Diss. (sammanfattning) Uppsala : Univ., 2001. / Härtill 4 uppsatser.

Made available in DSpace on 2016-03-07T19:20:25Z (GMT). No. of bitstreams: 0 Previous issue date: 2015-09-03. Added 1 bitstream(s) on 2016-03-07T19:24:03Z : No. of bitstreams: 1 000857370_20170430.pdf: 809498 bytes, checksum: 80b75f84f1c54021e456991ff49e7ef9 (MD5) Bitstreams deleted on 2017-05-05T11:53:10Z: 000857370_20170430.pdf,. Added 1 bitstream(s) on 2017-05-05T11:53:57Z : No. of bitstreams: 1 000857370.pdf: 3326185 bytes, checksum: 3f22efb9b253d3c96ffa4aefe4751ed0 (MD5) / O fungo Neurospora crassa tem sido amplamente utilizado como organismo modelo para o estudo de alguns aspectos da biologia em eucariotos. O sequenciamento de seu genoma permitiu analisar funcionalmente diversos fatores de transcrição e, portanto, atribuir função a proteínas anotadas como hipotéticas. Neste estudo, está sendo investigado o papel funcional do produto de ORF NCU01629, um fator de transcrição que pertence à família zinc-finger sem homólogos funcionais nos bancos de dados de fungos filamentosos. Análises de interação DNA-proteína in vitro foram previamente realizadas por pesquisadores colaboradores, permitindo a identificação do seu motif de ligação ao DNA, bem como os genes provavelmente regulados por este fator de transcrição. A partir destes dados, estes genes foram classificados pelo FunCat. Os resultados revelaram o envolvimento do fator de transcrição em eventos celulares relacionados ao estresse oxidativo, bem como morte celular, entre outros processos celulares. Análises do crescimento radial do fungo foram realizadas em placas de Petri contendo agentes indutores de diferentes tipos de estresse, tais como osmótico, térmico e oxidativo. A linhagem mutante mostrou crescimento semelhante à linhagem selvagem, em condições de estresse osmótico (NaCl 0,1-1,5M e sorbitol 1-1,5M), pH (4,2 e 7,8) e térmico (45ºC). Entretanto, o crescimento da linhagem mutante foi influenciado quando a linhagem foi exposta a diferentes agentes indutores de EROs, como o paraquat (10 μM), menadiona (50 μM), H2O2 (2 mM) e farnesol (10 μM). A linhagem mutante mostrou crescimento radial reduzido, quando comparado à linhagem selvagem no tratamento com diferentes concentrações de paraquat e farnesol e aumento da resistência quando expostos a H2O2 e menadiona. A expressão de genes relacionados a EROs (cat-1, cat-2, cat-3, gst-1, gst-2, sod e nox) e genes apoptóticos... / The fungus Neurospora crassa has been widely used as a model organism for the study of some aspects of biology in eukaryotes. The sequencing of its genome has enabled functionally analyze various transcription factors and therefore, assign function to hypothetical proteins. In this study, we investigated the functional role of the ORF NCU01629 product, a transcription factor that belongs to the zinc-finger protein family without functional homologues in fungi database. In vitro analysis of DNA-protein interaction, allowed the identification of its DNA binding motif and, as a consequence, the most likely genes regulated by this transcription factor. The genes were classified by FunCat. The results revealed the involvement of the transcription factor in multiple cellular processes including the response to oxidative stress and cell death. Analyses of radial growth were performed in Petri dishes containing agents that induce different types of stress such as osmotic, thermal and oxidative. The knockout strain showed similar growth to the wild type strain when exposed to osmotic (NaCl 0,1-1,5M and sorbitol 1-1,5M), pH (4.2 and 7.8) and heat (45°C) stresses. However, growth of the knockout strain was influenced when the strain was exposed to different ROS inducing agents, such as paraquat (10 μM), menadione (50 μM), H2O2 (2mM) and farnesol (10 μM). The knockout strain showed reduced radial growth, compared to the wild-type strain, when exposed to different concentrations of paraquat and farnesol and increased resistance to H2O2 and menadione. The expression of genes related to ROS (cat-1, cat-2, cat-3, gst-1, gst-2, sod, and nox) and apoptotic genes (bax, metascaspases, and p53) were analyzed by RT-qPCR. The results showed that the transcription factor is involved in the regulation of the oxidative stress response, controlling the expression of all genes. The gene encoding glutathione-S-transferase...

