京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第22254号 / 理博第4568号 / 新制||理||1656(附属図書館) / 京都大学大学院理学研究科物理学・宇宙物理学専攻 / (主査)教授 一本 潔, 准教授 浅井 歩, 教授 柴田 一成 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DFAM

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Coronal Mass Ejections (CMEs) and solar flares are energetic events taking place at the Sun that can affect the space weather or the near-Earth environment by the release of vast quantities of electromagnetic radiation and charged particles. Solar active regions are the areas where most flares and CMEs originate. Studying the associations among sunspot groups, flares, filaments, and CMEs is helpful in understanding the possible cause and effect relationships between these events and features. Forecasting space weather in a timely manner is important for protecting technological systems and human life on earth and in space. The research presented in this thesis introduces novel, fully computerised, machine learning-based decision rules and models that can be used within a system design for automated space weather forecasting. The system design in this work consists of three stages: (1) designing computer tools to find the associations among sunspot groups, flares, filaments, and CMEs (2) applying machine learning algorithms to the associations' datasets and (3) studying the evolution patterns of sunspot groups using time-series methods. Machine learning algorithms are used to provide computerised learning rules and models that enable the system to provide automated prediction of CMEs, flares, and evolution patterns of sunspot groups. These numerical rules are extracted from the characteristics, associations, and time-series analysis of the available historical solar data. The training of machine learning algorithms is based on data sets created by investigating the associations among sunspots, filaments, flares, and CMEs. Evolution patterns of sunspot areas and McIntosh classifications are analysed using a statistical machine learning method, namely the Hidden Markov Model (HMM).

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Les objectifs multiples étaient centrés autour d'une thématique générale : l'influence des processus physiques à mésoéchelle sur l'écosystème planctonique dans les upwellings côtiers. L'utilisation d'outils variés était nécessaire pour aborder les nombreux mécanismes impliqués. La variabilité physique et biogéochimique de l'upwelling de la péninsule Ibérique est d'abord étudiée à partir des données in-situ de la campagne MOUTON 2007. Ensuite, un front secondaire d'upwelling au niveau de la marge continentale a été observé dans ces données, puis expliqué grâce à un modèle numérique en 2D. Enfin, des données satellites et un outil lagrangien nous permettent de comparer le mélange horizontal de l'océan de surface des quatre zones d'upwelling de bord Est, en lien avec l'activité biologique. Nous mettons en évidence une relation négative entre la turbulence à mésoéchelle et les concentrations de chlorophylle. De par la diversité des approches, des progrès ont été faits sur la compréhension des effets des processus physiques à mésoéchelle sur les écosystèmes marins.

Centrinas são proteínas componentes essenciais nos centro organizadores de microtubulos em diversos organismos. Pertencem à família das proteínas EF-Hand ligantes de cálcio e podem ser divididas em duas subfamílias: uma definida pela centrina da alga Chlamydomonas reinhardtii CrCenp, associada a funções contráteis, e a outra pela centrina da levedura Saccharomices cerevisiae ScCdc31p, relacionada a duplicação de centros mitóticos. Curiosamente o fungo Blastocladiella emersonii possui duas formas de centrinas em seu genoma : BeCen1 mais parecida com a CrCenp, e BeCen3 com a ScCdc31p, enquanto todos os outros fungos já descritos possuem apenas uma forma, pertencente ao grupo ScCdc31p. Diante desse fato curioso, descrito em 2005, estudos estruturais e termodinâmicos comparativos entre as proteínas recombinantes BeCen1 e BeCen3, foram desenvolvidos para identificar e caracterizar diferenças relevantes, que pudessem justificar a presença dessas duas proteínas no fungo Blatocladiella emersonii. Ambas as centrinas foram expressas em E. coli e purificadas por cromatografia, resultando em um rendimento de aproximadamente 5mg/l. Analises estruturais foram realizadas utilizando técnicas de dicroísmo circular (CD) , fluorescência, espalhamento de luz (DLS e RALS), microscopias de força atômica (AFM) e eletrônica de transmissão (MET). Por calorimetria de titulação isotérmica (ITC) parâmetros termodinâmicos foram obtidos para BeCen1 e BeCen3 em relação a ligação de cálcio. Ambas apresentaram conteúdo predominante de hélices