The aim of this thesis is to comprehensively analyse presolar silicon carbide (SiC) grains from several primitive meteorites in order to investigate their complicated history. During their residence in the interstellar medium, presolar grains are predicted to be affected by many processes which may modify their original elemental and isotopic composition. Presolar SiC grains from three acid residues and two polished meteorite sections were analysed for their carbon, nitrogen and silicon isotope ratios with high spatial resolution, in order to compare the distribution of 14N/15N ratios compared to those found in the literature. As a result of this work, isotopic fractionation effects caused by the distortion of the electric field around the grain topography were identified. These effects have the potential to cause differential transmission of atomic and molecular secondary ions, particularly when small slits and apertures are selected during NanoSIMS analyses. The measured 14N/15N ratios of the presolar SiC grains analysed in this work match well with existing literature data, although many grains cluster at relatively low 14N/15N values. These low ratios do not appear to be the result of either terrestrial contamination or isotopic dilution, and may instead represent real differences between the SiC grain populations of different meteorites. The majority of mainstream SiC grains analysed in this work lie on a slope with a gradient of ~1.3 on a Si 3-isotope plot, in agreement with literature data. SiC grains from the JAMM and JA-MM2 acid residues appear to lie on shallower slopes, although these samples show significant scatter in the data. Neither terrestrial contamination nor isotopic dilution can explain the apparent fractionation of silicon isotopes in these samples. It is possible that these ratios may represent a difference in the Si ratios of grain populations of different meteorites, although fractionation during the sample preparation phase cannot be excluded. Ten presolar SiC grains from the KJG and JA-MM2 acid residues are comprehensively analysed for their trace element compositions using Time-of-Flight Secondary Ion Mass Spectrometry. The majority of analyses are significantly affected by the proximity of neighbouring grains, leading to high background counts which prevent the reliable determination of elemental abundances for many elements. Depth profiles of several elements are determined for two grains from the KJG residue. Each of the measured elements displays approximately homogeneous profiles through the grains, with abundances in agreement with existing literature data. The uniform depth profiles may represent formation in a stellar envelope with a stable composition, although homogenisation by secondary alteration processes cannot be ruled out.

A criptococose é uma doença invasiva capaz de apresentar-se de forma fatal podendo acometer pacientes imunocompetentes e imunocomprometidos. Os agentes etiológicos Cryptococcus neoformans var. grubii e C. neoformans var. neoformans apresentam distribuição cosmopolita, sendo as excretas de pombos o seu principal reservatório. Com o advento de terapias imunossupressoras e a pandemia de HIV, observou-se o aumento significativo de casos de pacientes com criptococose. Atualmente, o diagnóstico é baseado na apresentação clínica, na observação microscópica de líquor corado com tinta da Índia e/ou no isolamento em cultura. Neste trabalho desenvolveu-se um ELISA para detecção de anticorpos contra C. neoformans var. grubii em soro de pacientes utilizando como antígeno um extrato protéico total de uma linhagem clínica isolada de um paciente com criptococose (HC6). Foram testados através de ELISA 40 amostras de soros de pacientes com criptococose, sendo 67,5% positivos e 32,5% falsos negativos. Como controles negativos foram testados 82 amostras de soros de indivíduos hígidos, dos quais 26,82% apresentaram resultados positivos para os testes realizados. Para testar a reatividade cruzada, foram utilizadas 10 amostras de pacientes com histoplasmose (20% de reatividade cruzada), 9 amostras de pacientes com paracoccidioidomicose (66,6% de reatividade cruzada), 9 amostras de pacientes