Submitted by Irene Nascimento (irene.kessia@ufpe.br) on 2016-06-30T16:59:18Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Dissertação- Raphael Santana.pdf: 1198352 bytes, checksum: 2ddd13ab9df70bdaf76d80dd5d481f49 (MD5) / Made available in DSpace on 2016-06-30T16:59:19Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Dissertação- Raphael Santana.pdf: 1198352 bytes, checksum: 2ddd13ab9df70bdaf76d80dd5d481f49 (MD5) Previous issue date: 2015-02-24 / FACEPE / Actinobactérias são bactérias Gram-positivas formadoras de filamentos ramificados que se destacam pela produção de metabólitos secundários, como antimicrobianos, antitumorais, fitohormônios e corantes naturais. Diante disso, este trabalho teve o objetivo de determinar o potencial biotecnológico de actinobactérias da coleção UFPEDA contra Candida spp. Para avaliação da atividade biotecnológica, 32 actinobactérias foram testadas contra sete isolados clínicos de Candida spp. utilizando diferentes meios de cultura para o crescimento (ALA, ISP-4, AY, ISP-3) e temperaturas (37 ºC ou 45 ºC). No ensaio primário, foi evidenciada atividade apenas quando as actinobactérias foram cultivadas em meio ISP-3 a temperatura de 37 ºC. Dessas, apenas 2 linhagens (6,25 %) apresentaram atividade antifúngica com halo de inibição variando entre 11 mm e 18 mm. As duas linhagens produtoras de metabólitos secundários com atividades antifúngicas não apresentaram diferença estatística, por isso foi selecionada a linhagem G24 por apresentar um pigmento na cor vermelha para dar seguimento às análises. A fermentação da linhagem (G24) foi realizada para avaliar atividade antifúngica, biomassa e pH, durante 5 dias, utilizando diferentes meios (MPE, M1 e ISP-3),sendo tais parâmetros monitorados a cada 24 horas. O melhor meio para produção de metabólitos secundários foi ISP-3 fermentado durante 48 h em pH 7.0, sendo evidenciados halos de inibição de 13 a 18 mm e biomassa de 0,1 g/mL de meio. Estabelecidas às condições, foi realizada a extração do princípio bioativo, sendo evidenciada atividade apenas para biomassa quando extraído em acetato de etila. A concentração mínima inibitória (CMI) do extrato bruto variou de 125 μg/mL a 62,5 μg/mL para Candida spp testadas. Análise Cromatográfica do Extrato Bruto as frações semi-purificadas foram analisadas por cromatografia em camada delgada (CCD) sendo evidenciadas duas frações, uma com atividade antifúngica e outra um corante natural. As características morfológicas do isolado G24 foram analisadas por microscopia óptica, sendo observados esporos verticilados pertencente ao gênero Streptomyces. O gene 16S rDNA foi amplificado e enviado para sequenciamento, sendo identificada como Streptomyces sp. Diante destes resultados, podemos concluir que a linhagem (Streptomyces sp), isolado da rizosfera de Caesalpinia pyramidalis tul, do bioma Caatinga, apresenta uma significativa atividade antifúngica e necessita de estudos espectroscópios para caracterização do composto bioativo e do corante. / Actinobacteria are forming Gram-positive bacteria of branched filaments that stand out for the production of secondary metabolites such as antibiotics, antitumor, phytohormones and naturias dyes. Given this, this study aimed to determine the biotechnological potential of actinomycetes of UFPEDA collection against Candida spp. To evaluate the biotechnological activity, 32 actinomycetes were tested against seven clinical isolates of Candida spp., Using different culture media (ALA, ISP-4, AY, ISP-3) and temperatures (37 ° C and 45 ° C). In the primary test, activity was detected only when the actinomycetes were grown in ISP-medium 3 to a temperature of 37 ° C. Of these, only 2 strains (6.25%) showed antifungal activity with inhibition zone ranging between 11 mm and 18 mm. Fermentation of strain (G24) was used to evaluate antifungal activity, biomass and pH for 5 days, using different media (MPE M1 and ISP-3), these parameters being monitored every 24 hours. The best medium for production of secondary metabolites ISP-3 was fermented for 48 h at pH 7.0, being evidenced inhibition zones 13 to 18 mm and biomass of 0.1 g / ml medium. Established conditions, the extraction of bioactive principle has been performed and demonstrated activity only when biomass extracted into ethyl acetate. The minimum inhibitory concentration (MIC) of the crude extract ranged from 125 mg / mL to 62.5 mg / mL for Candida spp tested. In chemical prospecting, semi-purified fractions were analyzed by thin layer chromatography (TLC) was evidenced two fractions, one with antifungal activity and one with a natural dye. The morphological characteristics of isolated G24 were analyzed by optical microscopy, observed verticilados spores belonging to the genus Streptomyces. The 16S rDNA gene was amplified and sent to sequencing, being identified as Streptomyces sp. Given these results, we can conclude that the line (G24) (Streptomyces sp), isolated from the rhizosphere of Caesalpinia pyramidalis tul, the Caatinga biome, presents a significant antifungal activity and requires spectroscopes studies to characterize the bioactive compound and the dye.

