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published_or_final_version / abstract / toc / Zoology / Master / Master of Philosophy

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第22330号 / 医博第4571号 / 新制||医||1041(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 小西 靖彦, 教授 妹尾 浩, 教授 湊谷 謙司 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

The aim of this diploma thesis is determination of alfalfa (Medicago sativa) infestation in Agricaltural company Kvasicko a. s. The monitoring of infestation was doing from 2013 to 2016 on land Odšenkovna, sawn on 29. 8. 2013, and on land Novina levá, sawn on 11. 4. 2014. Evaluation was made by counting method. The results of this evaluation were processed with DCA analysis and canonical corespondence analysis (CCA). It was found 11 species of weeds on observed lands during the monitoring. The most frequently weeds were: Capsella bursa-pastoris, Stellaria media, Taraxacum sec. Ruderalia and Veronica.

The chicken bursa of Fabricius is a primary lymphoid tissue important for B-cell development. Our long-term goal is to understand the role of bursal microenvironment in an early B-cell differentiation event initiating repertoire development through immunoglobulin gene-conversion in the chick embryo. We hypothesize that early bursal B-cell differentiation is guided by signals through cytokine receptors. Our theory is based on previous evidence for expression of the receptor tyrosine kinase superfamily members and interleukin receptors in unseparated populations of bursal B-cells and bursal tissue. Knowledge of the expressed genes that are responsible for B-cell differentiation is a prerequisite for understanding the bursal microenvironment’s function. This project uses transcriptomic analysis to examine gene expression across an early B-cell differentiation event. RNA-seq was performed with total RNA isolated from developing B-cells at embryonic day (ED) 16 and ED 19 (n=3). Approximately 90 million high quality clean reads where obtained from the cDNA libraries. The analysis revealed differentially expressed genes involved in Wnt signaling pathway, Jak-STAT pathway, metabolic pathways, tyrosine metabolism, Toll-like receptor signaling pathway, MAPK signaling pathway, and cellhesion molecules. The transcripts for surface receptors, signal transduction and transcription factors identified in this study represent gene candidates for controlling B-cell differentiation in response to bursal microenvironmental factors.

Les « Maîtres de Tabriz » ont suscité un vif intérêt chez les chercheurs. Ces céramistes, qui ont orné des édifices ottomans au 15ème et 16ème siècle, demeurent pourtant mystérieux à bien des égards. L’absence de biographies rend leur identification incertaine et engendre par conséquent de nombreuses théories sur leur origine historique et géographique. Concrètement, ces maîtres ne sont connus qu’à travers leur nom figurant dans les inscriptions monumentales ou dans les archives ottomanes. Une investigation dans les textes anciens a alors été essentielle pour combler le manque d’indices. Cependant, certaines de ces sources écrites ont fait l’objet d’extrapolations et de spéculations aléatoires. Pourtant, elles sont considérées comme des éléments probants, ce qui fausse évidemment l’identification de ces céramistes. Il a été primordial de revenir sur les éléments d’identification. La relecture des sources primaires permet en effet de dégager les notions concrètes et d’écarter les hypothèses infondées. Tel est l’enjeu de la première partie de cette étude qui met en évidence les connaissances que l’on possède des « Maîtres de Tabriz ». La deuxième partie est consacrée à l’analyse technique et ornementale des céramiques architecturales. Les œuvres des « Maîtres de Tabriz » sont relativement bien connues. Elles ont fait l’objet de nombreuses publications, mais ont souvent été abordées de manière transversale. Cette étude propose une nouvelle approche en mettant en relation la production de chacun des quatre groupes de céramistes. Cette démarche permet ainsi de saisir l’évolution de cette production tout en mettant en avant les corrélations et les disparités artistiques. / The « Masters of Tabriz » generate high interest among researchers. These ceramists, who decorated ottoman buildings in the 15th and 16th centuries, remain mysterious in many respects. The absence of biographies makes their identification uncertain and hence leads to many different theories about their historical and geographical origins. In reality, these masters are only known for their names found on monumental inscriptions and from ottoman chancery documents. Thus, investigation into ancient texts became essential to fill in the lack of evidence. However, some of these written sources have led to extrapolations and uncertain speculations. Yet these have been accepted and considered as conclusive elements, which obviously misrepresent these master ceramists. It is thus essential to return to the elements of identification. Rereading primary sources written in Arabic, Persian and Ottoman gives evidence to concrete notions and dismisses unfounded suppositions. As the shadow zones round them tend to lead to myths, the objective of the first part of this study is to rectify the knowledge in our possession of the “Masters of Tabriz”.The second part consists of a technical and ornamental analysis of the architectural ceramic tiles. The productions of the “Masters of Tabriz”, principally found in Bursa, Edirne, Istanbul and Jerusalem, are relatively well known. They have been the subject of many publications, but have often been treated transversally. This study offers a new approach, comparing the productions of the four groups of ceramists. This procedure brings to light the progression of this production as it focuses on the artistic correlations and disparities.