Caulobacter crescentus sobrevive em baixas temperaturas e mostrou ser um organismo psicrotolerante e de alta resistência ao congelamento, característica resultante de múltiplos fatores. C. crescentus possui quatro genes codificantes para CSPs, sendo cspA e cspB induzidos em baixas temperaturas e cspB, cspC e cspD em fase estacionária. A ausência de cspA e cspB ou cspA e cspC confere grande deficiência de crescimento em baixas temperaturas. cspA e cspB não são autorregulados e são regulados pós-transcricionalmente via estabilização de seu mRNA e traducionalmente após o choque-frio. A expressão de cspB é influênciada por CspC a 30 graus e durante o choque-frio, e por CspC, SpdR e SpoT durante a fase estacionária. A ausência de CspC ou CspC e CspD compromete a adaptação à fase estacionária promovendo alterações morfológicas. Nenhuma das CSPs de C. crescentus é capaz de reverter o fenótipo de E. coli BX04 por expressão heteróloga, embora todas possuam atividade antiterminadora que, nestas proteínas, não depende dos mesmos aminoácidos que CspE de E. coli. / Characterization of Caulobacter crescentus cold response was performed. This bacterium showed to be psicrotolerant and have remarkable freezing resistance, which may be a result of multiple traits. C. crescentus has four CSP encoding genes, being cspA and cspB cold-induced and cspB, cspC and cspD stationary phase-induced. The absence of cspA and cspB or cspA and cspC led to growth deficiency under low temperature incubation. cspA and cspB are not self-regulated and are post-transcriptionally and translationally regulated during cold-shock. The cspB gene expression is affected by CspC at exponential growth phase and by CspC, SpdR and SpoT at stationary phase. The absence of CspC, or CspC and CspD, affects stationary phase fitness of this organism, also promoting morphological alterations. None of the C. crescentus CSPs were able to restore the phenotype of E. coli BX04 strain by heterologous expression. Although all of them have shown to be transcription antiterminators, this ability is not dependent on the same critical aminoacids displayed by CspE from E. coli.

A Mata Atlântica brasileira é apontada como um dos mais importantes refúgios da biodiversidade em todo o planeta. Este bioma é extremamente importante sob o aspecto da riqueza de espécies vegetais e animais na sua composição e interações, porém ainda pouco conhecido e explorado sob o ponto de vista microbiológico. Um grama de solo pode conter cerca de 10 bilhões de micro-organismos de diferentes espécies. A maioria dos micro-organismos presentes nos solos não é de fácil cultivo em laboratório (somente 0.1-10% são recuperados), sendo necessária à utilização de novas técnicas para superar este problema. Muitos micro-organismos presentes no solo tem grande importância biotecnológica por produzirem compostos bioativos. O filo Actinobacteria é abundante em solos e de grande importância econômica, tendo em vista que a maioria dos antibióticos comercializados é produzido por membros deste grupo. Porém a biodiversidade microbiana da Mata Atlântica, bem como, o seu potencial biotecnológico não tem sido plenamente estudado. Poucos trabalhos mostram produtos do metabolismo microbiano com potencial em uso em indústrias e mostram menos ainda antimicrobianos produzidos por isolados bacterianos desta região. Dentro deste contexto, o presente trabalho buscou em duas alternativas metodológicas como a técnica independente de cultivo, o metagenoma, verificar a presença de genes de uma importante via biossintética os policetídeos sintases e com a técnica dependente de cultivo, selecionar prováveis bactérias produtoras de composto bioativos. O metagenoma propõe fazer uma análise do DNA total de amostras do solo, visando conhecer a informação gênica destes compostos na complexa diversidade microbiana. Desta forma, várias abordagens foram empregadas para conseguir um DNA de alto peso molecular e de qualidade suficiente para construir bibliotecas metagenômicas, e procurar nestas, genes das vias de sínteses dos policetídeos (PKS) tipo I