Search

Made available in DSpace on 2016-10-10T03:52:57Z (GMT). No. of bitstreams: 5 Molecular phylogenetic diversity of bacteria associated with soil of the savanna-like Cerrado vegetation.pdf: 420658 bytes, checksum: 7499626b66cdeb1a2bcf72063c14976b (MD5) license_url: 52 bytes, checksum: 2f32edb9c19a57e928372a33fd08dba5 (MD5) license_text: 24372 bytes, checksum: 94b0a37ff5ec51de8c55507bff4a7ff9 (MD5) license_rdf: 24623 bytes, checksum: 378d22d8fe50e084ee2f354be78cbe62 (MD5) license.txt: 1887 bytes, checksum: 445d1980f282ec865917de35a4c622f6 (MD5) Previous issue date: 2009 The Braziliansavanna-likevegetationofCerradoisrapidlybeingconvertedto pasture andagriculturalfields.A16SrDNA-basedapproachwastakentostudythe bacterial communityassociatedwiththesoilofanativecerradoarea(sensu stricto) and anareathathasbeenconvertedtopasture.Thebacterialgroupmost abundantly identifiedincerrado sensu stricto soil wasthe a-Proteobacteriawhilein cerrado convertedtopasturetheActinobacteriawerethemostabundant. Rarefaction curvesindicatethatthespeciesrichnessofcerrado sensu stricto is greater thanthatofcerradoconvertedtopasture.Furthermore,lineage-through- time plotsshowthattheexpectedrichnessofspeciespresentincerrado sensu stricto soil isapproximately10timesgreaterthanthatofcerradoconvertedto pasture. Sim Publicado

Made available in DSpace on 2016-10-10T03:51:52Z (GMT). No. of bitstreams: 5 Diversity of soil fungal communities of Cerrado and its closely surrounding agriculture fields.pdf: 505497 bytes, checksum: 82c40856f7b51538e594dfadc7ea3182 (MD5) license_url: 52 bytes, checksum: 2f32edb9c19a57e928372a33fd08dba5 (MD5) license_text: 24259 bytes, checksum: f1f24f769b03eb8f9cd3f53c1090841c (MD5) license_rdf: 24658 bytes, checksum: 9d3847733d3c0b59c7c89a1d40d3d240 (MD5) license.txt: 1925 bytes, checksum: 7eeee87b74f804cd5a62ff1947665b5d (MD5) Previous issue date: 2008 Cerrado is a savanna-like region that covers a large area of Brazil. Despite its biological importance, the Cerrado has been the focus of few microbial diversity studies. A molecular approach was chosen to characterize the soil fungal communities in four areas of the Cerrado biome: a native Cerrado, a riverbank forest, an area converted to a soybean plantation, and an area converted to pasture. Global diversity of fungal communities in each area was assessed through Ribosomal intergenic spacer analysis which revealed remarkable diVerences among the areas studied. Sequencing of approximately 200 clones containing 18S rDNA sequences from each library was performed and, according to the genetic distance between sequences, these were assigned to operational taxonomic units (OTUs). A total of 75, 85, 85, and 70 OTUs were identiWed for the native Cerrado, riverbank forest, pasture, and soybean plantation, respectively. Analysis of sequences using a similarity cutoV value of 1% showed that the number of OTUs for the native Cerrado area was reduced by 35%; for the soybean plantation, a reduction by more than 50% was observed, indicating a reduction in fungal biodiversity associated with anthropogenic activity. This is the Wrst studydemonstrating the anthropogenic impact on Cerrado soil fungal diversity. Publicado

Made available in DSpace on 2016-10-10T03:52:15Z (GMT). No. of bitstreams: 5 Deciphering host resistance and pathogen virulence_the arabidopsis pseudomonas interaction as a model.pdf: 401934 bytes, checksum: 0b7ea0e1f11c9b4c9a18a6882dde12dd (MD5) license_url: 52 bytes, checksum: 2f32edb9c19a57e928372a33fd08dba5 (MD5) license_text: 24259 bytes, checksum: f1f24f769b03eb8f9cd3f53c1090841c (MD5) license_rdf: 24658 bytes, checksum: 9d3847733d3c0b59c7c89a1d40d3d240 (MD5) license.txt: 1887 bytes, checksum: 445d1980f282ec865917de35a4c622f6 (MD5) Previous issue date: 2003 The last decade has witnessed steady progress in deciphering the molecular basis of plant disease resistance and pathogen virulence. Although contributions have been made using many different plant and pathogen species, studies of the interactions between Arabidopsis thaliana and Pseudomonas syringae have yielded a particularly significant body of information. The present review focuses on recent findings regarding R gene products and the guard hypothesis, RAR1/SGT1 and other examples where protein processing activity is implicated in disease resistance or susceptibility, the use of microarray expression profiling to generate information and experimental leads, and important molecularand genome-level discoveries regarding P. syringae effectors that mediate bacterial virulence. The development of the Arabidopsis– Pseudomonas model system is also reviewed briefly, and we close with a discussion of characteristics to consider when selecting other pathosystems as experimentally tractable models for future research. Sim Publicado

Made available in DSpace on 2016-10-10T03:52:13Z (GMT). No. of bitstreams: 5 Diverse range of gene activity during arabidopsis thaliana leaf senescence includes ....pdf: 153859 bytes, checksum: d4c44a97a6137f1b737db33ff417e48e (MD5) license_url: 52 bytes, checksum: 2f32edb9c19a57e928372a33fd08dba5 (MD5) license_text: 24259 bytes, checksum: f1f24f769b03eb8f9cd3f53c1090841c (MD5) license_rdf: 24658 bytes, checksum: 9d3847733d3c0b59c7c89a1d40d3d240 (MD5) license.txt: 1887 bytes, checksum: 445d1980f282ec865917de35a4c622f6 (MD5) Previous issue date: 1999 To determine the range of gene activities associated with leaf senescence, we have identified genes that show preferential transcript accumulation during this developmental stage. The mRNA levels of a diverse array of gene products increases during leaf senescence, including a protease, a ribosomal protein, two cinnamyl alcohol dehydrogenases, a nitrilase and glyoxalase II. Two of the genes identified are known to be pathogen-induced. The senescence specificity of each gene was determined by characterization of transcript accumulation during leaf development and in different tissues. The increased expression of nitrilase in senescent leaves is paralleled by an increase in free indole-3-acetic acid (IAA) levels. Additionally, we have demonstrated that the induction of defense-related genes during leaf senescence is pathogen-independent and that salicylic acid accumulation is not essential for this induction. Our data indicate that the induction of certain genes involved in plant defense responses is a component of the leaf senescence program. Sim Publicado