alfa e diferenças físico-químicas e estruturais marcantes. BeCen1, após desnaturação a 90ºC e deixada a temperatura de 4°C por 24 horas horas, mostrou um espectro de CD compatível com um processo de reenovelamento; a TM foi de 42°C e aumentou cerca de 4°C na forma holo; os espectros de CD são modificados na presença de cálcio, mostrando uma forma característica de movimentação de hélices das proteínas ligantes de cálcio; pelos dados obtidos por ITC liga cálcio em três sítios EF-Hand por uma reação endotérmica; na presença de magnésio apresentou mudanças conformacionais, compatíveis com a ligação deste nos sítios de cálcio; a partir de 40°C é observado um processo de agregação chegando a formação de filamentos, que foram visualizados por AFM e MET. BeCen3 após ser desnaturada e colocada nas mesmas condições de BeCen1, permanece desnaturada; A TM é de 49°C e aumentou em aproximadamente 5°C na forma holo; os espectros de CD, na presença de cálcio, apresentam aspectos característicos de movimentação de -hélices das proteínas ligantes de cálcio; liga cálcio em apenas dois sítios EF-Hand por uma reação exotérmica, sofre mudanças conformacionais na presença de magnésio e a partir de 30°C já sofre um processo de agregação, formando filamentos. Neste trabalho foi estabelecido o primeiro protocolo para a expressão e purificação das centrinas de B. emersonii, além dos estudos de caracterização estrutural e termodinâmica destas proteínas. O estudo também foi pioneiro quanto a obtenção de imagens no processo de formação de filamentos destas centrinas na ausência de cálcio. As centrinas de B. emersonii apresentam diferenças importantes nas respostas em função da presença de cálcio e também do magnésio. Os dados obtidos são fortes indicativos que estas centrinas têm mecanismos de ação diferentes dentro do fungo B. emersonii. / Centrin proteins are essential component of the microtubule organizing centers in a large range of organisms. They belong to the EF-Hand calcium binding proteins family e can be divided in two subfamilies: one defined by the green algae Chlamydomonas reinhardtii CrCenp, related to contractile functions and the other centrin of the yeast Saccharomices cerevisiae ScCdc31p, related to duplication of centrossome mitotic centers. Interesantly, Blastocladiella emersonii fungus posses two centrin forms in it genome: BeCen1 closely related to CrCenp and BeCen3 closely related to ScCdc31p. All other known fungus have only one form of centrin: ScCdc31p. With this curious finding, described in 2005, compared structural and thermodynamics studies between recombinant proteins BeCen1 and BeCen3 were performed, in attempt to identify relevant differences that could explain the presence of two forms of centrins in this fungus. Both centrins were expressed in E. coli and purified by chromatography resulting in 5mg/l protein yield. Structural analyses were performed with circular dichroism (CD), fluorescence, light scattering (DLS AND RALS), atomic force microscopy (AFM) and transmission electronic microscopy (TEM). Using isothermal titration calorimetry (ITC) thermodynamics parameters about the calcium binding were defined. Both showed alpha helix predominant content and structural physical-chemistry differences. After denaturation at 90°C and cooled overnight at 4°C, BeCen1 showed a CD spectrum consistent to a renaturation process; the calculated TM was 42°C and raised 4°C in the holo state; CD spectra were modified under calcium presence showing characteristics changes of calcium binding proteins; ITC data exhibited tree calcium binding motifs through an endothermic reaction and the presence of magnesium also showed conformational changes; From 40°C a aggregation process leading to filament formation was observed and visualized with AFM and TEM. After denaturation at 90°C and cooled overnight at 4°C, BeCen3 remained denaturated; Calculated TM was 49°C and raised 5°C in the holo state; CD spectra were modified under calcium presence showing characteristics changes of calcium binding proteins; ITC data exhibited only two calcium binding motifs through an exothermic reaction and the presence of magnesium also showed conformational changes; From 30°C BeCen3 already suffered a aggregation process forming filaments. In this study it was established the first expression and purification protocol for B. emersonii centrins, besides the structural and thermodynamic characterization of these proteins. This is the first study containing filaments images of the centrins of B. emersonii. These centrins showed important response differences in calcium and magnesium binding. All the obtained data are strong indications that the two centrins have distinct functions in the fungus.

