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This dissertation is a compilation of published work and a manuscript that seeks to understand the role of polyamine metabolism in the regulation of pneumococcal physiology. Streptococcus pneumoniae (pneumococcus) is the major cause of community-acquired pneumonia, and otitis media worldwide. Genetic diversity and serotype replacement, and antibiotics resistance to confound existing therapeutic strategies and limit the effectiveness of the available capsule polysaccharide (CPS) based vaccines. Polyamines such as putrescine, spermidine and cadaverine are ubiquitous polycationic hydrocarbons that interact with negatively charged molecules and modulate important cellular processes. Intracellular polyamine concentrations are regulated by biosynthesis, degradation, and transport. This work investigated the impact of the deletion of polyamine biosynthesis gene, SP_0916 (cadA, lysine/arginine decarboxylase covered in the second, third and fourth chapters), on growth, Gram staining characteristics, capsule production, proteome and stress responses of virulent pneumococcal serotype 4 (TIGR4). We identified loss of capsular polysaccharide (CPS) in DELTA SP_0916 strain. Our proteome results showed a shift in metabolism towards the pentose phosphate pathway (PPP) that could reduce the availability of precursors for CPS and could explain the un-encapsulated phenotype of DELTA SP_0916. Since a shift towards the PPP is usually in response to stress, we compared the stress responses of DELTA SP_0916 to that of TIGR4. Our results show that the mutant was more susceptible to oxidative, nitrosative, and acid stress compared to the wild type. In the fifth chapter we compared the transcriptome, metabolome, stress responses and stress susceptibility of the polyamine transport deficient strain (DELTA potABCD) and S. pneumoniae TIGR4. Results in this chapter show that polyamine transport is essential for pneumococcal stress responses, and capsule biosynthesis. The impact of impaired polyamine synthesis (DELTA SP_0916), and transport (DELTA potABCD) on pneumococcal capsule is due to altered expression of Leloir pathway, reduced glycolysis, and increased PPP, possibly in response to impaired stress responses. These results demonstrate that alteration of polyamine pathways affects pneumococcal stress responses which in turn could limit the availability of precursors for capsule synthesis, and thus have an impact on virulence. Thus, polyamine metabolism is an attractive avenue for developing novel interventions for limiting the spread of S. pneumoniae, a versatile human pathogen.

Angiotensin-converting enzyme 2 (ACE2) has been identified as the cellular entry receptor for the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). High ACE2 tissue expression and low glycine levels were suggested to increase susceptibility for SARS-CoV-2 infection and increasing circulating ACE2 has been proposed as one possible strategy to combat COVID-19. In humans, aerobic physical exercise induces an increase in plasma ACE2 in some individuals. However, it is not clear whether glycine and ACE2 levels depend on intrinsic exercise capacity or on exercise training. We used rats selectively bred for high intrinsic exercise capacity (HCR) or low exercise capacity (LCR) and tested the influence of this genetic predetermination and/or aerobic exercise on metabolites, ACE2 tissue expression and circulating ACE 2. ACE2 expression was measured in different tissues in the sedentary animals and again after 4 weeks of high-intensity aerobic exercise in both LCRs and HCRs. Sedentary HCRs exhibited significantly higher circulating ACE2 concentrations compared to LCRs, but a lower expression of ACE2 in all investigated tissues except for adipose tissue. Body weight was negatively correlated with serum ACE2 and positively correlated with ACE2 expression in the heart. Aerobic exercise caused a significant decrease in ACE2 expression in the lung, heart, muscle, and kidney both in LCRs and HCRs. Our results suggest that ACE2 expression, circulating ACE2 and glycine serum concentration are related to aerobic intrinsic exercise capacity and can be influenced with exercise. These results may support the hypothesis that physically fit individuals have a lower susceptibility for COVID-19 infection.