com candidose (13,3% de reatividade cruzada) e 7 amostras de pacientes com aspergilose (14,28% de reatividade cruzada). Visando solucionar o problema da reatividade cruzada, identificamos proteínas antigênicas de C. neoformans var. grubii por eletroforese bidimensional seguida por western blot e espectrometria de massa (MALDI-TOF MS). Das 75 amostras analisadas, quatro foram identificadas: uma proteína hipotética, 2 isoformas de HSPs 70 e uma catalase-2. As proteínas identificadas apresentaram baixa similaridade com ortólogas de outros fungos patogênicos, sendo, dessa forma, possíveis alvos para a padronização do ELISA e diagnóstico da criptococose. / Cryptococosis is an invasive and potentially fatal disease. Cryptococcus neoformans is the etiological agent, which can affect both immunocompromised and immunocompetent individuals. C. neoformans var. grubii and C. neoformans var. neoformans are cosmopolitan and their major natural reservoir is the excrement from pigeons. With the advent of immunosupressor therapies and the pandemic HIV infection, a significant augmentation of cryptococosis cases in humans was observed. Nowadays cryptococcosis diagnosis is based on the clinical presentation, India ink sample preparation methods and/or in vitro culture isolation. In this work we had developed an ELISA to detect antibodies against C. neoformans var. grubii in serum from patients with cryptococcosis using as antigens a whole cell protein extract from a clinical cell line isolate (HC6). Sera from 40 patients with cryptococcosis were tested by ELISA. From these, 67.5% were positives and 32.5% were false-negatives. As a negative control 82 samples from health subjects were also tested, from these 26.82% were positives. To test cross-reactivity, samples from 10 patients with histoplasmosis (20% cross-reactivity), 9 from patients with paracoccidioidomicosis (66.6% cross-reactivity), 9 from patients with candidosis (13.3% cross-reactivity) and 7 from patients with aspergilosis (14.28% cross-reactivity) were tested. To solve the cross-reactivity problem, we searched immunogenic proteins which were specific to C. neoformans var. grubii applying two-dimensional polyacrylamide gel electrophoresis (2DE-PAGE) followed by western blot and mass spectrometry (MALDI-TOF MS). From the 75 sample analyzed, four were identified: one as a hypothetic protein, two HSPs 70 isoforms and the protein catalase 2. These proteins showed low similarity with orthologues from other pathogenic fungi, and are potential targets to further of the standardizing cryptococosis diagnosis by ELISA.

abstract: The ability of microalgae to be mass cultivated and harvested for production of pharmaceuticals, nutraceuticals, and biofuels has made microalgae a focal point of scientific investigation. However, negative impacts on production are essentially inevitable due to the open design of many microalgae mass culture systems. This challenge generates a need for the consistent monitoring of microalgae cultures for health and the presence of contaminants, predators, and competitors. The techniques for monitoring microalgae cultures are generally time-intensive, labor-intensive, and expensive. The scope of this work was to evaluate the use of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) as a viable alternative for the characterization of microalgae cultures. The studies presented here evaluated whether MALDI-TOF MS can be used to: 1) differentiate microalgae at the species and strain levels, 2) characterize simple mixtures of microalgae, 3) detect changes in a single microalgae culture over time, and 4) characterize growth phases of microalgae cultures. This research required the development of a MALDI-TOF MS microalgae analysis protocol for organism characterization. The results yielded in this research showed that MALDI-TOF MS was just as accurate, if not more so, than molecular techniques for the identification of microalgae at the species and strain levels during its logarithmic growth phase. Additionally, results suggest that MALDI-TOF MS is sensitive enough to characterize simple mixtures and detect changes in cultures over time. The data presented here suggests the next logical step is the development of protocols for the near-real time health monitoring of microalgae cultures and detection of contaminants using MALDI-TOF MS. / Dissertation/Thesis / Masters Thesis Biology 2016

