京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第19000号 / 工博第4042号 / 新制||工||1622(附属図書館) / 31951 / 京都大学大学院工学研究科分子工学専攻 / (主査)教授 田中 庸裕, 教授 今堀 博, 教授 阿部 竜 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DFAM

Los terpenos constituyen el mayor grupo de metabolitos secundarios, siendo componentes de las glándulas de aceites esenciales, de las flores y de las resinas defensivas de plantas aromáticas, a los que proporcionan sus aromas y sabores característicos. Los terpenos volátiles se asocian a la defensa de muchas especies de plantas, animales y microorganismos contra depredadores, patógenos y competidores. Por otra parte, estos compuestos parecen servir como señales para atraer a los polinizadores y agentes dispersores de semillas, así como a depredadores de plagas. El estudio de compuestos orgánicos volátiles emitidos durante el desarrollo del fruto y después del desafío con diferentes agentes bióticos puede ayudar a conocer las interacciones de los frutos carnosos no sólo con vertebrados dispersores y depredadores, sino también con insectos y microorganismos. Los frutos carnosos son particularmente ricos en volátiles. En los frutos cítricos, los monoterpenos son los principales componentes de las glándulas del aceite esencial de la cáscara (flavedo), siendo el D-limoneno el más abundante (hasta 95% en la naranja). Esta característica hace que los cítricos sean un buen sistema modelo para el estudio de la función de los terpenos en los frutos. La biología molecular moderna permite la realización de experimentos para comprobar la función de terpenos por medio del uso de organismos transformados genéticamente en los que se han manipulado los niveles de acumulación de dichos compuestos. En este trabajo, se ha utilizado un plásmido que alberga el cDNA completo del gen de una limoneno sintasa de cítricos (CiTMTSE1) en orientación antisentido (AS) o sentido (S) para modificar la expresión y la acumulación de D-limoneno en plantas de naranjo dulce (Citrus sinensis L. Osb.). La acumulación de D-limoneno en las frutas AS se redujo drásticamente pero la acumulación de otros terpenos también se modificó, afectando a compuestos tales como alcoholes monoterpenos, cuya concentración se incrementó en la cáscara de las frutas. Las plantas transformadas fueron morfológicamente indistinguibles de las plantas control (WT) y de las plantas transformadas con el vector vacío (EV). Los frutos transgénicos fueron desafiados con un insecto plaga y con diferentes patógenos para probar si la alteración de los niveles de acumulación de estos volátiles daba como resultado una mejora en la respuesta del flavedo frente a plagas y patógenos. Los machos de la mosca mediterránea de la fruta (Ceratitis capitata) expuestos a las frutas AS y EV en ensayos en túnel de viento fueron significativamente más atraídos por el aroma de los frutos control EV. En otros experimentos de desafío con el hongo de la podredumbre verde Penicillium digitatum y la bacteria causante de la cancrosis de los cítricos Xanthomonas axonopodis subsp. citri, las frutas transgénicas con un contenido reducido de D-limoneno mostraron elevada resistencia a estos patógenos. El alto contenido en D-limoneno en la cáscara de naranjas maduras puede ser una señal para la atracción de plagas y microorganismos que podrían estar involucrados en la facilitación del acceso a la pulpa de los frugívoros dispersores de semillas. El análisis de la expresión génica global en el flavedo de las frutas transgénicas vinculó la disminución de D-limoneno y la reducción de la expresión de genes del metabolismo de monoterpenos con la activación de la expresión de genes implicados en inmunidad innata, incluyendo factores de transcripción, genes de quinasas implicadas en la entrada de Ca2+ en la célula y genes implicados en la activación de las cascadas de MAPKs, con la consiguiente activación de la ruta de señalización de ácido jasmónico (JA), lo que provocó la activación del metabolismo de JA y un aumentó drástico de la acumulación de JA en la cáscara de la naranja tras el desafío con P. digitatum, lo que explicaría la resistencia al menos a hongos necrotrofos observada en las frutas. Estos resultados indican que la acumulación de D-limoneno en la cáscara de la naranja estaría implicada en la interacción trófica entre las frutas, insectos y microorganismos, lo cual proporciona una visión mucho más amplia de las funciones de los terpenos en la naturaleza. También representa una alternativa muy prometedora para incrementar la resistencia o tolerancia de las plantas frente a patógenos y plagas. / Terpenes, the largest group of secondary metabolites, are well known as constituents of essential oils, floral scents and defensive resins of aromatic plants, to which they impart their characteristic aromas and flavors. Terpene volatiles defend many species of plants, animals and microorganisms against predators, pathogens and competitors. Moreover, those compounds seem to serve as advertisements to attract pollinators and seed-dispersal agents as well as pest predators. The study of VOCs emitted during fruit development and after challenge with different biotic agents may help to determine the interactions of fleshy fruits not only with legitimate vertebrate dispersers and predators, but also with insects and microorganisms. Fleshy fruits are particularly rich in volatiles. In citrus fruits, monoterpenes are the main components of the essential oil glands of the peel, being D-limonene the most abundant one (up to 95% in orange fruits). This characteristic makes citrus a good model system for studying the function of terpenes in plants. Modern molecular biology now enable experiments to test terpenoid function by the use of genetically transformed organisms in which terpene levels have been manipulated. In this work, a plasmid harboring the complete cDNA of a citrus limonene synthase gene (CiTMTSE1) in antisense (AS) or sense (S) orientation was used to modify the expression and accumulation of D-limonene of sweet orange (Citrus sinensis L. Osb) plants. D-limonene accumulation in AS fruits was dramatically reduced but the accumulation of other terpenoids was also modified, such as monoterpene alcohols, whose concentration increased in the peel of fruits. Genetically transformed plants were morphologically indistinguishable from wild-type (WT) and empty vector (EV) control plants. Transgenic fruits were challenged against a pest and different pathogens to test whether volatile profile alteration results in an improvement in the response of the fruit flavedo against them. Males of the Mediterranean fruit fly (Ceratitis capitata) exposed to AS fruits versus EV in wind tunnel assays were significantly more attracted to the odor of EV control fruits. In separate experiments with the green mould rot of citrus fruits and citrus canker caused by Penicillium digitatum and Xanthomonas axonopodis subsp. citri, respectively, transgenic fruits with a reduced content in D-limonene showed resistance to both pathogens. High D-limonene content in mature orange peels may be a signal for attractiveness of pests and microorganisms which might be likely involved in facilitating the access to the pulp of seed dispersal frugivores. A global gene expression analysis of the flavedo of AS transgenic fruits linked the decrease of D-limonene and monoterpene metabolism to the up-regulation of genes involved in the innate immunity response, including transcription factors together with Ca2+ entry into the cell and activation of MAPK cascades, contributing to activation of jasmonic acid (JA) signaling, which triggered the up-regulation of JA metabolism and drastically increased the accumulation of JA in orange peels upon fungal challenge, explaining the resistance to necrotrophic fungi observed in AS fruits. These results indicate that limonene accumulation in the peel of citrus fruit appears to be involved in the successful trophic interaction between fruits, insects, and microorganisms and provide a much more comprehensive view of roles of terpenes in nature. It also represents a very promising alternative for increasing resistance or tolerance of plants to pathogens. / Rodríguez Baixauli, AM. (2013). Genetic engineering of plant volatiles in fleshy fruits: pest repellency and disease resistance through D-limonene downregulation in transgenic orange plants [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/31655