e tipo II, que ficam agrupados em clusters que variam de tamanho entre 20 a 100 kb. Otimizamos um método de extração de DNA do solo e conseguimos obter um DNA de aproximadamente 50kb, que foi amplificado por PCR utilizando primers para regiões conservadas dos genes policetídeos sintases tipo I e II (acetosintase ) de Actinomicetos. Os fragmentos obtidos, PKS I e PKS II, com tamanho entre 600pb a 700pb, foram clonados, construído-se duas bibliotecas metagenômicas (KSI e KS II). Os clones foram sequênciados e analisados em uma árvore filogenética. A análise filogenética de genes policetídeos tipo I demonstrou similaridade com estes genes de diversas divisões de bactérias, revelando a presença de prováveis genes novos não apenas relacionados a via de PKSI, como também aos genes de PKSI híbridos com peptídeos não ribossomais. Em complemento a filogenia de policetídeos tipo II apresentou uma similaridade com genes de Actinobacteria, formando um grupo que também está relacionados a presença de prováveis genes novos de importantes famílias de antibióticos. Através do cultivo utilizando meio seletivo para o crescimento de bactérias não cultivadas, foi possível isolar sete bactérias que possuem atividade antibacteriana e/ou antifúngica. / The Brazilian Atlantic Forest is considered as one of the most important reservoir of biodiversity in the planet. This biome is extremely important for its richness of plant and animal species but although with their composition and interactions poorly known and unexplored from a microbiological perspective. One gram of soil can contain near 10 billion microorganisms of different species. The majority of the soil microorganisms is not cultivable in laboratory (only 0.1-10% are recovered), being necessary to use new techniques to overcome this problem. Many of the soil microorganisms are biotechnologically important for the production of bioactive compounds. The Actinobacteria phylum is abundant in soil and important economically due to the capacity of synthesize many antibiotics. Nevertheless, the Atlantic Forest microbial biodiversity has not been properly study. Few works show microbial metabolic products with potential use in industries and, still less, antimicrobials isolated from this biome. The present work searched two new methodological alternatives: one culture independent, the metagenome, to verify the presence of polyketide synthases biosynthetic genes; and the second, the culture dependent, to select potential bacteria producers of bioactive compounds. The metagenome intend the total DNA analysis of a sample, focusing in to know the genetic information of the complex microbial diversity. Several approaches were used in order to obtain DNA of high molecular weight and quality toconstruct metagenomic libraries and search for polyketide synthases (PKS) genes types I and II, that usually are organized in clusters of 30 to 100 kb. A DNA extraction method was optimized obtaining DNA of approximately 50 kb, and used for the detection of PKS gens by PCR approaches using primers based in polyketide synthases type I and II (ketosynthase ) conserved regions of Actinomycetes. The PKS I and PKSII amplicons (600-700 bp) were cloned and two metagenoic libraries were obtained (KS I and KS II). The clones were sequenced and analyzed in a phylogenetic tree. Phylogenetic analysis of PKS I genes reveled high similarities with genes of several divisions of bacterias pointing the presence of provable new genes related with the synthesis of polyketides produzrd by PKS I and hybrid PKS with non ribosomal peptides (NRPs). Polyketide type I genes showed similarity with Streptomyces and uncultered bacteria. The analysis of polyketide II genes showed high similarity with genes of Actinobacteria gruped in two main groups, one of them with possible new genes related with the production of important antibiotics. Using selective medium for uncultered bacteria, seven isolates were obtained being studied taxonomically and tested for the production of secondary metabolites with antibacterial and antifungal activities.