Orientador: Anita Jocelyne Marsaioli / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Quimica / Made available in DSpace on 2018-08-04T15:13:44Z (GMT). No. of bitstreams: 1 Costa_LuizAntonioMendoncaAlvesda_D.pdf: 24416441 bytes, checksum: bec02c6b51213d77af83bf869644c046 (MD5) Previous issue date: 2005 / Resumo: O presente trabalho foi dividido em dois projetos: a avaliação do potencial biocatalítico de microrganismos isolados da abelha Trigonna sp e o estudo de biorremediação de ambiente contaminado por Alachlor®. A atividade catalítica de oxidação de sulfeto e a hidrólise de éster sulfínico de 12 linhagens de fungos foi avaliada durante a primeira parte deste trabalho, dentre das quais, 8 linhagens foram isoladas do corpo da abelha Trigonna sp em trabalhos anteriores do nosso grupo. Os melhores microrganismos na oxidação enantiosseletiva do etil fenil sulfeto foram os Fungo CCT 5553 e Cladosporium sp. CBMAI 0210 que produziram o (S)-etil-fenil-sulfóxido (ee > 99%) e (R)-etil-fenil-sulfóxido (ee 97%), respectivamente. O (S)-etil-fenil-sulfóxido (ee > 92%) foi aplicado na síntese da S-(+)-4-metil-3-heptanona, feromônio de alarme da formiga do gênero Atta, mas uma racemização durante a eliminação do grupo sulfinila impossibilitou a síntese total. Para a resolução enzimática de (±)-benzenossulfinato de cicloexila foi selecionado os fungos Penicillium sp. CBMAI 0208 e Aspergillus ochraceus CBMAI 0211 ambos fornecendo os produtos com excessos enantioméricos > 99%. Na segunda etapa, avaliou-se a capacidade de degradação do pesticida Alachlor® de 6 linhagens de bactérias (Streptomyces sp.) e as estruturas dos produtos de degradação foram sugeridas baseados em seus padrões de fragmentação. Entre esses 8-etil-quinolina e N-metil-8-etil-indol nunca foram citados nos estudos de biodegradação do Alachlor®. / Abstract: The work presented in this thesis is divided into two projects: the evaluation of the biocatalytic potential of microorganisms isolated from Trigonna bee and those deposited in two brazilian collections and bioremediation of Alachlor contamined soil. The sulfide oxidation and sulfinic esters hydrolysis catalytic activity was screened using 12 different fungi strains, 8 of which were previously isolated from a Trigonna sp. bee. The best microorganisms for the enantioselective oxidation of ethyl phenyl sulfide were Fungus CCT 5553 and Cladosporium sp. CBMAI 0210 WHICH PRODUCED (R)-ethyl phenyl sulfoxide (ee 97%) and (S)-ethyl phenyl sulfoxide (ee > 99%) respectively. The chiral (S)-ethyl phenyl sulfoxide which was applied in the synthesis of S-(+)-4-methyl-3-heptanone, ant alarm pheromone (genus Atta), of but racemization during sulfinyl group elimination step precluded the total asymmetric synthesis. For the enzymatic resolution of the cyclohexyl (±)-benzenosulfinate we have selected Penicillium sp. CBMAI 0208 and Aspergillus ochraceus CBMAI 0211 both with the capacity of resolving the sulfinate in over 99 enantiomeric excess. In the second part, the Alachlor® degradation potential of 6 bacterium strains (Streptomyces sp.) was evaluated and the structures of biodegradation products were suggested based on their mass fragmentation patterns. Among these 8-ethyl-quinoline and N-methyl-8-ethyl-indole have never been mentioned as Alachlor biodegradation products before. / Doutorado / Quimica Organica / Doutor em Quimica

Though this current study was initiated independently and was not a test laboratory for the taxonomic sub-committee's evaluative program, the problem outlined in this treatise was also designed in an effort to test certain characteristics of the actinomycetes of both a biochemical and morphological nature. This problem employed methods that might absolve or establish certain criteria for taxonomic use in the group of actinomycetes.

