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Metabolomics is a rising field combining bioinformatics and cheminformatics together. A major component of research is having a reliable data source, which usually comes in the form of metabolomic databases. This paper documents arising issues revolving categorizing metabolome compounds within databases, and a possible solution in the form of an R package that is capable of matching up various metabolome identifiers that originate from various metabolome databases. Then, by using this package we reflect on the average coverage of external reference between metabolome databases to highlight the lack of a universal compound primary identifier. / <p>The thesis presentation was held over Zoom due to the recent COVID19 pandemic.</p>

A demanda comercial de produtos derivados da cana-de-açúcar é a grande motivadora do aprimoramento genético com a finalidade de proporcionar a planta aumento no acúmulo de sucrose e/ou de resistência a ataques de herbívoros. Assim sendo, este trabalho abrange o estudo metabolomico de duas variedades transgênicas da cana-de-açúcar (Bowman-Birk-SBBI e Kunitz- SKTI) e seus respectivos controles através de duas metodologias distintas: a análise quimiométrica do perfil cromatográfico dos polifenóis existentes nas variedades transgênicas e o estudo metabolomico por ressonância magnética nuclear a fim de identificar possíveis diferenças entre as plantas transgênicas em relação aos seus respectivos controles. Nas amostras de folhas foram encontradas nove regiões cromatográficas representativas para a discriminação das variedades SBBI e SKTI. Análises de HPLC-MS/MS foram empregadas para a identificação parcial dos biomarcadores selecionados pelo método OPS, dentre eles: ácido cafeoílaquínico, ácido feruloílaquínico, shaftosídeo ou isoshafitosídeo, além de quatro substâncias parcialmente identificadas: um derivado de apigenina, um glicosídeo da tricina--O-(metoxicinamato), um derivado de flavonóide metoxilado e um derivado de catequina. Através do estudo metabolomico obteve-se uma visão geral sobre os metabólitos produzidos pelas variedades transgênicas e controles e através das análises dos espectros de RMN 1H, J-resolved, COSY 1H-1H, HMBC 13C-1H foi possível identificar a presença de ácidos orgânicos, amino-ácidos, açúcares, flavonóides e fenilpropanóides. Adicionalmente, a análise quimiométrica dos espectros de RMN 1H mostrou não haver diferença significativa entre folhas SBBI e controles e SKTI e controles. Como conclusão pôde-se sugerir que a inserção dos genes inibidores de protease na cana-de-açúcar não afeta as rotas biosintéticas da planta, mas apenas confere maior resistência contra a broca da cana-de-açúcar (Diatrea saccharilis). Entretanto diferenças significativas entre as variedades transgênicas foram encontradas: a variedade SBBI apresenta teor de açucares e fenilpropanóides mais elevados que a variedade SKTI. Conclui-se também que as alterações metabólicas encontradas neste trabalho não são provenientes dos genes inseridos na planta, mas por outro tipo de efeito sofrido nos controles das duas variedades, como por exemplo, variação somaclonal que antecedem a modificação genética. / Comercial demanding of industrial products from sugarcane plants are reponsable for researchs on genetic improvements with the aim to increase sucrose plant acumulation and/or provide resistence against herbivors. Thus, the present work covers metabolomic study of two transgenics varieties of sugarcane (Bowman-Birk-SBBI e Kunitz- SKTI) and their respectives wild (control) plants through two distinct methodologies: chemometrics analysis of polyphenols chromatography profile found into the transgenics varieties and the metabolomic study by nuclear magnetic resonance for identification of possible metabolic alterations comparing transgenics plants and their respective controls. Nine discriminants chromatography regions were detected on SBBI and SKTI leaves samples. HPLC-MS/MS analyses were performed for biomarkers identification selected by OPS method, among then: caffeoylquinic acid, feruloyl quinic acid, shaftoside or isoshaftoside, apigenin derivatives, tricin-O-(methoxycinamate)-glicosilated, methoxylated flavone and catechine derivative. A general vision about metabolites produced for transgenics and control plants could be achived through metabolomic study. Identification of organic acids, amino acids, sugars, phenylpropanoids and flavonoids were possible through 1H NMR, J-resolved, COSY 1H-1H, HMBC 13C-1H. Moreover, chemometrics analysis of the 1H NMR spectra had shown no significant differences between SBBI with wild plant and SKTI with control plants. These results suggest that the biosyntheses pathways are not affected by protease inhibitors genes introduced on sugarcane, but these genes just provides resistence against Diatrea saccharilis. However, metabolic alterations were found between the transgenic plants (SBBI and SKTI). Specially, the variety SBBI presents high levels of sugars and phenylpropanoids compared with SKTI variety. In conclusion, the metabolic variation found in the present are not due to genes introduction, but are originated by other type of effect on wild plants, such as, somaclonal variation before genetical modification.

