<p>With the full sequence of the human genome now available, anexciting era in biomedical research has started. The sequenceprovides information about all our genes and greatly increasesthe scope to compare genetic activities in different cells, toanalyze genetic variation between individuals and betweendifferent species and, most importantly, to investigatesystematically the whole genome in a gene-by-gene manner, andthus increase our understanding of gene function.</p><p>This thesis describes studies in which developments weremade in several areas of functional genomics. Messenger RNAlevels were analyzed by the use of an amplification procedure,in which the 3´-ends of the transcripts were selected inorder to amplify the mRNA population in an unbiased fashion. Bysonicating cDNA originating from expressed mRNA, uniformlysized representatives of the transcripts,“signaturetags”, were obtained. The mRNA levels in the original mRNApopulation correlated well with the levels in the amplifiedmaterial, as verified by microarray analysis and realtimequantitative PCR. The expressed transcripts can be identifiedusing pyrosequencing, by comparing the obtained sequenceinformation from the signature tags to information contained invarious sequence databases. In one of the articles, the use ofpyrosequencing is illustrated by efforts to find genes involvedin the disease progression of atherosclerosis.</p><p>More challenging than the study of mRNA levels is to analyzewhen, where and how proteins fulfill their wide-ranging rolesin all the various cellular processes. Proteins are morecomplex biomolecules than mRNA, each having unique properties.Current techniques for studying proteins need much improvement,and are often limited to investigations of a specific portionof the proteome. One approach for studying the whole proteomeis to systematically generate reagents with specific affinityfor the proteins encoded by the genome, one by one. Theaffinity reagents can be used as flags for their targets,providing a flag-specific detection system, so that the targetproteins can be sub-cellularly localized in the majority ofhuman tissues in an array format. One of the articles includedin the thesis presents a pilot project for large-scale affinityreagent production. The aim was to provide a sound basis forwhole proteome studies, but as a pilot study this investigationwas limited to the proteins encoded by human chromosome 21. Allputative genes on the chromosome were subjected to antibodygeneration in a systematic manner. Small, uniform, and easilyproduced representative portions of the full-length proteinswere expressed. These were denoted“Protein EpitopeSignature Tags”and were designed to be unique for theirfull-length counterparts. The antibodies were produced inrabbits and two of the articles in the thesis discuss differentapproaches for affinity purification of the antibodies toachieve the highest possible specificity towards the targets.The resulting“mono-specific”, but still“multi-epitope”, antibodies can be used for a widerange of additional biochemical studies, such as protein arrayand protein pull-out analyses.</p><p><b>Keywords:</b>functional genomics, 3´-end signaturetags, pyrosequencing, amplification, PrEST, chromosome 21,polyclonal antibodies, dual expression, affinitypurification.</p>

Biologging tools for investigating the study of fine-scale linkages between animal behavior and the physical microstructure of the marine habitat are technically limited by substantial size, high cost or low sensor resolution. However, recent advances in electronic technologies and process techniques present attractive alternatives to current tag designs. Motivated by the need for a low-cost, compact CTD biotag for medium-sized marine animals, the University of South Florida Center for Ocean Technology developed a multi-sensor biotag for quantitative measurements of ocean salinity. This dissertation describes the development and performance of a novel CTD biotag used for animal-borne measurements of the physical microstructure of marine ecosystems. Printed circuit board processes were used to fabricate a liquid crystal polymer- based conductivity, temperature and depth sensor board. Tests performed in the laboratory exhibited good sensor repeatability between the measured and the predicted variables indicating that the initial design and fabrication process is suitable for the construction of a CTD sensor board. The conductivity cells showed good sensor integrity for the entire conductivity range (0- 70 mS/cm), thus demonstrating the potential for a highly resolved salinity system. The CTD sensor board was integrated into two initial multi-sensor biologging systems that consisted of reconfigurable modular circuit boards. The design and initial performance of a 4-electrode conductivity cell circuit was discussed and preliminary tests showed a sensor accuracy of 0.0161 mS/cm. A potential packaging material was analyzed for use on the temperature and pressure sensors and initial tests showed good sensor sensitivities (-2.294 °C/kohms and 1.9192 mV/dbar, respectively). Underwater packaging of the biotag was presented in this work along with three different field observations. Vertical profiles of conductivity, temperature and depth in the Gulf of Mexico were obtained and compared to a commercial instrument. On the West Florida shelf, conductivity, temperature, depth and salinity data were obtained from loggerhead turtle deployments. Data collected showed that the tagged turtle encountered a highly variable salinity range (30.6- 35.3) while at depth (20 m). This data trend captured was in agreement with shelf characteristics (tidal fluxes and water mass features) and moored instruments. Finally, observations that were undertaken in Bayboro Harbor showed no biofouling to the conductivity electrodes during a 14 day deployment. This biotag is the first to use a PCB-based low-cost CTD to collect animal-borne salinity measurements.