<p>The interest for cooperative robots has increased considerably in recent years and one of the research issues within this domain is how to evolve heterogeneity in a team. The research today is however either focusing on diversity in hardware (e.g. sensory system) or diversity of behaviour. This dissertation extends this research and presents experiments that attempts to 'co-evolve' heterogeneity at both the hardware level and the behavioural level. The results show that the team behaviour evolved depends on the complexity of the task where adding constraints or increasing the difficulty of the problem lead to better team behaviour.</p><p>Our belief was that the performance of the team should benefit from using robots that has been evolved at the hardware level together with the behavioural level. This, however, could not be proved to be true, but the idea that these two should be kept together in order to evolve heterogeneity in a team is still believed.</p>

The interest for cooperative robots has increased considerably in recent years and one of the research issues within this domain is how to evolve heterogeneity in a team. The research today is however either focusing on diversity in hardware (e.g. sensory system) or diversity of behaviour. This dissertation extends this research and presents experiments that attempts to 'co-evolve' heterogeneity at both the hardware level and the behavioural level. The results show that the team behaviour evolved depends on the complexity of the task where adding constraints or increasing the difficulty of the problem lead to better team behaviour. Our belief was that the performance of the team should benefit from using robots that has been evolved at the hardware level together with the behavioural level. This, however, could not be proved to be true, but the idea that these two should be kept together in order to evolve heterogeneity in a team is still believed.

