Les champignons produisent une grande variété de composés/métabolites biologiquement actifs qui peuvent être utilisés à des fins médicinales et pharmaceutiques. Les mitorubrines, membres de la famille des azaphilones, constituent un ensemble particulièrement intéressant de métabolites secondaires, présentant une grande étendue d'activités biologiques (e.g. antimicrobienne, antibactérienne, antipaludique). Ce travail présente le développement de plusieurs approches de spectrométrie de masse permettant de résoudre la diversité structurelle naturelle et la complexité des azaphilones extraits des champignons Hypoxylon fragiforme. La première partie de ce manuscrit est dédiée au développement et à la validation d'une méthodologie analytique impliquant la chromatographie liquide couplée à la spectrométrie de masse haute résolution pour la détection efficace et précise de traces d'azaphilones dans des extraits fongiques complexes. En outre, des expériences de spectrométrie de masse en mode tandem (par dissociation induite par collision, CID) et d'échange hydrogène/deutérium ont été effectuées pour élucider et caractériser les azaphilones et leurs analogues azotés chez Hypoxylon fragiforme. La deuxième partie est consacrée à l'application de ces différentes stratégies analytiques pour la caractérisation approfondie d'une nouvelle famille de métabolites secondaires dérivés des azaphilones, les mitorubramines. Enfin, ces différents métabolites secondaires ont été purifiés pour confirmer leur structure chimique par spectroscopie RMN

In Chapter I is a general description of novel metal complexes which hydrolytically cleave peptides, proteins, DNA, and other biological molecules. These reagents are becoming the more important as potential therapeutic agents. A panel of ligands was investigated for coordination to ZrIV and other metals in groups 4, 5, and 6 to effect the greatest degree of hydrolysis. Chapter II describes a ZrIV complex which is capable of hydrolyzing a 30 amino acid peptide, insulin chain B, with amino acid specificity. Oxidized insulin chain B peptide was hydrolyzed after only 4 h of treatment at pH 7.0 and 60 °C using ZrCl4 in the presence of 4,13-diaza-18-crown-6. MALDI-TOF and ESI LC-MS mass spectra indicated that insulin chain B was hydrolyzed by ZrIV at the Gly8-Ser9, Ser9-His10, and Gly20-Glu21 amide bonds within the oligopeptide. To our surprise, the cysteine sulfonic acid sequences Cys(SO3H)7-Gly8 and Cys(SO3H)19-Gly20 were also cleaved. To the best of our knowledge, this constitutes the first example of metal-assisted hydrolysis of a Cys(SO3H)-Xaa amide bond. This is significant in light of the fact that cysteine sulfonic acid formation in proteins is triggered by oxidative stress and has been associated with amyloid fibril formation, Parkinson’s disease, and other deleterious, physiological processes. Chapter III describes the metal-assisted hydrolysis of sphingomyelin which is a principle phospholipid component of animal cell membranes. The sphingomyelin assays showed evidence of metal-assisted hydrolysis after 20 h of treatment at lysosomal pH 4.8 and cytosolic pH 7.0 at both physiological temperature 37 °C and 60 °C. The metal ion CeIV was the most reactive, followed by ZrIV, and then HfIV. The goal of this work is to develop metal-based reagents to reverse the lethal build-up of sphingomyelin that occurs in lysosomes of patients suffering from Niemann-Pick disease.