F-Aktin spielt eine wichtige Rolle bei der Steuerung der endothelialen Barrierefunktion. In dieser Arbeit verwendeten wir Colchicin, Vinca-Alkaloide (Vinblastin, Vincristin) und Paclitaxel um Mikrotubulussysteme (MT) auszulenken und den Effekt auf die Permeabilität zu untersuchen. Endothelzellen wurden auf Polycarbonatfiltermembranen gepflanzt und einem kontinuierlichen hydrostatischen Druck von 10 cm H2O ausgesetzt. Die Exposition von Endothelzell-Monolayern gegenüber Colchicin und Vinca-Alkaloiden führte innerhalb von 60 100 Minuten zeit- und dosisabhängig zu einem fünf zehnfachen Anstieg der hydraulischen Konduktivität. Dagegen war nach MT-Stabilisation durch Paclitaxel keine Permeabilitätszunahme festzustellen. Doppelimmunfluoreszenz-Mikroskopie zeigte, dass die MT-Depolymerisation durch Colchicin und Vinca Alkaloide zu F-Aktin-Umverteilung, Stressfaserbildung und Zellretraktionen mit ausgeprägter parazellulärer Lücken-Bildung führt. Diese Phänomene wurden durch Kombinationen von Vinblastin und Paclitaxel deutlich abgeschwächt. Die fluorometrische Messung des intrazellulären F-Aktins nach MT-Depolymerisation durch Vinblastin resultierte in einer signifikanten Zunahme der Aktinfilamente. Auf der anderen Seite resultierte F-Aktin Abbau durch Cytochalasin D und Clostridium difficile (TcdB-10463) morphologisch nicht in einer Veränderung von MT-Strukturen. Dabei zeigten in Interzellularbrücken gelegene MT-Filamente Kolokalisation mit F-Aktin Fragmenten. Unsere Ergebnisse demonstrieren, dass MT-Systeme an der Regulation der endothelialen Barriere beteiligt sind. Darüber hinaus verdeutlichen die Resultate eine enge Bindung von MT- und Aktin-Filamenten innerhalb endothelzellulärer Adhäsionskontakte. / The endothelian cytosceleton plays an important role in the regulation of endothelial permeability via cellular actin filaments. We tested the effect of agents known to perturb cellular microtubules on the permeability of endothelial cell monolayers. The agents chosen were colchicine, the vinca alkaloids vinblastine and vincristine and paclitaxel. Cell monolayers were prepared on polycarbonate filter membranes and exposed to a continuous hydrostatic pressure of 10 cm H2O. Colchicine and the vinca alkaloids caused a five to tenfold increase in the hydraulic conductivity of the monolayers within 60 100 min. The effect was dose and time dependent. The microtubule stabilizer paclitaxel caused no increase in permeability. Double-immunofluorescence microscopy showed that microtubule depolymerisation was associated with certain morphological features such as inter-endothelial gaps, cell retraction, f-actin reorganisation and some stressfibre appearance. These phenomena were significantly reduced when vinblastine and paclitaxel were combined. Measurement of intracellular f-actin following microtubule inhibition with vinblastine showed a significant increase in endothelial actin filaments. No changes in microtubule structures were seen when actin filaments were perturbed with cytochalasin D and Clostridium difficile (TcdB-10463). However, in this case the intercellular bridges showed that microtubules were co-localised with fragments of actin filaments from neighbouring cells. Our data demonstrate that microtubules are important for the regulation of endothelial permeability. Moreover, our results support evidens of binding between microtubules and actin filaments within endothelial cell adhesion contacts.