<p>A recent trend in evolutionary robotics and artificial life research is to maximize self-organization in the design of robotic systems, in particular using artificial evolutionary techniques, in order to reduce the human designer bias. This dissertation presents experiments in competitive co-evolutionary robotics that integrate and extend previous work on competitive co-evolution of neural robot controllers in a predator-prey scenario with work on the ‘co-evolution’ of robot morphology and control systems. The focus here is on a systematic investigation of tradeoffs and interdependencies between morphological parameters and behavioral strategies through a series of predator-prey experiments in which increasingly many aspects are subject to self-organization through competitive co-evolution. The results show that there is a strong interdependency between morphological parameters and behavioral strategies evolved, and that the competitive co-evolutionary process was able to find a balance between and within these two aspects. It is therefore concluded that competitive co-evolution has great potential as a method for the automatic design of robotic systems.</p>

A recent trend in evolutionary robotics and artificial life research is to maximize self-organization in the design of robotic systems, in particular using artificial evolutionary techniques, in order to reduce the human designer bias. This dissertation presents experiments in competitive co-evolutionary robotics that integrate and extend previous work on competitive co-evolution of neural robot controllers in a predator-prey scenario with work on the ‘co-evolution’ of robot morphology and control systems. The focus here is on a systematic investigation of tradeoffs and interdependencies between morphological parameters and behavioral strategies through a series of predator-prey experiments in which increasingly many aspects are subject to self-organization through competitive co-evolution. The results show that there is a strong interdependency between morphological parameters and behavioral strategies evolved, and that the competitive co-evolutionary process was able to find a balance between and within these two aspects. It is therefore concluded that competitive co-evolution has great potential as a method for the automatic design of robotic systems.

Software developers adapt to the fast-moving nature of software systems with agile development techniques. However, database developers lack the tools and concepts to keep the pace. Whenever the current database schema is evolved, the already existing data needs to be evolved as well. This is usually realized with manually written SQL scripts, which is error-prone and explains significant costs in software projects. A promising solution are declarative database evolution languages, which couple both schema and data evolution into intuitive operations. Existing database evolution languages focus on usability but do not strive for completeness. However, this is an inevitable prerequisite to avoid complex and error-prone workarounds. We present CODEL which is based on an existing language but is relationally complete. We precisely define its semantic using relational algebra, propose a syntax, and formally validate its relational completeness. Having a complete and comprehensive database evolution language facilitates valuable support throughout the whole evolution of a database. As an instance, we present VACO, a tool supporting developers with variant co-evolution. Given a variant schema derived from a core schema, VACO uses the richer semantics of CODEL to semi-automatically co-evolve this variant with the core.

Viruses are the most abundant biological entity on Earth and outnumber their hosts ten-to-one. Ocean viruses (phages) impact bacterial-driven global biogeochemical cycles through lysis, manipulating host metabolism, and horizontal gene transfer. However, knowledge of virus-host interactions and viral roles in ecosystems remains limited due to few cultured marine phage genomes and non-quantitative culture-independent metagenomes. Here, I develop and apply novel and well-tested bioinformatic techniques to explore Pacific Ocean viral communities using quantitative datasets derived from rigorously-tested preparation methods. To evaluate concentration and purification methods, I examined triplicate metagenomes from a single ocean sample using four protocols. Concentration protocols showed statistical differences in taxonomy whereas purification protocols did not. Specifically, TFF-concentrated metagenomes contained trace bacterial contamination and had fewer abundant taxa as compared to FeCl₃-precipitated metagenomes. K-mer analysis using the complete dataset revealed polymerase choice defined access to "rare" sequences.To explore unknown viral sequences, I organized known and unknown sequence space into 27K high-confidence protein clusters (PCs) from 32 diverse Pacific Ocean Virus (POV) metagenomes, which doubled available PCs and included the first pelagic deep-sea viral metagenomes. Using PCs as a whole-viral-community diversity metric revealed decreases from coastal to open ocean, winter to summer, and deep to surface, that correlate with data from microbial genetic diversity markers (no parallel viral markers exist).Biologically, POV metagenomes showed that viruses likely reprogram central metabolic pathways in microbial communities far beyond the "photosynthesis viruses" paradigm. Gene distribution patterns from 35 viral gene families (31 new) revealed niche-specific (photic vs aphotic zone) altered pathway carbon flux presumably optimized to best locally generate energy and drive viral replication. Further, these PCs define the first "core" (180 genes) and "flexible" (423K genes total) viral community genome. Functionally, core genes again suggest niche-differentation with extensive Fe-S cluster-related genes for electron transport and metabolic enzyme catalysis in photic samples, and manipulation of host pressure-sensitive genes in aphotic samples. Taxonomically, these data deconstruct the culture-based paradigm that tailed viruses dominate in the wild - instead they appear ubiquitous, but not abundant.

