Modern surgery of the 21st century relies in many aspects on computers or, in a wider sense, digital data processing. Department administration, OR scheduling, billing, and - with increasing pervasion - patient data management are performed with the aid of so called Surgical Information Systems (SIS) or, more general, Hospital Information Systems (HIS). Computer Assisted Surgery (CAS) summarizes techniques which assist a surgeon in the preparation and conduction of surgical interventions. Today still predominantly based on radiology images, these techniques include the preoperative determination of an optimal surgical strategy and intraoperative systems which aim at increasing the accuracy of surgical manipulations. CAS is a relatively young field of computer science. One of the unsolved "teething troubles" of CAS is the absence of technical standards for the interconnectivity of CAS system. Current CAS systems are usually "islands of information" with no connection to other devices within the operating room or hospital-wide information systems. Several workshop reports and individual publications point out that this situation leads to ergonomic, logistic, and economic limitations in hospital work. Perioperative processes are prolonged by the manual installation and configuration of an increasing amount of technical devices. Intraoperatively, a large amount of the surgeons' attention is absorbed by the requirement to monitor and operate systems. The need for open infrastructures which enable the integration of CAS devices from different vendors in order to exchange information as well as commands among these devices through a network has been identified by numerous experts with backgrounds in medicine as well as engineering. This thesis contains two approaches to the integration of CAS systems: - For perioperative data exchange, the specification of new data structures as an amendment to the existing DICOM standard for radiology image management is presented. The extension of DICOM towards surgical application allows for the seamless integration of surgical planning and reporting systems into DICOM-based Picture Archiving and Communication Systems (PACS) as they are installed in most hospitals for the exchange and long-term archival of patient images and image-related patient data. - For the integration of intraoperatively used CAS devices, such as, e.g., navigation systems, video image sources, or biosensors, the concept of a surgical middleware is presented. A c++ class library, the TiCoLi, is presented which facilitates the configuration of ad-hoc networks among the modules of a distributed CAS system as well as the exchange of data streams, singular data objects, and commands between these modules. The TiCoLi is the first software library for a surgical field of application to implement all of these services. To demonstrate the suitability of the presented specifications and their implementation, two modular CAS applications are presented which utilize the proposed DICOM extensions for perioperative exchange of surgical planning data as well as the TiCoLi for establishing an intraoperative network of autonomous, yet not independent, CAS modules. / Die moderne Hochleistungschirurgie des 21. Jahrhunderts ist auf vielerlei Weise abhängig von Computern oder, im weiteren Sinne, der digitalen Datenverarbeitung. Administrative Abläufe, wie die Erstellung von Nutzungsplänen für die verfügbaren technischen, räumlichen und personellen Ressourcen, die Rechnungsstellung und - in zunehmendem Maße - die Verwaltung und Archivierung von Patientendaten werden mit Hilfe von digitalen Informationssystemen rationell und effizient durchgeführt. Innerhalb der Krankenhausinformationssysteme (KIS, oder englisch HIS) stehen für die speziellen Bedürfnisse der einzelnen Fachabteilungen oft spezifische Informationssysteme zur Verfügung. Chirurgieinformationssysteme (CIS, oder englisch SIS) decken hierbei vor allen Dingen die Bereiche Operationsplanung sowie Materialwirtschaft für spezifisch chirurgische Verbrauchsmaterialien ab. Während die genannten HIS und SIS vornehmlich der Optimierung administrativer Aufgaben dienen, stehen die Systeme der Computerassistierten Chirugie (CAS) wesentlich direkter im Dienste der eigentlichen chirugischen Behandlungsplanung und Therapie. Die CAS verwendet Methoden der Robotik, digitalen Bild- und Signalverarbeitung, künstlichen Intelligenz, numerischen Simulation, um nur einige zu nennen, zur patientenspezifischen Behandlungsplanung und zur intraoperativen Unterstützung des OP-Teams, allen voran des Chirurgen. Vor allen Dingen Fortschritte in der räumlichen Verfolgung von Werkzeugen und Patienten ("Tracking"), die Verfügbarkeit dreidimensionaler radiologischer Aufnahmen (CT, MRT, ...) und der Einsatz verschiedener Robotersysteme haben in den vergangenen Jahrzehnten den Einzug des Computers in den Operationssaal - medienwirksam - ermöglicht. Weniger prominent, jedoch keinesfalls von untergeordnetem praktischen Nutzen, sind Beispiele zur automatisierten Überwachung klinischer Messwerte, wie etwa Blutdruck oder Sauerstoffsättigung. Im Gegensatz zu den meist hochgradig verteilten und gut miteinander verwobenen Informationssystemen für die Krankenhausadministration und Patientendatenverwaltung, sind die Systeme der CAS heutzutage meist wenig oder überhaupt nicht miteinander und mit Hintergrundsdatenspeichern vernetzt. Eine Reihe wissenschaftlicher Publikationen und interdisziplinärer Workshops hat sich in den vergangen ein bis zwei Jahrzehnten mit den Problemen des Alltagseinsatzes von CAS Systemen befasst. Mit steigender Intensität wurde hierbei auf den Mangel an infrastrukturiellen Grundlagen für die Vernetzung intraoperativ eingesetzter CAS Systeme miteinander und mit den perioperativ eingesetzten Planungs-, Dokumentations- und Archivierungssystemen hingewiesen. Die sich daraus ergebenden negativen Einflüsse auf die Effizienz perioperativer Abläufe - jedes Gerät muss manuell in Betrieb genommen und mit den spezifischen Daten des nächsten Patienten gefüttert werden - sowie die zunehmende Aufmerksamkeit, welche der Operateur und sein Team auf die Überwachung und dem Betrieb der einzelnen Geräte verwenden muss, werden als eine der "Kinderkrankheiten" dieser relativ jungen Technologie betrachtet und stehen einer Verbreitung über die Grenzen einer engagierten technophilen Nutzergruppe hinaus im Wege. Die vorliegende Arbeit zeigt zwei parallel von