Submitted by Sandra Pereira (srpereira@ufrrj.br) on 2016-10-17T16:03:22Z No. of bitstreams: 1 2015 - Paula Cardoso de Almeida Silva.pdf: 2121155 bytes, checksum: b827c0e7a20bdec7ae36fca85e2c8455 (MD5) / Made available in DSpace on 2016-10-17T16:03:22Z (GMT). No. of bitstreams: 1 2015 - Paula Cardoso de Almeida Silva.pdf: 2121155 bytes, checksum: b827c0e7a20bdec7ae36fca85e2c8455 (MD5) Previous issue date: 2015-11-06 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior - CAPES / Embryo transfer and other biotechnologies are intensivelyused for equine reproduction and other species as well. Even though there is an expansion of the mule market and an increase in the number of animals, researches working with reproduction of these animals are still scarce. The aim of this study was to evaluate aspects of embryo transfer, embryo morphology and gender identification of hybrid (horses x donkeys) embryos, checking either their similarity or divergence with the characteristics already known of equine embryos. Attempts of embryo collection on Day 6 -9 after OV were performed in mares previously bred with a P?ga donkey. The embryo recovery rates, the characteristics related to age, morphology and embryonic diameter were evaluated. After these assessments, a group of embryos was cut using an adapted technique, where, the cutting process was carried out with the aid of an ophthalmic scalpel blade. The resulting biggest cut portion was used for embryo transfer, and the smallest parts and the others whole embryos to determination of the embryo gender. Data were analyzed using Fisher's exact test, with 5% significance, except the daily growth of embryos, which was analyzed by linear regression. The overall embryo recovery rate was 55,9% (71/127), and for each group D6, D7, D8 and D9, was 57,1% (28/49), 51% (25/49), 63% (15/24) 60% (3/5), respectively. The developmental stage of the collected embryos were, morula: 18.3% (13/71); early blastocysts: 26,8% (19/71); blastocyst: 29,6% (21/71); and expanded blastocysts: 25,3% (18/71). The measured diameter revealed that the size of the embryos ranged from 147 to 1688?m, the mean diameter of all collected embryos was 438,04?m, and according to different groups, the average size (smallest and largest diameter) of embryos were D6 (n = 29) - 183,4?m (147 - 253?m), D7 (n = 24) - 463,2?m (168 - 886?m), D8 (n = 15) - 727,2?m (422 - 1224?m ) and D9 (n = 3) - 1350,6?m (844 - 1688?m), and daily growth rate was 312,7?m. After the section, the 23 embryos were transfered, only one recipient mare was diagnosed as pregnant at 15 days after ovulation, however after 30 days the embryo was lost. The efficiency of the sex identification by PCR using the primers SRY and ZFX / ZFY was 85,9% (61/71), being 55,7% (34/61) determined as female: and 39,3% (27/61) as male. Embryo transfer has shown to be favorable to aid mule reproduction, whereas the recovery rate and the characteristics of the embryos are similar to equine embryos. Altough, the methodology used to section of embryos had unable the gestational development, the most part of the biopsy derived cutting allowed sexing of the embryos / A transfer?ncia de embri?es e outras biotecnologias reprodutivas s?o cada vez mais utilizadas para a produ??o de equinos e de outros animais, entretanto, mesmo com a expans?o do mercado de muares e com crescimento do n?mero de animais, as pesquisas relacionadas com a produ??o desses animais ainda s?o raras. O presente estudo avaliou as caracter?sticas relacionadas ? transfer?ncia de embri?es, a morfologia e a identifica??o do sexo de embri?es h?bridos (muares), verificando sua semelhan?a ou diverg?ncia com as caracter?sticas j? conhecidas em equinos. Foram realizadas colheitas de embri?es provenientes do cruzamento de ?guas com um jumento P?ga, nos dias 6, 7, 8 e 9 ap?s a ovula??o, a taxa de recupera??o embrion?ria, e as caracter?sticas relacionadas com a idade, morfologia e di?metro embrion?rio foram avaliadas para os diferentes dias. Ap?s essas avalia??es, uma parte dos embri?es coletados foi seccionada, com uma t?cnica adaptada onde o corte foi realizado com o aux?lio de uma l?mina de bisturi oftalmol?gico. A