京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第19774号 / 農博第2170号 / 新制||農||1040(附属図書館) / 学位論文||H28||N4990(農学部図書室) / 32810 / 京都大学大学院農学研究科応用生命科学専攻 / (主査)教授 植田 充美, 教授 栗原 達夫, 教授 矢﨑 一史 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

Azotobacter vinelandii contains an iron-regulatory small RNA ArrF whose expression is dependent upon the levels of iron and ferric uptake regulator. The deletion of ArrF-encoding gene resulted in a 300old increase in the production of polyhydroxybutyrate (PHB), a polymer of industrial importance. This ∆arrF mutant exhibited wild-type growth and growth-associated PHB production. Limited iron and aeration elevated the PHB production in the mutant as well as wild type. SDS-PAGE and MALDI-MS/MS revealed the overexpression of acetyl-CoA reductase, a phbBAC operon enzyme and the proteins that would alleviate the stress due to PHB accumulation in the ∆arrF mutant. Real-time RT-PCR revealed that phbR, phbB, phbA and phbC were upregulated in the mutant. Increased levels of activator PhbR in the mutant elevates the expression of phbB, phbA and phbC, resulting in the PHB overproduction. The proteins differentially expressed in the ∆arrF mutant were determined by gel-based proteomics and confirmed by real time RT-PCR. 6-phosphogluconolactonase that involve in the production of NADPH and acetyl-CoA, was upregulated, while the proteins involved in the TCA cycle that consumes acetyl-CoA were downregulated. Heat-shock proteins such as HSP20 and GroEL were overexpressed in the mutant. In addition, antioxidant proteins such as Fe-containing supeoxide dismutase (FeSOD), a putative oxidoreductase with unknown function, alkyl hydroperoxide reductase, flavorprotein WrbA and cysteine synthase were also upregulated, indicating that the PHB accumulation is highly stressful to the cells. Upregulated in the ∆arrF mutant were acetyl-CoA carboxylase, flagellin, and adenylate kinase. Among the genes upregulated in the ∆arrF mutant, sodB gene coding for Fe-superoxide dismutase and phbF gene encoding PHB synthesis regulator appears to be negatively regulated by small RNA ArrF in an antisense mechanism. However, all the TCA cycle genes were downregulated in the ∆arrF mutant. In addition to the TCA cycles enzyme, glutamate synthetase, elongation factor-Tu, iron ABC transporter, and major outer membrane porin OprF were downregulated in the ∆arrF mutant. Based on the results, it is concluded that several factors are responsible for the overproduction of PHB polymer in the ∆arrF mutant and one of which is the direct effect of small RNA ArrF on the expression of PhbF .

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第20438号 / 農博第2223号 / 新制||農||1049(附属図書館) / 学位論文||H29||N5059(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 植田 充美, 教授 矢﨑 一史, 教授 森 直樹 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

Orientador: Lidiane Nunes Barbosa / Resumo: Combinações entre antimicrobianos, a exemplo de nisina (bacteriocina) e fármacos antibacterianos tradicionais, podem amenizar o problema da resistência bacteriana, pois o possível efeito sinérgico se torna estratégico, possibilitando o uso de doses menores no tratamento de doenças infecciosas com redução nos custos e na toxicidade, além de ter potencial na prevenção do surgimento das linhagens resistentes. No entanto, os mecanismos envolvidos na ação antibacteriana são importantes para pesquisas de novos fármacos. O objetivo do estudo foi investigar como a nisina, alguns fármacos antibacterianos e respectivas combinações interferem no metabolismo de Staphylococcus aureus Meticilina Resistente (MRSA) e Pseudomonas aeruginosa, através de ensaios de estresse oxidativo bacteriano, análises morfológicas por microscopia eletrônica de transmissão (MET) e análise do perfil de proteínas expressas nas bactérias quando expostas aos antimicrobianos e suas combinações em concentrações subletais. Inicialmente foram realizados ensaios visando obter os valores de concentração inibitória mínima (CIM) e concentração subletal máxima (CSM) para nisina e fármacos como tetraciclina, ciprofloxacina, vancomicina, polimixina B, oxacilina e cefalotina para ambas bactérias. Na sequencia, foram realizados ensaios para verificação de sinergismo entre nisina e antibacterianos utilizando metodologia da curva de sobrevivência, sendo escolhidas para ensaios posteriores, as combinações com demostração de sine... