Inflammatory bowel disease (IBD) is a chronic inflammatory disorder that occurs as a consequence of a genetic mutation that results in an overly aggressive immune response to normal bacteria. Metabolomics is a new born cousin to genomics and proteomics and involves a high throughput identification, characterization and quantification of small molecule metabolites generated by the organism. This study will show that metabolomics can be an effective tool in studying the differences between wild type and IL 10 KO mice as they age in axenic and conventional environments, and the onset of disease in a conventional environment. I show specific changes upon colonizing axenic mice with fecal bacteria that are similar to changes occurring over 16 weeks of conventional growth. Several bacterial metabolites have been identified that may play a role in the pathogenesis or provide clues to the interactions of the gut microbiota with the intestinal immune system. / Experimental Medicine

In spite of impressive recent progress, the aetiopathogenesis of Alzheimer’s disease (AD) remains incompletely understood. The distinctive neuropathological features of AD, in particular the plaques and tangles, have been the particular focus of most aetiological theories. It is well accepted that AD is a multifactorial disease, with alterations to a variety of brain structures and cell types, including neurons, glia and the brain vasculature. Studies of risk factors have revealed a diversity of genetic variables that interact with health, diet and lifestyle-related factors in the causation of AD. These factors influence the structure, aggregation and function of a set of proteins that are increasingly the focus of research. The work in this thesis has focused on the pathophysiological aspects of some of these proteins in a number of cellular compartments and brain. Several assays have been established and techniques utilized in the completion of this work, including; differential detergent fractionation of brain tissue, 1D and 2D PAGE, western blotting with chemiluminescence detection, ELISA assays of Abeta 1-40 and 1-42, quantitative ECNI GCMS of o- and m-tyrosine as well as metabolites of the kynurenine pathway, quantitative MALDI-TOF assay of hemorphins and LCMSMS based proteomics, to identify proteins with altered expression levels in AD relative to control brain tissue. A variety of regional differences have been observed in the biochemistry of the AD cortex which are probably the outcome of local response variations to AD pathology. One of the most consistent threads throughout this work has been an apparent resilience of the occipital lobe relative to the other brain regions, as reflected in lower overall levels of oxidative stress and increased levels of proteins associated with metabolic processes, neuronal remodeling and stress reduction.

Στην εποχή της συστημικής βιολογίας, οι υψηλής απόδοσης (-ομικές) τεχνικές βιομοριακής ανάλυσης επέτρεψαν την ολιστική ανάλυση των διαφόρων μοριακών επιπέδων κυτταρικής λειτουργίας μέσω της ταυτόχρονης μέτρησης εκατοντάδων έως χιλιάδων αντιπροσωπευτικών μοριακών ποσοτήτων. Η μεταβολομική αναφέρεται στην ποσοτικοποίηση του (σχετικού) προτύπου συγκέντρωσης των ελεύθερων μικρών μεταβολιτών. Λαμβάνοντας υπ’ όψιν, το ρόλο των μεταβολιτών ως, αντιδρώντα ή/και προϊόντα των μεταβολικών αντιδράσεων, το πρότυπο συγκέντρωσης τους επηρεάζει και επηρεάζεται από την κατανομή των μεταβολικών ροών, αποτελώντας επομένως ένα αποτύπωμα της μεταβολικής κατάστασης ενός βιολογικού συστήματος. Μεταξύ των πλεονεκτημάτων της μεταβολομικής ανάλυσης είναι ότι μπορεί να χρησιμοποιηθεί σε μεταβαλλόμενη κατάσταση φυσιολογίας, ενώ δεν απαιτεί ολοκληρωμένη γνώση του μεταβολικού δικτύου ενός οργανισμού. Αυτά τα χαρακτηριστικά είναι ιδιαίτερα πλεονεκτικά για τη μελέτη της μεταβολικής ενεργότητας του εγκεφάλου, λαμβάνοντας υπ’όψιν την ανατομική, μορφολογική και φαινοτυπική πολυπλοκότητα αυτού