Background: Human life without sperm is not possible. Therefore, it is alarming that the fertilizing ability of human spermatozoa is continuously decreasing. The reasons for that are widely unknown, but there is hope that metabolomics-based investigations may be able to contribute to overcoming this problem. This review summarizes the attempts made so far. Methods: We will discuss liquid chromatography–mass spectrometry (LC-MS), gas chromatography (GC), infrared (IR) and Raman as well as nuclear magnetic resonance (NMR) spectroscopy. Almost all available studies apply one of these methods. Results: Depending on the methodology used, different compounds can be detected, which is (in combination with sophisticated methods of bioinformatics) helpful to estimate the state of the sperm. Often, but not in all cases, there is a correlation with clinical parameters such as the sperm mobility. Conclusions: LC-MS detects the highest number of metabolites and can be considered as the method of choice. Unfortunately, the reproducibility of some studies is poor, and, thus, further improvements of the study designs are needed to overcome this problem. Additionally, a stronger focus on the biochemical consequences of the altered metabolite concentrations is also required

京都大学 / 新制・課程博士 / 博士(農学) / 甲第24673号 / 農博第2556号 / 新制||農||1099(附属図書館) / 学位論文||R5||N5454(農学部図書室) / 京都大学大学院農学研究科応用生命科学専攻 / (主査)教授 矢﨑 一史, 教授 梅澤 俊明, 教授 伊福 健太郎 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DGAM

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Doctor of Philosophy / Department of Statistics / Gary L. Gadbury / High-throughput metabolite analysis is an approach used by biologists seeking to identify the functions of genes. A mutation in a gene encoding an enzyme is expected to alter the level of the metabolites which serve as the enzyme’s reactant(s) (also known as substrate) and product(s). To find the function of a mutated gene, metabolite data from a wild-type organism and a mutant are compared and candidate reactants and products are identified. The screening principle is that the concentration of reactants will be higher and the concentration of products will be lower in the mutant than in wild type. This is because the mutation reduces the reaction between the reactant and the product in the mutant organism. Based upon this principle, we suggest a method to screen the possible lipid reactant and product pairs related to a mutation affecting an unknown reaction. Some numerical facts are given for the treatment means for the lipid pairs in each treatment group, and relations between the means are found for the paired lipids. A set of statistics from the relations between the means of the lipid pairs is derived. Reactant and product lipid pairs associated with specific mutations are used to assess the results. We have explored four methods using the test statistics to obtain a list of potential reactant-product pairs affected by the mutation. The first method uses the parametric bootstrap to obtain an empirical null distribution of the test statistic and a technique to identify a family of distributions and corresponding parameter estimates for modeling the null distribution. The second method uses a mixture of normal distributions to model the empirical bootstrap null. The third method uses a normal mixture model with multiple components to model the entire distribution of test statistics from all pairs of lipids. The argument is made that, for some cases, one of the model components is that for lipid pairs affected by the mutation while the other components model the null distribution. The fourth method uses a two-way ANOVA model with an interaction term to find the relations between the mean concentrations and the role of a lipid as a reactant or product in a specific lipid pair. The goal of all methods is to identify a list of findings by false discovery techniques. Finally a simulation technique is proposed to evaluate properties of statistical methods for identifying candidate reactant-product pairs.