maior por??o resultante do corte foi destinada para transfer?ncia de embri?es e a menor parte, juntamente com os embri?es inteiros, foram utilizados para verificar a efici?ncia dos primers SRY e ZFX/ZFY, na an?lise molecular para a determina??o do sexo dos embri?es. Os dados foram analisados pelo teste Exato de Fisher, com 5% de signific?ncia, exceto o crescimento di?rio dos embri?es que foi analisado atrav?s da regress?o linear. A taxa de recupera??o embrion?ria total foi de 55,9% (71/127), e para os diferentes dias de colheita D6, D7, D8 e D9, foi 57,1% (28/49), 51% (25/49), 63% (15/24), 60% (3/5), respectivamente. Os embri?es coletados apresentavam-se nos seguintes est?gios de desenvolvimento, m?rulas: 18,3% (13/71); blastocistos iniciais: 26,8% (19/71); blastocistos: 29,6% (21/71); e blastocistos expandidos: 25,3% (18/71). O di?metro mensurado revelou que o tamanho dos embri?es variou entre 147 - 1688?m, a m?dia do di?metro de todos os embri?es recolhidos foi de 438,04?m, e de acordo com os diferentes dias de colheita, o tamanho m?dio (maior e menor di?metro) dos embri?es foi de: D6 (n = 29) ? 183,4?m (147 - 253?m), D7 (n = 24) ? 463,2?m (168 - 886?m), D8 (n = 15) ? 727,2?m (422 - 1224?m) e D9 (n = 3) ? 1350,6?m (844 ? 1688?m), e a taxa de crescimento di?ria foi de 312,7?m. Ap?s a sec??o e transfer?ncia de 23 embri?es, apenas uma receptora foi diagnosticada como gestante aos 15 dias, mas aos 30 dias, o embri?o tinha sido absorvido. A identifica??o do sexo atrav?s da t?cnica de PCR, utilizando os primers SRY e ZFx/ZFy foi de 85,9% (61/71), sendo determinado f?meas: 55,7% (34/61) e machos: 39,3% (27/61). A transfer?ncia de embri?es ? favor?vel para auxiliar na produ??o de muares, a taxa de recupera??o e as caracter?sticas dos embri?es s?o semelhantes aos embri?es equinos. A metodologia de sec??o dos embri?es, inviabilizou o desenvolvimento gestacional, entretanto a biopsia oriunda do corte permitiu a sexagem da maioria dos embri?es coletados.

Der probiotische Stamm E. coli Nissle 1917 ist ein Fäkalisolat, das in der Medizin traditionell zur Behandlung verschiedener gastrointestinaler Erkrankungen eingesetzt wird. Durch erfolgversprechende klinische Studien zur Remissionserhaltung bei Colitis ulcerosa, bei denen EcN als therapeutische Alternative zur Standardmedikation eingesetzt wird, ist das Interesse an den Wirkmechanismen von Probiotika stark gestiegen. EcN gehört derzeit zu den am besten untersuchten Probiotika. Einige Wirkmechanismen konnten dadurch schon aufgeklärt werden. So sind vermutlich Strukturkomponenten und stammspezifische Syntheseleistungen an der Ausprägung des probiotischen Phänotyps von EcN beteiligt. Schlüssige Konzepte, die über Gene, Genprodukte und molekulare Mechanismen den probiotischen Effekt von EcN erklären, fehlen bislang. Im Rahmen dieser Arbeit wird das Genom von EcN analysiert und auf der Basis der Genomsequenz mit anderen E. coli-Stämmen verglichen. Mit Hilfe einer Promotor-Reporter-Fusionsbibliothek (Promotorbank) werden intestinal in vivo regulierte Gene identifiziert und dadurch neue Ansätze zur Untersuchung der probiotischen Eigenschaften von EcN geschaffen. Die Grundlage für die molekulare Analyse von EcN ist die manuelle Nachannotation seines sequenzierten Genoms. Die EcN-Sequenz wird mit 13 weiteren annotierten E. coli-Sequenzen verglichen. Nach dieser Analyse kodiert EcN derzeit 121 stammspezifische Gene. Die Genomstruktur ist mit den enthaltenen genomischen Inseln und Prophagen dem Genom des uropathogenen E. coli CFT073 sehr ähnlich. Mit wenigen Ausnahmen kodiert EcN alle in E. coli CFT073 vorhandenen Virulenz- und Fitnessfaktoren, so dass auf der Nukleotidebene die nahe Verwandschaft dieser beiden Stämme bestätigt werden kann. Zudem kann gezeigt werden, dass EcN in artifiziellen Systemen wie der Zellkultur oder gnotobiotischen Mäusen ein pathogenes Potenzial hat, obgleich die Kolonisierungsfähigkeit pathogener Bakterien durch Inkubation mit EcN herabgesetzt wird. Eine wichtige Rolle bei der Besiedlung des Intestinaltrakts und der Immunstimulation von Darmepithelzellen spielt auch die globale Regulation der Genaktivität bei EcN durch den alternativen