M.Tech. (Biomedical Technology) / Aflatoxins (AFs) are naturally occurring secondary metabolites produced principally by Aspergillus flavus and Aspergillus parasiticus in food and feed commodities worldwide. Contaminations of compound feeds by AFs do not only affect animal health, but the economy as well. It is for this purpose that a study was carried out to establish the quality of South African feeds with respect to AF-producing fungi, establish a correlation between levels of AFs and determinant gene (nor-1) responsible for producing these toxins. To this end, compound feeds (n=92) from various feed manufacturers in South Africa were sampled and analysed for aflatoxigenic fungi (Aspergillus flavus and Aspergillus parasiticus) and nor~1 genes using the conventional identification and real time- polymerize reaction (RT-PCR) methods, respectively. Data obtained revealed that 66.5 and 53.1% of samples were positive for A. flavus and A. parasiticus, respectively. Aflatoxins levels in similar samples were estimated by high performance liquid chromatography (HPLC) following an immune-affinity clean-up and multi mycotoxin extraction procedures. Accordingly, levels established ranged from 0.06 – 77.97 ppb (mean: 16.8 ppb) with feeds for poultry being the main contaminating substrate and no correlation (overall R2=0.093) was established between the concentrations of AFs and those of nor~1. The cytotoxic effect of some selected AF extracts from these feeds on human lymphocyte cells was performed in comparison to that of AFB1 standard. Data obtained from the cytotoxic assay revealed that cell viability was affected significantly (P<0.001) by both the dose and duration of exposure, which was much more noticeable when cells were exposed to AFB1 standard than for individual extracts. In conclusion, even though none of the feeds analysed contained levels of AFs above regulatory limits established in South Africa, such feeds when consumed on a continuous basis may pose some serious health problems especially when AFs is found in co-contamination with such significant mycotoxins as ochratoxins (OTs) and fumonisins (FBs). Thus, the continuous need to limit AFs levels in feed commodities from South Africa is imperative.

M.Tech. (Biomedical Technology) / A study was conducted with the aim to determine the incidence and contamination levels of fumonisin (FB) and FB producers in South African compound feeds. A total of 90 compound feed samples were screened for FB producing Fusarium species conventionally based on the morphological macroscopic and microscopic features. Data revealed that Fusarium spp. were most prevalent in feeds for chicken with an incidence rate of 34% recorded followed by cattle (6%) and pig feed (1%), meanwhile no Fusarium spp. was recovered from any of the horse feed analyzed. Similar samples were also analyzed for FB and in general, data indicate that 68% of samples were positive for FB1 which was the most frequent, ranging from 24 to 5515 μg/kg (mean concentration: 796.5 μg/kg). Quantification of fum 1 gene in 30 animal feed samples was performed by quantitative real time-polymerase chain reaction (qRT-PCR). Detection as well as quantification of fum 1 gene in animal feed was made possible but a positive correlation between fum 1 gene and FB levels was not established, however, an association between fungal contamination, FB and the determined fum 1 gene concentrations was evident in this study. The cytotoxic effect of FB extract from feeds was evaluated in vitro on human lymphocyte cells. Data obtained revealed that cell viability of lymphocytes was strongly influenced by both the concentration of toxin and duration of exposure. This study demonstrates that in South Africa, animals are constantly exposed to FB via consumption of feeds contaminated with the toxin even though the levels obtained are within the acceptable levels. Their presence thus highlights the need for proper quality control measures to be put in place at every step in the animal feed production chain.

