation]. Virginia Tech; 2013. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/10919/49596.

Council of Science Editors:

Hao W. A potential energy-saving heat treatment for re-circulated irrigation water and its biological mechanisms. [Doctoral Dissertation]. Virginia Tech; 2013. Available from: http://hdl.handle.net/10919/49596

24. 眞中, 章弘; マナベ, アキヒロ. Comparison of 16S ribosomal RNA gene sequence analysis and conventional culture in the environmental survey of hospital : 病院環境の細菌同定における細菌培養法と16S ribosomal RNA遺伝子解析法の比較.

Degree: 博士（医学）, 2017, Gunma University / 群馬大学

URL: http://hdl.handle.net/10087/11408

学位記番号：医博甲1604

Subjects/Keywords: 16S ribosomal RNA; Acinetobacter sp; Hospital environment; Infection control; Nosocomial infection

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APA (6^th Edition):

眞中, 章弘; マナベ, �. (2017). Comparison of 16S ribosomal RNA gene sequence analysis and conventional culture in the environmental survey of hospital : 病院環境の細菌同定における細菌培養法と16S ribosomal RNA遺伝子解析法の比較. (Thesis). Gunma University / 群馬大学. Retrieved from http://hdl.handle.net/10087/11408

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

眞中, 章弘; マナベ, アキヒロ. “Comparison of 16S ribosomal RNA gene sequence analysis and conventional culture in the environmental survey of hospital : 病院環境の細菌同定における細菌培養法と16S ribosomal RNA遺伝子解析法の比較.” 2017. Thesis, Gunma University / 群馬大学. Accessed March 03, 2021. http://hdl.handle.net/10087/11408.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

眞中, 章弘; マナベ, アキヒロ. “Comparison of 16S ribosomal RNA gene sequence analysis and conventional culture in the environmental survey of hospital : 病院環境の細菌同定における細菌培養法と16S ribosomal RNA遺伝子解析法の比較.” 2017. Web. 03 Mar 2021.

Vancouver:

眞中, 章弘; マナベ �. Comparison of 16S ribosomal RNA gene sequence analysis and conventional culture in the environmental survey of hospital : 病院環境の細菌同定における細菌培養法と16S ribosomal RNA遺伝子解析法の比較. [Internet] [Thesis]. Gunma University / 群馬大学; 2017. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/10087/11408.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

眞中, 章弘; マナベ �. Comparison of 16S ribosomal RNA gene sequence analysis and conventional culture in the environmental survey of hospital : 病院環境の細菌同定における細菌培養法と16S ribosomal RNA遺伝子解析法の比較. [Thesis]. Gunma University / 群馬大学; 2017. Available from: http://hdl.handle.net/10087/11408

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

25. Cassetari, Alice de Sousa. Diversidade de bactérias diazotróficas nodulíferas na Mata Atlântica.

Degree: Mestrado, Solos e Nutrição de Plantas, 2011, University of São Paulo

URL: http://www.teses.usp.br/teses/disponiveis/11/11140/tde-08022011-100010/ ;

►

A Mata Atlântica é um importante bioma da costa brasileira, apresenta grande diversidade de plantas e animais, porém, pouco se sabe sobre a diversidade microbiana.… (more)