του οργάνου και την έως τώρα κατανόηση των μεταβολικών του μηχανισμών. Πιο συγκεκριμένα για την επίδραση του ενήλικου υποθυρεοειδισμού στον μεταβολισμό του εγκεφάλου, η μέχρι σήμερα γνώση παραμένει αποσπασματική, ενώ προέρχεται από διαφορετικά πειράματα και διάφορες εγκεφαλικές περιοχές. Μια ολιστική θεώρηση του μεταβολισμού σε συνθήκες υποθυρεοειδισμού σε συγκεκριμένες εγκεφαλικές περιοχές αναμένεται να αυξήσει σημαντικά τη γνώση μας για την ασθένεια αυτή. Σε μια πρόσφατη μελέτη της ερευνητικής μας ομάδας, που ήταν η πρώτη μεταβολική ανάλυση εγκεφαλικού ιστού σε ζωικό μοντέλο μακρόχρονου υποθυρεοειδισμού, η πολυπαραμετρική στατιστική ανάλυση των μεταβολικών προτύπων της παρεγκεφαλίδας μυός έδειξε διαφορές στη μεταβολική φυσιολογία του ιστού στα ευ- σε σχέση με τα υποθυρεοειδικά ζώα, παρέχοντας ισχυρές ενδείξεις ότι ο μεταβολισμός της παρεγκεφαλίδας θηλαστικών επηρρεάζεται από τον μακρόχρονο υποθυρεοειδισμό. Στην παρούσα εργασία, συγκρίθηκε η επίδραση του μακρόχρονου υποθυρεοειδισμού στη μεταβολική φυσιολογία της παρεγκεφαλίδας μεταξύ αρσενικών και θηλυκών Balb/cJ μυών, αφού επεκτάθηκε για επιπλέον μεταβολίτες η αυτοματοποιημένη μέθοδος προσδιορισμού κορυφών στο χρωματογράφημα. Ο μακρόχρονος υποθυρεοειδισμός επήχθη με χορήγηση 1% υπερχλωρικού καλλίου για 64 μέρες στο πόσιμο νερό των ζώων. Αυτή είναι και η πρώτη μελέτη της επίδρασης του ενήλικου υποθυρεοειδισμού στην μεταβολομική φυσιολογία του 4 εγκεφάλου των θηλυκών μυών. Τα μεταβολικά πρότυπα αναλύθηκαν με το λογισμικό ανοικτού κώδικα ΤΜ4/ MEV(www.tm4.org/MEV) για την πολυπαραμετρική στατιστική ανάλυση των -ομικών δεδομένων. Τα αποτελέσματα συζητήθηκαν στο πλαίσιο ενός κατάλληλα ανακατασκευασμένου μεταβολικού δικτύου για την παρεγκεφαλίδα μυός με βάση τις μεταβολικές βάσεις δεδομένων KEGG και EXPASY και δεδομένα από τη βιβλιογραφία. Η ανάλυση των προτύπων έδειξε ότι η επίδραση της δίμηνης χορήγησης υπερχλωρικού καλλίου στη μεταβολική φυσιολογία της παρεγκεφαλίδας ήταν πιο οξεία στα αρσενικά απ’ότι στα θηλυκά ζώα. Αυτή η παρατήρηση υποστηριζόταν και απο την σημαντικά μικρότερη μείωση του μέσου βάρους των υποθυρεοειδικών σε σχέση με αυτό των ευθυρεοειδικών ζώων στο τέλος της δίμηνης χορήγησης στα θηλυκά σε σχέση με τα αρσενικά. Τέος, σύγκριση των μεταβολικών προτύπων της παρεγκεφαλίδας των ευθυρεοειδικών αρσενικών και θηλυκών μυών έδειξε τους μισούς από τους μεταβολίτες στην παρεγκεφαλίδα των αρσενικών να έχουν σημαντικά μεγαλύτερη συγκέντρωση απ’ ότι στον ιστό των θηλυκών. Αυτή η παρατήρηση καταδεικνύει την ανάγκη της παρεγκεφαλίδας των θηλυκών σε μικρότερες συγκεντρώσεις ελεύθερων μικρών μεταβολιτών για την εύρυθμη λειτουργία της ως ένα πιθανό παράγοντα «προστασίας» του μεταβολισμού της από την επίδραση του μακρόχρονου ενήλικου υποθυρεοειδισμού. Καθώς η παρεγκεφαλίδα των αρσενικών χρειάζεται μεγαλύτερες ποσότητες ελεύθερων μικρών μεταβολιτών, η αναμενώμενη μείωση της συγκέντρωσης των μεταβολιτών που λαμβάνει ο εγκέφαλος μέσω του αιματοεγκεφαλικού φραγμού λόγω του υποθυρεοειδισμού θα την επηρεάσει πιο γρήγορα και πιο δραστικά από αυτή των θηλυκών. Αυτές οι σημαντικές παρατηρήσεις χρειάζονται περαιτέρω διερεύνηση μέσω κατάλληλα σχεδιασμένων αναλύσεων μεταβολομικής και φυσιολογίας και άλλων εγκεφαλικών περιοχών, συνδυάζοντας επίσης μετρήσεις των επιπέδων των θυρεοειδικών ορμονών με μεταβολομική ανάλυση του εγκεφαλικού ιστού με Υγρή Χρωματογραφία- Φασματομετρίας Μάζας, καθώς και μετρήσεις ομικών αναλύσεων από άλλα επίπεδα κυτταρικής λειτουργίας, κυρίως της πρωτεωμικής. / In the systems biology era, the high-throughput “omic” technologies have enabled the holistic analysis of the various molecular levels of cellular function through the simultaneous measurement of hundreds to thousands of relevant molecular quantities. Metabolomics refers to the quantification of the (relative) concentration profile of the free small metabolites. Taking into consideration the role of the metabolites as reactants and products of the metabolic