Os actinomicetos são bactérias Gram positivas caracterizadas por sua habilidade em formar hifas, são amplamente distribuídos no ambiente e conhecidos pela diversidade na produção de moléculas biologicamente ativas. O presente trabalho teve por objetivo avaliar a atividade de compostos produzidos por quarenta isolados de actinomicetos contra isolados clínicos de Enterococcus sp, Staphylococcus aureus e Staphylococcus epidermidis. O perfil de suscetibilidade das amostras clínicas foi avaliado empregando a técnica de disco difusão em ágar. A atividade antimicrobiana dos actinomicetos foi avaliada pela técnica da dupla camada. Os isolados que apresentaram atividade foram cultivados em caldo amido caseína à temperatura de 30ºC por sete dias, com agitação constante. Após o crescimento, a cultura foi filtrada para obtenção do extrato bruto. A atividade antibiótica do extrato foi avaliada através da técnica de difusão em poço. O isolado que apresentou maior espectro de ação foi selecionado para otimização dos compostos. A otimização da produção dos compostos com atividade antibiótica foi realizada através da avaliação de curva de produção, variação da fonte de carbono, tempo de incubação, pH tamponado e pH não tamponado. No ensaio de sobrecamada os isolados 50 e 8S apresentaram atividade contra a 90% das amostras de microrganismos clínicos de Staphylococcus sp. e Enterococcus sp. No ensaio de difusão em poço o isolado 50 apresentou maior atividade antibiótica que o isolado 8S. Na otimização do extrato as melhores condições de produção foram: 72 h de crescimento, fonte de carbono amido e sem tamponamento de pH. Não foi observada influência de biomassa na produção dos compostos. A cromatografia em camada delgada revelou a presença de duas bandas com fator de retenção de 0,28 (Rf1) e 0,57 (Rf2). / Actinomycetes are Gram positive bacteria, characterized by their ability to form hyphae. They are widely distributed in the environment and known for their diversity in producing biological active molecules. This study aimed to evaluate the activity of compounds produced by forty isolates of Actinomycetes against clinical isolates of Enterococcus sp, Staphylococcus aureus and Staphylococcus epidermidis. The susceptibility profile of the samples was evaluated using the disk diffusion technique in agar. The antimicrobial activity of actinomycetes was assessed by means of the double layer. Isolates that showed activity were grown in starch casein broth at a temperature of 30 ºC for seven days, with constant agitation. After growth the culture was filtered to obtain a crude extract. The antimicrobial activity of the extract was evaluated by the well diffusion technique. The actinomycete that showed activity against most of the test samples was selected for optimization(s) of the compound(s) production. The optimization of the production was performed by evaluating: growth curve, the use of different carbon source, changes in the incubation time, and culture media with buffered and unbuffered pH. In the overlay assay isolates 50 and 8S presented activity against most of Staphylococcus sp. and Enterococcus sp samples. In diffusion assay isolate 50 showed higher antibiotic activity than the isolated 8S. Compiling the results the best production conditions were: 72 h of growth, carbon source starch without pH buffering at 30°C. There was no effect of biomass (s) compound (s) activity. The thin layer chromatography revealed the presence of two bands with a retention factor of 0.28 (Rf1) and 0.57 (Rf2).