"Optical vortices are singularities in phase fronts of laser beams. They are characterized by a dark core whose size may dramatically affect their behavior upon propagation. Previously, only large-core vortices have been extensively studied. The object of the research presented in this dissertation was to explore ways of generating small-core optical vortices (also called optical vortex filaments), and to examine their propagation using analytical, numerical and experimental methods. Computer-generated holography enabled us to create arbitrary distributions of optical vortex filaments for experimental exploration. We used hydrodynamic paradigms to develop an heuristic model which described the dependence of vortex motion on other vortices and the background beam, both qualitatively and quantitatively. We predicted that pair of optical vortex filaments will rotate with angular rates inversely proportional to their separation distance (just like vortices in a fluid). We also reported the first experimental observation of this novel fluid-like effect. It was found, however, that upon propagation in linear media, the fluid-like rotation was not sustained owing to the overlap of diffracting vortex cores. Further numerical studies and experiments showed that rotation angle may be enhanced in nonlinear self-defocusing media. The results presented in this thesis offer us a better understanding of dynamics of propagating vortices which may result in applications in optical switching, manipulation of micro-particles and optical limiting."

Submitted by Celso Magalhaes (celsomagalhaes@ufrrj.br) on 2018-09-24T15:13:44Z No. of bitstreams: 1 2017 - Enely Maris da Silveira Firmiano.pdf: 12307016 bytes, checksum: d58bee7e5ddc0113fa072ab4e9aabc29 (MD5) / Made available in DSpace on 2018-09-24T15:13:44Z (GMT). No. of bitstreams: 1 2017 - Enely Maris da Silveira Firmiano.pdf: 12307016 bytes, checksum: d58bee7e5ddc0113fa072ab4e9aabc29 (MD5) Previous issue date: 2017-08-29 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior - CAPES / Cap. I The aim of the current study is to investigate the histological and histochemical description, as well as the presence and immunohistochemical distribution of cytoskeleton proteins such as alpha smooth muscle actin, desmin and vimentin in the ovaries, testes and epididymis of Enyalius bilineatus, Enyalius perditus and Urostrophus vautieri. These species are representatives of family Leiosauridae, in order to help developing a database on the reproductive biology of these lizards, which could be compared to that of other reptile species and vertebrates. The herein studied specimens are deposited in the Herpetological Collection of Federal University of Juiz de Fora. The animals? ovaries, epididymis and testes were removed and sent to the Histology and Embryology Laboratory (UFRRJ), where they were fixed, processed and then subjected to histological, histochemical and immunohistochemical techniques. The ovaries of these leiosauridae are functionally-active paired organs filled with ovarian follicles at different follicular development stages. These organs are covered by a simple cubic epithelium, which presents an underlying connective tissue layer called tunica albuginea. The testes are covered by the tunica albuginea and hold septa forming lobes where the seminiferous tubules are located in. The epididymis of these lizards are convolute ducts internally coated by an epithelium, whose shape ranges from simple cylindrical to simple cubic with stereocilia. The immunohistochemical analysis applied to the ovaries of the herein studied lizards showed moderate to strong reaction to the alpha smooth muscle actin in the teak layer and in endothelial cells of blood vessels. With respect to the species? testes, this cytoskeleton protein showed strong reaction in the tunica albuginea, interstitial tissue, and in endothelial cells of blood vessels. As for the epididymis, the alpha-actin showed immunohistochemical reaction in the capsule and in the interstitial tissue of the lizards. The antibody ?desmin? showed strong immunostaining in the albuginea and ovarian stroma of E. perditus, only; however, the endothelial cells in the blood vessels of the three herein analyzed