Η έννοια του «Web2.0.» χρησιμοποιήθηκε για πρώτη φορά σε ένα συνέδριο για την ανταλλαγή ιδεών μεταξύ του εκδοτικού οίκου O’ Reilly και του Medialive International. Μέσα από αυτή τη σύσκεψη έγινε φανερό ότι το Web είναι πιο σημαντικό από ποτέ, με εντυπωσιακές νέες εφαρμογές και ιστότοπους, που κάνουν την εμφάνισή τους ολοένα και συχνότερα. Μισό χρόνο μετά, ο όρος Web2.0. έχει ξεκάθαρα λάβει χώρα, με περισσότερες από 9,5 εκατομμύρια αναφορές στη μηχανή αναζήτησης Google. Πιο συγκεκριμένα, το νέο Web αλλάζει επειδή αλλάζει η νοοτροπία των δημιουργών των ιστότοπων, των προγραμματιστών αλλά και των απλών χρηστών. Το Web2.0. είναι περισσότερο δημοκρατικό. Ο ρόλος των ισχυρών, παραδοσιακών δημιουργών και «εκδοτών» περιεχομένου αποδυναμώνεται. Η αλληλεπίδραση των χρηστών με το περιεχόμενο και άλλους χρήστες εντείνεται. Η νέα χρήση των ήδη υπαρχουσών τεχνολογιών και εργαλείων δίνει καινούριες διαστάσεις και προστιθέμενη αξία στο περιεχόμενο. Οι λέξεις «υλικό» και «λογισμικό» περνάνε σε δεύτερη μοίρα ενώ μια νέα, καθολική πλατφόρμα είναι αυτή που αναδεικνύεται. Ο νέος Παγκόσμιος Ιστός που ακούει στο όνομα Web2.0. ενθαρρύνει τη συμμετοχή των χρηστών και την παραγωγή ενός πλουσιότερου, πιο σύγχρονου και δυναμικότερου περιεχομένου. Προσφέρει σε όλους τους χρήστες του το ρόλο του δημιουργού και του εκδότη αφού ταυτόχρονα με τους web developers, και οι απλοί χρήστες είναι σε θέση να δημιουργούν χρησιμοποιώντας τη θέληση και τη φαντασία τους. Παράλληλα με τη διαμόρφωση του περιεχομένου, διαφόρων μορφών, όπως κείμενο, ήχος, εικόνα, βίντεο, στους χρήστες επαφίεται και η κατηγοριοποίηση, η αξιολόγηση και η κατάταξη του περιεχομένου, όπως για παράδειγμα ποια είδηση θεωρείται από αυτούς ως η περισσότερο σημαντική. Το Web2.0 αναφέρεται σε ένα σύνολο νέων δικτυακών υπηρεσιών, οι οποίες επιτρέπουν στους χρήστες να συνεργάζονται και να ανταλλάζουν δεδομένα online, με πιο αποδοτικό τρόπο σε σχέση με αυτόν που προσφέρανε οι παλιότερες υπηρεσίες. Η ειδοποιός διαφορά είναι ότι οι νέες υπηρεσίες παρέχουν στο χρήστη μια εμπειρία που πλησιάζει περισσότερο σε αυτή που έχει όταν εργάζεται στον προσωπικό του υπολογιστή. Με άλλα λόγια, οι εφαρμογές του Web2.0. μοιάζουν με τις εφαρμογές desktop. Επιπλέον, οι νέοι δικτυακοί τόποι είναι κατά κανόνα «δυναμικοί» και περισσότερο αλληλεπιδραστικοί, διαφέροντας από το «στατικό» Web1.0. Το Web2.0. είναι συμβατό με οποιοδήποτε λειτουργικό σύστημα κι αν χρησιμοποιεί ο εκάστοτε χρήστης. Μια εφαρμογή πλοήγησης του Διαδικτύου (web browser) (οποιαδήποτε κι αν είναι αυτή) αρκεί για να συμμετέχει ένα χρήστης στο νέο, πιο ζωντανό και εκπληκτικό Διαδίκτυο. Επιπρόσθετα, το Web2.0. είναι εκτός από πλούσιο και «ελαφρύ». Πολλές από τις εφαρμογές του έχουν σχεδιαστεί για να «τρέχουν» γρήγορα, χωρίς να «βαραίνουν» τους πόρους του συστήματος. Τέλος, το λογισμικό και το υλικό δεν απασχολούν πλέον τους προγραμματιστές στον ίδιο βαθμό με το παρελθόν, αφού το περιεχόμενο, η διαμόρφωση και η αξιοποίησή του είναι τα θέματα στα οποία επικεντρώνεται κυρίως το ενδιαφέρον. Η παρούσα μεταπτυχιακή διπλωματική εργασία μελετά τις αρχές που το Web2.0. πρεσβεύει, τα πρότυπα σχεδιασμού που ακολουθούνται, τις τεχνικές και τεχνολογίες που χρησιμοποιούνται, τις ικανότητες που πρέπει να έχουν οι εταιρείες