▼

A Mata Atlântica é um importante bioma da costa brasileira, apresenta grande diversidade de plantas e animais, porém, pouco se sabe sobre a diversidade microbiana. Da mesma forma, pouco se sabe sobre o papel funcional desses microrganismos. Vários microrganismos estão envolvidos na ciclagem do nitrogênio na Mata Atlântica, e dentre eles os diazotróficos são de particular interesse, pois contribuem para o aporte direto de nitrogênio nos ecossistemas. O objetivo deste trabalho foi avaliar a diversidade de bactérias diazotróficas que nodulam leguminosas em duas parcelas permanentes do Parque Estadual da Serra do Mar em diferentes altitudes. Nódulos de raízes foram coletados nas quatro estações do ano. As bactérias foram isoladas do interior dos nódulos, resultando em 105 isolados. A análise de diversidade genética destas bactérias foi feita utilizando-se BOX-PCR e sequenciamento parcial do gene 16S rRNA. A capacidade de nodulação dos isolados foi determinada através da formação de nódulos em caupi (Vignia unguiculata). Os resultados indicaram que há uma diferença na distribuição espacial e temporal dos nódulos nas áreas estudadas. A maior quantidade de nódulos foi encontrada na parcela de Picinguaba, em estações com menores índices pluviométricos. Os isolados apresentaram uma grande diversidade fenotípica, sendo separados em 6 grupos com características culturais semelhantes. Os perfis de BOX-PCR formaram 8 grupos genotípicos com mais de 80% de similaridade, agrupando tanto isolados de Picinguaba quanto de Santa Virgínia. Os perfis dos géis do BOX-PCR apresentaram variação no número e mobilidade das bandas. Os dados foram transformados em uma matriz binária de presença e ausência que possibilitou a análise de agrupamento hierárquicos com 8 grupos genotípicos com mais de 80% de similaridade, agrupando tanto isolados de Picinguaba quanto de Santa Virgínia. Através do sequenciamento parcial de fragmentos de gene rRNA 16S verificou-se que a estrutura das comunidades diazotróficas de Picinguaba e Santa Virgínia não apresentaram diferença estatisticamente significativa, indicando que não há seleção de populações bacterianas especificas nas áreas.Dos isolados testados, 88% apresentaram capacidade de nodular caupi, porém alguns não foram eficientes em promover o crescimento das plantas. Nas duas áreas predominou UTOs filogeneticamente associados ao gênero Paenibacillus nos nódulos, sugerindo que essas bactérias são importantes para nodulação de leguminosas na Mata Atlântica.

The Atlantic Rainforest is a major biome of the Brazilian coast, which harbors great diversity of flora and fauna, but little is known about its microbial diversity. Furthermore, little is known about the functional role of these abundant microorganisms. Several microorganisms are involved in cycling of the Atlantic Rainforests nitrogen, among them the diazotrophs which are of particular interest because they contribute to the direct input of nitrogen to ecosystems. The aim of this study was to evaluate the diversity of legumes nodulating diazotrophs in…

Advisors/Committee Members: Lambais, Marcio Rodrigues.

Subjects/Keywords: Atlantic Rainforest; Bactérias fixadoras de nitrogênio; Biodiversidade; Biodiversity; Biological Nitrogen Fixation; Diazotrophs; Diversidade genética; Fixação de nitrogênio; Leguminosae; Mata Atlântica; nifH; Nodulação; RNA ribossômico.; rRNA 16S.

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APA (6^th Edition):

Cassetari, A. d. S. (2011). Diversidade de bactérias diazotróficas nodulíferas na Mata Atlântica. (Masters Thesis). University of São Paulo. Retrieved from http://www.teses.usp.br/teses/disponiveis/11/11140/tde-08022011-100010/ ;

Chicago Manual of Style (16^th Edition):

Cassetari, Alice de Sousa. “Diversidade de bactérias diazotróficas nodulíferas na Mata Atlântica.” 2011. Masters Thesis, University of São Paulo. Accessed March 03, 2021. http://www.teses.usp.br/teses/disponiveis/11/11140/tde-08022011-100010/ ;.

MLA Handbook (7^th Edition):

Cassetari, Alice de Sousa. “Diversidade de bactérias diazotróficas nodulíferas na Mata Atlântica.” 2011. Web. 03 Mar 2021.

Vancouver:

Cassetari AdS. Diversidade de bactérias diazotróficas nodulíferas na Mata Atlântica. [Internet] [Masters thesis]. University of São Paulo; 2011. [cited 2021 Mar 03]. Available from: http://www.teses.usp.br/teses/disponiveis/11/11140/tde-08022011-100010/ ;.