einander (jedoch, im Sinne der Schnittstellenkompatibilität, nicht gänzlich unabhängig voneinander) zu betreibende Ansätze zur Integration von CAS Systemen. - Für den perioperativen Datenaustausch wird die Spezifikation zusätzlicher Datenstrukturen zum Transfer chirurgischer Planungsdaten im Rahmen des in radiologischen Bildverarbeitungssystemen weit verbreiteten DICOM Standards vorgeschlagen und an zwei Beispielen vorgeführt. Die Erweiterung des DICOM Standards für den perioperativen Einsatz ermöglicht hierbei die nahtlose Integration chirurgischer Planungssysteme in existierende "Picture Archiving and Communication Systems" (PACS), welche in den meisten Fällen auf dem DICOM Standard basieren oder zumindest damit kompatibel sind. Dadurch ist einerseits der Tatsache Rechnung getragen, dass die patientenspezifische OP-Planung in hohem Masse auf radiologischen Bildern basiert und andererseits sicher gestellt, dass die Planungsergebnisse entsprechend der geltenden Bestimmungen langfristig archiviert und gegen unbefugten Zugriff geschützt sind - PACS Server liefern hier bereits wohlerprobte Lösungen. - Für die integration intraoperativer CAS Systeme, wie etwa Navigationssysteme, Videobildquellen oder Sensoren zur Überwachung der Vitalparameter, wird das Konzept einer "chirurgischen Middleware" vorgestellt. Unter dem Namen TiCoLi wurde eine c++ Klassenbibliothek entwickelt, auf deren Grundlage die Konfiguration von ad-hoc Netzwerken während der OP-Vorbereitung mittels plug-and-play Mechanismen erleichtert wird. Nach erfolgter Konfiguration ermöglicht die TiCoLi den Austausch kontinuierlicher Datenströme sowie einzelner Datenpakete und Kommandos zwischen den Modulen einer verteilten CAS Anwendung durch ein Ethernet-basiertes Netzwerk. Die TiCoLi ist die erste frei verfügbare Klassenbibliothek welche diese Funktionalitäten dediziert für einen Einsatz im chirurgischen Umfeld vereinigt. Zum Nachweis der Tauglichkeit der gezeigten Spezifikationen und deren Implementierungen, werden zwei modulare CAS Anwendungen präsentiert, welche die vorgeschlagenen DICOM Erweiterungen zum perioperativen Austausch von Planungsergebnissen sowie die TiCoLi zum intraoperativen Datenaustausch von Messdaten unter echzeitnahen Anforderungen verwenden.

Αντικείμενο της παρούσας διπλωματικής εργασίας, είναι η μελέτη της συμπεριφοράς φωτοβολταϊκού πλαισίου λεπτής ταινίας CIS, σε πραγματικές συνθήκες λειτουργίας. Μελετάται η επίδραση διάφορων εξωτερικών παραγόντων και κυρίως της θερμοκρασίας, της ηλιακής ακτινοβολίας και της σκίασης. Με στόχο την εκτίμηση της παραγόμενης DC ισχύος σε διάφορες συνθήκες λειτουργίας., έχουν πραγματοποιηθεί μετρήσεις ρεύματος-τάσης στο χώρο του Πανεπιστημίου Πατρών, σε φωτοβολταϊκό πλαίσιο CIS ονομαστικής ισχύος 75W. Οι μετρήσεις ήταν συνήθως ημερήσιες και καταγράφονταν οι τιμές για διάφορες συνθήκες λειτουργίας και σε διαφορετικές εποχές του έτους. Με ένα μεταβλητό φορτίο συνδεδεμένο με το εν λόγω φωτοβολταϊκό πλαίσιο, ήταν δυνατός ο προσδιορισμός της χαρακτηριστικής I-V καμπύλης σε κάθε μέτρηση και ως εκ τούτου, ο υπολογισμός του σημείου μέγιστης ισχύος. Για κάθε μέτρηση καταγράφονταν, εκτός του ρεύματος και της τάσης, η λαμβανόμενη ηλιακή ακτινοβολία, η θερμοκρασία αέρα καθώς και οι θερμοκρασίες στις δύο όψεις του συλλέκτη. Αρχικά, υπολογίζεται η απόδοση του πλαισίου σε διαφορετικές θερμοκρασίες λειτουργίας ενώ σε αυτό προσπίπτουν ίδια ποσά της ηλιακής ακτινοβολίας. Επίσης, μελετάται ποιες χαρακτηριστικές παράμετροι επηρεάζονται περισσότερο όπου διαπιστώνεται πως η αύξηση της θερμοκρασίας προκαλεί μείωση της τάσης και μία μικρή αύξηση του ρεύματος η οποία όμως, δεν είναι ικανή να αντισταθμίσει την μείωση της τάσης, με αποτέλεσμα η αύξηση της θερμοκρασίας να επιδρά αρνητικά στην απόκριση ισχύος. Στη συνέχεια, γίνεται αντίστοιχος υπολογισμός και για την ηλιακή ακτινοβολία όπου παρουσιάζεται η θετική της επίδραση στην απόδοση του πλαισίου, ενώ ταυτόχρονα μελετάται η συμπεριφορά του CIS σε συνθήκες ηλιοφάνειας αλλά και συννεφιάς. Κατά την επεξεργασία των αποτελεσμάτων αυτών, ήταν δυνατός ο υπολογισμός μίας μέσης τιμής της αποδιδόμενης ισχύος τόσο για τη θερινή όσο και για τη χειμερινή περίοδο. Τέλος, προκαλώντας τεχνητή σκίαση στο 30% περίπου της επιφάνειας του φωτοβολταϊκού πλαισίου κατά τη διάρκεια κάποιων μετρήσεων, υπολογίζεται το ποσοστό μείωσης της παραγόμενης DC ισχύος, συγκριτικά με τις περιπτώσεις όπου κάτω από τις ίδιες εξωτερικές συνθήκες, το πλαίσιο δεν σκιάζεται. / The objective of this diploma thesis, is to study the behavior of a thin film photovoltaic module CIS, under real conditions of operation. The effect of various exterior factors is studied and mainly the factors of temperature, solar radiation and shading. To estimate the produced DC Power in various conditions, measurements has been took place at the University of Patras using a CIS photovoltaic module, of 75W Maximum Power. Measurements were usually daily and were taken in all seasons of year. With a variable load connected to the photovoltaic module, the determination of the I-V curve was possible for each measurement and consequently, the calculation of the Maximum Power Point could be made. At each measurement, were noted the current, the voltage and also the received solar radiation, the air temperature as well as the temperatures at the two sides of the module. At first, the output and the efficiency of the module in different temperatures of operation are calculated , while the received solar radiation is the same in every case. Also, it is studied witch parameters are more influenced by increasing temperature and it is proved that voltage is decreased and current is a little increased. However, the increasing current is not capable to compensate the decreasing voltage, so the increase of temperature affects negatively the output power and the efficiency. Afterwards, a similar calculation has been made, studying the influence of solar radiation at the characteristic parameters of the CIS photovoltaic module. During these calculations, except the positive effect of solar radiation it is presented the behavior of CIS in sunlight and also cloudy conditions. As a result, an average output power of the module has calculated for the aestival and the wintry period. Finally, causing artificial shading in about the 30% of the module's surface, it is determined the rate of reduction of produced DC power, comparatively the case where the module is not shading under the same exterior conditions.