Sigma-Faktor RpoS, der im Gegensatz zu rpoS-Deletionsmutanten zu einer gesteigerten mRNA-Expression des Tight-junction Proteins ZO-1 führt. Des Weiteren führte die Untersuchung von EcN-Deletionsmutanten zu der Schlussfolgerung, dass einige genomische Inseln für Eigenschaften, die das probiotische Verhalten erklären können, eine Rolle spielen. Durch den Einsatz einer Promotorbank von EcN in konventionellen und gnotobiotischen Mäusen werden erstmalig Sequenzen von intestinal in vivo aktiven Promotoren identifiziert. Der Aufbau eines Promotor-Reportergen-Assays mit dem Biolumineszenz erzeugenden luxCDABE-Operon ermöglichte die Untersuchung ausgewählter Promotoren in vitro. Mit einem In Vivo Imaging System (IVIS) kann in weiteren Experimenten die Aktivität dieser Promotoren in lebenden Mäusen untersucht werden. Im Rahmen dieser Arbeit wird gezeigt, dass EcN kein vollkommen harmloser probiotischer Stamm ist. Weitere Informationen über EcN sind dehalb wichtig für eine optimierte Anwendung als Therapeutikum. Die molekulare Analyse ist somit eine unbedingt notwendige Grundlage für weiterführende Untersuchungen der Eigenschaften von EcN, die für seinen probiotischen Charakter verantwortlich sind. / The probiotic E. coli Nissle 1917 is a fecal isolate which is traditionally used for treatment of various gastrointestinal disorders. In clinical trials where EcN was used as therapeutic alternative for remission maintenance of ulcerative colitis compared to standard medication, promising results led to an increased interest in probiotics. Today, EcN is one of the best studied probiotics. Therefore, several mechanisms of action could be enlightened. Structural components and strain-specific products are responsible for its probiotic effects. But conclusive concepts about genes, gene products and molecular mechanisms that really contribute to the probiotic character of EcN have not been offered so far. In order to create new possibilities to elucidate the probiotic traits of EcN the genome is analysed by taking this as a basis for comparison to other E. coli genomes and identification of intestinal in vivo regulated genes using a promoter-trap-library. The sequenced EcN genome is annotated and compared to 13 other so far annotated E. coli genomes. Concerning these analyses EcN encodes 121 strain-specific genes. The genome structure including the genomic islands and prophages is highly homolog to the uropathogenic E. coli CFT073. EcN encodes most of the virulence and fitness factors that are present in E. coli CFT073. Therefore, the close relationship of these two strains is confirmed at nucleotide level. Furthermore, it is shown that in artificial systems like cell culture assays and gnotobiotic mice EcN reveals a pathogenic potential although EcN is able to decrease colonization efficiency of pathogenic bacteria. The alternative sigma factor RpoS that is responsible for global regulation and activity of several genes seems to play an important role during colonization of EcN in the intestine and its immunostimulatory effects on intestinal epithelial cells. Investigation of EcN-deletion mutants lacking genomic islands and prophages lead to the conclusion that some genomic islands may play a role for specific probiotic traits. This is the first time where a promoter-trap-library was used in conventional and gnotobiotic mice for collection of intestinal in vivo active promoters. Constructing and establishing a promoter-reporter gene assay with the bioluminescent luxCDABE operon made the investigation of selected promoters in vitro possible as well as establishing a bioluminescence assay using an In Vivo Imaging System (IVIS) for investigation of promoter activity in living mice. In this research project was shown that EcN is not a completely harmless probiotic. The genome structure and regulatory mechanisms of gene expression are the strain’s molecular traits that lead to probiotic activity and immunostimulatory effects. Therefore, the molecular analyses presented here, together with the complete genome sequence, are a basis for further investigations of mechanisms that are responsible for the probiotic effects of EcN.