Philosophiae Doctor - PhD / Actinobacteria, a Gram-positive phylum of bacteria found in both terrestrial and aquatic environments, are well-known producers of antibiotics and other bioactive compounds. The isolation of actinobacteria from unique environments has resulted in the discovery of new antibiotic compounds that can be used by the pharmaceutical industry. In this study, the fynbos biome was identified as one of these unique habitats due to its rich plant diversity that hosts over 8500 different plant species, including many medicinal plants. In this study two medicinal plants from the fynbos biome were identified as unique environments for the discovery of bioactive actinobacteria, Aloe ferox (Cape aloe) and Sutherlandia frutescens (cancer bush).

The need for new antibiotics and other biologically active compounds is the reason for an increased interest in secondary metabolites of soil bacteria. The phylum Actinobacteria has the dominant position in the soil environment thanks to the potential of producing a broad spectrum of antibiotics and the presence of a number of defense mechanisms preventing the effects of antibiotics. The aim of this thesis was to determine the number of copies of selected secondary metabolic genes in the soils of two sites using designed primers and primers from literature. The design of effective new primers for the detection of selected genes in the soil environment was not achieved in this work, and therefore only primers from literature that had been verified for their specificity were used. In samples taken from soil profiles of two sites, abundances of bacteria, actinobacteria, type II polyketide synthase genes and Erm methyltransferase genes mediating resistance to MLSB antibiotics (macrolides, lincosamides and streptogramins B) were determined by digital PCR. The comparison of the determined copy numbers gave an information about the structure of the bacterial community and the relative abundance of bacteria carrying selected secondary metabolic genes depending on the soil condition changes due to the...

Ensyeh Sarikhani Soil microbial communities in agroecosystems and natural habitats contributing to resistance and resilience of the soil environment. Summary The control of common scab of potatoes (CS) includes resistant varieties (cultivars), precise fertilization, increase of soil moisture, and chemical treatments. Yet, these management practices do not have common or reproducible results at differing sites. A monitoring study was done in 32 sites to evaluate the relation between CS and biological/chemical soil parameters. Correlations were observed between scab severity and content of nutrients such as Fe, N, and Ca in soil and periderm, and between disease severity and abundance of actinobacteria and total bacteria, together with the pathogenicity determinant, txtB gene (biosynthetic gene of thaxtomin) in both soil and periderm of potatoes. The findings led to novel conclusions, which can help to understand relationships applicable in scab control. Peat and DTPA chelated iron were supplemented to pots filled with soil conducive for CS in order to determine the effects of soil organic matter, iron and pH on CS development. The results were compared with data obtained for a suppressive soil from a nearby field with naturally low CS severity. Both peat and iron supplements decreased CS and the combination...

Marineosins A and B are two spiroaminal-ring containing tripyrrole compounds isolated from the marine actinomycete, Streptomyces CNQ-617, and were found to possess potent and selective cytotoxic activity against leukemia and melanoma. Marineosins belong to the prodiginines class of natural products, examples of which are undecylprodiginine and streptorubin B. Unlike marineosins, prodiginines structures are characterized by the presence of fully conjugated tripyrrole nucleus linked to an alkyl chain (that lacks any oxygen). Cyclic prodiginines arise from an oxidative cyclization of the alkyl chain onto the tripyrrole, a step catalyzed by Rieske-oxygenase like enzymes such as RedG. The biosynthesis of prodiginines is directed via the red gene cluster. The unique structural differences between marineosin and other prodiginines spurred the proposal of a number of hypotheses for its biosynthesis, none of which have been experimentally tested. A red gene cluster homolog which has only one extra dehydratase-encoding gene; marA has been identified from the genomic library of Streptomyces CNQ-617, and the identified cluster was proposed to direct the biosynthesis of marineosin. In this study, the identified putative gene cluster was expressed in the heterologous host, S. venezuelae, and marineosin production in the new strain; JND2 was confirmed via LC/MS and 1H-NMR. The new engineered strain also produces a myriad of marineosin