A criptococose é uma doença invasiva capaz de apresentar-se de forma fatal podendo acometer pacientes imunocompetentes e imunocomprometidos. Os agentes etiológicos Cryptococcus neoformans var. grubii e C. neoformans var. neoformans apresentam distribuição cosmopolita, sendo as excretas de pombos o seu principal reservatório. Com o advento de terapias imunossupressoras e a pandemia de HIV, observou-se o aumento significativo de casos de pacientes com criptococose. Atualmente, o diagnóstico é baseado na apresentação clínica, na observação microscópica de líquor corado com tinta da Índia e/ou no isolamento em cultura. Neste trabalho desenvolveu-se um ELISA para detecção de anticorpos contra C. neoformans var. grubii em soro de pacientes utilizando como antígeno um extrato protéico total de uma linhagem clínica isolada de um paciente com criptococose (HC6). Foram testados através de ELISA 40 amostras de soros de pacientes com criptococose, sendo 67,5% positivos e 32,5% falsos negativos. Como controles negativos foram testados 82 amostras de soros de indivíduos hígidos, dos quais 26,82% apresentaram resultados positivos para os testes realizados. Para testar a reatividade cruzada, foram utilizadas 10 amostras de pacientes com histoplasmose (20% de reatividade cruzada), 9 amostras de pacientes com paracoccidioidomicose (66,6% de reatividade cruzada), 9 amostras de pacientes com candidose (13,3% de reatividade cruzada) e 7 amostras de pacientes com aspergilose (14,28% de reatividade cruzada). Visando solucionar o problema da reatividade cruzada, identificamos proteínas antigênicas de C. neoformans var. grubii por eletroforese bidimensional seguida por western blot e espectrometria de massa (MALDI-TOF MS). Das 75 amostras analisadas, quatro foram identificadas: uma proteína hipotética, 2 isoformas de HSPs 70 e uma catalase-2. As proteínas identificadas apresentaram baixa similaridade com ortólogas de outros fungos patogênicos, sendo, dessa forma, possíveis alvos para a padronização do ELISA e diagnóstico da criptococose. / Cryptococosis is an invasive and potentially fatal disease. Cryptococcus neoformans is the etiological agent, which can affect both immunocompromised and immunocompetent individuals. C. neoformans var. grubii and C. neoformans var. neoformans are cosmopolitan and their major natural reservoir is the excrement from pigeons. With the advent of immunosupressor therapies and the pandemic HIV infection, a significant augmentation of cryptococosis cases in humans was observed. Nowadays cryptococcosis diagnosis is based on the clinical presentation, India ink sample preparation methods and/or in vitro culture isolation. In this work we had developed an ELISA to detect antibodies against C. neoformans var. grubii in serum from patients with cryptococcosis using as antigens a whole cell protein extract from a clinical cell line isolate (HC6). Sera from 40 patients with cryptococcosis were tested by ELISA. From these, 67.5% were positives and 32.5% were false-negatives. As a negative control 82 samples from health subjects were also tested, from these 26.82% were positives. To test cross-reactivity, samples from 10 patients with histoplasmosis (20% cross-reactivity), 9 from patients with paracoccidioidomicosis (66.6% cross-reactivity), 9 from patients with candidosis (13.3% cross-reactivity) and 7 from patients with aspergilosis (14.28% cross-reactivity) were tested. To solve the cross-reactivity problem, we searched immunogenic proteins which were specific to C. neoformans var. grubii applying two-dimensional polyacrylamide gel electrophoresis (2DE-PAGE) followed by western blot and mass spectrometry (MALDI-TOF MS). From the 75 sample analyzed, four were identified: one as a hypothetic protein, two HSPs 70 isoforms and the protein catalase 2. These proteins showed low similarity with orthologues from other pathogenic fungi, and are potential targets to further of the standardizing cryptococosis diagnosis by ELISA.