reactions, their concentration profile affects and is affected by the metabolic pathway flux distribution. Thus, the metabolic profile provides a fingerprint of the metabolic state of a biological system. Among the advantages of the metabolomic analysis is that it can be easily used to monitor transient metabolic conditions without requiring extensive knowledge of the structure and regulation of the investigated metabolic networks. This characteristic is especially advantageous for the analysis of brain metabolism, considering the anatomical, morphological and phenotypic complexity of this organ and our current shortages in understanding its metabolic mechanisms. For the effect of adult onset hypothyroidism (AOH) on brain metabolism in particular, the current knowledge remains fragmented, concerning different experimental setups and recovered from various brain regions. A holistic view of metabolism under AOH in particular brain regions is expected to significantly enhance the current knowledge about the disease. In a recent study of our group, which was the first metabolomic analysis of brain tissue in a prolonged AOH mouse model, multivariate statistical analysis of the metabolic profiles of the mouse cerebella indicated differences in the metabolic physiology of the tissue in the eu- compared to the hypo- thyroid animals, providing strong evidence that the mammalian cerebellum is metabolically responsive to prolonged AOH. In the present work, we compared the effect of prolonged AOH on the cerebellar metabolic physiology between male and female Balb/cJ mice, after enhancing the metabolite peak identification method to include additional metabolites. The prolonged AOH was induced by a 64-day treatment with 1% potassium perchlorate in the drinking water of the animals. This is the first reported analysis of the effect of AOH on the brain metabolic physiology of female mice. The raw metabolic profiles were normalized and appropriately filtered. The normalized metabolic profiles were analyzed using the open-source TM4/MeV software (www.tm4.org/MeV) for the multivariate statistical analysis of “omic” data. The acquired results were interpreted in the context of an appropriately reconstructed metabolic network for the mouse cerebellum based on the metabolic databases, KEGG and Expasy, and a plethora of information mined from the literature. The analysis of the metabolic profiles 6 indicated that the effect of the 2-month potassium perchlorate treatment on the metabolic physiology of the cerebellum is more acute in the male with respect to the female mice. The time profile of the body weight of the female compared to the male mice indicated a significantly smaller decrease in the mean weight of the hypothyroid compared to the euthyroid mice in the female compared to the male population at the end of the KClO4 treatment, an observation that further supports the metabolic profiling results. Finally, comparison between the metabolic profiles of the euthyroid male and female cerebellum indicated a significantly higher concentration in half of the measured free metabolites in the male compared to the female animals. This indicates the “leanness” of the metabolic profile of the female cerebellum as a potential “protective” parameter to the effect of AOH on its metabolic physiology, in the sense that the expected due to AOH decrease in the concentrations of the metabolites that are transferred to the brain through the blood brain barrier may affect more the male cerebellum that requires higher levels of free metabolites for its regular activity. These significant observations are in need of further investigation through appropriately designed physiological and metabolomic studies, integrating also thyroid hormone measurements from Liquid Chromatography-MS metabolomic analysis of brain tissue as well as omic measurements from other molecular levels of cellular function, mainly from proteomics.

