Submitted by Ricardo Cedraz Duque Moliterno (ricardo.moliterno@uefs.br) on 2017-10-09T22:34:41Z No. of bitstreams: 1 MATHUES BRITO DE OLIVEIRA Disserta??ov.pdf: 5287293 bytes, checksum: 8d3e3b854b5799f16c0b61b6a5d33f1c (MD5) / Made available in DSpace on 2017-10-09T22:34:41Z (GMT). No. of bitstreams: 1 MATHUES BRITO DE OLIVEIRA Disserta??ov.pdf: 5287293 bytes, checksum: 8d3e3b854b5799f16c0b61b6a5d33f1c (MD5) Previous issue date: 2017-06-12 / The assembly of bacterial genomes consists of a process of reordering fragments so that the original genome can be represented. However, to maximize the results of genome assembly, some steps are required, for instance, read quality analysis and preprocessing, repetition identification and quality check. The process of assembly of genomes is a complex step that involves the type of sequencing that was used, there are several types of sequencers which imply different characteristics for each one for example: fragments size, throughput, among others. Analyzing these characteristics requires the use of several computational tools, to assist in all the processes mentioned above, and since the range of software available is quite broad and distinct, it is necessary for the user to learn to work with this computational diversity, dominating often knowledge that is not of the biological area, implying in less time for a deepening in biological questions. Based on this context, we developed a pipeline to perform an automated fragment analysis, read preprocessing, genome assembly and orientation of contigs, having as the assembly the main objective of the pipeline and that it will be managed by a Web application called GATOOL (Genome Assembly Tool). Aiming to evaluate the performance of the application, tests were carried out with two samples of prokaryotic organisms, which are: Bacillus amyloliquefaciens and Serratia marcescens. Also perform a test with seven SRA samples. Both organisms are sequenced on the Ion PGMTM platform. The tools used to perform the assembly were SPAdes and Velvet, both assemblers use de Bruijn graph algorithm as a paradigm for the assembly of the genome, after this stage the resulting set of contigs was ordered through the CONTIGuator, which is a reference ordering. We observed that the interface GATOOL allowed a quick and easy execution of several steps and processes in the field of genome assembly, including the assembly of two prokaryotic species in an automated way, thus facilitating the use and accomplishment of such processes by any user. / A montagem de genomas bacterianos ? um processo de reordena??o de fragmentos, de forma que se possa representar o genoma original. Entretanto, para que a montagem de um genoma seja realizada visando maximizar os resultados, ? preciso que algumas etapas sejam cumpridas, por exemplo: a an?lise dos fragmentos, o pr?-processamento destes fragmentos e novamente uma repeti??o do processo de an?lise, para verificar a efic?cia do pr?-processamento realizado. O processo de montagem de genomas ? uma etapa complexa, que envolve o tipo de sequenciamento que foi utilizado. Existem diversos tipos de sequenciadores, o que implica caracter?sticas distintas em cada um, como por exemplo: tamanho dos fragmentos, quantidade de fragmentos gerados por corrida, dentre outros. Analisando essas caracter?sticas, faz-se necess?ria a utiliza??o de diversas ferramentas computacionais para auxiliar a todos os processos citados anteriormente e, como a gama de softwares dispon?veis ? bem ampla e distinta, ? importante que o usu?rio domine essa diversidade computacional, contendo muitas vezes conhecimentos que n?o s?o da ?rea biol?gica, implicando menos tempo para um aprofundamento das quest?es biol?gicas. Com base neste contexto, prop?em-se um pipeline para a realiza??o da an?lise de fragmentos, pr?-processamento dos fragmentos, montagem de genomas e orienta??o de contigs, tendo como a montagem o objetivo principal do pipeline e este ser? gerenciado por uma aplica??o web chamada GATOOL (Genome Assembly Tool). Visando avaliar o desempenho da aplica??o, foram feitos testes com duas amostras de organismos procariontes, que s?o: Bacillus amyloliquefaciens e Serratia marcescens. Tamb?m foram realizados testes com sete amostras SRA. Ambos os organismos est?o sequenciados na plataforma Ion PGMTM. Os montadores usados foram o SPAdes e o Velvet, ambos montadores, utilizam o algor?tmo grafo de Bruijn como paradigma para a montagem do genoma; ap?s esta etapa, o conjunto de contigs resultante foi ordenado atrav?s do CONTIGuator, que ? uma ordena??o por refer?ncia. Observamos que a interface GATOOL permitiu uma execu??o r?pida e f?cil de diversas etapas e processos no campo da montagem de genomas, inclusive realizando a montagem de duas esp?cies procariontes de maneira automatizada, facilitando assim a utiliza??o e realiza??o de tais processos por qualquer usu?rio.