Blumeria graminis f. sp. hordei is a biotroph pathogen that causes powdery mildew disease in barley. In this study, Pallas01 and Pallas03 barley lines having Mla1, Ml (Al2) and Mla6, Mla14 R-genes were inoculated with Bgh103(64/01) race of the Blumeria graminis f. sp. hordei having avirulence and virulence to Pallas01 and Pallas03, respectively. The proteins were isolated from the three biological replicates of 12, 24, and 48 hpi samples following the method in Rampitsch et al., 2006. These there biological replicates of three time points together with the mock inoculated plant proteins were separated on 2D-PAGE using IPG strips of 4-7 pH values as three technical replicates, resulting 108 gels. The gels were analyzed using PdQuest (Bio Rad) in order to assess up- or down-regulated protein spots by comparing against controls and the samples having resistance or susceptible responses with each other. According to the analysis, 36 proteins were found to be differentiated and among them 18 proteins were found up-regulated and 8 proteins were found down-regulated. The spots were manually v excised and subjected to the nano-LC-ESI-MS/MS analysis (Proteome Factory, Germany). The MASCOT algorithm was used for identification of the possible proteins. The experimental pI and MW values were used for selecting the differentiated proteins from the mass results. The relative abundance of each of the 38 identified polypeptides was calculated in terms of spot intensity. The majority of the most abundant proteins were found to be carbohydrate metabolism related. The relative distribution of the proteins into four main functional categories was taken into consideration. Statistical tests (Students&amp / #8223 / T-test) were carried among the identified proteins in order to reveal statistically significant proteins throughout the study. By making a WoLF PSORT search, subcellular localization of the proteins was predicted. Accordingly, most of the proteins were found to be located in cytoplasm or chloroplast.

La dégradation protéolytique du collagène de type II est considérée comme étant un facteur majeur dans le processus irréversible de dégradation de la matrice cartilagineuse lors d’ostéoarthrose. Outre les collagénases de la famille des métaloprotéinases de la matrice (MMP-1, -8, -13), la cathepsine K est parmi les seules enzymes susceptibles de dégrader la triple hélice intacte du collagène de type II, devenant ainsi un élément pertinent pour les recherches sur l’ostéoarthrose. L’objectif à court terme de notre étude consiste en l’identification et la caractérisation de sites de clivage spécifiques de la cathepsine K sur le collagène de type II équin. La technique d’électrophorèse SDS-PAGE 1D permet la visualisation des produits de digestion et la validation des résultats de la caractérisation moléculaire des fragments protéolytiques. La caractérisation est réalisée en combinant la digestion trypsique précédant l’analyse HPLC-ESI/MS. Les résultats ont permis d’établir les sites, présents sur la carte peptidique de la molécule de collagène de type II équin, des 48 résidus prolines (P) et 5 résidus lysines (K) supportant une modification post-traductionnelle. De plus, 6 fragments majeurs, différents de ceux produits par les MMPs, sont observés par SDS-PAGE 1D puis confirmés par HPLC-ESI/MS, correspondant aux sites suivants : F1 [G189-K190], F2 [G252-P253], F3 [P326-G327], F4 [P428-G429], F5 [P563-G564] et F6 [P824-G825]. Le fragment F1 nouvellement identifié suggère un site de clivage différent de l’étude antérieure sur le collagène de type II bovin et humain. L’objectif à long terme serait le développement d’anticorps spécifiques au site identifié, permettant de suivre l’activité protéolytique de la cathepsine K par immunohistochimie et ÉLISA, dans le cadre du diagnostic de l’ostéoarthrose. / The proteolytic degradation of type II collagen is believed to be mainly an irreversible event in the process of cartilage matrix degradation in osteoarthritis. Cathepsin K is the most active enzyme protease outside the matrix metalloproteinase (MMP) family (MMP 13, -8, -1) capable of degrading the intact triple helical type II collagen. The short term objective of our study was to characterize the specific cleavage sites of CK on type II collagen. Our long term goal is to develop antibodies specific to these sites to develop biomarkers to detect it’s cleavage, for the early diagnosis of OA. Thus, in order to achieve our first goal, Cathepsin K cleavage of equine type II collagen was first examined by SDS-PAGE electrophoresis. Molecular characterization of proteolytic fragments, and therefore cleavage sites, was performed using tryptic digestion followed by LC-ESI/MS analysis to establish a comprehensive peptide map which was used as a template to identify specific proteolytic cleavage by cathepsin K. Comprehensive peptide mapping provided information on post-translational modifications and permitted the identification of 48 proline (P) and 5 lysine (K) residues that were subject to post translational modification. Six major fragments were observed on 1D SDS-PAGE and confirmed by HPLC-ESI/MS including F1 [189-190], F2 [252-253], F3 [326-327], F4 [428-429], F5 [563-564] and F6 [824-825]. The observed F1 fragment showed that cleavage was three residues N-terminal to the site reported previously for bovine type II collagen. These new findings will be used to develop new analytical methods to quantify biomarkers associate to equine type II collagen degradation in osteoarthritis patient and/or to support the development of new treatments.