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Combinations of antimicrobials, such as nisin (bacteriocin) and traditional antibacterial drugs, may assuage the problem of bacterial resistance because the possible synergistic effect becomes interesting, allowing the use of smaller doses in the treatment of infectious diseases and reduction in costs and toxicity , besides having potential in the prevention of the emergence of resistant strains. However, the mechanisms involved in antibacterial action are important for research on new drugs. The aim of this study was to investigate how nisin, antibacterial drugs and their combinations interfere in the metabolism of Methicillin Resistant Staphylococcus aureus (MRSA) and Pseudomonas aeruginosa, verified in bacterial oxidative stress assays, morphological analyzes by transmission electron microscopy (TEM) and analysis of the protein profile expressed in bacteria when exposed to antimicrobials and combinations in sublethal concentrations. Initially, assays were performed to obtain the minimum inhibitory concentration (MIC) and maximum sublethal concentration (MSC) for nisin and drugs such as tetracycline, ciprofloxacin, vancomycin, polymyxin B, oxacillin and cephalothin for both bacteria. Subsequently, assays were performed to verify the synergism between nisin and antibacterials using time kill curve methodology and the combinations with demonstration of synergism (reduction in final bacterial count above 2 logs of CFU / mL in relation to initial inoculum) were chosen for later... (Complete abstract click electronic access below) / Doutor

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第21808号 / 農博第2321号 / 新制||農||1066(附属図書館) / 学位論文||H31||N5180(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 植田 充美, 教授 渡邊 隆司, 教授 栗原 達夫 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

Palliative Therapie inklusive Chemotherapie und andere Behandlungsmethoden wie Hyperthermie ist oftmals die einzig verbleibende Option bei der Behandlung von bestimmten soliden Tumoren wie Magen- und Pankreaskarzinom. Leider ist der Erfolg dieser Therapien limitiert durch geringes Ansprechen der Tumoren auf die Behandlung und die Entwicklung einer Therapieresistenz. In dieser Arbeit wurde die globale Proteinexpression von chemo- und thermoresistenten Varianten der Magenkarzinomzellinie EPG85-257 und der Pankreaskarzinomzellinie EPP85-181 mit Hilfe von Proteomics (Kombination aus zweidimensionaler Elektrophorese, computergestützter Gel-Analyse und Massenspektrometrie) in vitro untersucht, um Kandidatenproteine zu finden, die potentiell mit Thermoresistenz bzw. Chemoresistenz assoziiert sind. In diesem Zusammenhang wurde eine mit Maldi-TOF kompatible Spezialsilberfärbung neu entwickelt. Es zeigte sich eine differentielle Expression einer Vielzahl von Proteinen in den thermoresistenten Zellen, darunter eine Hochregulation von Proteinen mit Chaperonaktivität aus nahezu allen subzellulären Kompartimenten sowie eine Überexpression von Enzymen des Arzneimittelmetabolismus in Zellen mit sowohl chemo- als auch thermoresistentem Phänotyp. Darüber hinaus wurden weitere Proteine identifiziert, welche hinsichtlich ihrer Beteiligung an Resistenzphänomenen im Vorfeld noch gar nicht charakterisiert worden sind (u.a. Aldehyd-Dehydrogenase 1, Transgelin, Phosphoglyceromutase). / Palliative treatment including chemotherapy and other modes of treatment, e.g. hyperthermia, is often the only remaining option in the management of certain solid tumours including gastric and pancreatic carcinoma. Unfortunately, its efficacy is poor due to low tumour sensitivity and the development of therapy resistance. The aim was to study in vitro global protein expression of chemo- and thermoresistant variants of the stomach cancer cell line EPG85-257 and the pancreatic cancer cell line EPP85-181 using proteomics (two-dimensional electrophoresis in combination with computer-assisted image analysis and mass spectrometry) to identify candidate proteins potentially associated with thermoresistance alone or in combination with chemoresistance. In this context, a special silver stain compatible with Maldi-TOF was developed. A large number of proteins was found to be differentially expressed in thermoresistant cells including up-regulation of molecular chaperones at practically every sub-cellular level as well as over-expression of enzymes involved in drug metabolism in both chemo- and thermoresistant cells. Furthermore, other proteins were identified that have not yet been linked to resistance phenomena (e.g. aldehyde dehydrogenase 1, transgelin, phosphoglycerate mutase).