Made available in DSpace on 2016-04-28T20:17:24Z (GMT). No. of bitstreams: 1 2006-Marcelo Carvalho Gomes.pdf: 324564 bytes, checksum: 3942a2feee43fca4762eb4590c899bfc (MD5) Previous issue date: 2006-03-31 / The present work was carried out in three different goat raisings and 27 females and 2 males were selected for identifying the present microbiota in the preputial and vaginal cavity of goats under three estrous cycle phases: In Februrary, 2005 in the pro-estrum, in May, 2005 in the post-copula and in October, 2005 in the post-partum. The samples were collected by swabs as well as vaginal and preputial washings for studying microbiota and by gynecological brushes for the females esfoliative cytological study. The two greatest bacteria genera prevalence were: Micrococcus spp (89,65 %) following by Bacillus spp. (29,90 %). Filamentous fungi as Cladosporium spp. (26,39 %) and Aspergillus spp. (11,46 %) were the most isolated. On the bacteria cytological test about 76 % of the investigations have been in accordance with the microscopic finding and bacteria isolation. In 89% appraised animal some yeasts presence on sheets was observed in spite of there was isolation just in 7,4 % of the animals. There was similarity between hifas observation and filamentous fungi isolation, in regarding to 53 % of hifas presence investigations. The bacterial and fungical microbiota found on this survey showed the goats vaginal and preputial microbiota diversity and pointed out to the fact that it might be carried during copulation. The number of isolated bacteria species in the post-copulation phase was upper, as well as for yeasts. The vaginal cytology performed significative association in relation to the bacterial isolation, observed by cocos and bacilli presence on the sheets with positive growth. Bacteria potentially pathogenic as Pseudomonas alcalinigenes, P. aeruginosa, and Corynebacterium spp. as well as opportunist fungi as Aspergillus flavus in healthy goats vaginal cavity were found. / O presente trabalho foi desenvolvido em tr?s criat?rios caprinos distintos, de onde tomamos 27 f?meas e 2 machos a fim de identificar a microbiota presente no prep?cio de bodes e na cavidade vaginal de cabras em tr?s fases do ciclo estral: fevereiro de 2005 no proestro, maio de 2005 ap?s a c?pula e outubro de 2005 ap?s o parto. As amostras foram coletadas atrav?s de swab, lavado vaginal e prepucial para o estudo da microbiota e com escovas ginecol?gicas para o estudo colpocitol?gico das f?meas. Os dois g?neros de bact?rias de maior preval?ncia foram os seguintes: Micrococcus spp. (89,65 %) e Bacillus spp. (29,90 %). Os dois g?neros de fungos de maior preval?ncia foram Cladosporium spp. (26,39 %) e Aspergillus spp. (11,46 %). No estudo colpocitol?gico para bact?rias, em 76 % das investiga??es houve concord?ncia entre os achados microsc?picos e isolamento bacteriano. Em 89 % dos animais avaliados foi observada a presen?a de leveduras nas l?minas, mas houve isolamento em apenas 7,4 % dos animais. Em 53 % das investiga??es da presen?a de hifas houve concord?ncia entre a observa??o de hifas e o isolamento de fungos filamentosos. A microbiota f?ngica e bacteriana encontrada no presente trabalho evidenciou a diversidade da microbiota vaginal e prepucial de caprinos e aponta para o fato de que podem ser carreados durante a c?pula. Observou-se que o n?mero de esp?cies isoladas de bact?rias ? superior na fase de p?s-c?pula enquanto que em fungos observamos este aumento no p?s-parto; O resultado da citologia vaginal teve correla??o com o isolamento bacteriano, observada pela presen?a de cocos e bacilos nas l?minas com crescimento bacteriano positivo; Bact?rias potencialmente patog?nicas como Pseudomonas alcaligenes, P. aeruginosa e Corynebacterium spp. foram encontrados na cavidade vaginal de cabras h?gidas, assim como fungos oportunistas como Aspergillus flavus.