related shunt metabolites and pathway intermediates. This study hence presents the first identified gene cluster proved to direct the biosynthesis of marineosin; the mar gene cluster and proves that the cloned cluster encodes most, if not all the enzymes required to direct the biosynthesis of marineosin. Deletion of the Rieske-oxygenase encoding gene; marG (a RedG homolog) from the mar gene cluster led to the accumulation of 2-hydroxyundecylprodiginine; G410 with an m/z 410.28 and molecular formula C25H35O2N3. This data proves that MarG is not responsible for the introduction of the spiromaminal ring oxygen on the alkyl chain, but is required for catalyzing macrocyclic ring formation between C-8 and C-9 of G410. Undecylprodiginine production in marG deletion mutant was not observed which indicates that undecylprodiginine is likely not an intermediate along the pathway for marineosin biosynthesis, and indicates that the spiroaminal ring oxygen is introduced early in the pathway, possibly due to the incorporation of a 3-hydroxy-butyric acid starter unit. Deletion of the dehydratase-encoding gene; marA, from the mar gene cluster led to the accumulation of compounds JN408 and JN422 with m/z 408.26 and 422.24 and molecular formulae C25H33O2N3, and C25H31O3N3, respectively. Purification and structure elucidation of JN408 proves it to be an oxidized marineosin analog which has fully aromatic tripyrrole rings while; purification and structure elucidation of JN422 proves it to be a 9-keto-JN408 derivative. Both JN408 and JN422 compounds have a spiroaminal ring which indicates that MarA does not catalyze spiroaminal ring formation but catalyzes the reduction of pyrrole ring B of JN408 to yield marineosin. Therefore, we are proposing that MarA acts as a dehydrogenase, rather than a dehydratase. We are proposing that the intramolecular spiroaminal ring formation is catalyzed by either MarG or occurs non-enzymatically. JN422 is a shunt metabolite produced due to promiscuous activity of either MarG or an unidentified oxidase in the mar cluster, possibly MarT. From the data generated in this study, we present the first experimentally supported pathway for the biosynthesis of marineosin and the opportunity to generate novel compounds with potentially useful biological activities.

Indiana University-Purdue University Indianapolis (IUPUI) / Taste-and-Odor (T&O) occurrences are a worldwide problem and can locally have extensive socio-economic impacts in contaminated waterbodies. Tracing odorous compounds in surface waters or controlling the growth of producing organisms is particularly challenging. These approaches require the understanding of complex interactions between broad climate heterogeneity, large-scale physical processes such basin hydrology, lake/reservoir circulation, responses of aquatic ecosystems and communities. Eagle Creek Reservoir (ECR), a eutrophic water body, located in central Indiana experiences annual odorous outbreaks of variable durations and intensities that can impair its water quality. Two major compounds, 2-methylisoborneol and geosmin, have been identified as the main culprits occurring seasonally when the reservoir receives high discharges and nutrient loads from its main tributaries. Under these conditions, the growth of T&O-producing bacteria tends to take over other phytoplanktic organisms. Discrete samples collected within the water column during severe outbreaks in 2013 revealed that some bacterioplankton members belonging to Actinobacteria (Streptomyces) and Cyanobacteria (Planktothrix) were involved in the generation of T&O compounds. Most of this production occurred in the upper layers of the water column where higher abundances of key enzymes from MIB and geosmin metabolic pathways were detected. Application of a copper-based algaecide to curb the biosynthesis of bacterial metabolites led to geosmin production (linked to Cyanobacteria) being quickly terminated, whereas MIB levels (linked to Actinobacteria) lingered for several weeks after the algaecide treatment. Significant chemical differences in the association of these metabolites were measured in ECR. Geosmin was dominantly found cell-bound and settling after cellular death increases susceptibility to biodegradation in bottom sediments. MIB was mostly found dissolved making it less susceptible to biodegradation in bottom sediments. Genetic data identified Novosphingobium hassiacum and Sphingomonas oligophenolica (α- Proteobacteria) as potential degraders of geosmin and, four Flavobacterium species (Bacteroidetes) as potential MIB degraders. The role of Eagle Creek natural sediments in the removal of bacterial metabolites via chemical adsorption was also tested but was not proven efficient. Bacterial breakdown activity was demonstrated to be the major loss mechanism of MIB and geosmin.