Αντικείμενο της παρούσας διπλωματικής είναι η μελέτη του παράγοντα ποιότητας για τρία διαφορετικά πλαίσια για διαφορετικές καιρικές συνθήκες. Τα πλαίσια που μελετήθηκαν ήταν ένα πλαίσιο μονοκρυσταλλικού πυριτίου CONERGY Q 80 MI , ένα πλαίσιο πολυκρυσταλλικού πυριτίου sharp NE-80E2EA και ένα πλαίσιο δισεληνοϊνδιούχου χαλκού (CIS) τεχνολογίας thin –film SHELL ECLIPSE 75 –C . Στο θεωρητικό μέρος παραθέτονται οι βασικές αρχές της φυσικής των ημιαγωγών και περιγράφονται οι τεχνολογίες των τριών πλαισίων που μελετάμε. Επίσης, αναλύονται τα ηλεκτρικά χαρακτηριστικά του ηλιακού στοιχείου και τέλος παρουσιάζονται οι πρόσφατες μελέτες σχετικά με τον παράγοντα ποιότητας οι οποίες χρησιμοποιήθηκαν ως αναφορά για τη διεξαγωγή της πειραματικής διαδικασίας. Για την διεξαγωγή του πειραματικού μέρους πραγματοποιήθηκαν πειραματικές μετρήσεις διάρκειας πέντε μηνών (Οκτώβριος 2009 – Φεβρουάριος 2010 ) . Οι μετρήσεις αφορούσαν όλα τα ηλεκτρικά χαρακτηριστικά των τριών πλαισίων και έγιναν σε πραγματικές συνθήκες στην ταράτσα του κτιρίου του τμήματος Ηλεκτρολόγων Μηχανικών του πολυτεχνείου Πάτρας για την κλίση των 38° . Τα πειραματικά δεδομένα οδήγησαν σε συμπεράσματα σχετικά με την συμπεριφορά του παράγοντα ποιότητας των τριών πλαισίων σε διαφορετικές καιρικές συνθήκες. Επιπλέον, μελετήθηκε η επίδραση της θερμοκρασίας υπό σταθερή ακτινοβολία και της ακτινοβολίας υπό σταθερή θερμοκρασία στον παράγοντα ποιότητας και στις παραμέτρους που τον επηρεάζουν. Η μελέτη ολοκληρώθηκε με τον υπολογισμό της αποδιδόμενης ενέργειας των τριών πλαισίων στο ίδιο διάστημα. Τέλος υπολογίστηκε η ετήσια αποδιδόμενη ισχύς για την ίδια κλίση για τα τρία πλαίσια με την βοήθεια του προγράμματος PV SOL και έγινε σύγκριση αυτών των τιμών με τις πειραματικές. / The purpose of this thesis is to study the fill factor for three different photovoltaic modules under different weather conditions. The modules under investigation were a mono-crystalline CONERGY Q 80 MI, a polycrystalline silicon sharp NE-80E2EA and a CIS technology thin-film SHELL ECLIPSE 75–C. In the literature review the basic physical principles of semiconductor technology are presented and the technical characteristics of the three modules under study are described. Also, the electrical characteristics of a solar cell are analyzed. Finally, recent studies on the fill factor of solar cells are presented. In order to conduct the experimental part of this thesis, extensive outdoor measurements have been realized during five months (October 2009 - February 2010). We have realized measurements of the electrical characteristics of the three modules under environmental conditions, on the roof of the building of the Department of Electrical and Computer Engineering of the University of Patras, at tilt angle of 38°. Conclusions were extracted, from experimental data, about the behavior of the fill factor of each of the three modules under varying weather conditions. Moreover, the effect of temperature and solar radiation on the fill factor of a solar cell was presented. The study was completed by calculating the energy yield from these modules during five months (October to February). Finally, the annual energy output was calculated using PV SOL software.