Submitted by Lucivânia Carmo (lucivania.carmo@ucb.br) on 2021-09-13T14:10:15Z No. of bitstreams: 1 Rodrigo Mauricio Marinsek SalesTCC2021.pdf: 1046433 bytes, checksum: 3eb8cd3a135f4e3d8bbdbeafaac3e1c6 (MD5) Approved for entry into archive by Sara Ribeiro (sara.ribeiro@ucb.br) on 2021-09-13T17:39:14Z (GMT) No. of bitstreams: 1 Rodrigo Mauricio Marinsek SalesTCC2021.pdf: 1046433 bytes, checksum: 3eb8cd3a135f4e3d8bbdbeafaac3e1c6 (MD5) Made available in DSpace on 2021-09-13T17:39:15Z (GMT). No. of bitstreams: 1 Rodrigo Mauricio Marinsek SalesTCC2021.pdf: 1046433 bytes, checksum: 3eb8cd3a135f4e3d8bbdbeafaac3e1c6 (MD5) Previous issue date: 2021-06-09 O mercado industrial de enzimas cresce em bilhões de dólares todos os anos, pois as enzimas desempenham papel importante na catálise de muitas reações químicas em processos industriais. As β-glicosidases exercem uma posição importante neste mercado, devido a sua alta versatilidade, criando a possibilidade de utilizá-las em diversos ramos industriais. A partir de bibliotecas metagenômicas e genômicas de microrganismos da biodiversidade brasileira, construídas em projetos anteriores da Embrapa Agroenergia, foi possível fazer triagens funcionais na busca de atividade de β-glicosidase. Alguns dos genes encontrados foram expressos em cepas de Escherichia coli. Duas β-glicosidases foram selecionadas para as etapas de purificação e caracterização bioquímica, a Bgl12 e Bgl08. Após análises in sillico, foi identificado que possivelmente, as enzimas Bgl12 e Bgl08 pertencem às famílias de enzimas GH1 e GH3 respectivamente. A Bgl08 apresentou melhores resultados na purificação e análise em SDS-PAGE em relação a Bgl12. A Bgl08 apresentou alta atividade em substrato pNPG, confirmando sua atividade de β-glicosidase, e também apresentou atividade secundária em outros substratos sintéticos. Este trabalho teve como objetivo prospectar, purificar e caracterizar bioquimicamente pelo menos uma β-glicosidase com potencial valor biotecnológico para o mercado industrial.

Submitted by Sara Ribeiro (sara.ribeiro@ucb.br) on 2019-05-20T18:48:23Z No. of bitstreams: 1 MarianaBotelhoGarciaDissertacao2019.pdf: 2502321 bytes, checksum: 555f937393902476c3cd126f02b3ba18 (MD5) Approved for entry into archive by Sara Ribeiro (sara.ribeiro@ucb.br) on 2019-05-20T18:48:34Z (GMT) No. of bitstreams: 1 MarianaBotelhoGarciaDissertacao2019.pdf: 2502321 bytes, checksum: 555f937393902476c3cd126f02b3ba18 (MD5) Made available in DSpace on 2019-05-20T18:48:34Z (GMT). No. of bitstreams: 1 MarianaBotelhoGarciaDissertacao2019.pdf: 2502321 bytes, checksum: 555f937393902476c3cd126f02b3ba18 (MD5) Previous issue date: 2019-02-25 Sustainable development has been widely discussed in the world and in Brazil, especially when it comes to biorefineries produced by lignocellulosic material. This material is basically composed of cellulose, hemicellulose and lignin. However, it is known that only cellulose and hemicellulose are used, leaving lignin, which is a complex heteropolymeric matrix and ends up being burned because it is difficult bioconversion. There are some fungi and bacteria capable of degrading aromatic compounds, including lignin. However, microbial diversity goes far beyond what we know within the laboratory, as some microorganisms are not easily grown. Prior to this work, microbial consortia were produced enriched for microorganisms capable of degrading lignin from the community present in the backyard. The soil was inoculated in minimal medium M9 with kraft lignin or lignin extracted by alkaline method as carbon source, at two temperatures (30??C or 37??C). Every two weeks, an aliquot was transferred to a new medium, making six passes. In addition, a metagenomic library was constructed with the DNA of sixth passage consortium grown with kraft lignin at 37??C. The objectives of this work were: to evaluate and to compare the bacterial and fungal diversity found in the successive passages during the enrichment; and perform the search for enzymes capable of degrading lignin in the metagenomic library. To this end, DNA samples were obtained from the passages and an iTags sequencing of the bacterial 16S rRNA gene and the fungal ITS region was performed. Analyzes were performed using the QIIME software to calculate richness and diversity indices: Chao1, Shannon-Wiener, Simpson, Good's coverage and Phylogenetic Diversity (PD). In addition, rarefaction curves were constructed, taking into account the number of OTUs observed in each consortium. Both analyzes showed that the original soil was extremely diverse and that, as the passages occurred, the richness and diversity decreased. Graphs of the taxonomic composition of the consortia were generated to analyze the dynamics of the communities. The graphs pointed out that the microorganisms present there became specific, as the passages occurred, according to the substrate and the temperature, showing that there was a selection within the communities, favoring specific classes in each situation. All the dominant classes in the sixth passage have already been described as lignin degrading, suggesting that the enrichment was sufficient to select the degrader lignin microorganisms present in the initial backyard. Bacterial and fungal non - metric multidimensional scaling (NMDS) graphs were generated with the purpose of identifying the dissimilarity among the analyzed samples. For bacteria, the substrate and the temperature were factors of great relevance in the differentiation of the communities. As for fungi, the substrate as the temperature had little influence on the differentiation between the consortia. In addition, the metagenomic library was inserted into two hosts, Escherichia coli HB101 and Pseudomonas putida KT2440, and a screening was performed using guaiacol as a substrate. In E. coli HB101, it was possible to identify three positive clones potentially capable of degrading the substrate used. After sequencing these clones, their ORFs were analyzed. The ORF3 belonging to the clone p8_a4 presented similarity with the enzyme fatty acid desaturase, belonging to Altererythrobacter sp. The reaction catalyzed by this enzyme uses O2 and a pair of electrons, releasing water. This also occurs during the oxidation reaction of guaiacol promoted by laccase. Thus, it is possible that this enzyme is performing the oxidation of guaiacol. After analysis of the other two clones, it was not possible to identify which ORF