A demanda comercial de produtos derivados da cana-de-açúcar é a grande motivadora do aprimoramento genético com a finalidade de proporcionar a planta aumento no acúmulo de sucrose e/ou de resistência a ataques de herbívoros. Assim sendo, este trabalho abrange o estudo metabolomico de duas variedades transgênicas da cana-de-açúcar (Bowman-Birk-SBBI e Kunitz- SKTI) e seus respectivos controles através de duas metodologias distintas: a análise quimiométrica do perfil cromatográfico dos polifenóis existentes nas variedades transgênicas e o estudo metabolomico por ressonância magnética nuclear a fim de identificar possíveis diferenças entre as plantas transgênicas em relação aos seus respectivos controles. Nas amostras de folhas foram encontradas nove regiões cromatográficas representativas para a discriminação das variedades SBBI e SKTI. Análises de HPLC-MS/MS foram empregadas para a identificação parcial dos biomarcadores selecionados pelo método OPS, dentre eles: ácido cafeoílaquínico, ácido feruloílaquínico, shaftosídeo ou isoshafitosídeo, além de quatro substâncias parcialmente identificadas: um derivado de apigenina, um glicosídeo da tricina--O-(metoxicinamato), um derivado de flavonóide metoxilado e um derivado de catequina. Através do estudo metabolomico obteve-se uma visão geral sobre os metabólitos produzidos pelas variedades transgênicas e controles e através das análises dos espectros de RMN 1H, J-resolved, COSY 1H-1H, HMBC 13C-1H foi possível identificar a presença de ácidos orgânicos, amino-ácidos, açúcares, flavonóides e fenilpropanóides. Adicionalmente, a análise quimiométrica dos espectros de RMN 1H mostrou não haver diferença significativa entre folhas SBBI e controles e SKTI e controles. Como conclusão pôde-se sugerir que a inserção dos genes inibidores de protease na cana-de-açúcar não afeta as rotas biosintéticas da planta, mas apenas confere maior resistência contra a broca da cana-de-açúcar (Diatrea saccharilis). Entretanto diferenças significativas entre as variedades transgênicas foram encontradas: a variedade SBBI apresenta teor de açucares e fenilpropanóides mais elevados que a variedade SKTI. Conclui-se também que as alterações metabólicas encontradas neste trabalho não são provenientes dos genes inseridos na planta, mas por outro tipo de efeito sofrido nos controles das duas variedades, como por exemplo, variação somaclonal que antecedem a modificação genética. / Comercial demanding of industrial products from sugarcane plants are reponsable for researchs on genetic improvements with the aim to increase sucrose plant acumulation and/or provide resistence against herbivors. Thus, the present work covers metabolomic study of two transgenics varieties of sugarcane (Bowman-Birk-SBBI e Kunitz- SKTI) and their respectives wild (control) plants through two distinct methodologies: chemometrics analysis of polyphenols chromatography profile found into the transgenics varieties and the metabolomic study by nuclear magnetic resonance for identification of possible metabolic alterations comparing transgenics plants and their respective controls. Nine discriminants chromatography regions were detected on SBBI and SKTI leaves samples. HPLC-MS/MS analyses were performed for biomarkers identification selected by OPS method, among then: caffeoylquinic acid, feruloyl quinic acid, shaftoside or isoshaftoside, apigenin derivatives, tricin-O-(methoxycinamate)-glicosilated, methoxylated flavone and catechine derivative. A general vision about metabolites produced for transgenics and control plants could be achived through metabolomic study. Identification of organic acids, amino acids, sugars, phenylpropanoids and flavonoids were possible through 1H NMR, J-resolved, COSY 1H-1H, HMBC 13C-1H. Moreover, chemometrics analysis of the 1H NMR spectra had shown no significant differences between SBBI with wild plant and SKTI with control plants. These results suggest that the biosyntheses pathways are not affected by protease inhibitors genes introduced on sugarcane, but these genes just provides resistence against Diatrea saccharilis. However, metabolic alterations were found between the transgenic plants (SBBI and SKTI). Specially, the variety SBBI presents high levels of sugars and phenylpropanoids compared with SKTI variety. In conclusion, the metabolic variation found in the present are not due to genes introduction, but are originated by other type of effect on wild plants, such as, somaclonal variation before genetical modification.