Os pacientes com Síndrome de Down (SD) possuem grande incidência de doença periodontal (DP), caracterizada por um curso precoce e com maior severidade. O estudo de metaboloma pode contribuir para o entendimento deste curso da doença, identificando possíveis metabólitos como biomarcadores nestes indivíduos. Para entender o perfil metabolômico dos indivíduos com síndrome de Down e a sua relação com a doença periodontal, realizamos a identificação de metabólitos salivares de adolescentes e adultos jovens, entre 12 e 21 anos, ambos os gêneros. Foram coletados dados sobre o estado geral de saúde e realizados exames clínicos bucais, como índice de higiene oral simplificado, sangramento e profundidade de sondagem. Para a análise do metaboloma foi coletada amostra de saliva não estimulada, analisadas por meio de cromatografia gasosa acoplada á espectrometria de massas. Saliva e fluido crevicular gengival também foram coletados para identificação microbiana através do MALDI-TOF. Os dados encontrados foram submetidos a análise estátisca por meio da Análise dos Componentes Principais (PCA) e quantificação relativa dos metabólitos foi avaliada por testes não paramétricos, Mann-Whitney e Kruskal-Wallis. Foi possível observar através dos modelos de PCA separação dos indivíduos com SD e controles, independente da doença periodontal. A quantificação relativa revelou maiores níveis de glicina, lprolina, l-leucina, l-serina, ácido palmítico, ácido pentanóico, ácido tetradecanóico, tirosina e l-fenilalanina nos grupos SD quando comparados aos controles. Controles com DP também apresentaram níveis elevados de glicina, l-alanina, l-serina e manopiranose quando comparados com controles saudáveis. A microbiota de indivíduos com SD apresentous diferenças siginificantes em relação aos individuos controles, principalmente para Rothia dentocariosa, Staphylococcus epidermidis, Tannerella forsythia quando avaliado a saliva e A. Actinomycetemcomitans, Micrococcus luteus, Rothia aeria, Treponema denticola no fluido crevicular gengival. Em conclusão, o perfil metabolômico impresso nos indivíduos com SD difere significativamente dos indivíduos controles, independente da doença periodontal. Entretanto, os metabólitos que diferenciam indivíduos controles com e sem DP, apresentam-se elevados em todos indivíduos com SD, promovendo novos \"insights\" para o perfil metabólico relacionado a DP na SD. / Down Syndrome (DS) patients have a high incidence of periodontal disease (PD), characterized by an early course and greater severity. The metabolome study may contribute to the understanding of the disease course, identifying possible metabolites as biomarkers in these individuals. To understand the metabolomic profile of the DS and their relationship with PD, we conducted the identification of salivary metabolites of adolescents and young adults between 12 and 21 years, both genders. Data were collected on general health and was performed oral clinical examination, as the IHOS, bleeding index and probing depth. For metabolome analysis was collected unstimulated saliva sample, analyzed by gas chromatography coupled to mass spectrometry. Saliva and gingival crevicular fluid were also collected for microbial identification by MALDI-TOF. Data were submitted to analysis-statistic by PCA and relative quantification of metabolites was evaluated by Mann-Whitney and Kruskal-Wallis tests. It can be observed through the PCA models separation of DS groups and controls groups, regardless of periodontal disease. Relative quantification showed higher levels of glycine, L-proline, L-leucine, L-serine, palmitic acid, pentanoic acid, tetradecanoic acid, tyrosine and L-phenylalanine in the SD groups when compared to controls groups. Controls with PD also showed high levels of glycine, L-alanine, L-serine and mannopyranose compared with healthy controls. The microbiota of individuals with DS groups show significant differences compared to control groups, especially for Rothia dentocariosa, Staphylococcus epidermidis, Tannerella forsythia when evaluated saliva and A. actinomycetemcomitans, Micrococcus luteus, Rothia aeria, Treponema denticola in gingival crevicular fluid. In conclusion, the printed metabolomic profile in individuals with Down syndrome differs significantly from control subjects, regardless of periodontal disease. However, the metabolites that distinguish controls group with and without PD, show up high in all DS individuals, promoting new \"insights\" to the metabolic profile related to PD in DS.

