Cette thèse a été consacrée à l’amélioration de méthodes en imagerie par spectrométrie de masse, et à leur utilisation pour l’analyse in situ de substances naturelles. Une première partie a été consacrée à développer une nouvelle méthode permettant d’acquérir en imagerie TOF-SIMS des images avec une résolution de 400 nm tout en préservant la résolution en masse. Pour cela, une extraction retardée des ions secondaires a été caractérisée et optimisée. Une seconde partie a eu pour objectif d’étudier le phénomène de duraminisation d’un arbre tropical de l’espèce Dicorynia guianensis, qui est l’un des plus exploités en Guyane française et dont le duramen est réputé être imputrescible. Les images par spectrométrie de masse TOF-SIMS enregistrées avec la méthode développée ont montré à l’échelle sub-micrométrique les changements métaboliques s’opérant autour de la zone de transition, où s’opère la duraminisation. Les techniques TOF-SIMS et MALDI-TOF ont ensuite été utilisées pour l’analyse d’une surface sur laquelle ont crû deux souches microbiennes en compétition. Les deux souches ont été extraites d’un if japonais (Cephalotaxus harringtonia), l’une étant un champignon endophyte (Paraconiothyrium variabile) et l’autre une bactérie pathogène à ce conifère (Bacillus subtilis). Les résultats ont montré que le champignon était capable d’hydrolyser les surfactines produites par la bactérie. Enfin, les imageries par spectrométrie de masse MALDI-TOF et TOF-SIMS sont deux méthodes de choix pour l’étude de modèle in vitro de ce qui pourrait se produire in vivo. / This thesis was devoted to the improvement of mass spectrometry imaging methods, and to their use for in situ analysis of natural substances. The first part of this thesis has been dedicated to the development of a new acquisition mode in TOF-SIMS imaging able to acquire images with a high spatial resolution of 400 nm while keeping a good mass resolution. For that, a delayed extraction of the secondary ions has been characterized and optimized. Then, a second part has been dedicated to the study of heartwood production in a tropical species named Dicorynia guianensis. This species is one of the most exploited in French Guiana for its heartwood which exhibits a good durability. Metabolic changes are shown by sub-micrometric resolution ion images recorded in and around the transition zone, where the heartwood formation occurs. Then, TOF-SIMS and MALDI-TOF have both been used to analyse the surface of a bacterial competition. Species have been isolated from a Japanese conifer (Cephalotaxus harringtonia), from which the stains are an endophitic fungi (Paraconiothyrium variabile) and a pathogenic bacteria of the conifer (Bacillus subtilis). The results have shown that the fungus is able to hydrolyze surfactines produced by the bacteria during the competition. Furthermore, both the MALDI-TOF and the TOF-SIMS mass spectrometry imaging are methods of choice to study in vitro models of what could happen in vivo.

Peanut skin, a low-value agriculture waste product, has drawn lots of research interest in recent years, due to its high content of A-type proanthocyanidins. A-type proanthocyanidins have been believed to contribute to cranberries' anti-UTI (urinary tract infection) effect. In this study, we compared the A-type proanthocyanidins in cranberry and peanut skin crude extracts using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Many similarities were found in the proanthocyanidin composition of cranberries and peanut skins. New oligomeric and polymeric proanthocyanidins in peanut skins, including heteroproanthocyanidins and proanthocyanidins with sugar moieties or galloyl esters, were tentatively identified. Solid phase extraction (SPE) and HPLC fractionation largely improved MALDI-TOF's ability to detect proanthocyanidins with high degrees of polymerization (DP). By analyzing the identified compounds in each fraction, we were also able to find some interesting elution pattern of the proanthocyanidins on the SPE cartridges and on the HPLC column. For example, the elution order on both the SPE cartridges and the diol phase column generally followed the DP. A-type proanthocyanidins tended to elute earlier than the B-type. Prodelphinidins retained much longer than other proanthocyanidins with the same DP. These findings may help researcher to identify future research directions and develop new separation methods to facilitate the identification of bioactive components in proanthocyanidin-rich plant extracts. / Ph. D.

The aim of this study was to optimize the sample preparation and methods for analysis of oligosaccharides of hyaluronic acid with MALDI- TOF-MS. The analysis was carried out on an Autoflex speed MADLI-TOF- MS instrument with both linear and reflectron mode. Matrices used in this study were 2,5-DHB and Super-DHB and type of matrix was chosen depending on the size of the analyzed oligosaccharides. The application of sample and matrix on the target that gave the most homogenous crystallization was sandwich and the laser power in the MALDI was kept at 65 %. Since it is known that salts and buffers interfere with the analysis, sample clean-up such as solid phase extraction (SPE) in pipette tips and dialysis was performed. SPE worked best for low mass oligosaccharides and provided high intensity and little noise. With SPE a concentration of the analyte could be done which was the advantage over dialysis. Dialysis worked well for larger oligosaccharides and mixtures of different sized oligosaccharides. Another way of using MALDI for biomolecule analysis is with TLC-MALDI. A fast and accurate separation was achieved and analysis could be done directly from the plate. The optimized methods were evaluated according to linearity and precision, LOD, mass accuracy and matrix stability. The linearity and precision was good in a higher concentration range (50 μg/mL and higher), but the test for limit-of-detection (LOD) indicated that concentrations from 20-30 μg/mL could be analyzed with no interference from the background. The mass accuracy was within the acceptable limits according to Bruker Daltonics when a mass calibration was done for each analyzed sample. The stability of the matrix in solution was difficult to study because of the day-to-day variation in intensities given by the MALDI-TOF-MS technique.