potentially is responsible for the phenotype of guaiacol oxidation. Despite the difficulties encountered, it was possible to enrich communities of microorganisms that are probably degrading lignin. In addition, from a metagenomic library, three positive clones were screened that possess the phenotype for the oxidation of guaiacol and, in the future, could be extensively studied and possibly applied during the degradation of lignin. O desenvolvimento sustent??vel tem sido bastante discutido no mundo e no Brasil, principalmente quando se trata das biorrefinarias produzidas a partir do material lignocelul??sico. Esse material ?? formado basicamente de celulose, hemicelulose e lignina. Por??m, sabe-se que apenas as duas primeiras s??o utilizadas, restando a lignina, que ?? uma matriz heteropolim??rica complexa e acaba sendo queimada por ser de dif??cil bioconvers??o. Existem alguns fungos e bact??rias capazes de degradar compostos arom??ticos, incluindo a lignina. Contudo, a diversidade microbiana vai muito al??m do que conhecemos dentro do laborat??rio, pois alguns microrganismos n??o s??o facilmente cultivados. Previamente a este trabalho, foram produzidos cons??rcios microbianos enriquecidos para microrganismos capazes de degradar lignina a partir da comunidade presente no solo de jardim. O solo foi inoculado em meio m??nimo M9 com lignina kraft ou lignina extra??da por m??todo alcalino como fonte de carbono, em duas temperaturas (30??C ou 37??C). A cada duas semanas, uma al??quota foi transferida para um novo meio, perfazendo-se seis passagens. Al??m disso, uma biblioteca metagen??mica foi constru??da com o DNA do cons??rcio da sexta passagem cultivada com lignina kraft a 37??C. Os objetivos deste trabalho foram: avaliar e comparar a diversidade bacteriana e f??ngica encontrada nas sucessivas passagens durante o enriquecimento; e realizar a busca por enzimas capazes de degradar lignina na biblioteca metagen??mica. Para tal, foram obtidas amostras de DNA das passagens e foi realizado um sequenciamento de iTags do gene rRNA 16S de bact??rias e da regi??o ITS de fungos. A partir das sequ??ncias obtidas, foram realizadas an??lises utilizando o software QIIME para c??lculo dos ??ndices de riqueza e diversidade: Chao1, Shannon-Wiener, Simpson, Good???s coverage e Phylogenetic Diversity (PD). Adicionalmente, foram constru??das curvas de rarefa????o, levando em considera????o o n??mero de OTUs observadas em cada cons??rcio. Ambas as an??lises mostraram que o solo original era extremamente diverso e que, conforme as passagens foram ocorrendo, a riqueza e diversidade diminu??ram. Tamb??m foram gerados gr??ficos de composi????o taxon??mica dos cons??rcios para analisar a din??mica das comunidades. Os gr??ficos apontaram que os microrganismos ali presentes se tornaram espec??ficos, conforme as passagens foram ocorrendo, de acordo com o substrato e a temperatura, mostrando que houve uma sele????o dentro das comunidades, favorecendo classes espec??ficas em cada situa????o. Todas as classes dominantes na sexta passagem j?? foram descritas como degradadoras de lignina, sugerindo que o enriquecimento foi suficiente para selecionar os microrganismos capazes de degradar lignina presentes no solo de jardim inicial. Foram gerados gr??ficos de Escalonamento multidimensional n??o m??trico (NMDS) bacterianos e f??ngicos, com a finalidade de identificar a dissimilaridade entre as amostras analisadas. Para bact??rias, o substrato e a temperatura foram fatores de grande relev??ncia na diferencia????o das comunidades. J?? com rela????o aos fungos, o substrato como a temperatura tiveram pouca influ??ncia na diferencia????o entre os cons??rcios. Adicionalmente, a biblioteca metagen??mica foi inserida em dois hospedeiros, Escherichia coli HB101 e Pseudomonas putida KT2440 e, posteriormente, foi realizada uma triagem utilizando guaiacol como substrato. Em E. coli HB101, foi poss??vel identificar tr??s clones positivos potencialmente capazes de degradar o substrato utilizado. Ap??s sequenciamento destes clones, suas ORFs foram analisadas. A ORF3 pertencente ao clone p8_a4 apresentou similaridade com a enzima ??cido graxo desaturase, pertencente a Altererythrobacter sp. A rea????o catalisada por esta enzima utiliza-se do O2 e de um par de el??trons, liberando ??gua. Isso tamb??m ocorre durante a rea????o de oxida????o do guaiacol promovida pela lacase. Sendo assim, ?? poss??vel que essa enzima esteja realizando a oxida????o do guaiacol. Ap??s a an??lise dos outros dois clones, n??o foi poss??vel identificar qual a ORF potencialmente ?? respons??vel pelo fen??tipo de oxida????o de guaiacol. Apesar das dificuldades encontradas, foi poss??vel realizar o enriquecimento de comunidades de microrganismos que provavelmente est??o degradando lignina. Al??m disso, a partir de uma biblioteca metagen??mica, foram triados tr??s clones positivos que possuem o fen??tipo para oxida????o do guaiacol e, futuramente, poder??o ser amplamente estudados e, possivelmente, aplicados durante a degrada????o da lignina.

Fatal yellowing disease (FY) is a bud rot-type disease that severely affects oil palm plantations in Latin America. Since 1974, when it was first reported in Brazil, this disorder has been responsible for severe economic losses in the oil palm industry; and, for nearly 50 years, several studies have tried to identify its causal agent, without success. The etiological studies regarding FY in oil palm explored either biotic and abiotic stress scenarios, in a single or combined manner. Most recently, the hypothesis in favor of one biotic cause has lost some grounds to the abiotic one, mainly due to new insights regarding deficient aeration in the soil, which reduces the potential for oxy-reduction, causing changes in the ionic composition of the soil solution. This review presents an overview of the history of this disease and the several efforts done to fulfill Koch’s postulates over the last 40 years, besides discussing recent studies that revisited this subject using some omics technics. We conclude by discussing further uses of omics via a multi-omics integration (MOI) strategy to help finally find out what is really behind the genesis of FY. Finding this elusive causal agent of FY out will allow either the development of a more efficient diagnostic tool and the advance in studies trying to find out the source of the genetic resistance hidden in the genome of the American oil palm.