Chronic, noncommunicable diseases such as chronic fatigue syndrome (also known as myalgic encephalomyelitis) are rapidly becoming a worldwide epidemic that profoundly affects public health and productivity. Chronic fatigue syndrome (CFS) is characterised by severe and debilitating fatigue and although its etiology is still unknown, recent studies have found considerable evidence that mitochondrial dysfunction and oxidative stress might be responsible for the underlying energy deficit in these patients. Adenine and pyridine nucleotides could be used as potential biomarkers for energy related disorders such as chronic fatigue syndrome because of their various functions in the energy and redox pathways. The first part of this study focussed on developing a liquid chromatography electrosprayionisation tandem mass spectrometry (LC-ESI-MS/MS) method for the quantification of these nucleotides in blood samples. Due to the instability of nucleotides in biological matrices it was also necessary to find a suitable extraction method that would be able to stop enzymatic activity via protein precipitation. Out of the four extraction methods investigated during this study, deproteinisation of whole blood samples with perchloric acid produced the highest nucleotide abundances. Although nucleotide standards were found to be stable in perchloric acid, nucleotide levels in blood samples were not stabilised by addition of perchloric acid. The second part of this study consisted of measuring the nucleotide levels in blood samples of controls and possible CFS patients in order to test the proof of concept of the new LCESI- MS/MS method. Despite changes in the nucleotide levels due to perchloric acid and problems with nucleotide instability, it was still possible to distinguish between the two groups based on the results obtained with the new LC-ESI-MS/MS method. The newly developed LC-ESI-MS/MS method proved to be reliable and adequate for nucleotide quantification in whole blood samples, thus the aim of this study was achieved. / MSc (Biochemistry), North-West University, Potchefstroom Campus, 2014

In the past couple of decades, the discovery that iron is a limiting nutrient in large regions of the ocean has spurred much research into characterizing the biogeochemical controls on iron cycling. While Fe(II) is soluble at circumneutral pH, it readily oxidizes to Fe(III) in the presence of oxygen. Fe(III) is highly insoluble at circumneutral pH, presenting organisms with a bioavailability paradox stemming from the physiological challenge of using a solid phase mineral for assimilatory or dissimilatory purposes. Interestingly, dissolved organic-Fe(III) complexes can be stable in seawater in the presence of oxygen, and an active flux of these complexes has recently been measured in estuarine sediments. Their sources and biogeochemical role, however, remain poorly understood. In this work, a suite of field and laboratory techniques were developed to quantify diagenetic processes involved in the remineralization of carbon in marine sediments in situ, investigate the role of these organic-Fe(III) complexes in sediment biogeochemistry, and characterize the composition of the ligands possibly involved in the solubilization of Fe(III) in marine sediments. The first-of-its-kind in situ electrochemical analyzer and HPLC was used to better constrain diagenetic processes that may lead to the formation of dissolved organic-Fe(III) complexes in the Altamaha estuary and Carolina slope. An intensive study of the Satilla River estuary reveals that dissimilatory iron-reduction contributes to the formation of sedimentary organic-Fe(III) complexes, which are demonstrated to serve as an electron acceptor in subsequent incubations with a model iron-reducing microorganism. Similar observations in deep-sea slope and abyssal plain sediments fed by the Mississippi and Congo Rivers suggest that dissimilatory iron reduction may represent an important component of carbon remineralization in river-dominated ocean margin sediments that may be currently underestimated globally. To confirm that these organic-Fe(III) complexes are produced during microbial iron reduction, novel separation schemes were developed to extract and identify Fe(III)-binding ligands from sediment pore waters. Preliminary results reveal the presence of a few select low-molecular weight compounds in all pore waters extracted, suggesting they might be endogenous ligands secreted by iron-reducing bacteria to non-reductively dissolve Fe(III) minerals prior to reduction.

