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.

Matrix assisted laser desorption/ionisation mass spectrometry (MALDI-MS) for small molecule analysis has been plagued with inherent problems associated with matrix interference. The matrix plays an important role in MALDI-MS where it has the ability to absorb UV energy from the laser employed and transfer it to the analyte, acts as a proton donor and protecting the analytes from being obliterated. For decades, research has been performed to eradicate matrix interference by matrix avoidance, finding alternative matrices, suppression through sample preparation methods and via chemical modification.In this investigation a number of the above mentioned approaches have been undertaken. First, a mesoporous silica powder, SBA-16, functionalised with a phenyl group to absorb UV from the MALDI-MS laser gave unfruitful results due to inhomogeneous dispersion of the SBA-16 powder. Therefore the same material was prepared but as a thin film and a homogeneously coated surface was generated with the phenyl group incorporated into the silica and this was compared with a conventional matrix, 2,5-dihydroxybenzoic acid (DHB). This was by far the most sensitive method which was accurate, with little background noise and importantly for small molecule analysis clear of matrix interference. Other surface systems were also tested such as graphene on copper and silver on copper, but the functionalised SBA-16 thin film remained the best. Graphite and 2B pencil were also investigated for MALDI-MS but were compared with conventional matrices (DHB and α-cyano-4-hydroxycinnamic acid (CHCA)) in a functional genomics study. The ability of all methods to find subtle phenotypic differences in various yeast strains was assessed with the help of multivariate data analysis (MVDA). Although DHB came out best, 2B pencil produce notably good separations that correlated nicely with the different genotypes. Therefore in addition to conventional matrices, 2B pencil should be considered for functional genomic studies when MALDI-MS is used as it is such a rapid and inexpensive method. Finally, chemical modifications were performed on amino acids where picolinic acid was used to attach a chromophore to the compounds, therefore, allowing UV absorption from the laser. Upon attaching the picolinate UV absorbing group, the amino acid compounds were detected LC-MS at an increased intensity of 10 to 100-fold. Moreover, enhanced separation in LC-MS was also observed.This project has successfully investigated alternative approaches to matrix-free MALDI-MS analysis. Functionalised SBA-16 thin films were by far the best method and this novel surface for MALDI-MS has the potential to transform small molecule analysis.

L’analyse d’échantillons du Patrimoine Culturel est primordiale pour la compréhension des techniques, la conservation des œuvres et leur restauration. Ces échantillons sont rares et précieux et l’analyse doit être effectuée sur une faible quantité de matière, ce qui nécessite le développement et l’optimisation de méthodes analytiques appropriées. L’objectif de ce travail de thèse a donc été de développer de nouvelles méthodes analytiques dans le but d’étudier les glycoprotéines et les polysaccharides de gommes végétales des échantillons du Patrimoine Culturel. Les macromolécules ont été séparées par chromatographie d'exclusion stérique et électrophorèse sur gel de polyacrylamide modifié, révélant la présence de poids moléculaires très élevés pouvant atteindre jusqu’à 1 à 2 millions de Dalton. Une stratégie analytique innovante basée sur la spectrométrie de masse a permis d’obtenir des empreintes caractéristiques de chaques gommes. La stratégie analytique développée a été appliquée avec succès sur un échantillon d'aquarelle daté de 1870 du Metropolitan Museum of Art (New York, USA). / The analysis of Cultural Heritage samples is critical for the understanding of the arstists' technique, the conservation and restoration of artworks. These objects under investigation are rare and precious and the amount of sample available for the analysis is usually very low, thus implying the development and the optimization of adapted analytical methodologies. The objective of this PhD was to develop new analytical methods to study glycoproteins and polysaccharides from plant gums in Cultural Heritage samples.These macromolecules have been separated by size exclusion chromatography and modified polyacrylamide gels, which allowed to reveal the presence of proteins with molecular weights up to 1-2 million Dalton. A novel analytical strategy based on mass spectrometry allowed to obtain the caracteristic fingerprint of each plant gum. This developed method was successfully applied on a watercolor sample dated from 1870 supplied by the Metropolitan Museum of Art (New York, USA).

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.“

Sepsis is a worldwide health condition. It is caused by disproportionatly large immunity system response for patogene presence. Fast and accurate diagnosis of sepsis can make difference between life and death. For clinical diagnosis of sepsis is used serum protein procalcitonin (PCT) as biomarker. Procalcitonin concentration level in patient bloodstream increases up to thousand times in short time period. Severity of sepsis can be determined by correlation with its concentration in bloodstream. To determine PCT level in patient bloodstream a broad variety of specialized instrument is used. All methods have same principle of measurement - PCT-antibody interaction. Procalcitonin level is then quantified by calibration curve method. During these measurements non-specific protein-antibody interactions can occur and distort the quantification of PCT level. Mass spectrometry due to its properties comes into consideration as an alternative method, that can be used for PCT determination. Aim of this diploma thesis was in situ enrichment of PCT on surface modified affinity carriers with immobilized antibody against PCT. These carriers are compatible with matrix assisted laser desorption/ionization time of flight mass spectrometry. Mass spectrometry provides mass spectrum, where PCT and other signals...