species showed positive reaction to this intermediate filament. Desmin showed immunoreactivity in the testicular albuginea and in the endothelial cells of the blood vessels in the herein analyzed leiosauridae testes; however, only E. bilineatus showed immunostaining in the interstitial region. Desmin showed positive immunoreaction in the epididymis of E. perditus and E. bilineatus, only. Vimentin did not show immunostaining in the ovaries, testes and epididymis of the three analyzed lizards. The consistent results found in the current study provide additional data on the reproductive biology of the investigated species. These data may be used for phylogenetic and behavioral comparisons between the herein studied species and other species belonging to family Leiosauridae or other reptiles Cap. II The aim of the current study is to investigate the histological description, as well as the presence and immunohistochemical distribution of alpha smooth muscle actin, desmin and vimentin in the testes and epididymis of Enyalius bilineatus, Enyalius perditus and Urostrophus vautieri, which are representatives of family Leiosauridae, in order to help developing a database on the reproductive biology of these lizards, which could be compared to that of other reptile species and vertebrates. The herein studied specimens are deposited in the Herpetological Collection of Federal University of Juiz de Fora. The animals? epididymis and testes were removed and sent to the Histology and Embryology Laboratory (UFRRJ), where they were fixed, processed and then subjected to histological and immunohistochemical techniques. The shape of the testes varies reasonably among the studied leiosauridae. These organs are covered by the tunica albuginea and hold septa forming lobes, where the seminiferous tubules are located in. The epididymis of these lizards are convolute ducts internally coated by an epithelium, whose shape ranges from simple cylindrical to simple cubic with stereocilia. The immunohistochemical analysis applied to the testes of the herein studied lizards showed strong positive reaction to the alpha smooth muscle actin in the tunica albuginea, interstitial tissue, and in endothelial cells of blood vessels. Desmin showed strong immunoreactivity in the testicular albuginea of E. bilineatus and moderate immunoreactivity in E. perditus and U. vautieri; however, only E. bilineatus showed immunostaining in the interstitial tissue region. The endothelial cells of blood vessels showed positive immunoreaction to desmin in the three herein analyzed species. The epididymis showed moderate immunohistochemical reaction to alpha smooth muscle actin in the capsule and in the interstitial tissue, whereas desmin showed positive immunoreaction in the epididymis of E. perditus and E. bilineatus, only. Vimentin did not show immunostaining in the testes and epididymis of the three analyzed lizards. The consistent results found in the current study provide additional data on the reproductive biology of the investigated species. These data may be used for phylogenetic and behavioral comparisons between the herein studied species and other species belonging to family Leiosauridae or other reptiles. / Cap. I Este trabalho investiga, al?m da descri??o histol?gica e histoqu?mica, a presen?a e distribui??o imuno-histoqu?mica de alfa-actina de m?sculo liso, desmina e vimentina nos ov?rios, test?culos e epid?dimos de Enyalius bilineatus, Enyalius perditus e Urostrophus vautieri, representantes da fam?lia Leiosauridae, para ajudar a formar uma base de dados sobre a biologia reprodutiva destes lagartos que possam ser comparados com outras esp?cies de r?pteis, bem como com outros vertebrados. Os esp?cimes estudados encontram-se depositados na Cole??o Herpetol?gica da UFJF. Os ov?rios, epid?dimos e test?culos dos animais foram removidos e encaminhados ao Laborat?rio de Histologia e Embriologia (UFRRJ), onde foram fixados, processados e ent?o submetidos ?s t?cnicas histol?gicas, histoqu?micas e imuno-histoqu?micas. Os ov?rios destes leiosaur?deos s?o ?rg?os pareados, repletos de fol?culos ovarianos, em distintos est?gios de desenvolvimento folicular. Estes s?o revestidos por epit?lio c?bico simples, com uma camada de