Council of Science Editors:

Cassetari AdS. Diversidade de bactérias diazotróficas nodulíferas na Mata Atlântica. [Masters Thesis]. University of São Paulo; 2011. Available from: http://www.teses.usp.br/teses/disponiveis/11/11140/tde-08022011-100010/ ;

26. Caruso, Vincent. Microbiome Community Inference In Low Microbial Biomass Environments.

Degree: MS, 2018, Oregon Health Sciences University

URL: doi:10.6083/M470810F ; https://digitalcommons.ohsu.edu/etd/4003

Subjects/Keywords: Microbiota; RNA; Ribosomal; 16S; Biomass; Cluster Analysis; Medicine and Health Sciences

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Caruso, V. (2018). Microbiome Community Inference In Low Microbial Biomass Environments. (Thesis). Oregon Health Sciences University. Retrieved from doi:10.6083/M470810F ; https://digitalcommons.ohsu.edu/etd/4003

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Caruso, Vincent. “Microbiome Community Inference In Low Microbial Biomass Environments.” 2018. Thesis, Oregon Health Sciences University. Accessed March 03, 2021. doi:10.6083/M470810F ; https://digitalcommons.ohsu.edu/etd/4003.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Caruso, Vincent. “Microbiome Community Inference In Low Microbial Biomass Environments.” 2018. Web. 03 Mar 2021.

Vancouver:

Caruso V. Microbiome Community Inference In Low Microbial Biomass Environments. [Internet] [Thesis]. Oregon Health Sciences University; 2018. [cited 2021 Mar 03]. Available from: doi:10.6083/M470810F ; https://digitalcommons.ohsu.edu/etd/4003.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Caruso V. Microbiome Community Inference In Low Microbial Biomass Environments. [Thesis]. Oregon Health Sciences University; 2018. Available from: doi:10.6083/M470810F ; https://digitalcommons.ohsu.edu/etd/4003

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

27. McElveen, Scott David. Characterizing Nodule Endophyte Communities in Glycine Max and Lablab Purpureus Using Next-Generation Sequencing.

Degree: Master of Natural and Applied Science in Agriculture, College of Agriculture, 2019, Missouri State University

URL: https://bearworks.missouristate.edu/theses/3415

► Biological nitrogen fixation by rhizobia in the root nodules of legumes is a significant source of agricultural nitrogen in global crop production systems. The… (more)

Subjects/Keywords: soybean microsymbionts; lablab microsymbionts; non-rhizobial endophytes; 16S ribosomal RNA (rRNA) and nifH gene high-throughput sequencing; Bradyrhizobium; Nitrobacter; Tardiphaga; Agriculture; Environmental Microbiology and Microbial Ecology

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

McElveen, S. D. (2019). Characterizing Nodule Endophyte Communities in Glycine Max and Lablab Purpureus Using Next-Generation Sequencing. (Masters Thesis). Missouri State University. Retrieved from https://bearworks.missouristate.edu/theses/3415

Chicago Manual of Style (16^th Edition):

McElveen, Scott David. “Characterizing Nodule Endophyte Communities in Glycine Max and Lablab Purpureus Using Next-Generation Sequencing.” 2019. Masters Thesis, Missouri State University. Accessed March 03, 2021. https://bearworks.missouristate.edu/theses/3415.

MLA Handbook (7^th Edition):

McElveen, Scott David. “Characterizing Nodule Endophyte Communities in Glycine Max and Lablab Purpureus Using Next-Generation Sequencing.” 2019. Web. 03 Mar 2021.

Vancouver:

McElveen SD. Characterizing Nodule Endophyte Communities in Glycine Max and Lablab Purpureus Using Next-Generation Sequencing. [Internet] [Masters thesis]. Missouri State University; 2019. [cited 2021 Mar 03]. Available from: https://bearworks.missouristate.edu/theses/3415.

Council of Science Editors:

McElveen SD. Characterizing Nodule Endophyte Communities in Glycine Max and Lablab Purpureus Using Next-Generation Sequencing. [Masters Thesis]. Missouri State University; 2019. Available from: https://bearworks.missouristate.edu/theses/3415

The Ohio State University

28. Ganesan, Sukirth M. Relative Contributions Of Tobacco Associated Factors And Diabetes To Shaping The Oral Microbiome.