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L'émergence de disciplines post-génomiques, telles que la protéomique et la métabolomique, requiert le développement d'outils analytiques toujours plus performants afin de déterminer, respectivement, l'ensemble des peptides et protéines et des composés organiques de faible masse moléculaire présents dans un milieu biologique. En raison de sa sensibilité, spécificité et rapidité d'acquisition des données, la désorption/ionisation laser assistée par une matrice (MALDI) constitue une des méthodes d'ionisation majeure en spectrométrie de masse (MS) permettant d'envisager les analyses de ces composés. Cependant, elle présente des limitations pour la détection de petites molécules (<700 Da) due à la présence des ions de matrice dans les basses masses du spectre. Dans ce contexte, le potentiel de différentes techniques LDI alternatives a été évalué dans le cadre de la détection de peptides synthétiques de compositions et de tailles variées. Dans le cadre de cette thèse, de nouvelles stratégies analytiques LDI-MS et LDI-MS/MS basées sur l'utilisation de matrices inertes ont été développées. Pour ce faire, des substrats, à base de silice et de titane présentant différentes structurations, ont été utilisés pour assister la désorption/ionisation sans ajout de matrice organique. L'optimisation des méthodologies a été réalisée, puis l'évaluation de la sensibilité et de la reproductibilité des techniques a ensuite été appréciée. Les problématiques de discrimination spectrale dans le cas d'analyses de mélanges de peptides synthétiques et ou issus de digestats trypsiques de protéines ont été abordées afin de valider ces méthodologies LDI pour des applications en protéomique. Les performances des méthodes ont été comparées à celles obtenues dans des stratégies LDI assistées par des matrices organiques (MALDI) pour des échantillons de peptides synthétiques seuls et en mélange ainsi que de quatre digestats trypsiques issus du Cytochrome C (12 kDa), de la β-Caséine (24 kDa), de l'albumine de sérum bovin (BSA, 66 kDa) et du fibrinogène (340 kDa). Un second aspect a consisté en l'analyse de peptide en spectrométrie de masse en tandem. Pour cela, des expériences de dissociation de peptides en fragmentation basse et haute énergie respectivement sur des appareillages de type ESI-QqTOF et MALDI-TOF/TOF ont été menées. Les résultats obtenus ont contribué à une meilleure compréhension du séquençage peptidique et ont démontré des comportements particuliers propres à certaines séquences observés quelles que soient les méthodes d'activation vibrationnelle employées. La présence de résidus basiques, à partir du moment où ils ne se trouvent pas en position C-terminale, a été déterminante pour déclencher des voies de fragmentation en compétition avec les dissociations bx-yn attendues. Ces comportements doivent être impérativement pris en compte par les logiciels de séquençage. / The advent of proteomics and metabolomics require the development of highly efficient analytical tool in order to detect and identify peptides and proteins as well as small organic compounds present in biological media. Due to its sensitivity, specificity and speed of data acquisition, Matrix-Assisted Laser Desorption/Ionization constitutes one of the major ionization methods in mass spectrometry suitable for the analyses of biomolecules. However the sensitive detection of low molecular weight compounds (<700 Da) is most of the time troublesome, being hampered by the production of matrix ions in the low mass range. In that case, the potency of various alternative LDI techniques based on inert ionization promoting substrates was evaluated for the detection of synthetic peptides presenting wide sequence diversity. Silicon and titanium based materials exhibiting different physico-chemical properties were probed for LDI-MS and LDI-MS/MS analyses of the designed model peptides. These methods, which were devoted of the use of any organic matrix, were optimized through a large set of experiments, taking particular attention to detection sensitivity and reproducibility. Spectral discrimination was another matter of concern, especially in the case of peptide mixture analyses which is encountered in proteomics for tryptic digest elucidation. The performances of the design LDI methods were compared with the original MALDI technique for peptide detection and sequencing from various samples i.e. pure and mixed synthetic peptides, and four tryptic digests issued from Cytochrome C (12 kDa), β-Casein (24 kDa), Bovin serum albumin (BSA, 66 kDa) and fibrinogen (340 kDa). A second research topic dealing with peptide sequencing by MS/MS technologies was pursued in order to contribute to the knowledge of the fragmentation rules. Vibrational activation methods through various mass analyzer configurations (MALDI-TOF/TOF, ESI-QqTOF) were investigated. Specific dissociation behaviors were extracted from the recorded MS/MS data sets. The presence of basic residues, provided that they are not located at the peptide C-terminal end, triggered specific backbone fragmentation in competition to the expected bx-yn pathway. This was found to be a critical issue to be considered by sequencing softwares.