No description available.

Die vorliegende Arbeit befaßt sich mit Nachweismöglichkeiten von Helicobacter pylori und deren Vergleich. Hierfür ist eine genaue Kenntnis der Helicobacter-Proteine notwendig. Zu diesem Zweck wurde die humorale Immunantwort gegenüber Helicobacter pylori unter Anwendung der Methodik des zweidimensionalen Immunoblots analysiert. Zunächst wurden Proteine des autologen Helicobacter pylori-Stammes über zweidimensionale Gelelektrophorese aufgetrennt, auf Nitrocellulose-Membranen geblottet und sodann mit Antikörpern aus autologem Plasma sowie Antikörpern aus dem Überstand von in vitro kultiviertem autologem Biopsiematerial detektiert. Zur Bestimmung einer Helicobacter-Infektion wurden andere invasive und nicht invasive Tests genutzt. In einer prospektiven Untersuchung wurden über 200 konsekutive Patienten mit gastrointestinalen Beschwerden und unbekanntem H. pylori-Status, die für eine Gastroskopie vorgesehen waren, routinemäßig untersucht. Bei jeder Gastroskopie wurden zwei Antrum- und zwei Korpusbiopsien zur Gastritis-Diagnostik und zur Bestimmung des H. pylori-Status entnommen. Es wurden Assoziationen zwischen einer Infektion mit Helicobacter pylori und Erkrankungen wie akute und chronische Gastritis, gastraler und duodenaler Ulkus, Magenkarzinom und Folgeerkrankungen der Gastritis überprüft. Dabei wurden auch die eindeutig Helicobacter pylori-negativen Seren mit den positiven Seren verglichen. Trotz ungleichmäßiger Verteilung der Patientenzahlen über die einzelnen Krankheitsgruppen (Gastritis, Ulkus, Karzinom) wurden bestimmte Proteine nur bei einer der Erkrankungen erkannt. Einige Proteinspots kamen deutlich intensiver bei einer einzigen Krankheitsgruppe vor. Anzustreben sind Studien mit größeren Patientenzahlen innerhalb der einzelnen Krankheitsgruppen, um mögliche weitere Assoziationen bestimmter Helicobacter-Antigene mit Folgeerkrankungen zu analysieren und zu verifizieren. Ferner wurde das Vorliegen einer Assoziation des zweidimensionalen Immunoblots mit anderen invasiven und nicht invasiven Nachweisverfahren der H. pylori-Infektion analysiert. Dabei wurde das Antigenprofil des H. pylori, sowohl qualitativ als auch quantitativ, berücksichtigt. Durch die Charakterisierung und Identifizierung einer bedeutenden Anzahl von Helicobacter-Proteinen erhöht sich die Wahrscheinlichkeit für ein zukünftig beschleunigtes Screening in Richtung protektiver Vakzine-Kandidaten. / The present study is concerned with practicable methods of detecting Helicobacter pylori and comparing them. As a precondition, a precise knowledge of the proteins of Helicobacter is necessary. To this end the humoral immune response of Helicobacter pylori was analysed by using the method of two-dimensional immuno blots. First, the proteins of each autologous Helicobacter pylori strain were separated by two-dimensional electrophoresis, then blotted onto nitrocellulose membranes and eventually detected by using antibodies from autologous plasma and antibodies taken from the overflow of in vitro cultivated autologous biopsy material. For determining a Helicobacter infection various invasive and non-invasive tests were carried out. In a prospective study on more than 200 patients with gastrointestianal disorders but unknown H. pylori status were consecutively tested. At each gastroscopy two bioptic specimen each were taken from the antrum and from the corpus region in order to determine the H. pylori status. Associations were assessed between Helicobacter pylori infections and manifestations such as acute or chronic gastritis, gastric or duodenal ulcers, gastric carcinoma and gastritis induced disorders. In the process, clearly Helicobacter pylori negative sera were also