Thesis (MSc)--Stellenbosch University, 2009. / ENGLISH ABSTRACT: Biotechnological applications are useful for adding value to the local medicinal plants and may provide an alternative source of pharmacologically-active compounds thus assisting with the conservation of wild populations. Salvia africana-lutea aromatic herb has long been used in folk medicine by traditional healers in the Western Cape Province (South Africa) for various ailments. As an in vitro conservation strategy, a continuous S. africana-lutea shoot culture was successfully established in solid MS medium containing BA (0.5 mg L-1) and NAA (0.2 mg L-1). The regeneration rate of the S. africana-lutea plants was high which produced approximately 720 plantlets in 20 culture bottles over a four week cycle. The microshoots were rooted in the MS medium without PGRs prior to acclimatisation. A survival rate of 92% was recorded for the greenhouse-acclimatised shoots. / AFRIKAANS OPSOMMING: Biotegnologiese toepassings is nuttig vir waarde toevoeging tot inheemse medisinale plante en kan ‘n alternatiewe bron van farmakologies aktiewe verbindings verskaf wat bydrae tot die bewaring van populasies in die natuur. Die aromatiese krui Salvia. Africana-lutea is reeds vir ‘n lang tydperk in volks medisyne deur tradisionele geneesheers in die Wes Kaap provinsie (Suid Afrika) vir ‘n verskeidenheid kwale gebruik. ‘n Kontinu S. africana-lutea lootkultuur in soliede Murashige en Skoog (1962) (MS) media wat BA (0.5 mg L-1) en NAA (0.2 mg L-1) bevat, is suksesvol as ‘n in vitro konservasie strategie ontwikkel. Die regenerasie tempo van die S. africana-lutea plante was hoog en het ongeveer 720 plante in 20 kultuur bottels tydens ‘n vier week siklus gelewer. Die mikrolote is op plant groei reguleerder vrye MS media gewortel voordat plante geaklimatiseer is. ’n Oorlewingstempo van 92% is vir die glashuis geaklimatiseerde lote waargeneem.

Les matières organiques dissoutes (MOD), en tant que sources de nutriments ou potentiels vecteurs de pollution, sont impliquées dans de nombreuses problématiques environnementales. Bien qu'elles fassent l'objet de nombreuses études depuis plusieurs décennies, les mécanismes gouvernant leur solubilisation et leur transfert depuis les sols vers les systèmes aquatiques demeurent sujets à discussion. En s'appuyant sur l'étude de la composition moléculaire des MOD par hydrolyse et méthylation assistée par température et couplée à la chromatographie en phase gazeuse et à la spectrométrie de masse (HMT-CPG-SM), cette thèse a pour objectif d'apporter une meilleure compréhension de leurs mécanismes de solubilisation et de transfert à l'échelle d'un bassin versant agricole. Ce travail s'est appuyé sur le bassin versant expérimental de Kervidy-Naizin (Morbihan, Observatoire de Recherche en Environnement AgrHys) afin d'observer les processus mis en jeux à deux échelles temporelles différentes. A l'échelle de la crue, ce travail a permis de préciser l'impact des conditions hydrologiques spécifiques sur la dynamique des MOD. A l'échelle annuelle, l'utilisation conjointe de la signature isotopique du carbone (δ13C) et de la composition moléculaire des MOD a permis de préciser les mécanismes de transfert de MOD impliqués à l'échelle du versant. L'utilisation de la HMT-CPG-SM s'est avéré un outil adéquat pour l'étude de la dynamique des MOD. L'ensemble des résultats ainsi obtenus ont permis de souligner l'importance des conditions hydrologiques et en particulier de la dynamique de nappe dans les processus de solubilisation et de transfert des MOD. / Dissolved organic matter (DOM), as sources of nutrient or pollutant dissemination pathway are implied in numerous environmental issues. Although DOM have been the subject of numerous studies for several decades, the mechanisms implied for their solubilization and their transport from soils to aquatic systems are still a matter of discussion. Based on DOM molecular composition determined using thermally assisted hydrolysis and methylation –gas chromatography – mass spectrometry (THM-GC-MS), this thesis aims to provide a better understanding of their solubilization and transfer mechanisms at the scale of an agricultural headwater catchment. This work was conducted on the experimental headwater catchment of Kervidy-Naizin (France, Environmental Research Observatory AgrHys) in order to determine the processes implied at two temporal scales. At the scale of a rain event, this work has clarified the impact of hydrological conditions on the DOM dynamics. At annual scale, the use of carbon isotope signature (δ13C) and DOM molecular composition allowed to clarify the DOM transfer mechanisms at the slope scale. The use of THM-GC-MS appears to be a suitable tool for the study of DOM dynamics. The results thus obtained allowed to highlight the role of hydrological conditions and in particular the water-table level in the solubilization and transfer of DOM.