Submitted by Automa??o e Estat?stica (sst@bczm.ufrn.br) on 2018-03-21T11:48:14Z No. of bitstreams: 1 JonathasDiegoLimaSantos_TESE.pdf: 8935214 bytes, checksum: 86433d89608ea11b99ac2a3911f14149 (MD5) / Approved for entry into archive by Arlan Eloi Leite Silva (eloihistoriador@yahoo.com.br) on 2018-03-23T11:23:51Z (GMT) No. of bitstreams: 1 JonathasDiegoLimaSantos_TESE.pdf: 8935214 bytes, checksum: 86433d89608ea11b99ac2a3911f14149 (MD5) / Made available in DSpace on 2018-03-23T11:23:51Z (GMT). No. of bitstreams: 1 JonathasDiegoLimaSantos_TESE.pdf: 8935214 bytes, checksum: 86433d89608ea11b99ac2a3911f14149 (MD5) Previous issue date: 2017-12-15 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior (CAPES) / Chromobcterium violaceum (C. violaceum) ? uma bact?ria Gram-negativa, encontrada em regi?es tropicais e subtropicais, considerada organismo modelo de vida livre. Alguns estudos prote?micos realizados com esta bact?ria demonstraram sua capacidade de adapta??o a desafios ambientais, como alta concentra??o de ferro e exposi??o ao estresse oxidativo. No entanto, nenhum estudo foi feito com esta esp?cie submetida ? microgravidade simulada (MGS), ou seja, em condi??es em que a gravidade ? artificialmente reduzida para menos de 1xg. Estudos MGS podem ser importantes para entender as modula??es em n?vel molecular sofridas pelos organismos vivos. Portanto, o objetivo deste estudo foi caracterizar a resposta de C. violaceum, como organismo modelo de vida livre, cultivado em MGS, usando t?cnicas de prote?mica para entender como a bact?ria responde a esse estresse. A MGS foi conseguida por meio da rota??o do vessel ao redor do eixo horizontal perpendicular ao vetor gravitacional nos sistemas de cultura de c?lulas rotativas - Rotating Cell Culture Systems ? (RCCS4). MGS foi conduzido a uma velocidade de 40 rpm por um per?odo de 12 horas para obter a curva de crescimento a cada 2 horas. Prote?nas totais foram extra?das de amostras de cultura de c?lulas bacteriana coletada ?s 5 e 12 horas, correspondendo as fases exponenciais inicial (MG5) e tardia (MG12), respectivamente, tendo a curva de crescimento como refer?ncia. Ap?s a tripsiniza??o, as amostras foram analisadas em espectr?metro de massas Q-TOF. Como resultado um total de 212 prote?nas durante ?s 5h de crescimento e 192 ?s 12h foram detectadas, das quais 144 delas foram comuns em ambos os per?odos. No proteoma de C. violaceum obitido em 5h de crescimento 195 prote?nas foram identificadas em gravidade normal (GN5) e 155 prote?nas foram identificadas em MG5, sendo 18 upreguladas, 19 downreguladas e 17 expressas somente na condi??o de MG5. No proteoma obtido em 12h de crescimento, 165 prote?nas foram identificadas em gravidade normal (GN12) e 173 em MG12, das quais, 17 foram upreguladas, 22 downreguladas e 28 expressas somente na condi??o de MG12 Al?m disso, foi poss?vel identificar 25 prote?nas com fun??o desconhecida em MG5 e MG12. Utilizando ferramentas computacionais foi poss?vel construir redes de intera??es prote?na-prote?na (PPI) e as sub-redes contendo grupo de prote?nas com fun??es correlacionadas, analisar vias metab?licas, processos biol?gicos, contexto gen?mico e busca por dom?nios conservados e sequ?ncias hom?logas de prote?nas com fun??o desconhecida. Como resultado, identificamos sub-redes relacionadas com a bioss?ntese de