The dense and diverse community of microorganisms inhabiting the gastrointestinal tract of ruminant animals plays critical roles in the metabolism and absorption of nutrients, and gut associated immune function. Understanding microbial colonization in the small intestine of new born ruminants is a vital first step toward manipulating gut function through interventions during early life to produce long-term positive effects on host productivity and health. Yet the knowledge of microbiota colonization and its induced metabolites of small intestine during early life is still limited. In the present study, we examined the microbiota and metabolome in the jejunum and ileum of neonatal sika deer (Cervus nippon) from birth to weaning at days 1, 42, and 70. The microbial data showed that diversity and richness were increased with age, but a highly individual variation was observed at day 1. Principal coordinate analysis revealed significant differences in microbial community composition across three time points in the jejunum and ileum. The abundance of Halomonas spp., Lactobacillus spp., Escherichia-Shigella, and Bacteroides spp. tended to be decreased, while the proportion of Intestinibacter spp., Cellulosilyticum spp., Turicibacter spp., Clostridium sensu stricto 1 and Romboutsia spp. was significantly increased with age. For metabolome, metabolites separated from each other across the three time points in both jejunum and ileum. Moreover, the amounts of methionine, threonine, and putrescine were increased, while the amounts of myristic acid and pentadecanoic acid were decreased with age, respectively. The present study demonstrated that microbiota colonization and the metabolome becomes more developed in the small intestine with age. This may shed new light on the microbiota-metabolome-immune interaction during development.

Human pathogenic yeasts of the genus Candida and 𝘊𝘳𝘺𝘱𝘵𝘰𝘤𝘰𝘤𝘤𝘶𝘴 𝘯𝘦𝘰𝘧𝘰𝘳𝘮𝘢𝘯𝘴 are responsible for about 10% of hospital-acquired infections. In addition, drug-resistant yeasts are rapidly emerging with the use of anti-fungal drugs. Common drugs such as Fluconazole and Amphotericin B target the ergosterol pathway in yeast. Learning about other metabolic differences in yeasts may also give a new understanding to their role as pathogens. Metabolomics is a field of study about the large spectrum of metabolites necessary for the growth and survival of an organism. Gas chromatography-mass spectrometry (GC-MS) was used to analyze the metabolome of different yeasts in three different studies. The first study was a targeted analysis of the ergosterol pathway in 𝘊𝘢𝘯𝘥𝘪𝘥𝘢 𝘢𝘭𝘣𝘪𝘤𝘢𝘯𝘴 and a double drug-resistant mutant was found to have several changes in its sterol composition while Fluconazole-resistant strains were similar to the wild-type. In the second study, a comprehensive analysis of the polar and lipid metabolite profiles of six pathogenic yeasts revealed that lipid profiles were more conserved than polar profiles, thereby better reflecting their taxonomical relationship according to 265 rRNA sequences. However, there were several potential species-specific metabolites and short regions in the metabolite profiles with enough peak differentiation that could be used to rapidly distinguish between these yeasts by visual inspection. In the third study, the metabolic phenotypes of three strains of 𝘊𝘳𝘺𝘱𝘵𝘰𝘤𝘰𝘤𝘤𝘶𝘴 𝘯𝘦𝘰𝘧𝘰𝘳𝘮𝘢𝘯𝘴 were analysed to determine the extent of contribution of the metabolite phenotypes from two parents to their hybrid offspring. While the lipid metabolite phenotypes of all strains resembled each other, the polar metabolite phenotype of the hybrid offspring strongly resembled one parent but not the other. / Thesis / Master of Science (MS)