L’élément L1 (Long Interspersed Nuclear Element 1 ou L1) est le seul rétrotransposon autonome et actif connu dans notre génome, représentant 17% de celui-ci. Capable de se répliquer grâce à un intermédiaire à ARN et un mécanisme de transcription inverse initiée au site d’intégration, il encode deux protéines ORF1p et ORF2p, qui s’associent à l’ARN L1 pour former une particule ribonucléoprotéique (RNP). L’élément L1 rétrotranspose préférentiellement en cis : un L1 défectif est complémenté en trans par un élément fonctionnel de façon inefficace. Ce travail s'intéresse à deux étapes clefs du cycle réplicatif du L1 : l'assemblage de la RNP L1 en cis ou en trans afin d’explorer le mécanisme de la cis-préférence et la spécificité de l’initiation de la reverse transcription initiée. Nous avons d’abord comparé deux méthodes d’analyse de l’activité RT. Puis, nous avons montré l’importance de la complémentarité entre queue poly(A) de l’ARN L1 et site d’intégration durant l’initiation de la RT, ainsi que l’impact de mésappariements terminaux éventuels. Enfin, nous avons étudié les bases biochimiques de la cis-préférence, à travers la coexpression et la purification de deux éléments distincts étiquetés, ce qui nous a permis de suivre l'assemblage et l'activité de leurs RNPs respectives. Nos données suggèrent que ORF1p et ORF2p peuvent lier en trans l’ARN L1 de façon efficace et que la cis-préférence pourrait nécessiter des quantités limitantes de L1. / The Long Interspersed Nuclear Element 1 (LINE-1 ou L1) is the only known active and autonomous retrotransposon in the human genome and constitutes around 17% of our genomic DNA. The L1 element is able to replicate through an RNA intermediate by a mechanism called target-primed reverse transcription and encodes two proteins ORF1p and ORF2p, which associate with the L1 RNA to form a ribonucleoprotein particle (RNP). L1 preferentially retrotranspose in cis: a defective L1 can only be rescued in trans at low levels by a replication-competent copy. During this work, we focused on two essential steps of the L1 replication cycle: the assembly of the L1 RNP in cis or in trans to explore the mechanism of the cis-preference and the specificity of L1 reverse transcription priming. First, we compared two different methods to detect L1 RT activity. Then, we showed the importance of base-pairing between the poly(A) tail of the L1 RNA and the integration site to prime reverse transcription and the impact of potential mismatches. Finally, we investigated the biochemical basis of the cis-preference through the coexpression and purification of two different tagged L1 elements, which allowed us to follow the assembly and activity of their RNP. Our data suggest that binding of ORF1p and ORF2p in trans is efficient and that the cis-preference might requires limiting L1 levels.

Atopic dermatitis (AD) is a common, chronic relapsing inflammatory skin disease associated with cutaneous hyper-reactivity to environmental triggers that are innocuous to normal nonatopic individuals. AD affects 10% to 15% of children and 2% to 10% of adults in industrialized countries. There has been increasing interest in this disease triggered by its increasing prevalence in western societies and its contribution to the increasing health care costs. Yet, the underlying pathophysiologic and genetic mechanisms leading to the manifestation of AD are not clear. AD results from a complex interplay between environmental triggers, susceptibility genes including mutations in the keratinocyte protein filaggrin and altered immune responses resulting in allergic CD4+ T cell (Th2) immunity to epidermally encountered antigens. Regulatory T cells (Tregs) play an important role in controlling responsiveness to self-antigens and preventing autoimmune diseases, as well as in limiting inflammatory responses during inflammation and infection. Currently, studies investigating the number and function of Tregs in patients with AD have shown controversial results. It has been long established that symptoms of AD improve on exposure to sunlight. Narrowband UVB (NB-UVB) phototherapy is a common treatment modality for a variety of skin diseases. Considering the adverse effects for systemic treatment for severe adult AD, phototherapy, especially NB-UVB phototherapy may be a more practical long-term treatment. However, approximately 50% of patients over an 8-week treatment course do not improve after NB-UVB phototherapy. Therefore, it is important to identify characteristics of AD patients to determine whether they will respond to phototherapy and to avoid adverse effects for unresponsive patients. UVB exposure has also been associated with induction of Tregs in mice and increasing their numbers and/or functional capacity may offer benefit to patients with chronic AD. Active vitamin D (1,25(OH)2D3), one of the factors induced by UV-B radiation induces Tregs and is suggested to contribute to the suppressive effect of NB-UVB phototherapy. However, UV radiation could also have beneficial effects through other pathways known to affect immunoregulation. UVB exposure upregulates production of nitric oxide (NO) in the skin which also affects immune cell function. The protein filaggrin is broken down in differentiating keratinocytes to form the natural moisturizer of the skin. The gene encoding filaggrin (FLG) has been shown to be a major predisposing factor for AD. A key breakdown product is urocanic acid (UCA) which also acts as a natural sunscreen and undergoes trans-cis isomerisation on exposure to UV-B. Cis-UCA is known to modulate immune responses, however, the mechanisms of its action remain elusive. The production of all three compounds, vitamin D, cis-UCA and NO might all increase in the circulation of patients undergoing UVB phototherapy. While the immunomodulatory effect of Vitamin D is well described, cis-UCA and NO may also affect the behaviour of T lymphocytes systemically. Therefore, I investigated the effect of NO and cis-UCA on the phenotype and function of CD4+T cells and monocyte-derived dendritic cells (Mo-DCs) derived from peripheral blood mononuclear cells (PBMCs) from healthy volunteers. I also investigated the correlation between plasma concentration of 25(OH) vitamin D and nitrate, FLG genotype, circulating Tregs and clinical efficacy of NB-UVB phototherapy. My results showed that NO did not affect the phenotype of human mo-DCs and directly affected peripheral CD4+ T cells by inducing functional CD25+Foxp3+CD127-Tregs from CD4+CD25lo/- effector T cells. Moreover, NO increased expression of the of skin homing marker CLA on these Tregs, suggesting an increased ability of NO-induced Tregs to migrate to the skin. These NO-induced CD25+Foxp3+CD127-Tregs had immunosuppressive functions and inhibited autologous CD4+ T cell proliferation. Cytokines, at least IL-10, secreted by NO-treated CD4+ T cells were not sufficient for the suppressive function of NOinduced Foxp3+Tregs. The immune regulatory function of NO-induced Fopx3+Tregs required cell-cell contact and was mediated by membrane bound TGFβ and PD-1/PD-L1 but not CTLA-4. Results also showed that cis-UCA might have both pro- and anti-inflammatory effects. Cis- UCA significantly decreased the proportion of CD25hi Foxp3+ cells from activated CD4+ T cells. It also decreased the expression of vitamin D receptor in CD4+ T cells which may interfere with the immune regulatory function of vitamin