Der probiotische Stamm E. coli Nissle 1917 ist ein Fäkalisolat, das in der Medizin traditionell zur Behandlung verschiedener gastrointestinaler Erkrankungen eingesetzt wird. Durch erfolgversprechende klinische Studien zur Remissionserhaltung bei Colitis ulcerosa, bei denen EcN als therapeutische Alternative zur Standardmedikation eingesetzt wird, ist das Interesse an den Wirkmechanismen von Probiotika stark gestiegen. EcN gehört derzeit zu den am besten untersuchten Probiotika. Einige Wirkmechanismen konnten dadurch schon aufgeklärt werden. So sind vermutlich Strukturkomponenten und stammspezifische Syntheseleistungen an der Ausprägung des probiotischen Phänotyps von EcN beteiligt. Schlüssige Konzepte, die über Gene, Genprodukte und molekulare Mechanismen den probiotischen Effekt von EcN erklären, fehlen bislang. Im Rahmen dieser Arbeit wird das Genom von EcN analysiert und auf der Basis der Genomsequenz mit anderen E. coli-Stämmen verglichen. Mit Hilfe einer Promotor-Reporter-Fusionsbibliothek (Promotorbank) werden intestinal in vivo regulierte Gene identifiziert und dadurch neue Ansätze zur Untersuchung der probiotischen Eigenschaften von EcN geschaffen. Die Grundlage für die molekulare Analyse von EcN ist die manuelle Nachannotation seines sequenzierten Genoms. Die EcN-Sequenz wird mit 13 weiteren annotierten E. coli-Sequenzen verglichen. Nach dieser Analyse kodiert EcN derzeit 121 stammspezifische Gene. Die Genomstruktur ist mit den enthaltenen genomischen Inseln und Prophagen dem Genom des uropathogenen E. coli CFT073 sehr ähnlich. Mit wenigen Ausnahmen kodiert EcN alle in E. coli CFT073 vorhandenen Virulenz- und Fitnessfaktoren, so dass auf der Nukleotidebene die nahe Verwandschaft dieser beiden Stämme bestätigt werden kann. Zudem kann gezeigt werden, dass EcN in artifiziellen Systemen wie der Zellkultur oder gnotobiotischen Mäusen ein pathogenes Potenzial hat, obgleich die Kolonisierungsfähigkeit pathogener Bakterien durch Inkubation mit EcN herabgesetzt wird. Eine wichtige Rolle bei der Besiedlung des Intestinaltrakts und der Immunstimulation von Darmepithelzellen spielt auch die globale Regulation der Genaktivität bei EcN durch den alternativen Sigma-Faktor RpoS, der im Gegensatz zu rpoS-Deletionsmutanten zu einer gesteigerten mRNA-Expression des Tight-junction Proteins ZO-1 führt. Des Weiteren führte die Untersuchung von EcN-Deletionsmutanten zu der Schlussfolgerung, dass einige genomische Inseln für Eigenschaften, die das probiotische Verhalten erklären können, eine Rolle spielen. Durch den Einsatz einer Promotorbank von EcN in konventionellen und gnotobiotischen Mäusen werden erstmalig Sequenzen von intestinal in vivo aktiven Promotoren identifiziert. Der Aufbau eines Promotor-Reportergen-Assays mit dem Biolumineszenz erzeugenden luxCDABE-Operon ermöglichte die Untersuchung ausgewählter Promotoren in vitro. Mit einem In Vivo Imaging System (IVIS) kann in weiteren Experimenten die Aktivität dieser Promotoren in lebenden Mäusen untersucht werden. Im Rahmen dieser Arbeit wird gezeigt, dass EcN kein vollkommen harmloser probiotischer Stamm ist. Weitere Informationen über EcN sind dehalb wichtig für eine optimierte Anwendung als Therapeutikum. Die molekulare Analyse ist somit eine unbedingt notwendige Grundlage für weiterführende Untersuchungen der Eigenschaften von EcN, die für seinen probiotischen Charakter verantwortlich sind. / The probiotic E. coli Nissle 1917 is a fecal isolate which is traditionally used for treatment of various gastrointestinal disorders. In clinical trials where EcN was used as therapeutic alternative for remission maintenance of ulcerative colitis compared to standard medication, promising results led to an increased interest in probiotics. Today, EcN is one of the best studied probiotics. Therefore, several mechanisms of action could be enlightened. Structural components and strain-specific products are responsible for its probiotic effects. But conclusive concepts about genes, gene products and molecular mechanisms that really contribute to the probiotic character of EcN have not been offered so far. In order to create new possibilities to elucidate the probiotic traits of EcN the genome is analysed by taking this as a basis for comparison to other E. coli genomes and identification of intestinal in vivo regulated genes using a promoter-trap-library. The sequenced EcN genome is annotated and compared to 13 other so far annotated E. coli genomes. Concerning these analyses EcN encodes 121 strain-specific genes. The genome structure including the genomic islands and prophages is highly homolog to the uropathogenic E. coli CFT073. EcN encodes most of the virulence and fitness factors that are present in E. coli CFT073. Therefore, the