Degree: PhD, Oral Biology, 2018, The Ohio State University

URL: http://rave.ohiolink.edu/etdc/view?acc_num=osu1529572658170786

► The oral cavity is an open ecosystem with niche-specific microbial colonization. Within a few hours after birth, bacteria colonize the oral cavity and form complex… (more)

▼ The oral cavity is an open ecosystem with niche-specific microbial colonization. Within a few hours after birth, bacteria colonize the oral cavity and form complex communities called biofilms. These biofilms constantly interact with the host immune system and play an important role in the maintenance of health. Dysbiotic bacterial communities are established as the underlying etiology of periodontitis, a disease that destroys structures tooth-supporting structures and results in tooth loss. Several factors are known to contribute to an individual’s susceptibility to periodontitis, notably, smoking and diabetes, however, the mechanisms by which they increase the risk for this bacterially induced inflammatory disease have not been well established. The purpose of this investigation was to examine the relative contributions of smoking and diabetes to shaping the subgingival microbiome. Cross-sectional and longitudinal cohort study designs using were combined with comprehensive systems biology approach to characterize the composition, functional characteristics, gene-expression patterns, and structure of the oral microbial ecosystem in response to these perturbations both in periodontal health and disease. In vitro models were used to validate the clinical findings and to explore a biological basis for the shifts. Smoking, diabetes, and e-cigarettes selectively enriched for disease-associated species and specific virulence functions in this ecosystem even in states of clinical health. Each of these perturbations exerted a unique effect on the microbiome, in terms of species composition, biofilm architecture and functional potential, thus enabling us to identify and validate microbial biomarkers unique to each perturbation. Finally, we investigated whether the associations between bacterial virulence and smoking was causal or casual by examining the responses of the subgingival microbiome to smoking cessation. Quitters demonstrated a significant shift in microbial composition and function within two weeks of cessation, while the microbiome of continuous smokers remained stable over 3 months of observation. Together, these studies demonstrated that the oral microbiome responds quickly to smoking and hyperglycemia and that these perturbations enrich these biomes for oro-pharyngeal pathogens along with increasing the immuno-inflammatory potential of these communities. This might be one mechanism by which smoking and diabetes increase susceptibility to disease. Advisors/Committee Members: Kumar, Purnima (Advisor).

Subjects/Keywords: Dentistry; Microbiology; Molecular Biology; Epidemiology; Ecology; Periodontology, Microbiome, Metagenome, Microbial Ecology, Smoking, E-cigarettes, Vaping, Diabetes, Metagenomics, RNA-seq, Metatranscriptomics, Periodontitis, Sub-gingival, 16S, Cigarette smoke, Smoking cessation, KEGG pathways

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Ganesan, S. M. (2018). Relative Contributions Of Tobacco Associated Factors And Diabetes To Shaping The Oral Microbiome. (Doctoral Dissertation). The Ohio State University. Retrieved from http://rave.ohiolink.edu/etdc/view?acc_num=osu1529572658170786

Chicago Manual of Style (16^th Edition):

Ganesan, Sukirth M. “Relative Contributions Of Tobacco Associated Factors And Diabetes To Shaping The Oral Microbiome.” 2018. Doctoral Dissertation, The Ohio State University. Accessed March 03, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=osu1529572658170786.

MLA Handbook (7^th Edition):

Ganesan, Sukirth M. “Relative Contributions Of Tobacco Associated Factors And Diabetes To Shaping The Oral Microbiome.” 2018. Web. 03 Mar 2021.

Vancouver:

Ganesan SM. Relative Contributions Of Tobacco Associated Factors And Diabetes To Shaping The Oral Microbiome. [Internet] [Doctoral dissertation]. The Ohio State University; 2018. [cited 2021 Mar 03]. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=osu1529572658170786.

Council of Science Editors:

Ganesan SM. Relative Contributions Of Tobacco Associated Factors And Diabetes To Shaping The Oral Microbiome. [Doctoral Dissertation]. The Ohio State University; 2018. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=osu1529572658170786

Universidade Estadual de Campinas

29. Saito, Daniel, 1974-. Caracterização das comunidades bacterianas associadas as infecções endodonticas : abordagem independente de cultivo: Characterization of bacterial communities associated with endodontic infections : culture-independent approach.