D. These results suggested that there might be a fine balance between UV-induced anti-inflammatory molecules’ effect on CD4+ T cells. However, Cis-UCA also modulated CD4+ T cell directly by decreasing CD4+ T cell proliferation, decreasing phosphorylation of ERK after TCR activation, enhancing immune suppressive cytokines secretion, and inhibiting the percentage of CLA+CD4+T cells suggesting a decreased ability to migrate to the skin, . Cis-UCA also affected the phenotype and function of antigen presenting cells by decreasing the expression of HLA-DR, CD86 and CD40 on immature mo-DCs, which led to increased proportion of CD25+Foxp3+CD127- T cells when co-cultured with allogenic CD4+ T cells. Results generated from the clinical study in which all 29 patients got better after phototherapy suggested although circulating 25 (OH) vitamin D concentration was significantly increased after NB-UVB phototherapy, the change of circulating 25 (OH) vitamin D concentration did not correlate with disease improvement. This suggests that vitamin D is not the only pathway involved and that other molecules contribute to UVB-induced immune-regulation. The data also show that of the levels of circulating nitrate and the FLG genotype did not correlate with improvement / change with phototherapy. However, the expression of CD69 and CLA on circulating CD4+ T cells was decreased after treatment suggesting that UVB affected T cell activation and migration to the skin, and their importance in determining clinical responses requires further investigation. Taken together, the results from my study provide evidence that vitamin D is not the only molecule responsible for the beneficial effect of NB-UVB phototherapy. NO and cis-UCA may down-regulate immune responses by affecting human peripheral CD4+ T cells and mo- DCs phenotype and function. A further understanding of the effect of NO and cis-UCA on skin resident immune cells will provide more insights for narrowing NB-UVB phototherapy which will help to select patients that most likely to benefit from a mechanism-based treatment.

Populações nativas da América do Sul apresentam diversidade genética reduzida em relação às demais populações do mundo e alta diferenciação interpopulacional dentro do continente. As pressões seletivas sobre a região cis-reguladora do CCR5 geram uma assinatura de diversidade oposta àquela esperada com base na história demográfica, reduzindo a variação interpopulacional e contribuindo para uma elevação das taxas de polimorfismo. No presente estudo investigamos a interação entre esses processos micro-evolutivos, analisando o polimorfismo da região cis-reguladora de ameríndios da América do Sul e comparando os resultados com aqueles obtidos em outras regiões do mundo. Sequenciamos 927 pares de base (pb) da região controladora do CCR5 em 7 tribos indígenas da região amazônica. Em ameríndios, nenhum haplótipo exclusivo foi encontrado em ameríndios e os dois haplogrupos mais comuns foram de diferentes clusters filogenéticos. A diversidade nucleotídica (&#960;) para a amostra total, foi a mais alta dentre todas as regiões do mundo já estudadas (&#960;=0,0027). A estimativa da diversidade genética populacional para ameríndios, baseada no número de sítios polimórficos (&#952;s), foi similar aos valores encontrados para as populações não-africanas, sendo que em africanos o valor foi praticamente o dobro. Conseqüentemente, foi observado um valor de D de Tajima positivo e estatisticamente significativo (D=2,82, p<0,01), maior do que aquele visto para outras regiões do mundo. Através de comparações empíricas e de simulações coalescentes verificamos que o alto valor de D de Tajima encontrado para ameríndios não é explicável por um recente modelo demográfico de evolução humana. O teste Ewens-Watterson indicou para a amostra ameríndia uma taxa de heterozigose maior do que esperada para um população neutra. O valor de Fst observado para comparação envolvendo asiáticos e ameríndios foi mais baixo que 1000 valores de Fst calculados a partir de 783 microssatélites genotipados em amostras de mesmo tamanho de regiões geográficas similares. Essas caraterísticas corroboram a hipótese de seleção balanceadora na região cis-reguladora do CCR5 de ameríndios da região amazônica brasileira. No presente estudo demonstramos também a existência de uma associação estatisticamente significativa (p<0,01) entre os alelos mantidos em freqüências intermediárias na população humana e regiões ativadoras de splicing localizadas em exons (ESEs). Finalmente, nós acreditamos que um modelo demográfico de evolução humana, complementar ao utilizado neste trabalho, deve ser testado para se refutar a hipótese de que a forte assinatura de seleção balanceadora observada em ameríndios não foi causada por seleção natural que atuou em população ancestral à de indígenas americanos / Native american populations show lower genetic diversity and higher interpopulational genetic differences than populations from other continents. Within South America groups from the non-andean geographic region shows extremely high genetic differentiation. The strong signature of balancing selection observed for 5\' cis-regulatory region of the CCR5 gene at the worldwide scale represents an opposite pattern of genetic variation to that expected by demographic process which acted in Amerindians. To evaluate the impact of complex demographic history on the 5\' cis-regulatory region of CCR5 we resequenced 927 bp of this locus in 62 individuals from different native groups located in the Brazilian Amazonian region. No new haplotype was detected and the two most common haplogroups observed were from different phylogenetic clusters, according with the pattern observed for other human populations. The level of heterozigosity of the total sample, measured by nucleotide diversity (&#960;) was the highest yet described for human populations (&#960;=0,0027) while values based on polymorphic sites (&#952;s) were similar among Amerindians and non-Africans populations. Consequently we observed a positive and significant Tajima\'s D value (D=2,82, p <0,01). This value was higher than all D values observed for the other human populations. Observed summary statistics (&#960; and D) were significantly higher than same statistics estimated from 2000 simulated samples assuming a recently proposed demographic model of human evolution. We also found significant deviations in Ewens-Watterson homozygosity test toward an excess of heterozygosity for Amerindian sample. Another striking feature of CCR5 cis-regulatory region was the low Fst value among populations. The Fst among Asians and Amerindians was an outlier among 1000 Fst values estimated by 783 microssatelites of samples from similar geographic regions and with the same sample sizes as those of the CCR5 5\' cis-regulatory data. These features corroborates the strong signature of balancing selection described for CCR5 5\'cis regulatory region. We also contributed to discussion about functional aspects of CCR5 cis-regulatory region demonstrating a significant association between intermediate frequency SNPs and exonic splicing enhancers (ESEs) regions (p<0,01). Finally, we believe that improved models of demographic human evolution must be tested to refute the hypothesis that the strong signature of balancing selection observed in Amerindians was not caused by a selection pressure which occurred in an ancestral population.