Alper e colaboradores demonstraram que a linhagem BY4741 recombinante portadora de cópias adicionais de um alelo SPT15 mutagenizado em três diferentes posições (spt15-300) utiliza mais rapidamente a glicose e aumenta a produção de etanol. Neste trabalho, foi realizada a clonagem deste alelo, aqui chamado spt15*. Inicialmente o DNA genômico da linhagem S. cerevisiae S288C foi utilizado como molde para amplificação por SOEing-PCR. O alelo spt15* foi clonado no plasmídeo pGEMT-Easy e, em seguida, introduzido no plasmídeo epissomal pMA91. Após construções moleculares, foi obtido o fragmento de DNA dpPGKspt15*tPGKd, empregado na transformação genética, da linhagem S. cerevisiae YPH252, por d-integração. Os clones recombinantes YHP252/pMA91spt15* e YHP252/dpPGKspt15*tPGKd consomem mais eficientemente a glicose e aumentam a produção de etanol. O seqüenciamento do alelo SPT15 da levedura industrial PE-2 revelou 100% de identidade com o alelo das linhagens BY4741 e S288C, criando ótimas perspectivas para trabalhos futuros. / Alper and colleagues demonstrated that the yeast S. cerevisiae BY4741 recombinant strain carrying additional copies of a SPT15 allele mutagenized in three different positions (spt15-300) uses glucose more speedily and produces more ethanol. In this work, this allele, here called spt15*, was cloned. The genomic DNA of the S. cerevisiae S288C strain was used for amplification through SOEing-PCR. The spt15* allele was cloned in the plasmid pGEMT-Easy and introduced in the episomal plasmid pMA91. After molecular constructions the DNA dpPGKspt15*tPGKd fragment was obtained to be employed in the genetic transformation of laboratory S. cerevisiae strains using d-integration. Both recombinant clones YHP252/pMA91spt15* and YHP252/dpPGKspt15*tPGKd consume glucose more speedily and produce more ethanol. The sequencing of the SPT15 allele of the industrial yeast PE-2 revealed 100% identity with BY4741 and S288C alleles, creating huge perspectives for future works.

Orientador: Maria Célia Bertolini / Co-orientador: Rodrigo Duarte Gonçalves / Banca: Iran Malavazi / Banca: Márcia Eliana da Silva Ferreira / Resumo: O fungo Neurospora crassa tem sido amplamente utilizado como organismo modelo para o estudo de alguns aspectos da biologia em eucariotos. O sequenciamento de seu genoma permitiu analisar funcionalmente diversos fatores de transcrição e, portanto, atribuir função a proteínas anotadas como hipotéticas. Neste estudo, está sendo investigado o papel funcional do produto de ORF NCU01629, um fator de transcrição que pertence à família zinc-finger sem homólogos funcionais nos bancos de dados de fungos filamentosos. Análises de interação DNA-proteína in vitro foram previamente realizadas por pesquisadores colaboradores, permitindo a identificação do seu motif de ligação ao DNA, bem como os genes provavelmente regulados por este fator de transcrição. A partir destes dados, estes genes foram classificados pelo FunCat. Os resultados revelaram o envolvimento do fator de transcrição em eventos celulares relacionados ao estresse oxidativo, bem como morte celular, entre outros processos celulares. Análises do crescimento radial do fungo foram realizadas em placas de Petri contendo agentes indutores de diferentes tipos de estresse, tais como osmótico, térmico e oxidativo. A linhagem mutante mostrou crescimento semelhante à linhagem selvagem, em condições de estresse osmótico (NaCl 0,1-1,5M e sorbitol 1-1,5M), pH (4,2 e 7,8) e térmico (45ºC). Entretanto, o crescimento da linhagem mutante foi influenciado quando a linhagem foi exposta a diferentes agentes indutores de EROs, como o paraquat (10 μM), menadiona (50 μM), H2O2 (2 mM) e farnesol (10 μM). A linhagem mutante mostrou crescimento radial reduzido, quando comparado à linhagem selvagem no tratamento com diferentes concentrações de paraquat e farnesol e aumento da resistência quando expostos a H2O2 e menadiona. A expressão de genes relacionados a EROs (cat-1, cat-2, cat-3, gst-1, gst-2, sod e nox) e genes apoptóticos... / Abstract: The fungus Neurospora crassa has been widely used as a model organism for the study of some aspects of biology in eukaryotes. The sequencing of its genome has enabled functionally analyze various transcription factors and therefore, assign function to hypothetical proteins. In this study, we investigated the functional role of the ORF NCU01629 product, a transcription factor that belongs to the zinc-finger protein family without functional homologues in fungi database. In vitro analysis of DNA-protein interaction, allowed the identification of its DNA binding motif and, as a consequence, the most likely genes regulated by this transcription factor. The genes were classified by FunCat. The results revealed the involvement of the transcription factor in multiple cellular processes including the response to oxidative stress and cell death. Analyses of radial growth were performed in Petri dishes containing agents that induce