Orientador: Kátia Cristina Kupper / Banca: Fabio Augusto / Banca: Alessandra Sussulini / Banca: Antonio de Góes / Banca: Jackson Antonio Marcondes de Souza / Resumo: O setor citrícola é o maior produtor de frutos no mundo, porém, encontra-se ameaçado por diversos patógenos, dentre esses, o fungo Phyllosticta citricarpa, agente causal da mancha preta dos citros. Como alternativa à utilização de fungicidas sintéticos para o controle do patógeno, o controle biológico, utilizando bactérias do gênero Bacillus, apresenta destaque. Tais microrganismos possibilitam o biocontrole pela produção de compostos orgânicos voláteis ou não voláteis. Sendo assim, este trabalho teve por objetivos: identificar os isolados de Bacillus spp. por meio de técnicas moleculares; avaliar a produção de compostos orgânicos voláteis produzidos por Bacillus spp. em diferentes meios de cultura; verificar os seus efeitos na evolução dos sintomas da doença em frutos de laranja, na morfologia de P. citricarpa em lesões de mancha preta e na indução de resistência, identificar os compostos voláteis por cromatografia gasosa unidimensional e finalmente, avaliar o efeito de diferentes meios de cultura no antagonismo e metabolismo secundário dos isolados de Bacillus. Os isolados bacterianos foram identificados como pertencentes às espécies de Bacillus subtilis, B. amyloliquefaciens e B. methylotrophicus. Os resultados mostraram que houve maior controle do patógeno, em decorrência da produção de voláteis, quando se utilizou os meios triptona de soja ágar (TSA) e caldo de triptona (TSB) para cultivo da bactéria, apresentando valores de inibição da colônia do fungo de até 73%. Com r... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The citrus sector is the largest producer of fruits in the world, but it is threatened by several pathogens, among them Phyllosticta citricarpa fungus, causal agent of the citrus black spot. As an alternative to the use of synthetic fungicides to control the pathogen, the biological control, using bacteria of the genus Bacillus, is highlighted. Such microorganisms enable biocontrol by the production of volatile or non-volatile organic compounds. Therefore, this work had as objectives: to identify the isolates of Bacillus spp. by means of molecular techniques; to evaluate the production of volatile organic compounds produced by Bacillus spp. in different culture media; to verify its effects on the evolution of orange disease symptoms, P. citricarpa morphology in black spot lesions and induction of resistance, to identify the volatile compounds by one-dimensional gas chromatography and, finally, to evaluate the effect of different culture in the antagonism and secondary metabolism of Bacillus isolates. The bacterial isolates were identified as belonging to the species of Bacillus subtilis, Bacillus amyloliquefaciens and Bacillus methylotrophicus. The results showed that there was greater control of the pathogen, due to the volatile production, when tryptone broth (TSA) and tryptone broth (TSB) were used to culture the bacteria, presenting inhibition values of the fungus colony up to 73%. With regard to the effect of volatile compounds on the evolution of disease symptoms, the best results in terms of inhibition (86%) of freckles that progressed to hard spots were obtained with ACB-65 and ACB-73, when cultured in TSB culture medium. Such antagonists have caused deformations in the hyphae of the pathogen, which may explain the non-evolution of the disease symptoms, as previously reported. The volatiles of Ba... (Complete abstract click electronic access below) / Doutor

Introduction Inflammatory bowel disease (IBD) is a chronic gastrointestinal disorder that encompasses two major subtypes; Crohn’s Disease (CD) and Ulcerative Colitis (UC). Our knowledge regarding disease pathogesis is rapidly increasing. However, these disease entities provide challenges in diagnosis, monitoring of disease activity and assessing individual response to treatment, because there is a lack of validated clinical biomarkers. Metabolomics involves the study of numerous analytes that have very diverse physical and chemical properties and occur in a wide concentration range. Early evidence suggests there is potential for metabolomic profiling to be used in the differentiation of CD and UC. However, knowledge is limited regarding the metabolic changes seen in relation to disease activity or to medical or surgical treatments. Aims A metabolomics approach was taken to determine whether metabolomic profiles could distinguish between patients with CD or UC and healthy controls. We also aimed to define the relationship between metabolomic profile and disease activity, and to determine the effect of medical (anti-TNFa agents) and surgical treatment on the metabolome. Methods A metabolomics approach was undertaken. Serum and urine sample sets were collected from a total of 41 patients with ulcerative colitis, 43 patients with Crohn’s disease, and 62 healthy controls (HC). In order to allow a comparison of metablomic profile and disease activity, 4 sample sets were taken from the same patient at 3 monthly intervals over the period of one year. Those patients undergoing either surgical or biological treatment had sample sets taken pre and post intervention. Metabolomic analysis using gas chromatography time of flight mass spectrometry (GC-ToF-MS) and ultra-high performance liquid chromatography Fourier Transform mass spectrometry (UHPLC-FTMS) was carried out on both serum and urine. Results Serum and urine GC-ToF-MS and UHPLC-FTMS metabolomic analyses show differentiation between UC, CD and healthy controls, most significantly in urine analyses. No significant differentiation was seen in pre- and post-surgical patients, or pre- and post-biological therapy patients. It was possible to differentiate surgical patients from healthy controls, especially in the urine analyses. Metabolite identification revealed consistently more dietary variation in the healthy controls than in the IBD patients. Significant differences (p < 0.05) were seen between healthy controls and IBD patients in classes of metabolites relating to the citric acid cycle and the uronic acid pathway, as well as amino acids, fatty acids and cholesterols. The behaviour or location of disease, or the disease activity score did not appear to influence the metabolome in either serum or urine analyses using GC-ToF-MS and UHPLC-FTMS. Conclusion Metabolomic profiling of urine and serum in IBD may provide a novel methodology aiding both clinical diagnosis through biomarker development, and advancing knowledge of disease pathogenesis.