Geólogo / La nanogeociencia así como la mineralogía ambiental son áreas de investigación que gracias a nuevos avances tecnológicos se están expandiendo rápidamente en múltiples direcciones enfocadas en la detección, caracterización y comprensión de fases no cristalinas, pobremente cristalinas y fases mixtas amorfo-cristalinas, así como también materiales nanométricos. En este contexto, los procesos no clásicos de nucleación y crecimiento cristalino presentes en soluciones acuosas representan un campo emergente que surge como alternativa al enfoque clásico con el cual ha sido abordado este tema (diferentes etapas de unión de monómeros básicos -átomos, iones o moléculas- entre sí). Estos procesos utilizan polímeros y nanopartículas más pequeñas como unidades básicas precursoras del crecimiento cristalino. La formación de nanopartículas de aluminio (comunes tanto en entornos naturales como procesos industriales), y más concretamente la precipitación de hidrobasaluminita (Al4SO4(OH)10 · 12-36H2O), puede ser considerada como el proxy perfecto para el estudio de estos procesos no clásicos. Para caracterizar las especies poliméricas generadas durante la síntesis acuosa de nanopartículas de hidrobasaluminita la metodología utilizada en este trabajo es el análisis mediante ionización por electrospray acoplada a un espectrómetro de masas de tiempo de vuelo (ESI-TOF/MS). Esta técnica fue aplicada a cuatro soluciones de Al2(SO4)3 · 18H2O resultando en la identificación de 38 especies poliméricas catiónicas, ratificando la utilidad de esta técnica en el estudio de estos procesos no clásicos de cristalización permitiendo generar un primer volumen de datos para la elaboración de una base de datos con la masa y la fórmula de los polímeros de aluminio más comunes detectados en el sistema acuoso Al-S-O-H. Los resultados mostraron una especiación variable, donde las especies reconocidas abarcan polímeros basados en Al, Al2, Al3, Al4, Al5, Al6 y algunos más complejos como Al11 o Al13. Dentro de los parámetros estudiados el efecto del pH fue el más notable de todos. Observándose una clara dependencia de este factor en la formación de complejos de mayor tamaño y carga. Por otra parte, la concentración de Al en la solución también mostró injerencia sobre la especiación de las muestras. Finalmente, la metodología y resultados obtenidos, a pesar de las limitaciones asociadas, permiten acercarse a una caracterización más certera de los procesos que rigen la precipitación de hidrobasaluminita y la naturaleza de las especies que participan en éstos.

Yeasts of genus Cryptococcus belong to the Basidiomycetes, a wide group with different geographical sharing in nature. Many of them rank among human pathogens that endanger immunocompromised patients. Thanks to the big diversity at the level of subspecies, various species of the genus Cryptococcus show different molecular characteristics. Their identification is difficult because of the presence of polysaccharide capsule that surrounds the cell of some species. This work deals with the identification of species occurring in meadows and gardens. The 79 yeasts samples are identified by MALDI-TOF MS. The influence of different culture media on the identification results is monitored simultaneously with the identification. Since a capsule is present in many species, another parameter to be monitored is the influence of the sample preparation method and the matrix on the identification. 51 samples of yeasts of the genus Cryptococcus are identified at the species level in the experimental part. Selected samples are further subjected to the determination of characteristics by conventional microbiological methods. The determined parameters are the presence of urease, radial growth constant, susceptibility to antimycotics, fermentation and assimilation of sugars, growth in the presence of alcohols and growth in the absence of vitamins. The yeast samples are classified into yeast species based on microbiological results. Biotyping resulted in identification of selected samples in the species Filobasidium magnum, Filobasidium oeirense and Filobasidium wieringae. Other samples showed ambiguous identification. As these species have the same properties, they could not be distinguished by the selected microbiological tests.