本論文旨在分析法國法蘭西研究院院士Michel Serres的思想及其在教育上的啟思。Michel Serres是一名著名的法國哲學家，但是在台灣他還是一名較不為人所熟知的學者。然而經過本論文對於其思想進行研究，發現其理論有許多重要的教育哲學思想。因此，本論文首先便由Serres的法文原著，探究他的理論定位及其思維特色。而後，本論文以「吟遊、尋渡與參化」之三向度作為分析的軸心，來探討Serres的理論在教育上的重要涵意：在吟遊的層面上，吟遊當中的旅程、漂流、孤獨、暴露、受苦、節制、愛、與創造等概念，蘊含的是Serres的教育人類學的想像；在尋渡的層面上，由於吟遊者在漂流中去執、受苦、節制、愛與創造，因此他將不斷轉化自身，也將不斷地在知識與知識之間，以及人於人之間尋找交融之渡，這蘊含的是Serres的教育倫理學的想像；而在參化的層面上，除了投入人群，吟遊者將轉化自身，投入自然以及萬事萬物之中，與人、與自然以及萬事萬物相互參化，這蘊含的是Serres的教育美學的想像。「吟遊、尋渡與參化」，這三者就是Serres對於「教育」這一概念的開展與想像。 / This study is to investigate the thought and implication for education of Michel Serres, a distinct member of L'Académie française. Michel Serres is a famous philosopher, but he is not well-known in Taiwan. Through examining Serres’s thought, we can find many inspiring ideas of educational philosophy. In the first part of this dissertation, it will focus on Serres’s original French texts in order to explore the orientation and the characteristic of his theories. Secondly, this dissertation will discuss the critical three axes of Serres’s theories: ‘Troubadour, Seeking Passage and Co-evolution.’ Troubadour entails the ideas of voyage, érrance (wanderings), solitude, expose to, suffering, temperance, love, and creation. These concepts imply the image of Serres’s educational anthropology. Seeking passage indicates the self-detachment, suffering, temperance, love, and creation of Troubadour. Because of érrance, Troubadour will never stop self-transforming and will constantly searching for the passages among different knowledge as well as the passages among people. This implies the image of Serres’s educational ethics. Co-evolution represents Troubadour’s engagement not only in human beings but also in nature and in all things on earth because of his self-transformation. The troubadour eagerly engages himself in the co-evolution with other human beings, nature and all things on earth. This implies the image of Serres’s educational esthetics. The ideas of ‘Troubadour, Seeking Passage and Co-evolution’ are the keystones of Serres’s discourses and images on education.

Entre as temporalidades de diferentes processos locais, este estudo etnográfico aprofunda-se em entender como esses diferentes ritmos relacionam-se e modulam as atividades de pescadores e de outros habitantes (humanos e não-humanos) na vila do Pontal do Leste - Ilha do Cardoso, Cananeia - SP. Relações essas sempre em processo de co-constituição, co-respondencia, co-evolução entre humanos e não-humanos, nunca formados e preexistentes de antemão. As percepções desses processos são fundamentais para o entendimento do comportamento de alguns animais não-humanos e plantas, das condições de tempo, da geomorfologia insular e da ecologia eólico-hídrica local, resultando em caracterizações sensíveis, que serão desdobradas nessa etnografia. Portanto, nessa malha de relações composta por paisagens multiespécies, onde diversas linhas de movimentos são traçadas por seres e processos, o intuito deste estudo foi descrever como essas linhas encontram-se e contaminam-se. E, acima de tudo, como esses encontros são traduzidos pelos habitantes e visitantes da vila. / Among the temporalities of different local processes, this ethnographic study deepens in understanding how these different rhythms relate and modulate the activities of fishermen and other inhabitants (human and non-human) in the village of Pontal do Leste - Cardoso Island, Cananeia - SP. These relations are always in the process of co-constitution, coresponse, co-evolution between humans and nonhumans never formed and preexisting inadvance. The perceptions of these processes are fundamental to the understanding of the behavior of some non-human animals and plants, of the weather conditions, insular geomorphology and local wind-hydric ecology, resulting in sensitive characterizations that will be unfolded in this ethnography. Therefore, in this meshwork of relationships composed of multispecies landscapes, where several lines of movement are traced by beings and processes, the purpose of this study was to describe how these lines meet and become contaminated. And, above all, how these meetings are translated by the inhabitants and visitors of the village.