Made available in DSpace on 2016-06-02T20:21:29Z (GMT). No. of bitstreams: 1 4330.pdf: 9783641 bytes, checksum: d254809e566158ecf10125a852fbdafa (MD5) Previous issue date: 2012-11-07 / Financiadora de Estudos e Projetos / The Amazon region has the largest hydrographic basin on the planet, the one that includes Amazon River, and it also has the largest rainforest in the world. Moreover, it presents a great biological diversity, both related to the fauna and flora, and microbiological. Microorganisms are responsible for most biogeochemical cycles that shape the terrestrial environment and the freshwater and marine ecosystems, and they can be widely exploited biotechnologically. It is estimated that less than 1% of all bacterial species is known due to our inability to simulate the environment in which they live. However, new techniques have allowed the study of these microorganisms. Through Metagenomics it is possible to study complex environmental samples without the need for isolation and individual cultivation of these organisms. For this purpose, the16S ribosomal DNA (16S rDNA) is used in bacteria and archaea in order to study phylogeny and diversity. This sequence is used because it has been fairly maintained during the processes of biological evolution and it may serve as an indicator of how organisms are closely related. For these studies, this region was amplified by the Polymerase Chain Reaction (PCR) and cloned into vectors through the recombinant DNA technology, thus enabling the construction of 16S rRNA libraries. These libraries were then sequenced and the microorganisms were identified by comparison with databases. In this study it was used DNA extracted from Solimões River filtered water, in addition to water from other rivers and adjacent lakes, to the construction of libraries, in order to study the biodiversity through 16S rRNA analysis. In all libraries, phylum Proteobacteria was the most abundant, and most of the genera observed belong to the Betaproteobacteria class. The freshwater cosmopolitan taxa Candidatus Planktophila limnetica and Polynucleobacter were observed, as well as primary producers were represented by the genera Synechococcus and Cyanobium. Samples in which the construction of 16S rRNA libraries was possible for Archaea, the phylum Crenarchaeota was the most abundant in all libraries. / A Região Amazônica apresenta a maior bacia hidrográfica do planeta, a do rio Amazonas, e também a maior floresta tropical do mundo. Além disso, apresenta uma grande diversidade biológica, tanto relacionada à fauna e flora, quanto microbiológica. Os micro-organismos são responsáveis pela maioria dos ciclos biogeoquímicos que moldam o ambiente terrestre e os ecossistemas de água doce e marinhos, e podem ser amplamente explorados biotecnologicamente. Estima-se que menos de 1% de todas as espécies bacterianas seja conhecida, devido à incapacidade de simulação do ambiente em que vivem. Contudo, novas técnicas têm possibilitado o estudo desses micro-organismos. Através do Metagenoma é possível estudar amostras ambientais complexas sem a necessidade de isolamento e cultivo individual desses organismos. Para tanto, utiliza-se, em bactérias e arquéias, o DNA ribossomal 16S (16S rDNA), para fins de estudos de filogenia e diversidade. Esta sequência é utilizada por se ter mantido bastante conservada durante os processos de evolução biológica, podendo servir como um indicador de como os organismos estão intimamente relacionados. Para estes estudos, esta região foi amplificada pela Reação em Cadeia da Polimerase (PCR) e clonada em vetores através da tecnologia do DNA recombinante, possibilitando, assim, a construção de bibliotecas de 16S rRNA. Estas bibliotecas foram então sequenciadas e os micro-organismos identificados por comparação com bancos de dados. Neste trabalho foi utilizado DNA extraído de filtrados de água do Rio Solimões, além de outros rios e lagos adjacentes, para construção de bibliotecas, com a finalidade de estudar a biodiversidade por meio de análise do 16S rRNA. Em todas as bibliotecas o filo Proteobacteria foi o mais abundante, e a maioria dos gêneros observados pertence à classe Betaproteobacteria. Os taxa cosmopolitas de água doce Candidatus Planktophila limnetica e Polynucleobacter foram observados, assim como os produtores primários foram representados pelos gêneros Synechococcus e Cyanobium. Nas amostras em que a construção das bibliotecas de 16S rRNA foi possível para Archaea, obteve-se o filo Crenarchaeota como o mais abundante em todas as bibliotecas.