close relationship of these two strains is confirmed at nucleotide level. Furthermore, it is shown that in artificial systems like cell culture assays and gnotobiotic mice EcN reveals a pathogenic potential although EcN is able to decrease colonization efficiency of pathogenic bacteria. The alternative sigma factor RpoS that is responsible for global regulation and activity of several genes seems to play an important role during colonization of EcN in the intestine and its immunostimulatory effects on intestinal epithelial cells. Investigation of EcN-deletion mutants lacking genomic islands and prophages lead to the conclusion that some genomic islands may play a role for specific probiotic traits. This is the first time where a promoter-trap-library was used in conventional and gnotobiotic mice for collection of intestinal in vivo active promoters. Constructing and establishing a promoter-reporter gene assay with the bioluminescent luxCDABE operon made the investigation of selected promoters in vitro possible as well as establishing a bioluminescence assay using an In Vivo Imaging System (IVIS) for investigation of promoter activity in living mice. In this research project was shown that EcN is not a completely harmless probiotic. The genome structure and regulatory mechanisms of gene expression are the strain’s molecular traits that lead to probiotic activity and immunostimulatory effects. Therefore, the molecular analyses presented here, together with the complete genome sequence, are a basis for further investigations of mechanisms that are responsible for the probiotic effects of EcN.

No description available.

Submitted by Ricardo Cedraz Duque Moliterno (ricardo.moliterno@uefs.br) on 2015-11-12T01:11:08Z No. of bitstreams: 1 Disserta??o Adriana Fidelis - Vers?o Definitiva.pdf: 9437752 bytes, checksum: f708082e56eba193c45496d67cab5993 (MD5) / Made available in DSpace on 2015-11-12T01:11:08Z (GMT). No. of bitstreams: 1 Disserta??o Adriana Fidelis - Vers?o Definitiva.pdf: 9437752 bytes, checksum: f708082e56eba193c45496d67cab5993 (MD5) Previous issue date: 2013-03-13 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior - CAPES / In the 1960? the mining company Plumbum Mineradora was installed in the Satate of Bahia, Brazil. This company, which produced lead ingots for 33 years, left over 400,000 tons of slag, which contained, among other pollutants, cadmium and lead. These metals are currently found in the soil surrounding the old factory, in concentrations considered highly toxic. A study was started to investigate possible bioremediation in the area with the isolation of bacteria from the rhizosphere of local plants, followed by the test in their performance in metals contaminant tolerance. Finally, identification of the bacteria was made based on molecular marker 16S rRNA. The isolation protocol was carry out using Nutrient Agar and after obtaining a pure culture. The isolates were then subjected to tests of Minimum Inhibitory Concentration (CIM). Each isolate served as a source for extraction of DNA for molecular analysis with 16S rRNA region. Among the rhizospheres collected, those from which the greatest number of species were isolated from plants with a perennial habit, among them the castor bean (Ricinus communis L.) and emba?ba (Cecropia pachystachya Tr?cul) which together comprised approximately 38% of all species of bacteria obtained. Interestingly, from the castor bean (an exotic plant in Brazil), 2/3 of the bacteria were Gram negative, while from the emba?ba (a native plant of Brazil), ? of the bacteria isolated were of Gram positive. Regardless of the classification of Gram, the bacteria studied showed higher tolerance to lead; 70% of Gram negative bacteria showed conspicuous morphological changes, whereas of those that were Gram positive, only 13% demonstrated. In addition, these bacteria have been identified by molecular analysis using the 16S rRNA marker. The used methodology based on analysis of parsimony and distance trees. As a result, the region 16S was able to identify only 22% of species while the remain species could only be identified to genus or to infra-generic groups. Therefore, the data suggest that the Gram negative and Gram positive bacteria have distinct mechanisms of adaptation in environments polluted by lead and cadmium and that the 16S region is not an efficient universal barcode marker, which should be used only as the first step on the identification of bacteria. Although this study does not provide a final parameter for ecological factors under consideration here, it provides an insight into the influence of the plant habitat on bacterial communites, and the role of Gram in the mechanisms of tolerance. It