prote?nas, regula??o da transcri??o e tradu??o, resposta ao estresse e metabolismo energ?tico, conclu?mos que as respostas celulares associadas ? express?o diferencial induzida pela MGS levaram ? diminui??o do crescimento de C. violaceum, acompanhado pela regula??o negativa de prote?nas relacionadas com processos transcricionais, traducionais e libera??o de energia por vias aer?bicas e pela regula??o positiva de prote?nas envolvidas no estresse oxidativo, na via anaer?bica e na sobreviv?ncia celular. / Chromobcterium violaceum (C.violaceum) is a Gram-negative bacteria, which has been found at tropical and subtropical regions, considered a free living model organism. Some proteomic studies performed with this bacterium have demonstrated its ability to adapt to environmental challenges such as high iron concentration and oxidative stress exposure. However, no study was made with this specie submitted to simulated microgravity (SMG), that is, under conditions in which the gravity is artificially reduced to less than 1xg. MGS studies may be important in understanding the molecular-level modulations undergone by living organisms. Therefore, the aim of this study was to characterize the response of C. violaceum, as free-living model organism, cultured at MGS, using proteomics techniques in order to understand how this bacterium response to this stress. The SMG was achieved by rotating the vessel around the horizontal axis perpendicular to the gravitational vector in Rotating Cell Culture Systems (RCCS4). SMG was conducted at a speed of 40 rpm for a period of 12 hours to obtain the growth curve every 2 hours. Total protein extraction was made in two times: 5 and 12 hours, corresponding to early (MG5) and late (MG12) exponential phase, respectively, taking the growth curve as a reference. After trypsinization, samples were analyzed with Q-TOF mass spectrometer. As a result a total of 212 proteins during 5h of growth and 192 at 12h were detected, of which 144 of them were common in both periods. We detected 155 proteins during MG5, from which 18 proteins were upregulated, 19 down-regulated and 17 proteins were exclusive when compared to GN5. In the proteome obtained in 12h of growth, 165 proteins were identified in normal gravity (GN12) and 173 in MG12, of which, 17 were upregulated, 22 were downregulated and 28 expressed only in MG12 condition. In addition, it was possible to identify 25 proteins with unknown function in MG5 and MG12. Using computational tools it was possible to construct networks of protein-protein interactions (PPI) and sub-networks containing group of proteins with correlated functions, to analyze metabolic pathways, biological processes, genomic context and search for conserved domains and homologous sequences of proteins with unknown function . As a result, we identified sub-networks related to protein biosynthesis, transcription regulation and translation, stress response and energetic metabolism, we conclude that the cellular responses associated with differential expression induced by MGS led to a decrease in the growth of C. violaceum, accompanied by the negative regulation of proteins related to transcriptional, translational and energy release by aerobic pathways and by the positive regulation of proteins involved in oxidative stress, anaerobic pathway and cell survival.