Two compounds of the class nitrophenyl-1,4-dihydropyridines (1 and 2), one from the quinone class - the β-lapachone (3) and one diazoquinone (4), the β- lapachone-derivative were analyzed by electrochemical methods. For the 1,4- dihydropyridines, the techniques used were cyclic voltammetry and square wave voltammetry, in aprotic (DMF + TBAP) and protic media (phosphate buffer, pH 6.9), on Hg and vitreous carbon electrodes. β-lapachone and its diazoderivative were studied in aprotic and protic media, using vitreous carbon as the working electrode. The reduction of the substituted nitrophenyl-1,4-dihydropyridines in protic medium, on both Hg and vitreous carbon electrodes showed electrochemical behavior typical of nitroaromatics, represented by one intense irreversible wave indicative of a 4e-/4H+ reduction process, with formation of the correspondent hydroxylamines, that showed different degrees of stability. In aprotic medium, the cyclic voltammograms showed, for 1, a first one-electron reversible wave corresponding to the generation of the nitro anion-radical, and a second irreversible wave that presented a complex mechanism, with the formation of reactive reduced intermediates. The acid (-COOH) derived nitrophenyldihydropyridine showed a more complex electrochemical feature, representative of an EC mechanism, with evidence of self-protonation. The electrochemical behavior of β-lapachone, in aprotic medium, was similar to the one of typical o-quinones and was represented by two one-electron waves, with reversible and quasi-reversible nature. However, the diazo derivative showed a different behavior, with only one reduction wave, without the anodic counterpart. The reduction mechanism corresponds to an EC process, with the irreversible electron transfer occurring at the diazo group, followed by a chemical reaction that involves the unimolecular loss of N2, generating the carbene anion radical. After successive protonations, the phenolic derivative (5) was obtained, as the main reduction product. The cyclic voltammogram reduction of the diazo derivative in protic medium (phosphate buffer, pH 6.9) showed only one wave without the anodic counterpart in potential of 0.419 V, differently from what is observed for o-quinones. Compound 4 didn t show antibacterial activity. / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Dois compostos da classe nitrofenil-1,4-diidropiridina (1 e 2), um da classe das quinonas - a β-lapachona (3) e uma diazoquinona derivada da β-lapachona, (4), foram analisados eletroquimicamente. Para as nitrofenil-1,4-diidropiridinas foram utilizadas as técnicas de voltametria cíclica e voltametria de onda quadrada, em meio aprótico (DMF + TBAP 0,1 mol/L) e prótico (tampão fosfato, pH 6,9), em Hg e carbono vítreo. Já a β-lapachona e seu diazoderivado foram estudados em meio prótico e aprótico, com o uso, como eletrodo de trabalho, de carbono vítreo. A redução das nitrofenil-1,4-diidropiridinas substituídas, em meio prótico tanto em eletrodo de Hg como em carbono vítreo, seguiu padrão de comportamento eletroquímico típico de nitrocomposto aromático, representado por uma onda intensa de natureza irreversível, indicativa de um processo de redução de 4e-/4H+, com formação de derivados hidroxilamínicos de diferentes estabilidades. Já em meio aprótico, os voltamogramas cíclicos evidenciaram, para a primeira delas (1), uma onda monoeletrônica, de caráter quase reversível correspondendo à geração do ânion-radical nitro e uma segunda onda irreversível apresentando mecanismo complexo, com formação de intermediários reduzidos reativos. A substância com grupamento ácido na molécula (-COOH) apresentou reação química acoplada após a primeira transferência eletrônica, em mecanismo típico de auto-protonação. O comportamento eletroquímico da β-lapachona, em meio aprótico, mostrouse similar ao de o-quinonas padrão, representado por duas ondas monoeletrônicas, uma de natureza reversível e outra quase-reversível. O diazo derivado da β- lapachona (4) apresentou comportamento diferente, com uma única onda de redução, sem correspondente anódica. O mecanismo de redução corresponde a um processo EC, onde a captura monoeletrônica irreversível ocorre no grupo diazo e a reação química acoplada envolve a perda unimolecular do N2, com geração do ânion radical carbeno intermediário, que após protonações sucessivas produz o derivado fenólico (5), majoritariamente. O voltamograma cíclico em meio prótico (tampão fosfato pH 6,9) de 4 apresentou uma única onda de redução sem contrapartida anódica em potencial de -0,419 V. O composto 4 não apresentou atividade antibacteriana.

