Agrobacterium are Alphaproteobacteria common in most soils that closely interact with plants in two respects. Firstly, they are rhizospheric bacteria saprophytically living in the rhizosphere of numerous plants and they are likely beneficial to plants. Secondly, when they harbor a dispensable Ti plasmid (i.e. tumor inducing plasmid), agrobacteria are plant pathogens able to cause the crown gall disease to most dicots and gymnosperms and some monocots. An epidemiological survey of crown gall thus also requires expert determination of the Agrobacterium taxonomy. In this thesis we evaluated the usefulness of MALDI-TOF MS technique as a high throughput tool to determine and classify agrobacteria. Then we set up a recA-based PCR method to accurately and exhaustively assess agrobacterial diversity either of isolated agrobacteria or directly in various biotopes. We applied standard biochemical, recA-based and Ti plasmid-based identification methods to study the prevalence of pathogenic and non-pathogenic agrobacteria at the country and local scales. Finally, we tested whether analyzing the internal composition of recA amplicons could be a way to directly assess the micro-diversity of agrobacterial populations using cloning sequencing or pyrosequencing approaches. The later methodology was applied to establish the actual field diversity of Agrobacterium and to evaluate whether plant genotypes differentially select agrobacteria in their root systems, providing first data upon biotic factors shaping the population structure of agrobacteria

Vibrio parahaemolyticus is an opportunistic human pathogen that occurs naturally in a non-pathogenic form in coastal estuarine and marine environments worldwide. Following the acquisition of virulence-associated genes, V. parahaemolyticus has emerged as a significant pathogen causing seafood-borne illnesses. The mechanisms and conditions that promote the emergence of disease causing V. parahaemolyticus strains are not well understood. In addition, V. parahaemolyticus clinical strains isolated from disease-associated samples and environmental strains from sediment, water, and marine organisms have been identified with considerable diversity; however, the evolutionary relationships of disease-causing strains and environmental strains are not known. In the following research, the evolutionary relationships of V. parahaemolyticus clinical and environmental strains are examined. In addition, the contribution of genetic elements and molecular mechanisms such as deficiency of DNA repair to the evolution of V. parahaemolyticus clinical and environmental strains is shown. Molecular analysis of the evolutionary relationships of V. parahaemolyticus clinical and environmental strains demonstrated separate lineages of pathogenic and non-pathogenic strains with the exception of several environmental strains that may represent a reservoir of disease-causing strains in the environment. Sequence characterization of plasmids isolated from diverse environmental Vibrios indicated a role of plasmids in strain evolution by horizontal transfer of housekeeping genes. In addition, analysis of plasmids from V. parahaemolyticus clinical and environmental strains indicated the existence of a plasmid family distributed among V. parahaemolyticus, V. campbellii, and V. harveyi environmental strains. Sequence characterization of a plasmid of this family from a V. parahaemolyticus environmental strain indicated the contribution of these plasmids to the emergence of the clonal pandemic strains. Investigation of the role of molecular mechanisms to the evolution of V. parahaemolyticus strains showed that inactivation of the DNA repair pathway methyl-directed mismatch repair (MMR) increased the accumulation of spontaneous mutations leading to increased nucleotide diversity in select genes. The research findings in the following chapters demonstrate a considerable contribution of genetic elements and molecular mechanisms to the evolution of genetic and phenotypic diversity.