is hope to explore these aspects in the further studies. / Na d?cada de 60, a empresa de minera??o Plumbum Mineradora foi instalada no Estado da Bahia, Brasil. Esta empresa, a qual produziu lingotes de chumbo por 33 anos, deixou mais de 400.000 toneladas de esc?ria, a qual continha, dentre outros poluentes, c?dmio e chumbo. Estes metais s?o, atualmente, encontrados no solo do entorno das antigas instala??es da f?brica, em concentra??es consideradas altamente t?xicas. Este estudo come?ou a investigar a biorremedia??o da ?rea com o isolamento de bact?rias das rizosferas de plantas locais, seguido por testar a toler?ncia das bact?rias a esses metais. Finalmente, a identifica??o de bact?rias foi feita baseada no marcador molecular 16S rRNA. O protocolo de isolamento foi realizado em meio de Agar Nutriente e ap?s a obten??o de cultura pura, os isolados foram submetidos a testes de Concentra??o Inibit?ria M?nima (CIM). Cada isolado serviu de fonte para extra??es de DNA para an?lise molecular com a regi?o 16S rRNA. Dentre as rizosferas coletadas, as que mais se destacaram em rela??o a quantidade de esp?cies isoladas foram as plantas de h?bito perene, dentre elas, a mamona (Ricinus comunis L.) e a emba?ba (Cecropia pachystachya Tr?cul), que abrigaram juntas aproximadamente 38% de todas as esp?cies de bact?rias obtidas. Interessante notar que da mamona (uma planta ex?tica no Brasil), 2/3 das bact?rias foram Gram negativas, enquanto que da emba?ba (uma planta nativa do Brasil), 3/4 das bact?rias isoladas foram Gram positivas. Independentemente da classifica??o do Gram, as bact?rias apresentaram maior resist?ncia ao chumbo; 70% das Gram negativas apresentaram mudan?as morfol?gicas acentuadas, enquanto que estas, nas Gram positivas, manifestaram-se em apenas 13%. Al?m disso, estas bact?rias foram identificadas por meio de an?lise molecular, com o uso do marcador 16S rRNA. A metodologia usada foi baseada em an?lise de ?rvores de parcim?nia e dist?ncia. Como resultado, a regi?o 16S foi capaz de identificar 22% das esp?cies, enquanto que para o restante mostrou-se eficiente para classifica??o at? g?nero ou para agrupamentos infragen?ricos. Portanto, os dados sugerem que as bact?rias Gram negativas e Gram positivas possuem mecanismos de adapta??es distintos em ambientes polu?dos por chumbo e c?dmio e que a regi?o 16S n?o ? eficiente como marcador universal tipo ?c?digo de barras?, o qual deve ser utilizado apenas como a primeira ferramenta de identifica??o de bact?rias isoladas. Apesar deste estudo n?o servir como par?metro definitivo para considera??es ecol?gicas, ele fornece conhecimento sobre a influ?ncia do h?bito da planta sobre a comunidade bacteriana e o papel da estrutura morfol?gica das bact?rias (Gram) nos mecanismos de toler?ncia. Espera-se que estes dados possam ser explorados em estudos posteriores.

Penicillium nordicum è un importante contaminante di salumi, rappresentanando il 10 % e il 26 % della popolazione di Penicillium spp . isolati , rispettivamente dall'aria e dai prodotti carnei stagionati in un'indagine gestita in Italia ( Battilani et al. , 2007). Diverse colonie di P. nordicum isolate dai salumi hanno dimostrato di essere importanti produttori di ocratossina A , OTA ( Sansom e Frisvad , 2004 . Pietri et al, 2006 ; . Battilani et al , 2010). Attualmente, l'impostazione appropriata delle condizioni ambientali (temperatura, umidità relativa e circolazione dell'aria ), è l'unico strumento accettato per impedire la crescita incontrollata di P. nordicum all'interno degli impianti di stagionatura attraverso una accurata analisi dei punti critici di controllo e l’ideazione di un relativo piano HACCP (Hazard Analysis and Critical Control Points) ben struttutato ( Asefa et al , 2011; Virgili et al , 2012). Anche se il sistema HACCP è stato applicato con successo nel settore alimentare ci sono rischi per la sicurezza alimentare non attentamente considerati. Questo è particolarmente vero per quanto riguarda i rischi micotossigeni associati ai prodotti alimentari di origine animale. Il termine "rischi micotossigeni" è utilizzato da Asefa et al. ( 2011) per descrivere lieviti patogeni e metaboliti secondari tossici prodotti da specie fungine tossigene che contaminano i prodotti alimentari e incidono sulla sicurezza alimentare. La maggior parte dei piani HACCP nelle attività di trasformazione alimentare, come ad esempio la produzione di formaggi e di prodotti carnei stagionati, tiene in considerazione principalmente il rischio derivante da agenti batterici (Arvanitoyannis e Mavropoulos, 2000; Barbuti e Parolari, 2002) anche se tali prodotti alimentari vengono spesso contaminati da funghi micotossigeni e dai loro metaboliti (Spotti et al 1989; Spotti et al , 