Le diabète de type 2 (DT2) progresse dans le monde entier de manière alarmante. Les complications sont graves et les traitements sont souvent inefficaces et donnent beaucoup d'effets indésirables. Le resvératrol (RSV) et la curcumine (Cur), des polyphénols naturels, sont connus pour leurs différentes activités pharmacologiques, y compris antidiabétiques. Les objectifs de cette étude ont été d'évaluer les effets de la combinaison de ces deux polyphénols sur l'amélioration de la tolérance au glucose. Nos résultats montrent que chez des souris soumises à un régime riche en graisse (HFD), le RSV améliore la tolérance au glucose alors que la Cur n'a pas d'effet significatif. De manière surprenante, lorsque les deux polyphénols sont administrés simultanément, la Cur inhibe l'effet du RSV sur l'amélioration de la tolérance au glucose. Pour expliquer cet antagonisme, nous avons évalué l'effet de ces polyphénols associés ou pas sur le métagénome. Nos résultats indiquent que la Cur et le RSV normalisent la flore intestinale altérée par le HFD. Lors d'une association de ces polyphénols, la Cur inhibe aussi l'effet du RSV sur la croissance de certaines espèces bactériennes. Ainsi, la Cur bloque l'effet inhibiteur du RSV sur Alistipes putredinis. Nos données indiquent que ces polyphénols sont en général anti-inflammatoires mais leur association peut être synergique in vitro ou bien, à l'opposé, antagoniste in vivo pour l'expression de certaines cytokines. Afin d'évaluer l'effet physiologique de la modification de la flore intestinale par les polyphénols, nous avons étudié le métabolome. Parallèlement au métagénome, chacun des polyphénols améliore le profil métabolomique altéré par le HFD. Cependant, la Cur s'oppose à l'effet du RSV. Les données de ce travail indiquent que la Cur n'est pas associable au RSV pour améliorer la tolérance au glucose. / Each year, the worldwide impact of type 2 diabetes (T2D) increases significantly. The complications are serious and treatments are often ineffective and provide a lot of side effects. Resveratrol (RSV) and curcumin (Cur) are natural polyphenols known for their different pharmacological activities, including anti-diabetic. The objectives of this study were to evaluate the effects of the combination of these polyphenols on glucose tolerance improvement. Our results show that in animals fed with a high fat diet (HFD), RSV improved glucose tolerance while Cur displayed no significant effect. Surprisingly, when both polyphenols were administered simultaneously, Cur inhibited the effect of RSV on glucose tolerance improvement. To explain this antagonism between both polyphenols on glucose tolerance, we have evaluated the effect of these compounds on the metagenome associated or not. Our results indicate that RSV and Cur normalized gut flora altered by HFD. When Cur and RSV were administrated simultaneously, Cur inhibited the effect of RSV on the growth of some bacterial species. Thus, Cur blocked the inhibitory effect of RSV on Alistipes putredinis. Our data indicate that these polyphenols displayed generally anti-inflammatory effects, but their combination may be either synergistic in vitro or antagonistic in vivo on the expression of some cytokines. To evaluate the physiological effect of the gut flora changes induced by polyphenols, we have drawn a parallel between metagenome and metabolome data. Each of the polyphenols improved by itself the metabolomic profile altered by HFD. However, Cur hindered the effect of RSV. In a whole, this study indicates that combination of Cur with RSV is not successful to further enhance the RSV-induced improvement of glucose tolerance.