Hypertrophic scarring is a common occurrence for severe burn victims leading to major functional, physiological, and aesthetic effects to the patients. Limiting the hypertrophic scarring of the patients alleviates the functional, physiological, and aesthetic effects. Silicone gels, over the past decade, have been widely used to remediate and limit hypertrophic scarring but the mechanism of action is yet to be determined. One explanation has been that hydration of the outermost area of the burn is induced by the silicone gel . However, non-silicone polymers which increase hydration could not mimic the effect. An alternative interpretation is that there may be silicone species that migrate from the silicone gel into the viable tissue to mediate reactions in the extra-cellular matrix that result in a decreased deposition of excessive amounts of collagen - a central feature of the hypertrophic scar. A novel and informative technique to study these species is MALDI-TOF/MS (Matrix Assisted Laser Desorption Ionisation-Time of Flight Mass Spectrometry) in conjunction with gel permeation chromatography. MALDI-TOF/MS, which has allowed the detection of intact molecular species that were not possible with more established mass spectrometric techniques. The mobile species that may migrate from polydimethylsiloxane medical gel sheeting into skin have been identified by MALDI-MS. The bulk gel contains predominantly cyclic oligomers with a mass distribution peaking at n = 19 (number of repeating siloxane units), but in an aqueous environment the species at the surface of the silicone medical gel are predominantly methyl/methylol-terminated linear siloxanes. By using a gelatine matrix as a model substrate, the distribution of silicon after application of the silicone gel for 16 weeks was determined by Energy-dispersive X-Ray mapping of the sectioned gelatine. The association of the linear and cyclic oligomers with proteins relevant in hypertrophic scarring are considered. The mobility of silicone species across stratum corneum was confirmed by Attenuated Total Reflectance Fourier Transform Infrared spectroscopy (ATR-FT/IR). This method confirms our hypothesis that not only are the low molecular weight silicone species mobile, but also that they do traverse the natural barrier, the stratum corneum, to levels that are detectable by ATR after a continuous application over approximately 11 days. Invitro studies of the effects of LMWS on primary line fibroblast cells indicate a response that down regulates the proliferation of fibroblast cells and protein production. Preliminary results indicate that a family of pendant functional LMWS are effective in down regulating hypertrophic-derived fibroblast primary cells. Studies on hypertrophic scar tissue treated with silicone medical gel indicate that LMWS permeate across the stratum corneum into viable scar tissue. In some areas, the LMWS tend to pool as detected by SEM/EDX elemental silicon analysis. These areas of LMWS pooling tend to be composed of highly disorganised collagen nodules.

Philosophiae Doctor - PhD / This study reports on a proteomic analysis of sorghum proteomes in response to salt and hyperosmotic stresses. Two-dimensional gel electrophoresis (2DE) in combination with mass spectrometry (MS) was used to separate, visualise and identify sorghum proteins using both sorghum cell suspension cultures and whole plants. The sorghum cell suspension culture system was used as a source of culture filtrate (CF) proteins. Of the 25 visualised CBB stained CF spots, 15 abundant and well-resolved spots were selected for identification using a combination of MALDI-TOF and MALDI-TOFTOF MS, and database searching. Of these spots, 14 were positively identified as peroxidases, germin proteins, oxalate oxidases and alpha-galactosidases with known functions in signalling processes, defense mechanisms and cell wall metabolism. / South Africa

Beta-N-methylamino-L-alanine (BMAA) is a non-protein amino acid produced by many cyanobacteria, and thought to induce neurotoxic effects through excitotoxicity, contributing to neurodegenerative diseases such as Amyotrophic Lateral Sclerosis/Parkinsonism-dementia complex (ALS-PDC) and Alzheimer’s. The ubiquitous nature of cyanobacteria, and evidence of biomagnification through our food web, creates a dire need for the development of an analytical platform that will provide accurate identification and quantification of BMAA amounts in our ecosystem and potential food supply. The present study evaluated the ability of a MALDI-ToF-MS method to detect and quantify BMAA in a variety of biological matrices. Through validation procedures, it was demonstrated that this MALDI-ToF-MS method provided comparable data to currently accepted analytical methods, specifically LC-MS/MS. Further, the development of said method reduced sample preparation and data acquisition time (1-2 seconds per sample), while providing high throughput analysis and eliminating the need for derivatization, chromatographic separation, and modification of amino acids.

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第22148号 / 医博第4539号 / 新制||医||1039(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 坂井 義治, 教授 小西 靖彦, 教授 滝田 順子 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

(EN) Vernix caseosa is a white creamy substance that covers the skin of a newborn. It is produced during the third trimester by the skin of the baby and remains there until the age of one or even two weeks. It is uniquely human. In utero, vernix protects the skin from maceration, during the birth it serves as a lubricant and after the delivery it protects the baby against infection and regulates the temperature. As vernix is produced in third trimester, prematurely born infants lack it and this may lead to, among other things, suffering from desiccation and therefore heat loss. It is important to study it thoroughly and to find a suitable substitute of vernix for the preterm infants. Vernix consists of lipids, proteins and 80 % water. This project is aimed at the lipids. Vernix is composed of 10 % of lipids. Basic analytical methods of pocessing vernix were searched. The methods of isolation, separation and transesterification have been optimized for the lipids. For separation, thin-layer chromatography has been chosen. The method of the lipid analysis of intact molecules by MALDI-TOF MS has been optimized for these lipids. The results were confirmed using fragmentation spectra and transesterification. Esterified lipids were measured by gas chromatography coupled with mass spectrometry detection....

