The extensive use of tetrachloroethene (PCE) and trichloroethene (TCE) as cleaning solvents has resulted in widespread contamination of groundwater systems with vinyl chloride (VC). VC, a known human carcinogen, is primarily formed in groundwater via incomplete anaerobic reductive dechlorination of PCE and TCE. Aerobic, methane-degrading bacteria (methanotrophs), which are capable of VC cometabolism while growing on methane, could be important in natural attenuation of VC plumes that escape anaerobic treatment. Real-time PCR (qPCR) represents an innovative approach for detecting and quantifying the presence and activity of these VC-degrading microbes. Immediate applications of this technique include use in a laboratory setting to help elucidate the potential bacterial-substrate interactions occurring in the subsurface environments at these contaminated sites; interactions that could ultimately affect the role of methanotrophs in VC degradation. This technique could also provide lines of evidence for natural attenuation of VC, thus support existing anaerobic bioremediation technologies that generate VC as a metabolic intermediate. In this work, we evaluated several PCR primer sets from the literature for use in methanotroph qPCR assays of groundwater samples. PCR primers targeting two functional genes involved in VC cometabolism, pmoA (sub-unit of particulate methane monooxygenase (pMMO)) and mmoX (sub-unit of soluble MMO (sMMO)), as well as 16S rRNA gene primers that targeted Bacteria, and Type I and Type II methanotrophs were tested. These assays were made quantitative by constructing standard curves with DNA from Methylococcus capsulatus (Type I) and Methylocystis sp. strain Rockwell (Type II). Primer sets were evaluated by comparing gene abundance estimated against known amounts of Type I and Type II methanotroph DNA. After primer validation, an effort to substantiate this methanotroph qPCR method was made by attempting to investigate methanotroph populations in groundwater samples from VC-contaminated sites. Some samples studied were also subjected to 16S rRNA gene pyrosequencing, allowing for relative abundance comparisons with qPCR analyses. Following our primer assessment experiments, effective primer sets were used to estimate the presence of methanotrophs at environmental sites in Soldotna, Alaska; Naval Air Station Oceana, Virginia Beach, Virginia; and Carver, Massachusetts. Results showed that methanotrophs were present in nearly all wells sampled from all environmental sites. Estimations of methanotroph relative abundance in environmental samples were determined by comparing the Type I and Type II primer estimates to those of the 16S universal primers. Methanotrophs in these groundwater samples ranged from 0.2% to 6.6% of the total bacterial population. Pyrosequencing analysis of the same samples showed methanotroph relative abundances that ranged from 1.7% to 54%. In groundwater samples where both DNA and RNA was extracted, the quantities of functional gene transcripts per gene copy was compared, revealing that the transcripts/gene ratio for both pmoA and mmoX was less than one, implying relatively low methanotroph activity. Analysis of mmoX environmental sample dissociation curves revealed a double peak, indicating possible non-specific PCR products. Our data suggests that most of the qPCR primer sets used in the environmental samples adequately detect methanotrophs, though the mmoX primers need to be further validated. These primer sets will be useful for supporting VC bioremediation strategies by providing a rapid, convincing, and cost effective alternative the enrichment culture technique currently employed. Comparison of qPCR and pyrosequencing analysis revealed biases in either one, or both techniques. Finally, our preliminary transcripts/gene data suggests that the methanotrophs at the Carver site are not actively expressing pMMO and sMMO genes above basal levels.

En la producción de vinagres no se cuenta con cultivos iniciadores en los que se conozca su composición microbiológica y tampoco se conocen las propiedades oxidativas que presentan. La falta de cultivos iniciadores en la producción de vinagres se ve reflejada en una iniciación lenta de la acetificación o en paradas de acetificación. La utilización de inóculos permite, a la vez, la uniformización en la calidad final del producto, asegurando los parámetros de calidad predeterminados. Las bacterias acéticas son los microorganismos responsables de la biotransformación de vino a vinagre gracias a su capacidad para oxidar el etanol a ácido acético y acumularlo en el medio sin gran toxicidad para ellas. Esta oxidación tiene lugar en dos pasos iniciándose por la acción de la enzima ADH (Alcohol deshidrogenasa). Este trabajo estudia las diferencias en la expresión de la ADH-PQQ en medios con diferentes fuentes de carbono. Las diferencias en la expresión pueden ser utilizadas como indicador de la capacidad acetificadora de diferentes especies de bacterias acéticas. Se propone el uso de la RT-QPCR (real-time quantitative reverse transcription polymerase chain reaction), como técnica para cuantificar la expresión relativa de la ADH. Esto permite poner a punto la metodologia para el análisis de la expresión relativa de la ADH y aplicarla posteriormente a otros genes de las bacterias acéticas. Se logró establecer la relación entre la actividad de la ADH con la producción de ácido acético en la producción de vinagres. Esta relación se observo especialmente en el género Acetobacter. Siendo la primera vez que se utiliza esta técnica en el área de las acetificaciones, proponemos esta técnica como una herramienta para el estudio del metabolismo de las bacterias acéticas.