κατασκευής λογισμικού και εφαρμογών προκειμένου να θεωρούνται ότι ακολουθούν τα πρότυπα του Web2.0. Επιπλέον, παρουσιάζονται οι βασικότερες Web2.0. εφαρμογές, οι οποίες είτε πρόκειται για καινοτόμα στοιχεία, είτε αποτελούν νέες εκδόσεις των ήδη Web1.0. υπαρχουσών εφαρμογών, με τις οποίες και συγκρίνονται. Τελικά, παρουσιάζονται μια σειρά από ιστοτόπους, ελληνικούς και ξένους, στους οποίους γίνεται φανερή η επίδραση και παρουσία του Web2.0., ενώ παράλληλα προτείνεται η χρήση συγκεκριμένωνWeb2.0. στοιχείων και τεχνολογιών ανάλογα με την κατηγορία και το είδος του ιστοτόπου. Ωστόσο, υπάρχει και ένα μεγάλο ποσοστό που αντιμετωπίζει το Web2.0. με επιφυλακτικότητα. Ενώ κάποιοι το θεωρούν μια καινοτομία, κάποιοι άλλοι το θεωρούν μια χωρίς νόημα λέξη, που αποσκοπεί στην επικράτηση στην αγορά και την αύξηση των κερδών, των εφαρμογών και υπηρεσιών που φέρονται ως αντιπρόσωποι του όρου. Η παρούσα εργασία έχει ως σκοπό να παρουσιάσει αντικειμενικά και αμερόληπτα τη νέα γενιά του Διαδικτύου και αφήνει στον αναγνώστη να βγάλει τα δικά του συμπεράσματα για το τι τελικά είναι το Web2.0. και ποια είναι η αξία του. / The concept of “Web2.0” began with a conference brainstorming session between O’ Reilly and MediaLive International. In the year and a half since, the term “Web2.0” had clearly taken hold, with more than 9.5 million citations in Google. In the new generation of Web, users are treated as co-developers. They obtain the role of author and publisher and use their willingness and imagination to add value and create the content of the web. Leverage customer-self service and algorithmic data management are used in order to reach out to the entire web, to the edges and not just the centre. As a result, the new projects can be seen to have a natural architecture of participation. In some cases, the service automatically gets better the more people use it. Moreover, Web2.0 era software is delivered as a service, not as a product. That leads to an end of the software release cycle. Furthermore, the Web2.0 mindset is good at re-use. When commodity components are abundant, developers can create value simply by assembling them in novel or effective ways. The purpose of this master thesis is to analyse the principles that Web2.0. advocate, the techniques and technologies that are used, the core competencies of Web2.0. companies, the design patterns, the new applications and projects. Its target is to recommend which of the Web2.0’ components should be used in each case, depending on the needs, the requirements and the kind of the website or application. However, there’s still a huge amount of disagreement about just what Web2.0 means, with some people decrying it as a meaningless marketing buzzword, and others accepting it as the new conventional wisdom. This thesis presents Web2.0 impartially, letting readers to decide what is Web2.0 and its value.

This study has successfully identified transcripts differentially expressed in the salivary gland and midgut and provides candidate genes that are critical to response to parasite invasion. Furthermore, an open-source Glossina resource (G-ESTMAP) was developed that provides interactive features and browsing of functional genomics data for researchers working in the field of Trypanosomiasis on the African continent.