Ahlberg Cameras is a company that manufactures advanced camera systems and inspection equipment for the nuclear industry. Every nuclear plant shuts down their reactors approximately every 18 months to perform visual inspections of the vessels to find cracks and other damage. The company has received a request from Electric Power Research Institute (EPRI) to develop a distance meter that will operate in the reactor vessel, placed in an inspection camera. The device should measure the distance between the camera and an object, and the angle between them. The measurement is performed in air and underwater and the device has therefore a requirement to be waterproof and radiation tolerant.   This thesis work has studied different possible technologies and technically excluded the ones that are not suitable for the intended application. A large part of the study has been about whether sound or light is a good enough source to use in the different technologies. The study has excluded to use sound mainly because the reflection back to the receiver at large angles becomes too weak. The choice of technology stands between structured light and a self-designed trigonometry technology, both using lasers. Tests have been made to determine if laser light underwater can be observed by the camera and the results indicates that lasers work well enough for this kind of application. Further in-depth studies into the sources of errors and measurement accuracy are needed for determining which of the two technologies is the most suitable.

Aim: To assess SELDI-TOF MS technology as a tool for biomarker discovery in the stool and serum of colorectal cancer patients. Materials and Methods: 1.Initially a technique of analysis was developed and optimised using tumour samples and matched normal mucosa, obtained from the Tayside Tissue Bank. These samples were then analysed using SELDI on a PBS II Protein Chip Mass Spectrometer to identify abundant proteins. 2. A technique of stool preparation and subsequent SELDI analysis was developed and then optimised (CM10 chip at pH4) to allow comparison of faecal samples from cancer and controls. Faecal samples were then collected from cancer patients and controls and analysed. In addition, FOB testing was carried out on all stool samples from cancer and controls and subgroup analysis of spectras was performed controlling for FOB status. 3. A test set of cancer and normal serum samples was used to optimise the method of analysis using 4 different chip surfaces at differing pH. Serum samples were collected from cancer patients and normal controls and were analysed on the H50 chip. Serum was then depleted of major proteins in an attempt to improve the detection of peaks. The mass spectra from each sample type were compared to identify any common protein peaks. Results: 1. Tumour analysis methods were optimised using an initial 4 samples of tumour and normal mucosa. Analysis of 8 further paired samples showed protein peaks at 2826, 3374, 3444, 3489 and 10854 Da which were abundant in tumour and reduced in the normal mucosa. 2. In serum analysis the initial experiment of 10 cancer versus 10 normal revealed 4 peaks on the H50 chip (3479, 3364, 3434, 3700 Da) that had significantly higher mass to charge ratios in cancer. The experiment was repeated on the H50 chip using 92 cancers and 92 controls and 5 different peaks were identified (7901, 8124, 8566, 8799 and 17 409Da) as being significant but these had higher mass to charge ratios in the controls. After depletion of the serum samples of albumin, transferrin, haptoglobin, anti-trypsin, IgG and IgA SELDI-TOF analysis showed a greatly reduced profile that yielded no meaningful spectra. 3. Stool analysis revealed 5 protein peaks (4633, 16511, 33423, 37087 and 47026 Da) in colorectal cancer patients, which were absent in stools from controls with a sensitivity of 83% when using all 5 peaks. Degradation of the spectra was observed after prolonged storage of stool samples. Conclusions: A method of stool analysis has been developed that yielded valid peaks differentiating between cancer and normal, which warrant further research through protein identification. Serum analysis was not reproducible across experiments and depletion of major proteins failed to reveal the sub-proteome raising doubts about whether discovery-based serum proteomics can accurately detect cancer. SELDI-TOF was not able to demonstrate that any of the peaks present in the tumour analysis were present in the stool or the serum samples.

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Metronidazole is an essential component of the triple therapy regimen against Helicobacter pylori infection. The development of resistance towards metronidazole results in failure to eradicate H. pylori completely. The main aim of the investigation was to understand further the mechanism(s) of resistance in H. pylori. The investigation focussed upon studying the role and function of NADH oxidase in metronidazole resistance. The NADH oxidase levels were shown to be significantly higher in metronidazole susceptible strains than in resistant strains. The purification and characterisation of the enzyme responsible for the oxidation of NADH resulted in isolation of a protein shown to be catalase. The results suggest that NADH oxidase activity in susceptible strains is a function of a bifunctional catalase rather than that of a distinct enzyme. This was confirmed by isolation of catalase from E. coli cells containing cloned H. pylori catalase and demonstration that catalase and NADH activities co-purified. The catalase activity of the purified protein from the bacterial strains used was retained but the oxidation of NADH was not significant in the resistant strain. The base sequence of the catalase gene from the susceptible strain was determined and shown to be 99% identical to that from the cloned gene. The comparison of the derived amino acid sequence of catalase from H. pylori and Proteus mirabilis showed that the heme-binding site is highly conserved. The amino acids in the NAD(P)H binding site are conserved in both strain NCTC 11639 (Mtz s ) and the genomic strain ATCC 26695 (Mtz s) of H. pylori but show significant differences compared with P. mirabilis. A three-dimensional model of catalase from a metronidazole-susceptible H. pylori strain showed stearic hindrance around the NAD(P)H binding site and a substitution of an acidic for a basic residue within the phosphate binding site. Both effects could result in NAD(P)H being less tightly bound and, hence able to leave the catalase in exchange for NADH. Other substitutions may account for the ability of the modified binding site to oxidise NADH. The oxidation of NADH aids in the activation of metronidazole, which damages DNA. The absence of NADH oxidase activity in resistant strains results in the inability of the enzyme to activate metronidazole leading to resistance. The finding that this NADH oxidase activity is a function of a modified catalase in susceptible strains suggests a novel mechanism of metronidazole resistance in H. pylori.

Zugl.: München, Techn. Univ., Diss., 2009

Erlangen-Nürnberg, Univ., Diss., 2009.

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.