Submitted by Franciene Aguiar (franciene.aguiar@ucb.br) on 2019-07-10T18:52:39Z No. of bitstreams: 1 BrunoRafaelDeLimaMoraesTCCGraduacao2016.pdf: 1438964 bytes, checksum: 41dbdf82890cb1a658b28501c2fa91d3 (MD5) Approved for entry into archive by Sara Ribeiro (sara.ribeiro@ucb.br) on 2019-07-12T18:43:48Z (GMT) No. of bitstreams: 1 BrunoRafaelDeLimaMoraesTCCGraduacao2016.pdf: 1438964 bytes, checksum: 41dbdf82890cb1a658b28501c2fa91d3 (MD5) Made available in DSpace on 2019-07-12T18:43:48Z (GMT). No. of bitstreams: 1 BrunoRafaelDeLimaMoraesTCCGraduacao2016.pdf: 1438964 bytes, checksum: 41dbdf82890cb1a658b28501c2fa91d3 (MD5) Previous issue date: 2016 O óleo diesel é um produto originado do petróleo que funciona em motores a diesel, com composição baseada em hidrocarbonetos. Este combustível é tóxico, inflamável e de forte odor, sendo usado em vários tipos de transportes e máquinas (PETRÓLEO BRASILEIRO S. A. PETROBRAS, 2015). A resolução ANP nº 50 (2013) estabelece duas classificações de óleo diesel para uso rodoviário: óleo diesel A e B, o primeiro sem adição de biodiesel e o segundo com adição de biodiesel.

Submitted by Kelson Anthony de Menezes (kelson@ucb.br) on 2016-11-23T11:36:50Z No. of bitstreams: 1 DaivaDomenechTupinambaDissertacao2015.pdf: 12204296 bytes, checksum: db4048c47ac3f9f47171655f6bfb3e91 (MD5) Made available in DSpace on 2016-11-23T11:36:50Z (GMT). No. of bitstreams: 1 DaivaDomenechTupinambaDissertacao2015.pdf: 12204296 bytes, checksum: db4048c47ac3f9f47171655f6bfb3e91 (MD5) Previous issue date: 2015-03-12 The Amazon rainforest is home to huge diversity of macro-species. However, little is known about the microbial diversity. The effect of land-use after deforestation is of great importance in the development of public policies. The metagenome were extracted from soils of native forest and an adjacent cultivated area with oil palm and pyrosequencing of 16S rRNA genes of archaea communities present in those soils was used for phylogenetic characterization of the archaeal microbiota, in an unprecedented characterization of native Amazonian soil and soils cultivated with oil palm. All OTUs of the native forest soils and cultivated area with oil palm were classified into two phyla: Euryarchaeota and Thaumarchaeota. Thaumarchaeota phylum was predominant only in native forest. Euryarchaeota, especially methanogenic archaea, were prevalent in cultivated area with oil palm. Various genera involved in biogeochemical cycles, as AOA and methanogenic archaea, were identified in all samples. In native forest the genera with larger representation were Candidatus Nitrosotalea and Candidatus Nitrososphaera, AOAs. In the cultivated area with oil palm the genus with larger representation was Rice Cluster I. There is a direct correlation between levels of organic matter and total carbon and the diversity of archaea in Amazonian soils. In addition, anthropization also showed impact on this diversity. This is the first study to characterize the microbiota of archaea in Amazonian soils using specific primers and high-throughput sequencing. This work also characterize the archaeal communities in soils cultivated with oil palm with and without symptoms of Fatal Yellowing. The growth of world energy demand and concern with climate changes lead to a worldwide increase in the search for alternative sources of energy. Within this scenario, agroenergy presents itself as a viable alternative. However, there are still several limitations to the production of biofuels, such as efficiency and cost of the production process as well as the quality of the energy feedstock available. Palm oil is one of the most promising sources of oil for biodiesel production in Brazil, and the Fatal Yellowing (FY), a disease with unknown etiology, is limiting the use of palm. From the metagenome extracted from soils associated to oil palms with and without symptoms of FY was used pyrosequencing of 16S rRNA genes of archaeal communities for phylogenetic characterization, in an attempt of an association of some microorganism with FY, and an unprecedented characterization of soils cultivated with oil palms with and without FY. In the comparison among oil palms with and without FY symptoms, the three groups were different among then; group 8 showed higher diversity and had lower coverage. All groups presented two phyla: Thaumarchaeota and Euryarchaeota. There was prevalence of the second in all groups, with an increase in abundance of methanogenic archaea with FY. In the analysis of genera, significant differences between the groups were observed, especially for genera Rice Cluster I and Ca. Nitrosotalea, which showed an increase in abundance directly proportional to the increase of the FY symptoms. The genera Ca. Nitrososphera and Methanocella showed the opposite; a decrease in abundance with the increase of FY symptoms. However, it???s not possible to say that these genera are related to FY. This work is complementary to the study of bacterial microbiota of these soils, already performed; and the study of fungal microbiota, in progress. This is an unpublished study, which will contribute to future studies on the Fatal Yellowing. A floresta Amaz??nica ?? ber??o de enorme diversidade de macroesp??cies. Entretanto, pouco se sabe sobre a diversidade microbiana. O efeito do uso da terra ap??s o desmatamento das florestas ?? de grande import??ncia no desenvolvimento de pol??ticas p??blicas. A partir do metagenoma extra??do do solo de mata nativa Amaz??nica e de uma ??rea adjacente cultivada com dendezeiros foi utilizado o pirosequenciamento do 16S rRNA das comunidades de arqueias presentes nesses solos para caracteriza????o filogen??tica e an??lise comparativa das comunidades de arqueias. Todas as OTUs dos solos de mata nativa e ??rea cultivada com dendezeiros foram classificadas em apenas dois filos: Euryarchaeota e Thaumarchaeota. O filo Thaumarchaeota foi predominante apenas na mata nativa, sendo Euryarchaeota, especialmente arqueias metanog??nicas, predominantes nos solos cultivados com dendezeiros. Diversos g??neros envolvidos com os ciclos biogeoqu??micos, como arqueias oxidadoras de am??nia e metanog??nicas, foram identificados nas duas amostras. Na mata nativa os g??neros classificados que apresentam a maior representa????o foram Candidatus Nitrosotalea e Candidatus Nitrososphaera, AOAs. J?? na ??rea cultivada com dendezeiros