Conselho Nacional de Desenvolvimento CientÃfico e TecnolÃgico / A tendÃncia crescente pela elaboraÃÃo de produtos alimentÃcios com propriedades melhoradas e que apresentem, ao mesmo tempo, processo de fabricaÃÃo, estocagem e aplicaÃÃo simples, rÃpido e econÃmico tem motivado a indÃstria de alimentos a investigar novas tÃcnicas no controle de qualidade de processos e a consequente reduÃÃo dos riscos à saÃde do consumidor e ao meio ambiente. O objetivo deste trabalho à avaliar a influÃncia do binÃmio tempo/temperatura sobre o perfil de metabÃlitos do suco de melÃo submetido a tratamento tÃrmico. A metodologia adotada consiste nas seguintes etapas: ObtenÃÃo do suco - Tratamento TÃrmico - PreparaÃÃo das amostras - AnÃlise CromatogrÃfica - BioinformÃtica - AvaliaÃÃo estatÃstica. As variÃveis estudadas foram o tempo (0,16-31min) e a temperatura (66-94ÂC), empregando um Delineamento Composto Central Rotacional 22. Foram encontrados 101 picos, 57 (56.44%) foram degradados, formados ou mantiveram-se sem alteraÃÃes em alguns ensaios e 44 (43.56%) estavam presentes em todos os tratamentos, sendo que apenas 37 foram submetidos à anÃlise estatÃstica por apresentarem coeficiente de variaÃÃo abaixo de 30% nos pontos centrais. Dentre os metabÃlitos do suco de melÃo tratado termicamente que estavam presentes em todos os tratamentos foram selecionados os picos 4 (1- metil-ciclo-hexanol), 17 (Ãcido isovalÃrico) e 20 (glicina), por estarem distribuÃdos em nÃveis variados nos grÃficos de curvas de contorno da superfÃcie de resposta e apresentarem termos que exerceram efeito estatisticamente significativo sobre a formaÃÃo e/ou degradaÃÃo dos mesmos no diagrama de Pareto. As informaÃÃes quantitativas e qualitativas obtidas referentes ao comportamento do perfil de metabÃlitos de suco de melÃo submetido a tratamento tÃrmico podem ser utilizadas para monitorar e controlar o processamento tÃrmico do produto. / The increasing trend for the elaboration of nourishing products with improved properties and that they present, at the same time, process of manufacture, simple stockage and application, fast economic e has motivated the food industry to investigate new techniques in the quality control of processes and the consequent reduction of the risks to the health of the consumer and the environment. The objective of this work is to evaluate the influence of the time and temperature on the metabolic profile of the submitted melon juice the thermal treatment. The adopted methodology consists of the following stages: Attainment of the juice - Thermal Treatment - Sample preparation - Chromatographic Analysis - Bioinformatics - Evaluation statistics. The studied variable had been the time (0,16-31min) and the temperature (66-94ÂC), using a central composite delineation 22. Found 101 peaks, 57 had been found (56,44%) had been degraded, formed or had been remained without alterations in some assays and 44 (43,56%) were present in all the treatments, being that only 37 had been submitted to the analysis statistics for presenting coefficient of variation below of 30% in the points central offices. Amongst the metabolics of the treat melon juice that they were present in all the treatments had been thermally selected peaks 4 (methyl ciclohexane), 17 (isovaleric acid) and 20 (glycine), for being distributed in levels varied in the graphs of curves of contour of the reply surface and to present terms that had statistical exerted significant effect on the formation and/or degradation of the same ones in the diagram of Pareto. Referring the quantitative and qualitative information gotten to the behavior of the metabolic profile of submitted melon juice the thermal treatment can be used to monitor and to control the thermal processing of the product.

Cyanobacteria are notorious for their potential to produce toxins with human health effects, particularly the hepatotoxic microcystins (MCs), but cyanobacteria also produce other bioactive compounds. A wide variety of oligopeptides including aeruginosins, cyanopeptolins and cyanobactins may be as toxic as MCs. To investigate the production of these compounds, an UPLC QTOF-MS/MS method was developed to compare the metabolomic profiles of various strains of a common bloom-forming and toxigenic species, Microcystis aeruginosa, as well as those obtained from lakes with mixed cyanobacterial assemblages. Although many compounds could not be confirmed, MCs were rarely the dominant secondary metabolite in any sample. Since the biological role of MCs remains unknown, I tested the hypothesis that MCs provide protection against oxidative stress as induced through exposure to the herbicide atrazine and UV radiation in pure cultures of toxic vs non-toxic strains. Results were inconclusive and varied between strains suggesting other mechanisms exist to counter oxidative stress.

京都大学 / 0048 / 新制・課程博士 / 博士(生命科学) / 甲第18626号 / 生博第317号 / 新制||生||42(附属図書館) / 31526 / 京都大学大学院生命科学研究科統合生命科学専攻 / (主査)教授 上村 匡, 教授 西田 栄介, 教授 James Hejna / 学位規則第4条第1項該当 / Doctor of Philosophy in Life Sciences / Kyoto University / DGAM