compared with positive sera. Inspite of the unequal distribution of numbers of patients over different groups of disorders (gastritis, ulcers, carcinoma) certain proteins were only detected in connection with one group of disorder. Several of the protein spots only occurred in a single group of disorders. More studies will be necessary using greater numbers of patients within each group of diseases in order to analyse and verify associations between Helicobacter antigenes and other disorders. Further, evidences of an association between two-dimensional immunoblots and other invasive and non-invasive methods of assessing H. pylori were analysed with regard to respective antigene profiles, qualitatively as well as quantitatively. Based upon the presented characterizations and identifications of an unusually great number of Helicobacter proteins the probability is thus increased considerably with regard to improved screening methods towards protective vaccine candidates.

L’hépatite allo-immune post-greffe de moelle osseuse (GMO) est très mal définie. Le premier objectif de notre thèse était d’identifier, par analyse sérologique du protéome, les antigènes (Ag) cibles d’auto-anticorps (Ac) présents dans le sérum de patients. Cinq patients, ayant reçu une GMO, ont développé des troubles hépatiques à l’arrêt du traitement immunosuppresseur, avec des signes histologiques ressemblant à ceux des hépatites auto-immunes (HAI). Avant et pendant l’épisode hépatique, des serums ont été testés sur des immunoblots réalisés avec des protéines nucléaires, cytosoliques, microsomiques et mitochondriales obtenues à partir d’homogénat de foie de rat, séparées par électrophorès bi-dimensionnelle et transférées sur membrane de nitro-cellulose. Après digestion trypsique, les protéines d’intérêt, marquées uniquement ou plus intensément par les sérums en phase d’hépatite, étaient identifiées par spectrométrie de masse MALDI-TOF/TOF et nanoHPLC LTQ-Orbitrap®. Un nombre total de 103 protéines antigéniques a été identifié, parmi lesquelles 12 sont reconnues par les sérums de 3 patients. A l’issue de cette première description immunologique des hépatites allo-imunes post-GMO, nous formulons des hypothèses physiopathologiques permettant d’expliquer l’évolution d’un mécanisme allo-immun vers une réaction auto-immune. En outre, nous recommandons la réduction très progressive des doses d’immunosuppresseur après GMO.La protéine hnRNP A2/B1 est une cible des anticorps anti-nucléaires (AAN) dans le lupus érythémateux disséminé (LED), la polyarthrite rhumatoïde (PR) et l’HAI. Dans la deuxième partie de la thèse, le but était de caractériser les interactions Ag-Ac en fonction de la pathologie, en utilisant la résonance plasmonique de surface par imagerie (SPRi). Trente-neuf peptides chevauchants de 17 acides aminés, couvrant l’ensemble de l’isoforme B1 de la protéine humaine, ont été immobilisés à la surface d’un prisme. Les interactions entre les peptides immobilisés et les sérums de 8 patients de chaque pathologie et de donneurs sains (D) ont été étudiées en temps réel. Les constantes de vitesse de dissociation koff, calculées pendant la phase de dissociation des complexes Ag-Ac formés, reflètent la stabilité de ces complexes.Plusieurs interactions significatives ont été observées : i) avec une stabilité élevée entre P55-70 et les sérums d’HAI par rapport aux contrôles (p= 0.003); ii) avec une faible stabilité entre P118-133 et P262-277 et les serums de LED, P145-160 et les sérums de PR par rapport aux serums D (p=0, 006; p=0,002; p=0,007). Le peptide P55-70 est donc un biomarqueur potentiel dans l’HAI. Les courbes d’interaction et les koff observés après la formation de complexes avec des anticorps