Os pacientes com Síndrome de Down (SD) possuem grande incidência de doença periodontal (DP), caracterizada por um curso precoce e com maior severidade. O estudo de metaboloma pode contribuir para o entendimento deste curso da doença, identificando possíveis metabólitos como biomarcadores nestes indivíduos. Para entender o perfil metabolômico dos indivíduos com síndrome de Down e a sua relação com a doença periodontal, realizamos a identificação de metabólitos salivares de adolescentes e adultos jovens, entre 12 e 21 anos, ambos os gêneros. Foram coletados dados sobre o estado geral de saúde e realizados exames clínicos bucais, como índice de higiene oral simplificado, sangramento e profundidade de sondagem. Para a análise do metaboloma foi coletada amostra de saliva não estimulada, analisadas por meio de cromatografia gasosa acoplada á espectrometria de massas. Saliva e fluido crevicular gengival também foram coletados para identificação microbiana através do MALDI-TOF. Os dados encontrados foram submetidos a análise estátisca por meio da Análise dos Componentes Principais (PCA) e quantificação relativa dos metabólitos foi avaliada por testes não paramétricos, Mann-Whitney e Kruskal-Wallis. Foi possível observar através dos modelos de PCA separação dos indivíduos com SD e controles, independente da doença periodontal. A quantificação relativa revelou maiores níveis de glicina, lprolina, l-leucina, l-serina, ácido palmítico, ácido pentanóico, ácido tetradecanóico, tirosina e l-fenilalanina nos grupos SD quando comparados aos controles. Controles com DP também apresentaram níveis elevados de glicina, l-alanina, l-serina e manopiranose quando comparados com controles saudáveis. A microbiota de indivíduos com SD apresentous diferenças siginificantes em relação aos individuos controles, principalmente para Rothia dentocariosa, Staphylococcus epidermidis, Tannerella forsythia quando avaliado a saliva e A. Actinomycetemcomitans, Micrococcus luteus, Rothia aeria, Treponema denticola no fluido crevicular gengival. Em conclusão, o perfil metabolômico impresso nos indivíduos com SD difere significativamente dos indivíduos controles, independente da doença periodontal. Entretanto, os metabólitos que diferenciam indivíduos controles com e sem DP, apresentam-se elevados em todos indivíduos com SD, promovendo novos \"insights\" para o perfil metabólico relacionado a DP na SD. / Down Syndrome (DS) patients have a high incidence of periodontal disease (PD), characterized by an early course and greater severity. The metabolome study may contribute to the understanding of the disease course, identifying possible metabolites as biomarkers in these individuals. To understand the metabolomic profile of the DS and their relationship with PD, we conducted the identification of salivary metabolites of adolescents and young adults between 12 and 21 years, both genders. Data were collected on general health and was performed oral clinical examination, as the IHOS, bleeding index and probing depth. For metabolome analysis was collected unstimulated saliva sample, analyzed by gas chromatography coupled to mass spectrometry. Saliva and gingival crevicular fluid were also collected for microbial identification by MALDI-TOF. Data were submitted to analysis-statistic by PCA and relative quantification of metabolites was evaluated by Mann-Whitney and Kruskal-Wallis tests. It can be observed through the PCA models separation of DS groups and controls groups, regardless of periodontal disease. Relative quantification showed higher levels of glycine, L-proline, L-leucine, L-serine, palmitic acid, pentanoic acid, tetradecanoic acid, tyrosine and L-phenylalanine in the SD groups when compared to controls groups. Controls with PD also showed high levels of glycine, L-alanine, L-serine and mannopyranose compared with healthy controls. The microbiota of individuals with DS groups show significant differences compared to control groups, especially for Rothia dentocariosa, Staphylococcus epidermidis, Tannerella forsythia when evaluated saliva and A. actinomycetemcomitans, Micrococcus luteus, Rothia aeria, Treponema denticola in gingival crevicular fluid. In conclusion, the printed metabolomic profile in individuals with Down syndrome differs significantly from control subjects, regardless of periodontal disease. However, the metabolites that distinguish controls group with and without PD, show up high in all DS individuals, promoting new \"insights\" to the metabolic profile related to PD in DS.