2001a; Battilani et al 2007). Pertanto, dovrebbe essere cruciale definire un piano HACCP specificamente incentrato sui rischi micotossigeni. L'identificazione, il controllo e la standardizzazione della micoflora superficie dei salumi è fondamentale per preservare la sicurezza delle produzioni e la salute dei consumatori . Questo è il contesto in cui deve essere valutata l’efficacia e l’affidabilità per l’identificazione delle popolazioni di Penicillium spp di interessante per la produzione alimentare. In questo contesto , il progetto di ricerca di questa tesi di dottorato ha cercato di approfondire le conoscenze su tali tematiche con l'intento di limitare il rischio micotossigeno nella catena di produzione dei prodotti carnei stagionati. Sono stati affrontati i seguenti argomenti: 1 . studio della composizione e dinamica della microflora fungina presente sulla superficie dei salumi (prodotto testato, salame) e l'aria di ambienti di stagionatura tenendo conto dell'influenza di alcuni parametri di processo (inoculo starter, temperatura, fase produttiva). 2 . sviluppo di un metodo MALDI TOF MS per l'identificazione di Penicilium a livello di specie per le prospettive future di screening diretti della microflora presente sui salumi. 3 . confronto e integrazione di diverse tecniche, come l'analisi morfologica, l’analisi molecolare e l’analisi tramite spettrometria di massa, per l'identificazione delle specie di Penicillium presenti nei salumi. 4 . valutazione dei lieviti selezionati, isolati dalla superficie di prosciutto crudo, per competere con P. nordicum ed inibire l'accumulo di OTA nella prospettiva del loro uso come starter superficiali con funzione di agenti di biocontrollo. / Penicillium nordicum is an important contaminant of cured meat products, representing 10% and 26% of the Penicillium spp. isolated, respectively, from the air or the products in a survey managed in Italy (Battilani et al., 2007). Several P. nordicum cured meat isolates proved to be important producers of ochratoxin A, OTA (Sansom and Frisvad, 2004; Pietri et al., 2006; Battilani et al., 2010). Currently, the appropriate setting of environmental conditions (temperature, relative humidity and air circulation), is the only accepted tool to prevent the uncontrolled growth of P. nordicum inside dry-curing plants through a carefully structured Hazard Analysis Critical Control Point (HACCP) plan (Asefa et al., 2011; Virgili et al., 2012). Even if the HACCP system has been successfully applied in the food industry, there are food safety hazards not carefully considered. This is especially true with regard to mycotoxigenic hazards associated with animal food products. The term “mycotoxigenic hazards” is used by Asefa et al. (2011) to describe pathogenic yeasts and toxic secondary metabolites of toxigenic moulds that contaminate food products and affect food safety. Most HACCP plans in food processing activities, such as the production of cheese and dry-cured meat products, considered mainly bacterial agents (Arvanitoyannis and Mavropoulos, 2000; Barbuti and Parolari, 2002), even if such food products get often contaminated with mycotoxigenic fungi and their metabolites (Spotti et al 1989; Spotti et al., 2001a; Battilani et al 2007). Therefore, it should be crucial to define a HACCP plan specifically focused on the mycotoxigenic hazards. The identification, control and standardization of the surface mycoflora of cured meat products is mandatory to preserve the productions safety and the consumers health. This is the context of the effectiveness and reliability evaluation for the Penicillium spp. identification methods of interesting species for food production. In this context, the research project of this PHD thesis tried to fill some gaps of knowledge with the attempt to limit the mycotoxigenic risk in the cured meat products chain. The following topics were faced: 1. study of the composition and dynamic of fungal microflora present on the surface of cured meat products (salami) and the air of seasoning environments taking into account the influence of some process parameters (starter inoculum, curing temperature, stage of seasoning). 2. development of a MALDI TOF MS method for the identification of Penicilium at species level for future direct screening perspectives of the microflora present on cured meat products. 3. comparison and integration of different techniques, as morphological, molecular and mass spectral analysis, for the identification of Penicillium species in cured meat products. 4. evaluation of selected yeasts, isolated from dry-cured ham surface, to compete with P. nordicum and to inhibit OTA accumulation in the perspective of their use as surface starter biocontrol agents.