Das Plattenepithelkarzinom stellt mit über 90% die häufigste maligne Neubildung innerhalb der Mundhöhle mit gravierenden funktionellen Einschränkungen für die betroffenen Patienten und hoher Mortalität dar. In den meisten Fällen bestehen bereits vor der malignen Transformation visuell erkennbare Veränderungen mit höherem Entartungspotential, sogenannte potenziell maligne Veränderungen. Die vorliegende Arbeit beschäftigt sich mit einem experimentellen Verfahren zur oralen Tumorfrüherkennung und Dignitätsabklärung von potenziell malignen Veränderungen der Mundschleimhaut. Grundlage bildet das Verfahren des „intact cell peptidome profiling“ (ICPP) mittels MALDI-TOF MS anhand von Präparaten oraler Bürstenbiopsien. Untersucht wurden 16 Proben oraler Plattenepithelkarzinome, 69 Fälle von oralem Lichen planus, 26 orale Leukoplakien, 21 andere orale Veränderungen sowie 56 Mundschleimhautläsionen an Fanconi-Anämie erkrankter Patienten. Die Methode eignet sich zur Unterscheidung zwischen gesunder Mundschleimhaut und maligne verändertem Gewebe, wie mit einer Sensitivität von 86 % und einer Spezifität von 100 % belegt wurde. Eine Differenzierung zwischen den einzelnen Mundschleimhautveränderungen und gesundem Gewebe konnte nicht erreicht werden. Die Untersuchungsreihe ist als vielversprechend einzuschätzen, um ein weiterführendes diagnostisches Verfahren zu entwickeln, dass den Untersucher durch eine objektive Messmethode unterstützen und Sensitivität und Spezifität der Bürstenbiopsie steigern könnte.

Philosophiae Doctor - PhD / Sorghum (Sorghum bicolorï, a drought tolerant cereal crop, is not only an important food source in the semi arid/arid regions but also a potential model for studying and gaining a better understanding of the molecular mechanisms of drought and salt stress tolerance in cereals. This study reports on a proteomic analysis of sorghum proteomes in response to salt and hyperosmotie stresses. Two-dimensional gel electrophoresis (2DE) in combination with mass spectrometry (MS) was used to separate, visualise and identify sorghum proteins using both sorghum cell suspension cultures and whole plants. The sorghum cell suspension culture system was used as a source of culture filtrate (CF) proteins. Of the 25 visualised CBB stained CF spots, 15 abundant and well-resolved spots were selected for identification using a combination of MALDI- TOF and MALDI- TOFTOF MS, and database searching. Of these spots, 14 were positively identified as peroxidases, germ in proteins, oxalate oxidases and alpha-galactosidases with known functions in signalling processes, defense mechanisms and cell wall metabolism. Following 200 mM NaCl and 400 mM sorbitol stress treatments, the expression/abundance of a protein spot similar to a rice wall-associated protein kinase was upregulated in the sorghum secretome in response to both stresses. Amino acid sequence alignment of the matching peptides between these two proteins showed that the sorghum CF spot possesses a protein kinase domain. Therefore, this protein could possibly participate in cell signalling functions, which link the external environment with the cell's cytoplasm. Using whole plant systems, a comparative study of leaf protein expression between two sorghum varieties, AS6 (salt sensitive) and MN1618 (salt tolerant) was conducted. Forty well resolved spots of varying abundances were picked for MS analysis. Of these, 28 were positively identified, representing proteins with functions in carbohydrate metabolism (60.7%), proton transport (17.9%), protein synthesis (7.1%), hydrolytic functions (7.1%), nucleotide metabolism (3.6%) and detoxification (3.6%). Using PDQuest™ Advanced 2D Analysis Software version 8.0.1 (BIO-RAD), a comparative analysis of leaf proteome expression patterns between the two sorghum varieties was conducted. The results indicated proteins with similar expression patterns as well as qualitative and quantitative differences between the two leaf proteomes. The effect of 100 mM NaCI on leaf proteome expression between the two sorghum varieties was also studied. Western blotting analysis of leaf, sheath and root tissues using Hsp70 antibodies showed that this treatment induced Hsp70 expression, a known stress protein, in both varieties. Thereafter, the partially annotated leaf proteome map was used to landmark other salt responsive proteins. Examples of differential expression patterns included glutathione S transferase and hydroxynitrile lyase proteins whose abundances were upregulated in both varieties, while the large subunit of RuBisCo was downregulated in AS6 but upregulated in MN1618. Qualitative spot expression differences in response to salt stress were also observed between the two sorghum varieties but these remained unidentified after both MALDI-TOF and MALDI-TOF-TOF MS, possibly indicating novel and previously uncharacterised sorghum proteins. The results of this study can be used as reference tools by proteomics researchers worldwide as well as a foundation for future studies.

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