The 21st Century has seen a rise in incidence of complex diseases such as cancer and in the quest to develop essential new therapeutic options, the study of drug-cell interactions can yield powerful information. Acute myeloid leukaemia (AML) is an aggressive cancer that causes life-threatening deficits of functional blood cells in humans for which current treatment options are highly toxic and often poorly tolerated. A combination of two existing drugs, bezafibrate and medroxyprogesterone acetate in a drug redeployment situation has shown promise in vitro and in vivo and further investigations are crucial to elucidate the mode of action of this treatment. This project investigated the mechanistic action of BaP at a cellular level. Orthogonal spectroscopic and mass spectrometric platforms were employed to probe the biochemical composition of two AML cell lines, HL60 and K562 in the presence and absence of this combined drug treatment. Analysis was performed on single living cells, dehydrated cells, fixed cells and cell extracts to give a large and detailed data set. A consideration of the main spectral differences obtained by Synchrotron-FTIR and ATR-FTIR in conjunction with multivariate statistical analysis revealed a significant change to the cellular lipid composition with drug treatment; furthermore, this response was not caused by cell apoptosis. In particular, the ratio of CH2:CH3 was observed to increase with BaP treatment and this was determined to be a significant change in both cell lines (p &lt;0.05). An overall increase in lipid unsaturation suggests that BaP targets cellular lipid biosynthesis. Raman microspectroscopy added a further dimension to the spectroscopic study by providing spatial information of lipid distribution which suggested that BaP-induced saturation change is uniform across a single cell. UHPLC-MS was employed for global metabolomics analysis of AML cell extracts and revealed a number of biochemical pathways that were indicated as targets of BaP therapy in both cell lines. Univariate and multivariate analysis determined statistically significant metabolites for which putative identifications were made. Pyrimidine metabolism was the most significant pathway identified for changes consistent in both HL60 and K562 cell lines. The complementarity of ToF-SIMS and UHPLC-MS provided large coverage of the lipidome of AML cells through untargeted and targeted approaches. For data derived by both techniques, a general increase in polyunsaturated species for BaP treated cell extracts was observed which correlated well with findings from spectroscopic investigations. Adopting a multi-disciplinary approach to cell analysis can afford a powerful insight into understanding drug mode of action at a cellular level and novel information regarding BaP mechanistic action in AML cell lines was revealed. This analytical approach could be extended to the future study of drug-cell interactions for other oncological systems.

Orientador: Prof. Dr. Danilo da Cruz Centeno. / Dissertação (mestrado) - Universidade Federal do ABC, Programa de Pós-Graduação em Biotecnociência, 2015. / A bioenergia destaca-se como um substituto relevante para os combustíveis fósseis e os biocombustíveis vem ganhando destaque nos últimos anos, assim como as tecnologias para a transformação dessa biomassa. No Brasil, os biocombustíveis mais utilizados são o etanol e o biodiesel, provenientes de tecidos vegetais. A demanda de etanol tem aumentado nos últimos anos tendo a produção de etanol em 2011/2012 atingido aproximadamente 27,67 bilhões de litros. Entretanto esta produção ainda é baixa frente à demanda por combustíveis renováveis. O etanol produzido a partir da cana-de-açúcar é proveniente do processo de fermentação da sacarose acumulada nos colmos. A produção de açúcares em organismos vegetais ocorre por meio de processos bioquímicos complexos envolvendo diferentes componentes subcelulares. Esses processos são um conjunto de reações que coordenam o metabolismo e a transferência de nutrientes e fotoassimilados entre os diferentes órgãos das plantas. Esses processos bioquímicos são dinâmicos e podem ser afetados em suas diferentes vias por interferências diversas, como estresses abióticos e bióticos, entre outros. Além da sacarose, outros açúcares são importantes para o acúmulo de carbono em plantas, sendo estes utilizados em diferentes vias metabólicas. Nesse estudo foram analisados colmos maduros de quatro variedades de cana-de-açúcar, divididos em terço superior, médio e inferior, sendo essas variedades RB72454, RB855156, RB867515 e RB92579, através da análise de perfil metabólico e quantificação de açúcares solúveis totais (AST), de modo a avaliar as relações do acúmulo de AST e outros metabólitos em cana-de-açúcar. Os resultados mostram correlações positivas entre alguns compostos chave do metabolismo primário em colmo de cana-de-açúcar e sugere ainda a importância do estudo de açúcares álcool nestas plantas com o intuito de avaliar a contribuição de outros açúcares, como oligossacarídeos da série da rafinose, no armazenamento de carbono em colmo. Estes resultados trazem uma nova perspectiva para estratégias futuras de obtenção de plantas com maior produtividade. / Bioenergy stands out as an important substitute for fossil fuels and biofuels has been gaining momentum in recent years, as well as technologies for the transformation of biomass. In Brazil, the most commonly used biofuels are ethanol and biodiesel from plant tissues. The demand for ethanol has increased in recent years and the production of ethanol in 2011/2012 reached about 27.67 billion liters. However, this production is still low against the demand for renewable fuels. Ethanol produced from sugarcane comes from the fermentation process of the accumulated sucrose in the stalks. The production of sugars in plant bodies occurs by means of complex biochemical processes involving different subcellular components. These processes are a set of reactions that coordinate the transfer and metabolism of nutrients and assimilates among the different plant organs. These biochemical processes are dynamic and can be affected in their different ways by various interferences such as abiotic and biotic stresses, among others. In addition to sucrose, other sugars are important for carbon accumulation in plants, which are used in different metabolic pathways. In this study, mature stalks of four varieties of sugarcane (RB72454, RB855156, RB867515 and RB92579), divided into upper, middle and lower third, were analyzed , through metabolic profiling and quantification of total soluble sugars (TSS) in order to assess the relationship of TSS accumulation and other metabolites in sugarcane. The results show positive correlations among some key compounds of primary metabolism in sugarcane stalks and also suggests the importance of the study of alcohol sugars in these plants in order to assess the contribution of other sugars such as oligosaccharides of the raffinose series, the stem in carbon storage. These results provide a new perspective for future strategies to obtain plants with higher productivity.