tecido conjuntivo subjacente, a t?nica albug?nea. Os test?culos encontram-se envolvidos pela t?nica albug?nea e em seu interior cont?m septos que formam l?bulos, nos quais se localizam os t?bulos semin?feros. Os epid?dimos destes lagartos s?o ductos convolutos, revestidos internamente por um epit?lio que varia de cil?ndrico simples a c?bico simples com estereoc?lios. A imuno-histoqu?mica, nos ov?rios dos lagartos estudados, mostra uma rea??o moderada a acentuada para alfa-actina de m?sculo liso na camada da teca e em c?lulas endoteliais dos vasos sangu?neos, enquanto nos test?culos destas esp?cies nota-se uma acentuada rea??o para esta prote?na do citoesqueleto, na t?nica albug?nea, no tecido intersticial e nas c?lulas endoteliais dos vasos sangu?neos. Nos epid?dimos observa-se imunomarca??o para alfa-actina na c?psula e no tecido intersticial destes lagartos. Quanto ao anticorpo desmina, apenas em E. perditus, foi poss?vel imunorrea??o na albug?nea e no estroma ovariano, no entanto, nas tr?s esp?cies analisadas, as c?lulas endoteliais dos vasos sangu?neos demonstraram rea??o positiva a este filamento intermedi?rio. Nos test?culos dos leiosaur?deos estudados, a desmina foi imunolocalizada na albug?nea testicular e nas c?lulas endoteliais dos vasos sangu?neos, entretanto, apenas em E. bilineatus ocorreu imunomarca??o, na regi?o do interst?cio. Nos epid?dimos, a desmina demonstrou imunorrea??o positiva apenas em E. perditus e E. bilineatus. N?o houve rea??o imuno-histoqu?mica para vimentina nos ov?rios, test?culos e epid?dimos dos tr?s lagartos analisados. Este estudo obteve resultados consistentes, fornecendo assim mais dados sobre a biologia reprodutiva das esp?cies aqui investigadas, que poder?o ser utilizados para compara??es filogen?ticas e comportamentais com outras esp?cies da fam?lia Leiosauridae e outros r?pteis. Cap. II Este trabalho investiga, al?m da descri??o histol?gica, a presen?a e distribui??o imuno-histoqu?mica de alfa-actina de m?sculo liso, desmina e vimentina nos test?culos e epid?dimos de Enyalius bilineatus, Enyalius perditus e Urostrophus vautieri, representantes da fam?lia Leiosauridae, para ajudar a formar uma base de dados sobre a biologia reprodutiva destes lagartos que possam ser comparados com outras esp?cies de r?pteis, bem como com outros vertebrados. Os esp?cimes estudados encontram-se depositados na Cole??o Herpetol?gica da Universidade Federal de Juiz de Fora. Os epid?dimos e test?culos dos animais foram removidos e encaminhados ao Laborat?rio de Histologia e Embriologia (UFRRJ), onde foram fixados, processados e ent?o submetidos ?s t?cnicas histol?gicas e imuno-histoqu?micas. O formato dos test?culos varia razoavelmente entre os leiosaur?deos estudados. Estes ?rg?os encontram-se envoltos pela t?nica albug?nea e no seu interior cont?m septos que formam l?bulos incompletos, nos quais se localizam os t?bulos semin?feros. Os epid?dimos destes lagartos s?o ductos convolutos. Estes ductos s?o revestidos internamente por um epit?lio que varia de cil?ndrico simples a c?bico simples com estereoc?lios. A imuno-histoqu?mica revela uma acentuada rea??o positiva para alfa-actina de m?sculo liso nos test?culos dos leiosaur?deos analisados, na t?nica albug?nea e no tecido intersticial, assim como, nas c?lulas endoteliais dos vasos sangu?neos. A desmina apresentou acentuada imunorreatividade na albug?nea testicular em E. bilineatus e moderada em E. perditus e U. vautieri, entretanto, na regi?o do tecido intersticial, apenas em E. bilineatus ocorreu imunomarca??o. Nas tr?s esp?cies analisadas, as c?lulas endoteliais dos vasos sangu?neos demostraram imunorrea??o positiva para desmina. Nos epid?dimos observou-se rea??o imuno-histoqu?mica moderada para alfa-actina de m?sculo liso na c?psula e no tecido intersticial, enquanto a desmina demonstrou imunorrea??o positiva apenas em E. perditus e E. bilineatus. N?o houve imunomarca??o para vimentina nos test?culos e epid?dimos dos tr?s lagartos analisados. Este estudo obteve resultados consistentes, fornecendo assim mais dados sobre a biologia reprodutiva das esp?cies aqui investigadas, que poder?o ser utilizados para compara??es filogen?ticas e comportamentais com outras esp?cies da fam?lia Leiosauridae e outros r?pteis.