Mass spectrometry was used to study two disparate transformations: in an applied project, the supposed degradation of perfluorooctanesulfonate (PFOS); and in a fundamental study, the Suzuki-Miyaura (SM) reaction was investigated in detail. The first investigation revealed that published methods to degrade PFOS were ineffectual, with apparent decreases being associated with adsorption onto available surfaces. In the Suzuki-Miyaura reaction, a dynamic series of equilibria were observed, and there is no direct evidence of a single pathway. Instead, there appear to be two mechanisms which are active in different conditions (one fluoride, one aqueous). Studies were initiated into the related SM polycondensation reaction and the hydrolysis of aryltrifluoroborates, the former indicating a step-growth mechanism, and the latter indicating a dynamic series of equilibria which are very sensitive to experimental conditions. Processing and interpretation of mass spectrometric data was a significant part of all of these projects, so a python framework was developed to assist in these tasks and its features are also documented herein. / Graduate / 0488 / 0486 / larsy@uvic.ca

La diversité et la distribution des cyanobactéries dans les écosystèmes aquatiques conduisent à des effets nuisibles dans l’eau par la production d’une variété de toxines cyanobactériennes qui présentent des risques pour la faune et la santé humaine. Différentes techniques analytiques émergentes ont été développées pour détecter et quantifier les toxines cyanobactériennes dans l'environnement. Dans ce mémoire nous avons examiné la présence de cyanotoxines multi-classes, dont 12 microcystines, les anatoxines, la cylindrospermopsine (CYN), les anabaenopeptines (AP-A, AP-B) et la cyanopeptoline-A dans les eaux de surface et les poissons sauvages. L'échantillonnage a été conduit pendant l’été 2018, dans l'écosystème fluvial de la réserve écologique de la Rivière aux Brochets (QC, Canada) près de la Baie Missisquoi (Lac Champlain). La méthode analytique employée combine la chromatographie liquide ultra haute performance et une ionisation par électronébuliseur (UHPLC-ESI) avec l’usage d’un spectromètre de masse triple quadripôle. Sur les 18 cyanotoxines ciblées, 14 ont été détectées dans des échantillons d'eau de surface impactés par la floraison ; les toxines ont culminé au début de la mi-septembre avec les concentrations les plus élevées de MC-LR (3,8 μg L-1) et MC-RR (2,9 μg L-1). Parmi les 71 poissons prélevés sur le terrain (10 espèces au total), 38% avaient des détections positives d'au moins une cyanotoxine. Dans les échantillons positifs, les plages de concentration dans le muscle du poisson étaient les suivantes : la somme des microcystines ΣMC (0,16-9,2 μg kg-1), la CYN (46-75 μg kg-1), et les anabaénopeptines AP-A (1,1-5,4 μg kg-1) et AP-B (0,01 à 5,0 μg kg-1). Dans l'ensemble, 17% des échantillons de poisson étaient positifs pour AP-A ou AP-B. A notre connaissance, ceci constitue le premier signalement de bioaccumulation d'anabaénopeptines dans la faune. La somme maximale des concentractions des microcystines ΣMC dans les poissons était 1,15 fois plus élevées que la recommandation de l'apport quotidien (8 μg kg-1 de tissu-1) de l'Organisation mondiale de la santé (OMS) pour les adultes et équivalaient presque à la valeur dérivée pour les jeunes enfants 9.3 μg kg-1. La concentration de CYN était également environ 3 fois plus élevée que la limite dérivée des valeurs recommandées pour la santé humaine. / The diversity and widespread distribution of cyanobacteria in aquatic ecosystems lead to harmful effects in water through the production of a variety of cyanobacterial toxins, which pose a great danger to fauna and human health. Different emerging analytical techniques have been developed to detect and quantify cyanobacterial toxins in the environment. In this thesis we examined the presence of multi-class cyanotoxins, including 12 microcystins, anatoxins, cylindrospermopsin (CYN), anabaenopeptins (AP-A, AP-B) and cyanopeptolin-A in surface water and wild fish. Sampling was conducted during the 2018 summer season in the fluvial ecosystem of the Pike River ecological reserve (QC, Canada) near Missisquoi Bay, Lake Champlain. This study was carried out using an analytical method combining ultra-high-performance liquid chromatography and ionization by electrospray (UHPLC-ESI) with the use of a triple quadrupole mass spectrometer. Of the 18 cyanotoxins targeted, 14 were detected in surface water samples impacted by the bloom; toxins peaked in early mid-September with the highest concentrations of MC-LR (3.8 μg L-1) and MC-RR (2.9 μg L-1). Among the 71 fish sampled in the field from 10 species, 38% had positive detections of at least one cyanotoxin. In positive samples, the concentration ranges in fish muscle were as follows: the sum of microcystins ΣMC (0.16-9.2 μg kg-1), CYN (46-75 μg kg-1), AP -A (1.1-5.4 μg kg-1) and AP-B (0.01 to 5.0 μg kg-1). Overall, 17% of the fish samples were positive for AP-A or AP-B; to our knowledge, this is the first report of accumulation of anabaenopeptins in wildlife. The maximum sum ΣMC of microcystin concentrations in fish was 1.15 times higher than the recommendation of the World Health Organization (WHO) Daily Intake (8 μg kg-1 tissue-1) for adults and was almost equivalent to the derived value for young children 9.3 μg kg-1. The concentration of CYN was also approximately 3 times higher than the limit derived from the recommended human health values.