Submitted by MARCEL PRATAVIEIRA null (marcelprata93@hotmail.com) on 2016-03-07T15:52:49Z No. of bitstreams: 1 Dissertação - Marcel Pratavieira - 2016.pdf: 8130455 bytes, checksum: a459e73ed4ef0757431f12802bc7f15b (MD5) / Approved for entry into archive by Ana Paula Grisoto (grisotoana@reitoria.unesp.br) on 2016-03-07T19:51:13Z (GMT) No. of bitstreams: 1 pratavieira_m_me_rcla.pdf: 8130455 bytes, checksum: a459e73ed4ef0757431f12802bc7f15b (MD5) / Made available in DSpace on 2016-03-07T19:51:13Z (GMT). No. of bitstreams: 1 pratavieira_m_me_rcla.pdf: 8130455 bytes, checksum: a459e73ed4ef0757431f12802bc7f15b (MD5) Previous issue date: 2016-02-23 / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / As abelhas têm sido utilizadas como modelos robustos e influentes para o estudo de memória e aprendizagem, contribuindo para o melhor entendimento das bases da cognição. Nesse contexto, diferentes metabólitos foram caracterizados por desempenharem funções distintas no processo de aprendizagem e formação de memória em insetos. Considerando que pouco se sabe sobre os metabólitos em relação ao desenvolvimento das habilidades cognitivas em A. mellifera, ou mesmo em relação aos comportamentos reflexos (condicionados e/ou não condicionados), o presente estudo teve como objetivo a análise metabolômica do cérebro de abelhas submetidas ao ensaio comportamental de reflexo de extensão de probóscide (REP). Para isto, foi padronizada a técnica de análise metabolômica com o uso do sistema LC-ESI- MS e MSn, construindo-se inicialmente uma biblioteca de compostos característicos de cérebro de abelhas (neurotransmissores, aminoácidos livres, poliaminas, nucleotídeos, nucleosídeos, ácidos orgânicos, etc). Nesta primeira abordagem, dentre os 112 compostos da biblioteca, 48 foram identificados e quantificados; alguns destes compostos foram únicos para o grupo controle (cadaverina, espermina, glicose, uracila e n-acetil-L-glutamato 5-semialdeido), enquanto que outros foram únicos para o grupo REP (fenilalanina, betaína, espermidina, serina e creatina). Dentre os compostos identificados em ambos os grupos, apenas 5 compostos apresentaram diferenças quantitativas estatisticamente significantes (arginina, asparagina, guanosina monofosfato, putrescina e 4-guanitinobutanoato). Visando o estudo dos perfis metabólicos regionais (em cada região do cérebro), foi também padronizado o protocolo experimental utilizando-se a estratégia MALDI Spectral Imaging e o desenvolvimento de um método semi-quantitativo de metabólitos. Esta estratégia permitiu o mapeamento e o estudo da distribuição espacial dos metabólitos identificados em cortes de cérebro de abelhas, bem como uma melhor compreensão da distribuição dessas moléculas nas diferentes estruturas do cérebro e sua correlação com o comportamento ensaiado. As duas estratégias aplicadas mostraram-se complementares e fundamentais para a compreensão da cognição em abelhas. De modo geral, o ensaio de REP parece estimular intensa atividade cerebral, alto gasto energético, intensa sinalização química e a ativação de algumas cascatas metabólicas específicas, tais como a rota metabólica da prolina e arginina. Nos indivíduos do grupo REP a arginina provavelmente foi catabolizada nas sínteses de creatina, 4-guanidinobutanoato, putrescina e espermidina. Esses processos bioquímicos provavelmente foram importantes para coordenar o reconhecimento da molécula de sacarose, e associar esse odor com um comportamento reflexo para a extensão da probóscide (estímulo não condicionado). / The honeybee Apis mellifera has long served as an invertebrate model organism for learning and memory research, contributing to a better understanding of cognition bases. In this context, different metabolites (especially neurotransmitters) were characterized by play distinct roles in learning process and in memory formation in insects. Whereas little is known about the metabolites in relation to the development of cognitive skills in A. mellifera, the present study aims to perform a metabolomic analysis of the honeybee brains submitted to the behavioral test of proboscis extension reflex (PER). For this, has been standardized a metabolomic analysis technique through the use of LC-ESI-MS and MSn system. Initially a low molecular weight compounds library was created, containing characteristic compounds of bee