anti-IgG et anti-IgM d’une part, et le traitement des sérums par des nucléases d’autre part, montrent que : i) les IgM sont majoritaires et ii) des acides nucléiques, présents ou non selon la maladie auto-immune, participent aux interactions entre les anti-hnRNP B1 et le peptide AA55-70 ainsi qu’entre les autres peptides et les sérums témoins, et contribuent à la stabilité des complexes Ag-Ac. Les résultats de nos travaux et les innovations technologiques en spectrométrie de masse et en SPR permettent d’envisager la mise au point de nouveaux tests pour le suivi des patients atteints d’hépatites auto et allo-immunes. / Alloimmune hepatitis following bone marrow transplantation (BMT) is poorly characterized. The first goal of this thesis was to identify antigens (Ag) targets of autoantibodies (auto-Ab) in sera from patients, using serological proteome analysis. Five patients who received an allogeneic BMT developed liver dysfunctions with histological features suggestive of autoimmune hepatitis (AIH) after the withdrawal of immunosuppressive therapy. Before and during the onset of hepatic dysfunction, sera were tested on immunoblots performed with cytosolic, microsomal, mitochondrial and nuclear proteins from rat liver homogenate, resolved by two-dimensional electrophoresis and transferred onto nitrocellulose membranes. After tryptic digestion, antigenic targets were identified by two tandem mass spectrometry techniques: MALDI-TOF/TOF and nanoHPLC LTQ Orbitrap®. A total of 103 different proteins were identified. Twelve of them were recognized by sera from three patients. This is the first immunological description of hepatitis occurring after BMT, enabling a discussion of the mechanisms that transform an alloimmune reaction into an autoimmune response. Any decision to withdraw immunosuppression after allogeneic BMT should be made with caution and hepatic parameters monitored systematically.Heterogeneous nuclear ribonucleoprotein (hnRNP) A2/B1 is a target for antinuclear autoantibodies in systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), and autoimmune hepatitis (AIH). In the second part of the thesis, the goal was to characterize Ag-Ab interactions as a function of pathology, using surface plasmon resonance imagery (SPRi). Sera from 8 patients from each pathology and healthy donors (D) were passed across a SPRi surface containing 39 overlapping peptides of 17 mers covering the human hnRNP B1. Interactions involving the immobilised peptides were followed in real time and dissociation rate constants koff for each interaction were calculated. koff values reflect the stability of the complex. Several significant interactions were observed: i) high stability (lower koff values) between P55-70 and the AIH sera compared to controls (p= 0.003); ii) lower stability (higher koff values) between P118-133 and P262-277 and SLE sera, P145-160 and RA sera compared to controls (p=0.006, p=0.002, p=0.007). These results indicate that P55-70 of hnRNP B1 is a potential biomarker for AIH in immunological tests.The binding curves and koff values observed after the formation of complexes with anti-IgM and anti-IgG antibodies and after nuclease treatment of the serum indicate that i) IgM isotypes are prevalent and ii) circulating nucleic acids, present or absent according to the autoimmune disorders, participate in the interaction between anti-hnRNP B1 and P55-70 and also between controls and the peptides studied and are involved in antigen-antibody stability. Results from our work as well as promising innovations in mass spectrometry and SPR technologies lead us to consider the development of new tests, usable in monitoring patients with auto and alloimmune liver diseases.