Made available in DSpace on 2014-08-20T13:25:43Z (GMT). No. of bitstreams: 1 Tese_Clauber_Mateus_Priebe_Bervald.pdf: 1713348 bytes, checksum: c9ae92634bc72e4a44156ded5d351214 (MD5) Previous issue date: 2009-08-09 / The use of sequences of DNA has been the base of comparative genomics for evolutionary studies. The transfer of information from model species to agricultural species has been revolutionizing the molecular genetics and strategies of crop improvement. The combination of classic methods of genetics and breeding with molecular technologies of genomic analysis opens a new perspective for the increase of the understanding of the genetic basis and the acceleration of breeding programs. Bioinformatics is becoming a tool that will be an essential part of the plant scientific research contributing to this challenge, and allowing inferences of function, structure and evolution of genes and genomes, search of markers, primers design, among other possibilities. In this sense, three studies of comparative genomics in grasses were accomplished, using bioinformatics tools. In the first work, the objective was to analyze the microsatellite abundance in genome fractions of 13 species of the genus Oryza, describing the rates, frequencies and pattern of distribution of the different microsatellites. The microsatellite frequency varies inversely proportional to the size of the genome of the specie of the genus Oryza. The A genome species presented the highest occurrences and frequencies for all types and total microsatellites. The trimers composed by cytosines and guanines presented the percentile largest of occurrence among the species, without direct relationship with the GC content of the species. In the second work, the promoter region of 1,000 bases pairs of the genes OsNramp of Oryza sativa subsp japonica cv. Nipponbare was investigated as for the abundance of cis-acting elements. The sequences were analyzed using the software Signal Scan Search of the website Plant Cis-acting Regulatory DNA Elements (PLACE) to the identification of different cis-acting elements present in each one of the promoter regions. Were detected 170 different cis-acting elements in the upstream region of the genes members of the family OsNramp subsp japonica cv. Nipponbare. A total of 14 elements were common to the eight members of the family OsNramp subsp japonica cv. Nipponbare. The element CACTFTPPCA1 was the most frequent motif in the promoter region of the genes of the family OsNramp of Oryza sativa subsp japonica cv. Nipponbare. The objective of the last work was to compare the sequences of oats with the species Arabidopsis, barley, rice, sugarcane, Sorghum, wheat and corn, looking for to infer evolutionary relationships of those species with the oats. Sequences of eight species of plants evaluable at the present moment, in the Unigene data bank in the National Center for Biotechnology Information - NCBI were downloaded and comparisons with oat made using the BLASTn and tBLASTx tools. It was observed that the bank of ESTs of oats UNIGENE-NCBI consists from many sequences a little similar to other species compared to nucleotides (46,72%) and aminoacids (74,97%). Only 4,56% of the sequences present in the UNIGENE-NCBI oat EST bank presents high similarity with sequences of mono and dicotyledonous species. / O uso de seqüências de DNA tem sido à base da genômica comparativa para estudos evolucionários e a transferência de informações de espécies modelo para espécies agrícolas tem revolucionado a genética molecular e estratégias de melhoramento das culturas. A combinação de métodos clássicos de genética e melhoramento com tecnologias moleculares de análise genômica abre uma nova perspectiva para a ampliação do conhecimento das bases genéticas e aceleração de programas de melhoramento. A bioinformática está se tornando em uma ferramenta que será parte essencial na pesquisa científica de plantas e que poderá contribuir muito para este desafio, permitindo fazer inferências de função, estrutura e evolução de genes e genomas, busca de marcadores, desenho de primers, entre outras possibilidades. Neste sentido, três estudos de genômica comparativa em gramíneas foram realizados, utilizando a bioinformática como ferramenta. No primeiro trabalho, o objetivo do trabalho foi analisar a abundância de microssatélites no genoma de 13 espécies do gênero Oryza obtidas do GeneBank do National Center for Biotechnology Information NCBI, com programa SSRLocator, descrevendo as taxas, freqüências e padrão de distribuição dos diferentes microssatélites. A freqüência de microssatélites varia inversamente proporcional ao tamanho do genoma da espécie no gênero Oryza. As espécies de genoma A apresentam as maiores freqüências para todos os tipos de microssatélites e totais no gênero Oryza. Os trímeros compostos por citosinas e guaninas apresentam o maior percentual de ocorrência entre as espécies de gênero Oryza, sem relação direta com o conteúdo GC da espécie. No segundo trabalho, a região promotora de 1000 pares de bases dos genes OsNramp de Oryza sativa subsp japonica cv. Nipponbare foi investigada quanto à abundância de elementos cis-acting. As seqüências foram analisadas utilizando o programa Signal Scan Search do portal Plant Cis-acting Regulatory DNA Elements (PLACE) para a identificação dos diferentes elementos cis-acting presentes em cada uma das regiões promotoras. Foram detectados 170 diferentes elementos cis-acting na região promotora dos genes membros da família OsNramp, sendo um total de 14 elementos comuns a região promotora dos oito membros da família gênica OsNramp de Oryza sativa subsp. japonica. O elemento CACTFTPPCA1 foi o motivo mais freqüente na região promotora dos genes membros da família OsNramp de Oryza sativa subsp. japonica. O objetivo do último trabalho foi comparar as seqüências de ESTs de aveia com as espécies Arabidopsis, cevada, arroz, cana-de-açúcar, sorgo, trigo e milho, buscando inferir relações evolutivas dessas espécies com a aveia. Seqüências de oito espécies de plantas disponíveis atualmente, no banco de dados Unigene no National Center for Biotechnology Information - NCBI foram baixadas e as comparações com a aveia foram feitas utilizando as ferramentas de BLASTn e tBLASTx. Observou-se que o banco de ESTs de aveia UNIGENE-NCBI consiste de muitas seqüências pouco similares a outras espécies comparados a nucleotídeos (46,72%) e aminoácidos (74,97%). Uma minoria de 4,56% das seqüências presentes no banco de ESTs de aveia UNIGENE-NCBI apresentam alta similaridade com seqüências de espécies de mono e dicotiledôneas.