Real-time quantitative polymerase chain reaction (real-time qPCR) assays are an effective technique to detect biological warfare agents and surrogate organisms. In my study, primers were designed to detect chromosomal DNA of biological warfare agent surrogates B. thuringiensis and S. marcescens (representing B. anthracis and Y. pestis, respectively) via real-time qPCR. Species-level specificity of the primers was demonstrated through comparisons with a bacterial strain panel and corroborated by qPCR data. Additionally, the primer efficacy was tested when template DNA was spiked into metagenomic DNA extracted from clinical lung microbiome samples. The results showed that while detection of B. thuringiensis or S. marcescens was still largely successful, the addition of metagenomic DNA did significantly inhibit amplification in most cases. The present study is significant not only for the design of multiple novel primer pairs able to detect bacterial agents in metagenomic DNA, but also the quantitative insight to the influence of background DNA on single species detection at low DNA concentrations.

Globally, vector borne diseases cause more than a million deaths each year and more than a billion infections in humans. Ticks are of big medicinal importance since they can transmit pathogens that can cause serious infections. Some recently discovered pathogens that can cause infections in humans are Anaplasma phagocytophilum (A. phagocytophilum) that can cause human granulocytic anaplasmosis (HGA) and Candidatus Neoehrlichia mikurensis (N. mikurensis) that can cause Neoehrlichiosis. It is still widely unknown how prevalent these pathogens are, if ticks can be infected with both of these pathogens and if these pathogens can be transovarially transmitted from adult female to egg and larvae. This study aims to screen for these pathogens in collected ticks from southern Sweden and to detect eventual co-infections and transovarial transmission. A real-time qPCR assay targeting the 16S rRNA gene of N. mikurensis and other Anaplasmataceae was applied on 1356 Ixodes ricinus (I. ricinus) ticks collected from 5 sites in southern Sweden. Positive samples were subjected to Sanger sequencing. A. phagocytophilum occurred in 4.64 % of the ticks, N. mikurensis occurred in 1.33 % of the ticks and also Rickettsia was found to occur in 6.27 % of the ticks. No co-infection was detected. Some samples of tick larvae showed positive results after qPCR, indicating transovarial transmission, but none of the sequences were readable.