brain (neurotransmitters, free amino acids, polyamines, nucleotides, nucleosides, organic acids, etc.). In this first approach, from the library of 112 compounds, 48 compounds were identified and quantified; some of these compounds were only identified in the control group (cadaverine, spermine, glucose, uracil and N-acetyl-L-glutamate 5- semialdehyde), while others were only identified in PER group (phenylalanine, betaine, spermidine, serine and creatine). Among the compounds identified in both groups, only five compounds showed statistically significant differences in quantitative results (arginine, asparagine, guanosine monophosphate, putrescine and 4-guanidinebutanoate). In order to study the metabolic profiles by regions (within each brain region) it was also standardized an experimental protocol using a novel semi-quantitative method of MALDI Spectral Imaging strategy. This strategy allowed the study and the mapping of the spatial distribution of metabolites identified in honeybee brain sections, as well as a better understanding of the distribution of molecules in the different brain structures and their correlation with the behavior tested. Both strategies applied proved to be complementary and essential to the understanding of cognition in bees. Overall, in this study the PER test seems to stimulate intense brain activity, high energy expenditure, intense chemical signaling and activation of some specific metabolic pathways, such the arginine and proline metabolic pathway. In individuals of PER group arginine was probably catabolized in the synthesis of creatine, 4-guanidinobutanoato, putrescine and spermidine. This biochemical process were probably important to coordinate the recognition of sucrose molecule and associate this odor with a reflex behavior for the proboscis extension (unconditioned stimulus). / FAPESP: 2014/05376-1

abstract: Obesity is a worldwide epidemic accompanied by multiple comorbidities. Bariatric surgery is currently the most efficient treatment for morbid obesity and its comorbidities. The etiology of obesity is unknown, although genetic, environmental, and most recently, microbiome elements have been recognized as contributors to this rising epidemic. The role of the gut microbiome in weight-loss or weight-gain warrants investigation, and bariatric surgery provides a good model to study influences of the microbiome on host metabolism. The underlying goals of my research were to analyze (i) the factors that change the microbiome after bariatric surgery, (ii) the effects of different types of bariatric surgeries on the gut microbiome and metabolism, (iii) the role of the microbiome on the success of bariatric surgery, and (iv) temporal and spatial changes of the microbiome after bariatric surgery. Roux-en-Y gastric bypass (RYGB) rearranges the gastrointestinal tract and reduces gastric acid secretions. Therefore, pH could be one of the factors that change microbiome after RYGB. Using mixed-cultures and co-cultures of species enriched after RYGB, I showed that as small as 0.5 units higher gut pH can aid in the survival of acid-sensitive microorganisms after RYGB and alter gut microbiome function towards the production of weight loss-associated metabolites. By comparing microbiome after two different bariatric surgeries, RYGB and laparoscopic adjustable gastric banding (LAGB), I revealed that gut microbiome structure and metabolism after RYGB are remarkably different than LAGB, and LAGB change microbiome minimally. Given the distinct RYGB alterations to the microbiome, I examined the contribution of the microbiome to weight loss. Analyses revealed that Fusobacterium might lessen the success of RYGB by producing putrescine, which may enhance weight-gain and could serve as biomarker for unsuccessful RYGB. Finally, I showed that RYGB alters the luminal and the mucosal microbiome. Changes in gut microbial metabolic products occur in the short-term and persist over the long-term. Overall, the work in this dissertation provides insight into how the gut microbiome structure and function is altered after bariatric surgery, and how these changes potentially affect the host metabolism. These findings will be helpful in subsequent development of microbiome-based therapeutics to treat obesity. / Dissertation/Thesis / Doctoral Dissertation Microbiology 2016