CoordenaÃÃo de AperfeiÃoamento de Pessoal de NÃvel Superior / Objetivaram-se neste trabalho: avaliar a resistÃncia de genÃtipos de feijÃo de corda [Vigna unguiculata (L.) Walp.] ao pulgÃo preto [Aphis craccivora Koch 1854] e estudar a variabilidade genÃtica desses genÃtipos para esta caracterÃstica; avaliar a aÃÃo indutora da cis-jasmona para a resistÃncia a esta praga; estudar a dispersÃo espacial do pulgÃo na cultura de feijÃo de corda; e estabelecer o nÃmero de amostras necessÃrias para a estimativa da populaÃÃo da praga para o uso em programas de Manejo Integrado de Pragas. Para a avaliaÃÃo da resistÃncia foi conduzido um experimento de preferÃncia em casa de vegetaÃÃo na Universidade Federal do Cearà (UFC), em Fortaleza, CearÃ. O delineamento utilizado foi o de blocos casualizados com 51 tratamentos, representados pelos genÃtipos, e quatro repetiÃÃes. Foram estimadas as distÃncias generalizadas de Mahalanobis e o agrupamento dos genÃtipos foi realizado utilizando o mÃtodo de otimizaÃÃo de Tocher. Para a avaliaÃÃo da cis-jasmona foram conduzidos trÃs experimentos, sendo o primeiro em QuixadÃ, CearÃ, no delineamento de blocos casualizados com cinco repetiÃÃes e cinco tratamentos sendo: uma testemunha; aplicaÃÃo dos inseticidas endosulfan e deltamethrin; e a aplicaÃÃo da cis-jasmona em dose Ãnica de 60 g.i.a. ha-1, em trÃs aplicaÃÃes de 20 g.i.a. ha-1 e seis de 10 g.i.a. ha-1 sobre a cultivar Vita 7. No segundo, no mesmo local, as sementes das cultivares TVu 408 P2, BRS GurguÃia e Vita 7 foram embebidas em uma soluÃÃo de cis-jasmona na concentraÃÃo de 60 g.i.a. ha-1 ou em Ãgua por 24 horas. O delineamento utilizado foi em blocos casualizados no arranjo fatorial 3x2. No terceiro experimento, conduzido na UFC, utilizou-se o delineamento de blocos casualizados com quatro repetiÃÃes e quatro tratamentos que consistiam de uma testemunha; e aplicaÃÃes de cis-jasmona nas doses de 50 g.i.a. ha-1, 100 g.i.a. ha-1 e 200 g.i.a. ha-1. A cultivar utilizada foi a Vita 7. Para as avaliaÃÃes foi contado o nÃmero de colÃnias de pulgÃo presentes em toda planta. Para estudo da dispersÃo do pulgÃo foram cultivados dois campos experimentais na UFC. O primeiro campo tinha uma Ãrea de 216 m e o segundo 576 mÂ. Os campos foram divididos em 15 e 25 parcelas, respectivamente. A cultivar utilizada foi a Vita 7 no espaÃamento de 0,25 m x 0,8 m. Foram realizadas seis coletas de dados em cada campo onde foram avaliadas dez plantas por parcelas. Foi contado o nÃmero de colÃnias de pulgÃo presentes em toda a planta. Os resultados demonstram que os genÃtipos BRS Guariba, TVu 410, BRS ParaguaÃu, TVu 36, Sempre Verde, TVu 408 P2, SetentÃo e Epace 10 apresentam maior resistÃncia ao pulgÃo. As maiores divergÃncias encontradas foram entre o BRS Guariba e Sete Semanas e entre TVu 410 e Sete Semanas, enquanto o BRS Guariba e TVu 410 foram os mais similares. Foi observada a divisÃo dos genÃtipos em oito grupos e o caractere que mais contribui para a divergÃncia à o nÃmero de ninfas. O cruzamento entre o genÃtipo SetentÃo e os genÃtipos BRS Guariba,TVu 410, BRS ParaguaÃu, TVu 36, TVu 408 P2 e entre o Epace 10 e o Sempre Verde, BRS Guariba e TVu 410 podem resultar em novas combinaÃÃes genÃticas visando o melhoramento da resistÃncia ao pulgÃo. Em todos os experimentos a cis-jasmona nÃo reduziu a infestaÃÃo de A. craccivora concluindo-se que essa substÃncia, em condiÃÃes de campo, nÃo induz a resistÃncia. Quanto a dispersÃo os Ãndices de agregaÃÃo utilizados indicam que do tipo agregada o que foi confirmado pelo ajuste dos dados a distribuiÃÃo de frequÃncia Binomial Negativa. Quarenta e cinco à o nÃmero de amostras adequado para a estimativa da populaÃÃo de A. craccivora em campos de V. unguiculata para aplicaÃÃo em programas de Manejo Integrado de Pragas. / The objective of this work were: to evaluate resistance of cowpea genotypes [Vigna unguiculata (L.) Walp.] to the black aphid [Aphis craccivora Koch, 1854] and to study the genetic variability of these genotypes for this feature; to evaluate the possible inducible action of cis-jasmone to resistance to this pest; to study the spatial dispersion of the aphid in cowpea culture, and to establish the number of samples required to estimate the population of the pest to use in integrated pest management programs. To evaluate the resistance preference, an experiment was conducted in a greenhouse at the Universidade Federal do Cearà (UFC) in Fortaleza, CearÃ. The experimental design was randomized blocks with 51 treatments, represented by genotypes and four replications. We estimated the generalized Mahalanobis distances and grouping of genotypes was performed using the Tocher optimization method. For the evaluation of cis-jasmone three experiments were conducted, the first in QuixadÃ, CearÃ, in the design of randomized blocks with five replications and five treatments as follow: untreated control; application of the insecticide endosulfan and