Uma avaliação da concentração dos aminoácidos primários em amostras de urina de crianças com refluxo vésico-ureteral (VUR) em busca de caminhos para o diagnóstico não invasivo desta doença. Dois métodos analíticos por eletroforese capilar com detecção UV/vis foram desenvolvidos para a quantificação dos analitos. No método 1 empregou-se a detecção UV/vis direta em 200 e 214 nm com as condições eletroforéticas eletrólito tampão fosfato 90 mmol L-1 pH 2,1; tensão de +15 kV; injeção de 7 s a 0,5 psi; capilar de 75 µm de diâmetro interno; 40,2 cm de comprimento total e 30,0 cm de comprimento efetivo. No método 2, fez-se uso da detecção indireta em 254 nm, com as condições eletroforéticas eletrólito tampão TEA 20 mmol L-1 e DNB 10 mmol L-1 pH 10,84; modificador de fluxo DDAB a 4 mmol L-1; tensão de -15 kV; injeção de 7 s a 0,5 psi; capilar de 75 µm de diâmetro interno; 50,2 cm de comprimento total e 40,0 cm de comprimento efetivo. O método 1 apresentou parâmetros de validação linearidade, precisão intra-dia e inter-dia, seletividade, robustez e recuperação satisfatórios. A quantificação de creatinina, fenilalanina (Phe), histidina (His), triptofano (Trp), tirosina (Tyr) nas amostras de urina foi possível pelo método 1, porém inviável para quantificação de arginina (Arg). O método 2 apresentou valores de robustez e recuperação satisfatórios para os aminoácidos alanina (Ala), aspartato (Asp), glutamato (Glu) e glicina (Gly) satisfatórios, mas a quantificação dos mesmos na maioria das amostras de urina diluída não foi possível por estarem em nível de concentração abaixo da detecção ou quantificação. Para avaliar a potencialidade dos resultados como ferramenta no diagnóstico do VUR, os aminoácidos His, Phe, Trp e Tyr, quantificados em todas as amostras, foram empregados como variáveis na classificação das amostras em dois grupos distintos (1) grupo de crianças saudáveis e (2) grupo de crianças diagnosticadas com VUR. A classificação realizada pelo método de análise de componente principal (PCA) apresentou valores estatísticos satisfatórios e poder de predição: R2 (capacidade de ajuste) e Q2 (capacidade de predição) foram 0.9993 e 0.65, respectivamente com os dois componentes principais (PC1 e PC2). A separação total com valor de Q2 desejável (acima de 0,8) poderia ser alcançada com uma quantidade maior de informação, sendo neste caso, número maior de aminoácidos quantificados. Assim, este trabalho abre caminho para estudos mais aprofundados na investigação da concentração dos aminoácidos primários em pacientes com VUR, objetivando o desenvolvimento de um potencial biomarcador para VUR. / An assessment of the concentration of primary amino acids in urine samples from children with vesicoureteral reflux (VUR) using capillary electrophoresis separation with UV/vis detection has been proposed to help establishing a means for non invasive diagnosis of the disease. Two analytical methods were developed. Method 1 used direct UV/vis detection at 200 and 214 nm, 90 mmol L-1 phosphate buffer at pH 2.1, high voltage separation at +15 kV, injection of 0.5 psi during 7 s, and a fused-silica capillary of 75 µm inner diameter, 40.2 cm total length, and 30.0 cm effective length. Method 2 used indirect UV/vis detection at 254 nm, TEA at 20 mmol L-1 and DNB at 10 mmol L-1 electrolyte at pH 10.84, 4 mmol L-1 DDAB as flow modifier, separation voltage at -15 kV, injection of 0,5 psi during 7 s, fused-silica capillary of 75 µm inner diameter, 50.2 cm total length, and 40,0 cm effective length. Method 1 presented satisfactory results for linearity, intra-day and inter-day precision, selectivity, robustness, and recovery. By method 1 it was possible to quantify creatinine, phenylalanine (Phe), histidine (His), tryptophan (Trp), tyrosine (Tyr) but not arginine (Arg) in the urine samples under investigation. Method 2 presented satisfactory robustness and recovery for alanine (Ala), aspartate (Asp), glutamate (Glu) and glycine (Gly), but the contents of these metabolites in the urine samples were not established because they lay below the limits of detection and quantitation. To assess the potentiality of the results as diagnostic tool for VUR condition, the concentrations of the amino acids His, Phe, Trp and Tyr, quantified in all samples, were used as variables in a classification procedure where samples were divided in two distinct groups: (a) a group of healthy children and (b) a group of children diagnosed with VUR. The classification by principal component analysis (PCA) showed a partial separation with good statistics and prediction power: R2 (goodness of fit) and Q2 (goodness of prediction) were 0.9993 and 0.65, respectively with two components analysis (PC1 and PC2). Values of Q2 greater than 0.8 are usually desired and it could be provided if more information was available, such as a greater number of amino acids being quantified. Thus, this research opens the way for further investigative studies of amino acids concentration in patients with primary VUR, aimed at developing a potential biomarker for VUR.