Cryptococcus laurentii has been classically considered a saprophytic species, although several cases of human and animal infection have been already reported. This species is reported to be heterogenous. The taxonomy of yeast Cryptococcus laurentii was always highly ambiguous. The application of molecular biology and bioinformatic methods led to dividing of searched strains to two distinct phylogenetic groups, some varieties were recognized as species and the locution „Cryptococcus laurentii group“ was introduced. The taxonomy of this group is likely not definitive and with advancing knowledge will change. Our aim was the identification of individual species within this group based on matrix-assisted laser desorption/ionization – time of flight mass spectrometry (MALDI – TOF MS), which has recently been described as a rapid, reliable, cost-effective and powerful tool for analyzing of microorganisms, even on variety level. Generally, the yeasts of genus Cryptococcus form highly resistant polysaccharide capsules and produce large amount of extracellular polysaccharides, therefore belong to so called „difficult“ cases for biotyping. The experimental protocol has been optimized for MS analysis of this genus on the selected strains of Cr. neoformans, Cr. laurentii and Cr. magnus from the Culture Collection of Yeasts (CCY).Thirty-three strains, originally classified as Cryptococcus laurentii has been identified by chosen method. These strains were distributed into six different groups according their spectra similarities. It was selected at least one strain of each group, which was classified based on the sequence analysis of the D1/D2 domains of the LSU rRNA gene. This strain (with known sequence) became representative for its group. Type strain of Cryptococcus laurentii (CCY 17-3-2) belongs to the group I. Its MS spectrum of ribosomal proteins differ from mass spectra of all other biotyped species, even with strains identified as Cryptococcus laurentii was the similarity of the spectra low, which could be caused by identification of two different varieties. The group II is represented by Cryptococcus laurentii CCY 17-3-17. Except this strain, thirteen more strains belong to the group II. The group III represents Cryptococcus flavescens CCY 17-3-29. This group included 12 additional strains with almost identical mass spectra. Group IV included only one strain (CCY 17-3-13), which was identified as Cryptococcus carnescens based on gene sequence analysis. Similarly, one representative (CCY 17-3-5) has the group V. Strain CCY 17-3-5 was identified as Cryptococcus flavus. The last group VI of three members represents strain 17-3-35 identified as Bulleromyces albus. While Cr. laurentii and Cr. flavescens belong to phylogenetic group I and Cr. carnescens to the phylogenetic group II, four strains giving two types of different MS spectra and identified as Cr. flavus (1 strain) and Bulleromyces albus (3 strains) were excluded from „Cr. laurentii group.“

We studied the topic of depth sensing camera calibration. Two devices Microsoft Kinectand Swissranger SR-4000, that work on different physical principles, were investigated.Both 3D cameras were described and subjected to experiments in order to evaluatetheir performance. Several systematic error sources were identified and we proposedmethods to compensate for them. A comparison of reconstruction performance of both3D cameras and a stereo-pair of conventional cameras was presented. Finally, we showedan application of the depth sensing camera together with conventional color camera inarea of complex scene reconstruction. / <p>Validerat; 20110825 (anonymous)</p>

The goal of this thesis is to determine if Sinorhizobium meliloti can be useful as a sentinel soil microorganism for assessing the impacts of contaminant stressors on the metabolome of a microorganism. Not only is a good deal known about this organism, but it is an important organism in agriculture. Moreover, the currently available gene array and a large library of gene fusion can be used as facile pathways to explore genetic and genomic impacts in addition to metabolomic impacts of contaminants, should such studies be deemed worthwhile. In this study, the polar metabolome of the soil microorganism, Sinorhizobium meliloti, has been analyzed by LC-ESI-MS using a HILIC column coupled to a medium mass resolution time-of-flight mass spectrometer. This approach has resulted in the retention (k' > 0.7) of over 300 polar metabolites as detected in both positive ion and negative ion modes. These data do not include ions corresponding to adduct ions, isotopic features or ions resulting from in-source decay processes. The retained peaks showed excellent linear responses and did not suffer