o g??nero de maior representa????o foi Rice Cluster I. Foi encontrada um correla????o direta entre os n??veis de mat??ria org??nica e carbono total e a diversidade de arqueias nos solos amaz??nicos. Al??m disso, a antropiza????o tamb??m apresentou impacto sobre essa diversidade. Este ?? o primeiro estudo de caracteriza????o da microbiota de arqueias em solos amaz??nicos usando primers espec??ficos e sequenciamento de alto desempenho. Este trabalho tamb??m caracterizou as comunidades de arqueias em solos cultivados com dendezeiros com e sem sintomas de Amarelecimento Fatal. O crescimento da demanda energ??tica mundial e preocupa????o com as mudan??as clim??ticas levou a um aumento da busca mundial por fontes alternativas de energia, o que est?? levando diversos pa??ses a buscarem na bioenergia uma alternativa. Entretanto, ainda existem diversas limita????es na produ????o de biocombust??veis, seja na efici??ncia e custo do processo produtivo, seja na qualidade das fontes energ??ticas dispon??veis. O dend?? ?? uma das fontes mais promissoras de ??leo para a produ????o de biodiesel no Brasil, sendo o Amarelecimento Fatal, doen??a com fator etiol??gico desconhecido, um limitante no uso do dend??. A partir do metagenoma extra??do dos solos associados a dendezeiros com e sem sintomas de AF foi utilizado o pirosequenciamento do 16S rRNA das comunidades de arqueias para caracteriza????o filogen??tica. Foi realizada uma an??lise comparativa das comunidades de arqueias de solos de dendezeiros com e sem sintomas de AF, numa tentativa de associa????o de algum microrganismo com essa doen??a. Na compara????o entre dendezeiros com e sem sintomas de AF, os tr??s grupos estudados diferiram entre si; o grupo 8 apresentou maior diversidade e obteve menor cobertura. Todos os grupos apresentaram dois filos: Thaumarchaeota e Euryarchaeota. Houve preval??ncia do segundo em todos os grupos, com aumento na abund??ncia de arqueias metanog??nicas com o AF. Na an??lise entre g??neros, foram observadas diferen??as significativas entre os grupos, especialmente para os g??neros Rice Cluster I e Ca. Nitrosotalea, que apresentaram um aumento em suas abund??ncias diretamente proporcional ao aumento dos sintomas do AF. Os g??neros Ca. Nitrososphaera e Methanocella apresentaram uma rela????o inversa; uma queda na abund??ncia com o aumento dos sintomas do AF. Entretanto, n??o se pode afirmar que estes grupos est??o relacionados ao AF. Este trabalho ?? complementar ao estudo da microbiota bacteriana desses solos, j?? realizado; e pelo estudo da microbiota f??ngica, em andamento. Trata-se de um estudo in??dito, que ir?? contribuir para os estudos futuros sobre o Amarelecimento Fatal.

Submitted by Kelson Anthony de Menezes (kelson@ucb.br) on 2016-12-19T18:17:11Z No. of bitstreams: 1 LuisFelipeSchroederDissertacao2014.pdf: 2932891 bytes, checksum: 9867ac60d140318b946ef45528984bca (MD5) Made available in DSpace on 2016-12-19T18:17:11Z (GMT). No. of bitstreams: 1 LuisFelipeSchroederDissertacao2014.pdf: 2932891 bytes, checksum: 9867ac60d140318b946ef45528984bca (MD5) Previous issue date: 2014-09-30 There are different process being developed for cellulosic ethanol production, with possible different pretreatments with varying temperatures and pH, in addition to several biomasses can be used as the source of fermentable sugars. Among the important enzymes for deconstruction of plant biomass, stand out xylanases. These enzymes are responsible for deconstruction of the hemicellulose present in the structure of the plant cell walls. There are several ways to accomplish the identification of these enzymes: purification from an isolated microorganism is one. In this study, genomic and metagenomic approaches were used to carry out the prospection of the genes responsible for coding these enzymes. Clones from two libraries were used for detection and evaluation of activity on solid medium, supplemented with xylan and acid pretreated sugarcane bagasse. Nineteen clones of a goat rumen metagenomic library and five clones from an AB60 bacterium genomic library, with 15,000 clones constructed in this study, were selected initially. Fourteen clones from the metagenomic library were completely sequenced and their ORFs were analyzed. Four clones from the genomic library were partially sequenced and one clone had its sequence completely determined and 104 ORFs were obtained for all clones completely or partially sequenced ORFs were analyzed. Eleven ORFs showed some similarity to genes of importance for the degradation of complex polysaccharides. Among the most important ORFs and most likely to be related to the detected activity, are genes coding for ??-glucosidase, ??-xylosidase and ??-glucuronidase. Furthermore, also other ORFs with lower probability of relation with the activity or necessity to full sequencing of the clones for a few more conclusive analysis were identified. About 40% of the ORFs present in the rumen clones and 37.8% of the ORFs present in Acidobacteria clones showed similarity with hypothetical or uncharacterized proteins, which could be important in the activity detected. A ??-glucuronidase gene detected in a clone from the goat rumen metagenomic library was synthesized, its sequence was optimized for expression in Escherichia coli. However, in the present work, it was not possible to sub-cloning, made expression and purification of this enzyme. Some ORFs detected can be used for future studies of expression and characterization in order to improve knowledge about biotechnological potential present in the rumen and acidobacteria AB60, besides the ecological role of these microorganisms in their environment. Existem diversos processos em desenvolvimento para a produ????o de etanol celul??sico, havendo diferentes poss??veis pr??-tratamentos, com temperaturas e pH variados, al??m das diversas biomassas que podem ser utilizadas como fonte de a????cares ferment??veis. Dentre as enzimas importantes para a desconstru????o de biomassa vegetal, destacam-se as xilanases. Estas enzimas s??o respons??veis pela desconstru????o da estrutura hemicelul??sica presente na parede celular das plantas. H?? diversas maneiras para alcan??ar a identifica????o destas enzimas: purifica????o a partir de micro-organismo isolado sendo uma delas. No presente trabalho, foram utilizadas abordagens gen??mica e metagen??mica a fim de realizar a prospec????o dos genes respons??veis pela codifica????o para estas enzimas. Foram utilizados clones oriundos de duas bibliotecas para a detec????o e avalia????o da atividade em meio s??lido suplementado com xilana e baga??o de cana-de-a????car pr??