different types of stress such as osmotic, thermal and oxidative. The knockout strain showed similar growth to the wild type strain when exposed to osmotic (NaCl 0,1-1,5M and sorbitol 1-1,5M), pH (4.2 and 7.8) and heat (45°C) stresses. However, growth of the knockout strain was influenced when the strain was exposed to different ROS inducing agents, such as paraquat (10 μM), menadione (50 μM), H2O2 (2mM) and farnesol (10 μM). The knockout strain showed reduced radial growth, compared to the wild-type strain, when exposed to different concentrations of paraquat and farnesol and increased resistance to H2O2 and menadione. The expression of genes related to ROS (cat-1, cat-2, cat-3, gst-1, gst-2, sod, and nox) and apoptotic genes (bax, metascaspases, and p53) were analyzed by RT-qPCR. The results showed that the transcription factor is involved in the regulation of the oxidative stress response, controlling the expression of all genes. The gene encoding glutathione-S-transferase... / Mestre

Cronobacter sakazakii is a gram-negative opportunistic pathogen known to survive in dry environments and food matrices, such as infant formula. This foodborne bacterium can cause fatal human infections of the blood, central nervous system, and gastrointestinal tract; it is also problematic in wounds and urinary tract infections. Preterm infants and immunocompromised individuals are in higher risk categories related to necrotizing enterocolitis, neonatal sepsis, and meningitis due to this organism. Therefore, there is a need for increased understanding of how this bacterium is able to persist in thermally treated low-moisture products that do not support growth. The objective of this research is to identify genes and mechanisms in C. sakazakii that contribute to its resistance to desiccation and survival in low-moisture food matrices, including powdered infant formula. C. sakazakii sequence type 4 (ST4) is of particular interest as it is often the cause of neonatal infections originating from contaminated feedings of powder infant formula. The method chosen to explore these genetic patterns is massively parallel transposon insertion sequencing (Tn-seq). The E. coli strain MFDpir was used to facilitate transposon insertional mutagenesis to create a library of mutated C. sakazakii. Three different C. sakazakii ST4 isolates of different origins (clinical, environmental, and infant formula-derived) were selected for this study. Once transposon mutagenesis occurred with the aid of E. coli MFDpir, the three mutant libraries were subjected to desiccation stress in a closed system equilibrated to 11.3% relative humidity. The surviving mutant genomes were analyzed with Tn-seq. The sequencing data revealed that, while transposition events did occur successfully within the genomes of each of the selected C. sakazakii isolates, these events were not dense enough to draw biological conclusions nor statistical inferences concerning which genes contribute to this organism’s uncanny desiccation tolerance. However, we concluded that the Tn-seq method is a promising tool with this organism of interest, despite incomplete results in this first round of experimentation.

Effective treatment of tuberculosis requires at least six months of combination therapy involving four antibiotics. Alterations in the physiological state of Mycobacterium tuberculosis during infection may reduce drug efficacy and prolong treatment, but these adaptations are incompletely defined. To investigate the mechanisms limiting antibiotic efficacy, I performed a comprehensive genetic study to identify M. tuberculosis genes and pathways important for bacterial survival during antibiotic treatment in vivo. First, I identified mutants in the glycerol kinase enzyme, GlpK, that promote survival under combination therapy. Similar glycerol catabolic mutants are enriched in extensively drug-resistant clinical isolates, indicating that these mutations may promote survival and the development of resistance in humans. A majority of these mutations are frameshifts within a homopolymeric region of the glpK gene, leading to the hypothesis that M. tuberculosis may reversibly produce drug-tolerant phenotypes through genetic variation introduced at homopolymer sites as a strategy for survival during antibiotic treatment. Second, I identified bacterial mutants with altered susceptibility to individual first-line anti-mycobacterial drugs. Many of these mutations did not have obvious effects in vitro, demonstrating that a wide variety of natural genetic variants can influence drug efficacy in vivo without altering standard drug-susceptibility tests. A number of these genes are enriched in drug-resistant clinical isolates, indicating that these genetic variants influence treatment outcome. Together, these data suggest new targets for improving therapy, as well as mechanisms of genetic adaptations that can reduce antibiotic efficacy and contribute to the evolution of resistance.