Made available in DSpace on 2014-06-11T19:27:23Z (GMT). No. of bitstreams: 0 Previous issue date: 2009-07-17Bitstream added on 2014-06-13T18:56:06Z : No. of bitstreams: 1 davolos_cc_me_jabo.pdf: 358910 bytes, checksum: 020446e7d045944b95dfcb371b8ab71e (MD5) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Bacillus thuringiensis é entomopatogênica muito utilizada no controle de insetos-praga e a predição de sua atividade tóxica é realizada por PCR na identificação de genes cry. Assim sendo, este trabalho objetivou elaborar novos oligonucleotídeos iniciadores para a detecção das subclasses cry1Ab, cry1Ac, cry1Ca, cry1Ea e cry1Fa, estudar o potencial de controle de 31 isolados de B. thuringiensis à duas populações de Spodoptera frugiperda por meio de bioensaios e analisar a taxa de expressão dos genes presentes nos isolados por qPCR em tempo real. Um par de oligonucleotídeo iniciador foi elaborado para cada subclasse e dentre os isolados testados 6,5% e 48,5% apresentaram os genes cry1Ab e cry1Ac, respectivamente, nenhum dos isolados apresentou os genes cry1Ca, cry1Ea e cry1Fa. Dentre os 31 isolados, 13 apresentaram mortalidade acima de 75% para as larvas da população de campo e apenas nove para a população de laboratório, mostrando que os isolados controlaram com maior eficiência as larvas da população de campo. A presença dos genes cry1Ab e cry1Ac conjuntamente foi associada à elevado potencial de controle às larvas da população de campo e baixo às larvas da população de laboratório. A expressão do gene cry1Ab, não foi constatada em nenhum dos isolados nas condições analisadas e, para o gene cry1Ac, todos os isolados apresentaram taxa de expressão. Os resultados de expressão foram associados ao potencial de controle das larvas de S. frugiperda das populações testadas, sendo que os elevados níveis de expressão do gene cry1Ac foram associados diretamente a elevado potencial de controle da população de laboratório. / Bacillus thuringiensis is entomopathogenic used for insect control and the prediction of the toxic activity is performed by PCR on the identification of cry genes. Thus, the aim of this research was develop news primers for detection the subclasses cry1Ab, cry1Ac, cry1Ca, cry1Ea and cry1Fa, study the potential control of 31 isolates of B. thuringiensis against two Spodoptera frugiperda populations by bioassays and analyze the rate of gene expression present on the isolates by real-time qPCR. A pair of primer was prepared for each subclass, the genes cry1Ab and cry1Ac were found in 6.5% and 48.5% of the isolates, respectively, and the genes cry1Ca, cry1Ea and cry1Fa were not detected on the isolates. Among the 31 isolates, 13 showed over 75% mortality for the larvae of field population and only nine isolates to the laboratory population, showing that the isolates controlled more efficiently the larvae of the field population. The presence of cry1Ab and cry1Ac genes were correlated to high levels of insecticidal activity for the larvae of field population and low levels control to the laboratory population. The expression of cry1Ab was not found in any of the isolates analyzed and the rates expression of cry1Ac gene was detected in all isolates. The results of gene expression were associated with the potential control to S. frugiperda, and the high levels of cry1Ac gene expression were linked directly to high levels of insecticidal activity for the laboratory population.

Resumo: Bacillus thuringiensis é entomopatogênica muito utilizada no controle de insetos-praga e a predição de sua atividade tóxica é realizada por PCR na identificação de genes cry. Assim sendo, este trabalho objetivou elaborar novos oligonucleotídeos iniciadores para a detecção das subclasses cry1Ab, cry1Ac, cry1Ca, cry1Ea e cry1Fa, estudar o potencial de controle de 31 isolados de B. thuringiensis à duas populações de Spodoptera frugiperda por meio de bioensaios e analisar a taxa de expressão dos genes presentes nos isolados por qPCR em tempo real. Um par de oligonucleotídeo iniciador foi elaborado para cada subclasse e dentre os isolados testados 6,5% e 48,5% apresentaram os genes cry1Ab e cry1Ac, respectivamente, nenhum dos isolados apresentou os genes cry1Ca, cry1Ea e cry1Fa. Dentre os 31 isolados, 13 apresentaram mortalidade acima de 75% para as larvas da população de campo e apenas nove para a população de laboratório, mostrando que os isolados controlaram com maior eficiência as larvas da população de campo. A presença dos genes cry1Ab e cry1Ac conjuntamente foi associada à elevado potencial de controle às larvas da população de campo e baixo às larvas da população de laboratório. A expressão do gene cry1Ab, não foi constatada em nenhum dos isolados nas condições analisadas e, para o gene cry1Ac, todos os isolados apresentaram taxa de expressão. Os resultados de expressão foram associados ao potencial de controle das larvas de S. frugiperda das populações testadas, sendo que os elevados níveis de expressão do gene cry1Ac foram associados diretamente a elevado potencial de controle da população de laboratório. / Abstract: Bacillus thuringiensis is entomopathogenic used for insect control and the prediction of the toxic activity is performed by PCR on the identification of cry genes. Thus, the aim of this research was develop news primers for detection the subclasses cry1Ab, cry1Ac, cry1Ca, cry1Ea and cry1Fa, study the potential control of 31 isolates of B. thuringiensis against two Spodoptera frugiperda populations by bioassays and analyze the rate of gene expression present on the isolates by real-time qPCR. A pair of primer was prepared for each subclass, the genes cry1Ab and cry1Ac were found in 6.5% and 48.5% of the isolates, respectively, and the genes cry1Ca, cry1Ea and cry1Fa were not detected on the isolates. Among the 31 isolates, 13 showed over 75% mortality for the larvae of field population and only nine isolates to the laboratory population, showing that the isolates controlled more efficiently the larvae of the field population. The presence of cry1Ab and cry1Ac genes were correlated to high levels of insecticidal activity for the larvae of field population and low levels control to the laboratory population. The expression of cry1Ab was not found in any of the isolates analyzed and the rates expression of cry1Ac gene was detected in all isolates. The results of gene expression were associated with the potential control to S. frugiperda, and the high levels of cry1Ac gene expression were linked directly to high levels of insecticidal activity for the laboratory population. / Orientador: Manoel Victor Franco Lemos / Coorientador: Odair Aparecido Fernandes / Banca: Jackson Antônio Marcondes de Souza / Banca: Celso Omoto / Mestre