-tratado com ??cido. Dezenove clones de uma biblioteca metagen??mica de r??men de caprinos e cinco clones de uma biblioteca gen??mica da bact??ria AB60, com 15.000 clones constru??da no presente trabalho, foram selecionados inicialmente. Quatorze clones da biblioteca metagen??mica foram sequenciados completamente e tiveram as suas ORFs analisadas. Quatro clones da biblioteca gen??mica foram parcialmente sequenciados e um clone teve a sua sequ??ncia completa determinada e as ORFs analisadas. Das 104 ORFs obtidas de todos os clones completamente ou parcialmente sequenciados, onze ORFs apresentaram alguma similaridade com genes de import??ncia para a degrada????o de polissacar??deos complexos. Dentre as ORFs de maior import??ncia e com maior probabilidade de estarem relacionadas com a atividade detectada, est??o genes codificantes para ??-glicosidase, ??-xilosidase e ??-glicuronidase. Al??m disso, tamb??m foram identificadas outras ORFs com menor probabilidade de rela????o com a atividade ou necessidade de sequenciamento completo de alguns dos clones para uma an??lise mais conclusiva. Cerca de 40% das ORFs presentes nos clones selecionados de r??men e 37,8% das ORFs presentes nos clones selecionados de Acidobacteria apresentaram similaridade com prote??nas hipot??ticas ou prote??nas n??o caracterizadas que podem ter import??ncia na atividade detectada. Um gene de ??-glicuronidase detectado em um clone da biblioteca metagen??mica de r??men de caprino foi sintetizado, otimizando-se sua sequ??ncia para express??o em Escherichia coli . Entretanto, n??o foi poss??vel a sub-clonagem, express??o e purifica????o desta enzima no presente trabalho. Algumas ORFs detectadas podem ser utilizadas para estudos futuros de express??o e caracteriza????o a fim de aprimorar o conhecimento a respeito do potencial biotecnol??gico presente no r??men e na Acidobact??ria AB60, al??m do papel ecol??gico destes micro-organismos em seu ambiente.

Submitted by Kelson Anthony de Menezes (kelson@ucb.br) on 2016-11-23T11:53:28Z No. of bitstreams: 1 OhanaYonaradeAssisCostaDissertacaoparcial2015.pdf: 2702312 bytes, checksum: 31ec065175a2d2c39c8a0c2121900693 (MD5) Made available in DSpace on 2016-11-23T11:53:28Z (GMT). No. of bitstreams: 1 OhanaYonaradeAssisCostaDissertacaoparcial2015.pdf: 2702312 bytes, checksum: 31ec065175a2d2c39c8a0c2121900693 (MD5) Previous issue date: 2014-03-31 The interest in biofuels started in the 2000s, due to a greater concern with the production of cleaner and renewable energy sources needed to decrease global dependency on fossil fuels. Brazil is the largest producer of sugar cane and the second largest producer of ethanol. Although the process is already well established, microbial contamination can be an obstacle, resulting in decreased productivity. The aim of this work was to study the microbial diversity of contaminants in six stages of ethanol production process using classical microbiology techniques and cultureindependent techniques. Triplicate samples from different stages of ethanol production were collected: sugarcane juice, mixed juice, clarified juice, evaporated juice, must and wine. Each sample was diluted and plated on four culture media: PCA, MRS and YPD CZAPEK. The colonies were counted, isolated and stored in glycerol at -80?? C. DNA extraction of samples was done, and the DNA of each one of the replicates of each sample was used for pyrosequencing of Bacteria and Archaea 16S rRNA genes, and Fungi ITS gene. The sequences generated were subjected to bioinformatics analysis using a specific database to the genes. It were isolated and stored in 64 bacteria, 30 yeasts, 20 filamentous fungi, which were identified by Sanger sequencing. The pyrosequecing showed 322 genera for the domain Bacteria, 21 genera for the domain Archaea and 184 genera for the domain Fungi. Among the predominant genera of bacteria in samples of sugarcane juice, mixed juice, clarified juice, evaporated juice and must are Leuconostoc, unclassified Enterobacteriales and unclassified Actinomycetales, while in the wine sample, the predominant genus was Lactobacillus, one of the major contaminants of ethanol production. For the domain Fungi, only sequenced in the sugarcane juice and mixed juice, the predominant groups were Lachancea, unclassified Hypocreales and unclassified Sordariomycetes. For the domain Archaea, also sequenced only in the sugarcane juice and mixed juice, the predominant group was unclassified Soil Crenarchaeotic group. Rarefaction curves showed that the samples of sugarcane juice, mixed juice and clarified juice did not have diversity at the genus level covered, and for sugarcane juice and mixed juice samples, the diversity was not covered in any of the domains, showing that further studies involving the diversity of these samples are needed. O interesse na produ????o de biocombust??veis se iniciou na d??cada de 2000, devido a uma maior preocupa????o com a produ????o de fontes de energia mais limpas e renov??veis, necess??rias para diminui????o da presente depend??ncia mundial dos combust??veis f??sseis. O Brasil ?? o maior produtor mundial de cana-de-a????car e o segundo produtor mundial de etanol. Embora o processo de produ????o do etanol esteja bem estabelecido, a contamina????o microbiana pode ser um obst??culo, gerando diminui????o da produtividade. O objetivo desse trabalho foi estudar a diversidade microbiana de contaminantes em seis etapas do processo de produ????o de etanol utilizando t??cnicas de dependentes e independentes de cultivo. Amostras triplicadas de diferentes est??gios da produ????o de etanol foram coletadas: caldo da cana crua, caldo misto, caldo clarificado, caldo evaporado, mosto e vinho. Cada amostra foi dilu??da e semeada em quatro meios de cultura: PCA, MRS, CZAPEK e YPD. As col??nias foram contadas, isoladas e armazenadas em glicerol a -80??C. Foi feita a extra????o de DNA das amostras, e o DNA das replicatas de cada amostra foi utilizado para o pirosequenciamento dos genes do RNAr 16S dos dom??nios Bacteria e Archaea e da regi??o ITS do reino Fungi. As sequ??ncias geradas foram submetidas a an??lise bioinform??tica utilizando-se