Photoperiodism refers to the organism’s ability to detect and respond to seasonal changes in the daily duration of light and dark and thus constitutes one of the most significant and complex examples of the interaction between the organism and its environment. This thesis attempts to describe the prevalence of variation in a photoperiodic response, its adaptive value, and its putative genetic basis in a common cruciferous weed, Capsella bursa-pastoris (Brassicaceae). Furthermore, the thesis presents a first comprehensive comparative overview of the circadian clock mechanism in an early land plant, Physcomitrella patens (Bryophyta), thus providing insights into the evolution of the plant circadian system. In an introductory survey of global gene expression changes among early- and late flowering accessions of C. bursa-pastoris we found an enrichment of genes involved in photoperiodic response and regulation of the circadian clock. Secondly, by phenotyping circadian rhythm variation in a worldwide sample of accessions with known flowering time, we detected robust latitudinal clines in flowering time and circadian period length, which constitute strong indications of local adaptation to photoperiod in the shaping of flowering time variation in this species. In an attempt to elucidate putative genetic causes for the correlated variation between circadian rhythm and flowering time, we found that sequence variation and diverged expression in components regulating light input to the clock, PHYTOCHROME B (PHYB) and DE-ETIOLATED 1 (DET1) make them strong candidate genes. Finally, we present a comparative study of circadian network topology in the moss P. patens. Phylogenetic analyses and time series expression studies of putative clock homologues indicated that several core clock genes present in vascular plants appeared to be lacking in the moss. Consequently, while the clock mechanism in higher plants constitutes at least a three-loop system of interacting components, the moss clock appears to comprise only a single loop. We conclude that C. bursa-pastoris is a highly suitable model system for the further elucidation of the molecular variation that influences adaptive change in natural plant populations. Furthermore, we believe that the continuing study of the seemingly less complex circadian network of P. patens not only can provide insights into the evolution of the plant circadian system, but also may help to clarify some of the remaining issues of the circadian clock mechanism in higher plants.

The theme of the thesis is the influence of the urban development activities on the historic commercial areas. Hence, the thesis focuses on the evaluation of these factors which cause alterations and transformations within the area and aims to propose compatible solutions against the problems in order to achieve the sustainability of the historic texture within the commercial area. In this thesis, Yeni Galle Pazari Hani,, one of the 16th century Ottoman Hans in the Hanlar District of Bursa, is studied together with its immediate surrounding. In order to define necessities and requirements of a transformed historic commercial area, it is aimed to conduct research, analysis, and decision stages concerning the studied area. For this purpose, the values, the problems and the potentials of the study area are defined and alternative conservation solutions are proposed. It is also aimed to present the principles and decisions on the preservation and rehabilitation of the study area, called as &amp / #8216 / Yeni Galle Pazari Hani and its immediate surrounding&amp / #8217 / , in environmental scale. Therefore, the main aim of the thesis is to determine the principles and the tools of an urban conservation project within the context of environmental scale and to re-gain the unity of Yeni Galle Pazari Hani as much as possible by integrating it into the current atmosphere of Hanlar District in Bursa together with the traditional texture surrounding it. In this study, the insufficiency observed in preparatory stages of most of current restoration projects was emphasized. Hence, before intervention of such kind of traditional areas, it is aimed to take care of documentation, to make a comprehensive study on unobserved parts of traditional texture such as archeological excavation, and to form a worksheet containing principles and decisions for future studies that would be done under various disciplines. The proposal for the case of Yeni Galle Pazari Hani is significant as being composed of documentation, observation and decision parts of a proper intervention, although it can be accepted as an incomplete project, since being the first step of a comprehensive restoration project for the study area. In conclusion, this study exemplifies the documentation and the evaluation of the transformation in a historic commercial area and the suggestion to solve the general problems among the Historical Commercial Center of the cities by taking decisions on conservation and rehabilitation for the sustainability of the study area.

In the present investigation, microarray analysis was used to identify potential TCDD gene targets. Three microarray experiments were performed to study the effect of TCDD in an established chicken B-cell line (DT40), in a chicken macrophage cell line (HD11), and in the bursa of Fabricius from embryos exposed in ovo at 6 days of incubation. From the DT40 microarray analyses, clones with sequence similarity to the apoptotic genes caspase 8 and caspase 9, and the transcription factor NFΜB, among others, were identified. Real-time quantitative polymerase chain reaction (RT-PCR) revealed that TCDD elicits aryl hydrocarbon receptor (AhR)-mediated apoptosis in the avian DT40 pre-B-cell line through activation of caspases 9 and 3 (see chapter III). During the course of the HD11 microarray analyses, a consistent down-regulation of the matrix metalloprotease MMP-2 was observed. This finding was the basis for the hypothesis that TCDD has an effect on the gene expression of the MMP-2 and MMP-9 in macrophages. Then, gene expression analysis and functional zymography showed that TCDD impairs the MMP-2 and MMP-9 response to LPS stimulation in HD11 chicken macrophages (see chapter V). The microarray analyses of the embryonic bursa of Fabricius provided the basis to further study of the effect of TCDD in the chicken embryo. The shifted genes were classified according to their function. The down-regulated genes included: precursor of matrix metalloprotease-inhibitor, histone acyl-transferase 1, homeobox protein CUX-2, Death Associated Protein Kinase, and UDPglucosyl transferase, among others. The up-regulated genes included: phosphoinositidespecific phospholipase, acyl Co-A oxidase, and protein effector of Cdc42, among others. Together, these microarray analyses produced a database of genes of interest that will provide sufficient hypotheses to inspire multiple investigations aimed at confirming and refining the gene expression alterations as a consequence of TCDD exposure.

The need for the public areas within urban environments is increasing day by day. This thesis focuses on urban balconies as one of the important element of public open areas. Their historical backgrounds, contribution to the cities, categorization and exemplification form important topics for explaining the concept. The study also searches the important natural features that effect the urban development of Bursa and questions the place of urban balconies between them. While explaining the past and the present situations, types and the usages of urban balconies&amp / #8217 / of Bursa / this thesis emphasizes their existing but neglected qualitative and quantitative values, that have the potential to play an important role for the physical shaping of the city so as the formation of urban image. Related to this, also the importance of the revitalization of the urban balconies as public open areas takes part in this study. Key Words: Urban Balconies, Vista Points, Topographical Features, Public Open Areas, Bursa.