There is much evidence that herbivory is a key innovation for the tremendous success of insect. In this thesis I have investigated different aspects of host plant utilization and phenotypic plasticity using the polyphagous comma butterfly, Polygonia c-album. Even though external conditions affect a phenotypic plastic response, the outcome is often influenced by a genetic background which may differ among populations. In Paper I we suspected the genetic background to seasonal polymorphism to be X-linked. However, results from interspecific hybridization between two populations suggested that diapause response is instead inherited in a mainly autosomally additive fashion, with a possible influence of sexual antagonism on males. In Paper II we showed that female oviposition preference is not a plastic response influenced by larval experience, but has a genetic background coupled to host plant suitability. Further, there is a strong individual correlation between larval host plant acceptance and female host plant specificity (Paper III). We believe this to be a larval feed-back genetically linked to female host specificity: offspring to ‘choosy’ specialist mothers benefit by remaining on the original host while offspring to less discriminating generalist mothers should risk inspecting the surroundings, thus compensating for potential poor female choice. In the larval mid-gut, genes are differentially expressed depending on host plant diet (Paper IV). Therefore, we expected to find fitness consequences of host plant switch. However, although growth rate was affected in a few treatments, larvae were generally surprisingly good at adjusting to new diets (Paper V). To conclude, host plant choice in both female and larval life stage is connected to performance. Combined with increased understanding about the plastic response to diet intake and seasonal polymorphism we have gained further insights into the processes of local adaptations and speciation in the Lepidoptera. / At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Submitted Manuscript; Paper 5: Manuscript

Microbial DNA was isolated from lysed cells of Lactobacillus genus in probiotic products. Reversible adsorption DNA on the surface of carboxyl coated nonporous poly(2-hydroxyethyl methacrylate-co-glycidyl methacrylate) (P(HEMA-co-GMA)) magnetic particles and silicagel coated manganase Perovskite nanoparticles. DNA was adsorbed on the surface of the particles in the presence of 16 % poly(ethylenglycol) (PEG 6000) and 2 M sodium chloride (NaCl) concentrations. The adsorbed DNA was released from particles by low ionic strength TE buffer (pH= 8.0). The quality of isolated DNA was checked by spectrofotometric measurement and PCR amplification. DNA samples isolated using magnetic particles and phenol extraction method (control method) were PCR-ready. The DNA isolated from lysed cells of probiotic products was quantificated in real-time qPCR.

Magister Scientiae (Medical Bioscience) - MSc(MBS) / This study investigated the effects of TKIs on the growth and proliferation of MCF-7 breast carcinoma cells in culture. MCF-7 cells were exposed to different concentrations of TKIs alone and in combination with each other. Inhibition of cell growth by TKIs used individually occurred in a dose- and time-dependent manner. When EGFR Inhibitor I, EGFR Inhibitor II/BIBX1382 and the multi-specific EGFR/ErbB-2/ErB-4 Inhibitor were used in combination with each other at equimolar log dose concentrations, the combined effects on cell growth was significantly different to inhibitors used individually as reflected in a decreased EC50 (IC50) during combination treatments. Generally, for the combinations with DOX, CPL and the TKIs, synergistic as well as antagonistic effects were observed at isoeffective concentrations with resultant decreases in dose reduction indices (DRIs) implying greater efficacies with the respective combinations. In this study, conventional PCR was used to detect and illustrate the presence of the EGFR gene in the samples, while RT-qPCR was used to determine the mRNA expression levels of this gene in MCF-7 breast carcinoma cells