banco de dados espec??ficos para os genes em quest??o. Foram isolados, armazenados e identificados por sequenciamento de Sanger 64 bact??rias, 30 leveduras e 18 fungos filamentosos. O pirosequenciamento demonstrou a presen??a de 322 g??neros/grupos n??o classificados para o dom??nio Bacteria, 21 g??neros/grupos n??o classificados para o dom??nio Archaea e 184 para o reino Fungi, no total. Entre os g??neros de bact??rias predominantes nas amostras de caldo da cana crua, caldo misto, caldo clarificado, caldo evaporado e mosto est??o Leuconostoc, Enterobacteriales n??o classificados e Actinomycetales n??o classificados, enquanto que na amostra de vinho, o g??nero predominante ?? Lactobacillus, um dos maiores contaminantes da produ????o de etanol. Para o reino Fungi, sequenciado apenas no caldo da cana crua e no caldo misto, foram predominantes os grupos Lachancea, Hypocreales n??o classificados e Sordariomycetes n??o classificados. Para o dom??nio Archaea, tamb??m sequenciado apenas no caldo da cana crua e no caldo misto, predominaram sequ??ncias n??o classificadas do Soil Crenarchaeotic Group. As curvas de rarefa????o mostraram que as amostras de caldo da cana crua, caldo misto, caldo clarificado n??o tiveram sua diversidade coberta em n??vel de g??nero, sendo que para as amostras de caldo da cana crua e caldo misto a diversidade n??o foi coberta em nenhum dos dom??nios, de modo que s??o necess??rios mais estudos envolvendo a diversidade dessas amostras.

Conselho Nacional de Desenvolvimento Científico e Tecnológico The screening for genes in metagenomic libraries from soil creates opportunities to explore the enormous genetic and metabolic diversity of microorganisms. Rivers are ecosystems with high biological diversity, but few were examined using the metagenomic approach. With this objective, a metagenomic library was constructed from DNA soil samples collected at three different points along the Jundiaí-river (Rio Grande do Norte-Brazil). The points sampled are from open area, rough terrain and with the direct incidence of sunlight. This library was analyzed functionally and based in sequence. For functional analysis Luria-Bertani solid medium (LB) with NaCl concentration varied from 0.17M to 0.85M was used for functional analysis. Positives clones resistant to hypersaline medium were obtained. The recombinant DNAs were extracted and transformed into Escherichia coli strain DH10B and survival curves were obtained for quantification of abiotic stress resistance. The sequences of clones were obtained and submitted to the BLASTX tool. Some clones were found to hypothetical proteins of microorganisms from both Archaea and Bacteria division. One of the clones showed a complete ORF with high similarity to glucose-6-phosphate isomerase which participates in the synthesis of glycerol pathway and serves as a compatible solute to balance the osmotic pressure inside and outside of cells. Subsequently, in order to identify genes encoding osmolytes or enzymes related halotolerance, environmental DNA samples from the river soil, from the water column of the estuary and ocean were collected and pyrosequenced. Sequences of osmolytes and enzymes of different microorganisms were obtained from the UniProt and used as RefSeqs for homology identification (TBLASTN) in metagenomic databases. The sequences were submitted to HMMER for the functional domains identification. Some enzymes were identified: alpha-trehalose-phosphate synthase, L-ectoina synthase (EctC), transaminase L-2 ,4-diaminobutyric acid (EctB), L-2 ,4-diaminobutyric acetyltransferase (EctA), L-threonine 3 dehydrogenase (sorbitol pathway), glycerol-3-phosphate dehydrogenase, inositol 3-phosphate dehydrogenase, chaperones, L-proline, glycine betaine binding ABC transporter, myo-inositol-1-phosphate synthase protein of proline simportadora / PutP sodium-and trehalose-6-phosphate phosphatase These proteins are commonly related to saline environments, however the identification of them in river environment is justified by the high salt concentration in the soil during prolonged dry seasons this river. Regarding the richness of the microbiota the river substrate has an abundance of halobacteria similar to the sea and more than the estuary. These data confirm the existence of a specialized response against salt stress by microorganisms in the environment of the Jundiaí river A busca por genes baseada na construção e análise de bibliotecas metagenômicas a partir de solo gera oportunidades para explorar uma enorme diversidade genética e metabólica de microrganismos. Os rios são ecossistemas com alta diversidade biológica, mas ainda pouco explorados por meio de metagenômica. Com o objetivo de explorar a diversidade microbiana, uma biblioteca metagenômica foi construída a partir de DNA extraído de substrato de rio em três pontos ao longo do rio Jundiaí (Rio Grande do Norte-Brasil). Os pontos de amostragem são derivados de área aberta, terreno acidentado e com a incidência direta da luz solar. Esta biblioteca foi analisada funcionalmente e também com base em sequências. Para a análise funcional foi utilizado meio de cultura sólido LB com concentração de NaCl variando de 0,17M a 0,85M. Foram obtidos 15 clones positivos com características halotolerantes. Os DNAs recombinantes foram extraídos e retransformados em cepa de Escherichia coli DH10B e curvas de sobrevivência foram obtidas para confirmação e quantificação da resistência ao estresse abiótico. As sequências dos clones foram obtidas e submetidas a ferramenta BLASTX e assim foi comprovado que alguns clones codificavam proteínas hipotéticas. Um dos clones apresentou uma ORF completa com elevada similaridade de glucose-6-fosfato-isomerase que participa na síntese do precursor de glicerol, sendo um soluto compatível para equilibrar a pressão osmótica no interior e no exterior das células. Posteriormente, para identificação de genes que codificam osmólitos relacionados com halotolerância e identificação da diversidade microbiológica, amostras de DNA ambiental do substrato do rio e da coluna d´água do estuário e oceano foram coletadas e pirosequenciadas. As sequências de osmólitos de diferentes microrganismos foram obtidas a partir do UniProt e utilizadas como RefSeqs para a identificação por homologia (TBLASTN) nos bancos de dados metagenômicos. As sequências identificadas nos bancos de dados ambientais