Mass spectrometry with electrospray ionization is an excellent method for structural analysis of coordination compounds with outstanding sensitivity and selectivity. However, it fails to detect some low-polar rhenium complexes. This master thesis describes derivatization method of non-ionizable rhenium complexes with 1,2-dihydroxybenzene and 2,3- dihydroxytoluenene. Fragmentation mechanisms and structure of prepared complexes was studied using high resolution mass spectrometry and collision-induced dissociation (CID). Furthermore, density functional theory (DFT) computational method was used for prediction of bond cleavage based on bond lengthening.

The catfish industry suffers losses primarily due to enteric septicemia of catfish and columnaris disease caused by Edwardsiella ictaluri and Flavobacterium columnare, respectively. Understanding the host-pathogen interactions is vital for prevention and eradication of these diseases. Hence, the overall objective of this study was to analyze whole cell proteomes of these two bacteria, and to determine the changes in E. ictaluri protein expression against in vitro iron-restriction and host serum treatment. High-throughput proteomic analysis of these bacteria was conducted using two-dimensional liquid chromatography followed by electrospray ionization tandem mass spectrometry (2-D LC ESI MS/MS) and two-dimentional gel electrophoresis coupled with matrix-assisted laser desorption/ionization time-oflight mass spectrometry (2-DE MALDI TOF/TOF). Identified proteins were clustered into functional groups using clusters of orthologous groups, and subcellular locations as well as possible functional relationships were determined. A total of 788 unique E. ictaluri and 621 unique F. columnare proteins were identified, which represented 12 and 28 pathways, respectively. Vertebrate hosts tend to chelate free iron of their body and make the environment hostile for bacteria. Hence, reduced availability of iron may cause significant stress for pathogens and is considered a signal that leads to alteration in virulent gene expression. Similarly, E. ictaluri might use the catfish blood stream effectively for quick systemic invasion. Hence, exposure to catfish serum components might reveal the ability of E. ictaluri to protect against host defense mechanisms. Using two-dimensional difference gel electrophoresis, responses of E. ictaluri due to in vitro iron-restriction and host serum treatment were determined. A total of 50 and 19 proteins were identified to be differentially expressed due to in vitro iron-restriction and catfish serum treatment, respectively. Among the differentially expressed proteins, several putative virulent determinants, immunogenic proteins, chaperones, and housekeeping genes were noted. To initiate functional studies, four differentially expressed E. ictaluri genes (lamB, glyS, malE, and sdhA) were mutated by inrame deletion. Results from this study provided experimental evidence for many predicted proteins. In addition, identification of differentially expressed proteins provided targets for further functional analysis, which could help elucidate pathogenic mechanisms of E. ictaluri.