deltamethrin, and the application of cis-jasmone a single dose of 60 g.ha-1, three applications of 20 g ha-1 and six of 10 g ha-1 on the cultivar Vita 7. In the second, in the same place, the seeds of the TVu 408 P2, BRS GurguÃia and Vita 7 were soaked in a solution of cis-jasmone with 60 g ha-1 or in water for 24 hours. The design was factorial 3x2 in blocks. In the third experiment, conducted in the UFC, we used a randomized block design with four replications and four treatments consisting of an untreated control, and applications of cis-jasmone at doses of 50 g ha-1, 100 g ha-1 and 200 g ha-1. The cultivar was Vita 7. For the evaluations, the number of colonies of aphids present in every plant was counted. To evaluate the spatial distribution of aphid were grown in two field trials in the UFC. The first field had an area of 216 m and second 576 mÂ. The fields were divided into 15 and 25 plots, respectively. The cultivar used was Vita 7 spaced in 0.25 m x 0.8 m. On those fields were performed six collections of data in each field where they were evaluated ten plants per plot. It was count the number of colonies of aphids present throughout the plant. The results show that the genotypes BRS Guariba, TVu 410, BRS ParaguaÃu TVu 36, Sempre Verde, TVu 408 P2, SetentÃo e Epace 10 have greater resistance to the aphid than the others. The largest differences were found between BRS Guariba and Sete Semanas and between Tvu 410 and Sete Semanas, while the BRS Guariba and TVu 410 were the most similar. We observed the division of the genotypes in eight groups and the character that contributes to the most divergence was the number of nymphs. The crosses among the genotype SetentÃo and the genotypes BRS Guariba ,TVu 410, BRS ParaguaÃu, TVu 36, TVu 408 P2 and between Epace 10 and Sempre Verde, BRS Guariba and TVu 410 may result in new genetic combinations intended to improve resistance to aphid. In all experiments, cis-jasmone did not reduce the infestation of A. craccivora and so concluding that this product, under field conditions, does not induce resistance. The dispersion indices indicate that aggregate was the case in this study, which was confirmed by data fitting the frequency distribution of the Negative Binomial. Forty five is the appropriate number of samples to estimate the population of A. craccivora in the fields of V. unguiculata to be used in Integrated Pest Management programs.

Résumé confidentiel / Résumé confidentiel

Il est connu que les 4,5-méthano-L-prolines ont des conformations et des caractéristiques différentes que la L-proline. L’aplatissement du cycle pyrrolidine dans la proline joue un rôle important dans sa stabilité et la conformation spatiale des analogues 4,5-méthano- de la L-proline. Ainsi, des études approfondies ont été menées pour analyser les différences de structure et les modèles de pliage des cis- et trans-4,5-méthano-L-prolines et leurs oligomères en corrélation avec la délocalisation électronique n→π∗ entre les carbonyles adjacents. Dans cette thèse, la stabilisation n→π∗ entre les groupes carbonyl d’une amide et un ester a été analysée, divulguant des propriétés structurelles supplémentaires des 4,5-méthano-L-prolines. Les études spectroscopiques en RMN ont révélé les caractéristiques spatiales des cis- and trans-4,5-méthano-L-prolines corrélant avec l’équilibre d’isomérisation de l’amide trans : cis dans des environnements différents. En outre, le mécanisme de la cyclisation intramoléculaire des dimères cis-cis, trans-trans, et du mélange trans,cis-4,5-méthano-L-proline dans la formation des dicétopipérazines a révélé l'importance de la stabilisation n→π∗ sur les caractéristiques conformationnelles et de pliage. Des études de modélisation DFT ont également été menées afin de compléter nos résultats et de fournir des explications soutenant nos résultats expérimentale. / It is well known that 4,5-methano-L-prolines have different conformational properties and characteristics than proline. The flattening of the pyrrolidine ring plays a role in the stability and conformation of L-proline methanologs. Thus, extensive studies have been conducted to analyze the structural differences and folding patterns of cis- and trans-4,5-methano-L-prolines and their oligomers in correlation with the n→π∗ electron delocalization between the adjacent carbonyls of amide and ester groups. In this thesis, the n→π∗ stabilization of each derivative is analyzed, disclosing additional structural properties of 4,5-methano-L-prolines. NMR spectroscopic studies revealed the spatial characteristics of cis- and trans-4,5-methano-L-prolines in correlation to the amide trans : cis isomerization equilibrium in different solvents. In addition, the tendency of diketopiperazine formation from the cis-cis, trans-trans, and mixed trans,cis-4,5-methano-L-proline dimers reflected the importance of the n→π∗ stabilization on the conformation and folding characteristics.