foram submetidas ao programa HMMER com o fim de identificar domínios funcionais. Foram identificadas as enzimas: alfa-trealose-fosfato sintase, L-ectoina sintase (ectC), transaminase do ácido L-2,4-diaminobutírico (EctB), ácido L-2 ,4-diaminobutírico acetiltransferase (EctA), L-treonina 3-desidrogenase (via de síntese do sorbitol), Glicerol-3-fosfato desidrogenase, inositol-3-fosfato desidrogenase, chaperonas, L-prolina glicina betaína ligação transportador ABC, mio-inositol-1-fosfato sintase, a proteína simportadora de prolina/sódio -PutP e trealose-6-fosfato fosfatase. Estas são enzimas que participam da síntese de osmólitos comumente relacionados a ambientes salinos, no entanto a identificação desses solutos em ambiente de rio é justificada pela elevada concentração salina no solo durante prolongadas estações de seca neste rio. Quanto à riqueza da microbiota foi identificado que o substrato do rio possui uma abundância de halobactérias semelhante a do mar e superior a do estuário. Esses dados confirmam a existência de uma resposta especializada contra o estresse salino por microrganismos no ambiente do rio Jundiaí

Made available in DSpace on 2016-06-24T04:01:16Z (GMT). No. of bitstreams: 1 TESEELISAFINAL_1_.pdf: 1434864 bytes, checksum: eb5b73e0ceb889cc60fabac5d882537f (MD5) Previous issue date: 2005-09-08 Brazil is the largest producer of Carica papaya in the world. Besides the economical importance of this crop it has a very important social role since it is produced all year long, generating new jobs annually. The discrete position of papaya fruit on the exportation market of fresh fruit in Brazil is due to fruit fragility and diseases after harvest, which makes the fruit inappropriate for exportation. The control of postharvest diseases of papaya fruit has been accomplished almost exclusively by mean of fungicides dip or drench after harvest. Due to increasing concerns with fungicide toxicity and development of resistance by pathogens most chemicals used for the control of papaya postharvest diseases have been withdrawn from the market. The search for quality associated to lower costs and environment safety concerns have directed efforts to search for new control alternatives such as the use of hot bath, irradiation (gama and UV) and natural compounds. In general, plants respond to attack of pathogenic microorganisms by the induction of expression of a large number of genes, which controls the expression of many proteins among which are the chitinases and the ??-1,3-glucanases. The objective of the present study was, therefore, to determine if the gene of ??-1,3-glucanase is present in the genome of C. papaya. Using Polymerase Chain Reactions, it was possible to amplify, identify and clone two different types of ??-1,3-glucanases. Based on the sequence analysis of the protein, it was possible to construct a phylogenetic tree and to predict the secondary and tertiary structure of these proteins. The identification of these two distinct types of ??-1,3-glucanases is, probably, explained by the fact that either these could be different alleles of the same gene, be different genes or it could be both. Other facts may contribute for the existence of these distinct types of the same enzyme in C. papaya. First, the necessity of a high expression level of the enzyme in the plant or differential localization of the expression in the plant. Considering that in many plant pathogen systems ??-1,3-glucanases are involved in resistance to diseases, knowing the gene sequence of these enzymes could help to produce transformed papaya with high level of resistance against fungi. This could increase fruit quality and shelf life, reducing losses and increasing growers profit O Brasil ?? o primeiro produtor mundial de Carica papaya que ?? cultivado em quase todo territ??rio brasileiro. Al??m de sua import??ncia econ??mica deve ser ressaltada sua fun????o social, pois o mamoeiro produz durante o ano todo, necessitando de renova????o peri??dica das lavouras, o que gera empregos e absorve m??o-de-obra continuamente. A discreta posi????o do mam??o na pauta das exporta????es de frutas frescas deve-se, entre outras raz??es, ?? sua fragilidade na fase de p??s-colheita que dificulta seu transporte e exporta????o. O controle de doen??as de p??s-colheita do mam??o tem sido feito quase que exclusivamente por meio do uso de fungicidas protetores, entretanto, tais produtos est??o se tornando menos efetivos porque os pat??genos est??o desenvolvendo resist??ncia. Nessa busca por qualidade associada ao menor custo t??m sido usados tratamentos com calor, irradia????o (gama e UV) e compostos naturais. Em geral, as plantas respondem ao ataque de microorganismos patog??nicos com a indu????o de express??o de um grande n??mero de genes que codificam diversas prote??nas, entre as quais est??o as quitinases e b-glucanases. O objetivo do presente estudo foi, portanto, determinar se o gene de b- 1,3 glucanase est?? presente em Carica papaya. Tal estudo poder?? subsidiar futuros estudos de transforma????o em mam??o, visando ?? produ????o de plantas transg??nicas superexpressando essa prote??na com o objetivo de controlar doen??as de pr?? e p??s-colheita. Para isto foi realizada uma PCR (Polimerase Chain Reaction), a partir da qual foi poss??vel a amplifica????o, a identifica????o e a clonagem de dois tipos de b- 1,3 glucanases. Com base na an??lise da seq????ncia prot??ica foi poss??vel construir uma ??rvore filogen??tica al??m de permitir a realiza????o da predi????o das estruturas secund??ria e terci??ria da prote??na. A identifica????o destes dois tipos de b-1,3 glucanases distintas sugere que estas sejam produto de alelos diferentes do mesmo gene, ou que as mesmas sejam produto de genes diferentes, ou ambas as situa????es. Outros fatores podem contribuir para o aparecimento desses dois tipos de uma mesma enzima em uma ??nica esp??cie, como a necessidade de um n??vel de express??o elevado ou a localiza????o distinta da express??o nos tecidos da planta. De posse destes resultados ser?? poss??vel produzir plantas com elevada express??o desta prote??na o que poderia garantir elevada resist??ncia a fungos. Desta forma, os produtos teriam a vida de prateleira aumentada, a perda de produtos seria menor, assim como o preju??zo para os agricultores, pois os frutos estariam mais protegidos durante o transporte e o armazenamento