Degree: 2007, Universidade Estadual de Campinas

URL: http://repositorio.unicamp.br/jspui/handle/REPOSIP/288628

► Abstract: The objective of the present study was to characterize the bacterial communities associated with endodontic infections by use of culture-independent molecular techniques. Overall, 34… (more)

▼ Abstract: The objective of the present study was to characterize the bacterial communities associated with endodontic infections by use of culture-independent molecular techniques. Overall, 34 intraradicular samples from teeth harboring endodontic infections were evaluated. 16S ribosomal DNA (16S rDNA) clone library analysis allowed the identification of 2 to 14 bacterial phylotypes (species) per tooth (mean= 9.6), with a total of 46 distinct phylotypes. Among the latter, 4 (9%) were considered previously unreported and further taxonomically classified as members of the order Clostridiales. Well-known endodontic representatives of Campylobacter, Eubacterium, Peptostreptococcus, Selenomonas, Treponema e Veillonella were detected, as well as members of less frequently reported genera, such as Burkholderia, Filifactor and Megasphaera. The application of the Real Time PCR technique permitted the detection of P. gingivalis, T. forsythia and a coexistence of both in 24%, 56% e 18% of the subjects, respectively. No significant correlations were evidenced among the levels of P. gingivalis and T. forsythia, individually or conjointly, and spontaneous endodontic pain. The use of T-RFLP in the analysis of bacterial community structures revealed a total of 123 (HhaI endonuclease) and 122 (MspI endonuclease) distinct terminal restriction fragments (T-RFs), with 20.8 and 20.0 mean T-RFs per tooth, respectively. Approximately 50% of the detected fragments were exclusive to one or two patients, indicating a high inter-subject variability in the bacterial assemblages. Cluster and multivariate statistical analyses did not demonstrate significant differences in the bacterial community profiles among the asymptomatic, tender to percussion and symptomatic study groups. Taken together, the results of this study reiterate the concept that the microbiota associated with endodontic infections is essentially polymicrobial, highly variable among individuals, and predominantly composed of Gram-positive anaerobic bacteria from the phylum Firmicutes. The species P. gingivalis and T. forsythia, although relatively prevalent in root canal infections, did not present significant correlations with the development of symptomatic features. Lastly, the absence of clusters of bacterial profiles according to symptomatic parameters suggests that the intraradicular bacterial community structures, as a whole, do not bear significant influence on the development of pain of endodontic origin Advisors/Committee Members: UNIVERSIDADE ESTADUAL DE CAMPINAS (CRUESP), Gonçalves, Reginaldo Bruno, 1966- (advisor), Universidade Estadual de Campinas. Faculdade de Odontologia de Piracicaba (institution), Programa de Pós-Graduação em Biologia Buco-Dental (nameofprogram), Fiore, Marli de Fatima (committee member), Camargo, Luis Eduardo Aranha (committee member), Höfling, José Francisco (committee member), Line, Sergio Roberto Peres (committee member).

Subjects/Keywords: Reação em cadeia da polimerase; RNA ribossômico 16S; Polimorfismo de fragmento de restrição; Polymerase chain reaction; 16S ribosomal RNA; Restriction fragment lenght polymorphism

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Saito, Daniel, 1. (2007). Caracterização das comunidades bacterianas associadas as infecções endodonticas : abordagem independente de cultivo: Characterization of bacterial communities associated with endodontic infections : culture-independent approach. (Thesis). Universidade Estadual de Campinas. Retrieved from http://repositorio.unicamp.br/jspui/handle/REPOSIP/288628

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Saito, Daniel, 1974-. “Caracterização das comunidades bacterianas associadas as infecções endodonticas : abordagem independente de cultivo: Characterization of bacterial communities associated with endodontic infections : culture-independent approach.” 2007. Thesis, Universidade Estadual de Campinas. Accessed March 03, 2021. http://repositorio.unicamp.br/jspui/handle/REPOSIP/288628.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Saito, Daniel, 1974-. “Caracterização das comunidades bacterianas associadas as infecções endodonticas : abordagem independente de cultivo: Characterization of bacterial communities associated with endodontic infections : culture-independent approach.” 2007. Web. 03 Mar 2021.