from ion suppression, a common problem in flow-injection ESI analysis. This methodology has been applied to the analysis of S. meliloti exposed to fluorene, a common PAH contaminant, and to a coal tar fraction containing low molecular mass PAHs. Multiple cultures of S. meliloti were grown on M9 glucose minimal medium in the absence and presence of fluorene (0.14 mg/L and 1.4 mg/L) and a PAH mixture (total PAH concentrations of 0.14 mg/L and 1.4 mg/L). Analyses of biological replicates were performed in pentuplicate. The retention times of the resulting chromatograms were aligned, peak areas determined and the resulting data processed using PCA and OPLS-DA methods. The retention time reproducibilities of peaks were within ± 10 seconds and the biological variabilities of over 700 components averaged 23% ± 15% (n=25) . The impacts of fluorene exposures and PAH mixture exposures on the S. meliloti metabolomes (polar) caused significant changes in the metabolome. The lower concentration exposures had less of an impact than the higher dosages. Low dosages of both fluorene and the PAH mixture produced a similar metabolic response in S. meliloti, while at higher dosages the responses were more specific to each toxin. The use of SUS plots coupled with S-plots of the OPLS-DA analysis were particularly advantageous for the identification of metabolites of interest. Changes were seen in the levels of adenine, adenosine, glutamate, and aspartate, among others. In the future, the profiles of the non-polar metabolites of each of sample will be analyzed using a previously developed 'shotgun lipidomics' method. / Thesis / Master of Science (MS)

En contrôlant le passage para- et transcellulaire des composés du sang vers le cerveau (et inversement), la barrière hémato-encéphalique (BHE) constitue la « gardienne » du compartiment cérébral. Bien que relativement connu dans son aspect physiologique, le phénotype BHE des cellules endothéliales des capillaires cérébraux (BCECs) reste mal compris au regard des mécanismes moléculaires qui gouvernent son établissement et son maintien. Dans cette optique, à l’aide du modèle in vitro de BHE développé au laboratoire (co-culture de BCECs bovines et de cellules gliales de rats), nous avons réalisé deux études protéomiques comparatives afin d’identifier les protéines cytoplasmiques potentiellement impliquées dans l’induction et le maintien de ce phénotype: d’une part une approche qualitative sans marquage (label free) et d’autre part une approche quantitative grâce à un marquage isotopique préalable des protéines (isotope-coded protein label, ICPL). Les deux approches, label free et ICPL se sont révélées complémentaires et ont permis, respectivement, l’identification de 447 et de 412 protéines (dont 290 quantifiées). Quatre protéines d’un intérêt particulier dans le domaine de la BHE (phosphatase alcaline tissu-non spécifique, TNAP ; protéine 1 possédant un domaine d’homologie à Eps15, EHD1 ; superoxyde dismutase, SODC et homologue 7 de la protéine de la maladie de Parkinson PARK7, DJ-1) ont fait l’objet de caractérisations biochimiques approfondies et ouvrent des pistes d’investigation sur des potentielles voies cellulaires induites par les cellules gliales et impliquées dans le phénotype BHE. / The blood-brain barrier (BBB) controls the para- and transcellular crossing of compounds from blood to brain (and inversely) and establishes the “gatekeepers” of the brain. The major part of therapeutic drugs developed to fight the brain diseases is deemed inefficient in vivo due to the presence of the BBB that they are unable to cross. Although relatively well known in its physiological aspect, the BBB phenotype of brain capillary endothelial cells (BCECs) remains largely under known and misunderstood in regards of the molecular mechanisms that govern its establishment and its maintenance. To this goal, using the in vitro BBB model developed in the laboratory (co-culture of bovine BCECs with rat glial cells), we performed two differential proteomic studies to identify the main cytoplasmic proteins involved in the establishment and maintenance of this phenotype: a qualitative label free approach and a quantitative isotope-coded protein labeling (ICPL) approach.The two different approaches, label free and ICPL, are complementary and led to the identification of 447 and 412 proteins, respectively. Four proteins of particular interest for BBB (tissue-non specific alkaline phosphatase, TNAP; Eps15 homology domain containing protein 1, EHD1; superoxide dismutase, SODC and Parkinson disease protein 7 homolog PARK7, DJ-1) have been more deeply studied and they open new discovery prospects related to cellular pathways induced by glial cells and involved in the BBB phenotype.