Submitted by Automa??o e Estat?stica (sst@bczm.ufrn.br) on 2017-07-04T11:53:11Z No. of bitstreams: 1 MariliaAugustaRochaDeQueirozPinheiro_DISSERT.pdf: 2148471 bytes, checksum: 3eaabda0264457ba7881c728daf88eb8 (MD5) / Approved for entry into archive by Arlan Eloi Leite Silva (eloihistoriador@yahoo.com.br) on 2017-07-11T12:42:03Z (GMT) No. of bitstreams: 1 MariliaAugustaRochaDeQueirozPinheiro_DISSERT.pdf: 2148471 bytes, checksum: 3eaabda0264457ba7881c728daf88eb8 (MD5) / Made available in DSpace on 2017-07-11T12:42:03Z (GMT). No. of bitstreams: 1 MariliaAugustaRochaDeQueirozPinheiro_DISSERT.pdf: 2148471 bytes, checksum: 3eaabda0264457ba7881c728daf88eb8 (MD5) Previous issue date: 2014-05-27 / A terapia larval ? a utiliza??o de larvas est?reis no desbridamento de feridas. Atualmente essa t?cnica vem sendo bastante utilizada na Europa, Estados Unidos da Am?rica e Israel, dentre outros pa?ses, entretanto, ainda n?o foi implementada rotineiramente no Brasil e n?o h? relatos de sua aplica??o utilizando larvas da mosca Chrysomya megacephala em pacientes humanos. O presente trabalho objetivou avaliar o desbridamento de ?lceras de dif?cil cicatriza??o utilizando larvas de C. megacephala. Cinco pacientes com ?lceras cr?nicas foram inclu?dos no estudo ap?s responderem a um question?rio, serem esclarecidos sobre os poss?veis riscos e benef?cios da terapia larval e assinarem o Termo de Consentimento Livre e Esclarecido ? TCLE. Antes das aplica??es, foram colhidas amostras para identifica??o das bact?rias presentes nas ?lceras. Ap?s essa etapa, as ?lceras foram avaliadas antes e durante o tratamento atrav?s de registro fotogr?fico, mensura??o de di?metros e avalia??o dos percentuais de tecido necr?tico e de granula??o. A avalia??o foi seguida da aplica??o de aproximadamente cinco larvas est?reis de 2? est?dio de C. megacephala por cm2 de les?o. Os curativos com larvas foram trocados ap?s 48 horas e com 48 horas de intervalo entre as aplica??es. As ?lceras dos pacientes inclu?dos no trabalho apresentaram car?ter polimicrobiano e em todas elas foi isolada a esp?cie Pseudomonas aeruginosa. Todos os pacientes submetidos ? terapia larval apresentaram redu??o significativa do percentual de necrose e aumento do tecido de granula??o na superf?cie das ?lceras e uma consequente melhora no decorrer do tratamento. / Larval therapy is the use of sterile larvae in the debridement of wounds. Currently this technique has been widely used in Europe, the U.S.A., and Israel, among other countries, however, has not been implemented in Brazil yet, and there are no reports of its application using larvae of the fly Chrysomya megacephala in human patients. This study aimed to evaluate the debridement of ulcers difficult to heal by using larvae of C. megacephala. Five patients with chronic ulcers were included in the study after answering a questionnaire, to be informed about the possible risks and benefits of larval therapy and signed a Free, Prior and Informed Consent. Before the applications, samples were collected for identification of the bacteria in the ulcers. After this step, the ulcers were evaluated before and during treatment by photographic recording, measurement and evaluation of diameters, percentage of necrotic tissue and granulation. The evaluation was followed by the application of approximately 5 second instar sterile larvae of C. megacephala per cm2 of lesion. Dressings with larvae were exchanged after 48 hours with 48 hours between applications. The patients? ulcers included in this study had polymicrobial nature and in all of them was isolated Pseudomonas aeruginosa species. All patients underwent larval therapy showed a reduction in the percentage of necrosis, increase of granulation tissue on the surface of ulcers and a consequent improvement during treatment.