Vancouver:

Saito, Daniel 1. Caracterização das comunidades bacterianas associadas as infecções endodonticas : abordagem independente de cultivo: Characterization of bacterial communities associated with endodontic infections : culture-independent approach. [Internet] [Thesis]. Universidade Estadual de Campinas; 2007. [cited 2021 Mar 03]. Available from: http://repositorio.unicamp.br/jspui/handle/REPOSIP/288628.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Saito, Daniel 1. Caracterização das comunidades bacterianas associadas as infecções endodonticas : abordagem independente de cultivo: Characterization of bacterial communities associated with endodontic infections : culture-independent approach. [Thesis]. Universidade Estadual de Campinas; 2007. Available from: http://repositorio.unicamp.br/jspui/handle/REPOSIP/288628

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Washington University in St. Louis

30. Nawrocki, Eric. Structural RNA Homology Search and Alignment Using Covariance Models.

Degree: PhD, Biology and Biomedical Sciences: Computational and Systems Biology, 2009, Washington University in St. Louis

URL: https://openscholarship.wustl.edu/etd/256

► Functional RNA elements do not encode proteins, but rather function directly as RNAs. Many different types of RNAs play important roles in a wide range… (more)

▼ Functional RNA elements do not encode proteins, but rather function directly as RNAs. Many different types of RNAs play important roles in a wide range of cellular processes, including protein synthesis, gene regulation, protein transport, splicing, and more. Because important sequence and structural features tend to be evolutionarily conserved, one way to learn about functional RNAs is through comparative sequence analysis - by collecting and aligning examples of homologous RNAs and comparing them. Covariance models: CMs) are powerful computational tools for homology search and alignment that score both the conserved sequence and secondary structure of an RNA family. However, due to the high computational complexity of their search and alignment algorithms, searches against large databases and alignment of large RNAs like small subunit ribosomal RNA: SSU rRNA) are prohibitively slow. Large-scale alignment of SSU rRNA is of particular utility for environmental survey studies of microbial diversity which often use the rRNA as a phylogenetic marker of microorganisms. In this work, we improve CM methods by making them faster and more sensitive to remote homology. To accelerate searches, we introduce a query-dependent banding: QDB) technique that makes scoring sequences more efficient by restricting the possible lengths of structural elements based on their probability given the model. We combine QDB with a complementary filtering method that quickly prunes away database subsequences deemed unlikely to receive high CM scores based on sequence conservation alone. To increase search sensitivity, we apply two model parameterization strategies from protein homology search tools to CMs. As judged by our benchmark, these combined approaches yield about a 250-fold speedup and significant increase in search sensitivity compared with previous implementations. To accelerate alignment, we apply a method that uses a fast sequence-based alignment of a target sequence to determine constraints for the more expensive CM sequence- and structure-based alignment. This technique reduces the time required to align one SSU rRNA sequence from about 15 minutes to 1 second with a negligible effect on alignment accuracy. Collectively, these improvements make CMs more powerful and practical tools for RNA homology search and alignment. Advisors/Committee Members: Sean Eddy.

Subjects/Keywords: Biology, Bioinformatics; Computer Science; Biology, Molecular; 16S, alignment, covariance models, homology search, non-coding RNA, RNA

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Nawrocki, E. (2009). Structural RNA Homology Search and Alignment Using Covariance Models. (Doctoral Dissertation). Washington University in St. Louis. Retrieved from https://openscholarship.wustl.edu/etd/256

Chicago Manual of Style (16^th Edition):

Nawrocki, Eric. “Structural RNA Homology Search and Alignment Using Covariance Models.” 2009. Doctoral Dissertation, Washington University in St. Louis. Accessed March 03, 2021. https://openscholarship.wustl.edu/etd/256.

MLA Handbook (7^th Edition):

Nawrocki, Eric. “Structural RNA Homology Search and Alignment Using Covariance Models.” 2009. Web. 03 Mar 2021.

Vancouver:

Nawrocki E. Structural RNA Homology Search and Alignment Using Covariance Models. [Internet] [Doctoral dissertation]. Washington University in St. Louis; 2009. [cited 2021 Mar 03]. Available from: https://openscholarship.wustl.edu/etd/256.

Council of Science Editors:

Nawrocki E. Structural RNA Homology Search and Alignment Using Covariance Models. [Doctoral Dissertation]. Washington University in St. Louis; 2009. Available from: https://openscholarship.wustl.edu/etd/256

Open Access Theses and Dissertations