RFID has been characterized as a “disruptive technology” that has the potential to revolutionize numerous key sectors. A key advantage of passive RFID applications is the ability to wirelessly transmit automatic identification and related information using very little power. This paper presents an experimental investigation to inform the optimal configuration for programming passive ultra-high frequency (UHF) RFID media in dynamic applications. Dynamic programming solutions must be designed around the tag’s functionality, the physical programming configuration and environment. In this investigation, we present a methodology to determine an optimal configuration to maximize the systems programming efficiency for dynamic applications.

The purpose of this thesis is to design a secure and optimized cryptographic stream cipher for passive type Radio Frequency Identification (RFID) tags. RFID technology is a wireless automatic tracking and identification device. It has become an integral part of our daily life and it is used in many applications such as electronic passports, contactless payment systems, supply chain management and so on. But the information carried on RFID tags are vulnerable to unauthorized access (or various threats) which raises the security and privacy concern over RFID devices. One of the possible solutions to protect the confidentiality, integrity and to provide authentication is, to use a cryptographic stream cipher which encrypts the original information with a pseudo-random bit sequence. Besides that RFID tags require a resource constrained environment such as efficient area, power and high performance cryptographic systems with large security margins. Therefore, the architecture of stream cipher provides the best trade-off between the cryptographic security and the hardware efficiency. In this thesis, we first described the RFID technology and explain the design requirements for passive type RFID tags. The hardware design for passive tags is more challenging due to its stringent requirements like power consumption and the silicon area. We presented different design measures and some of the optimization techniques required to achieve low-resource cryptographic hardware implementation for passive tags. Secondly, we propose and implement a lightweight WG-5 stream cipher, which has good proven cryptographic mathematical properties. Based on these properties we measured the security analysis of WG-5 and showed that the WG-5 is immune to different types of attacks such as algebraic attack, correlation attack, cube attack, differential attack, Discrete Fourier Transform attack (DFT), Time-Memory-Data trade-off attack. The implementation of WG-5 was carried out using 65 nm and 130 nm CMOS technologies. We achieved promising results of WG-5 implementation in terms of area, power, speed and optimality. Our results outperforms most of the other stream ciphers which are selected in eSTREAM project. Finally, we proposed RFID mutual authentication protocol based on WG-5. The security and privacy analysis of the proposed protocol showed that it is resistant to various RFID attacks such as replay attacks, Denial-of-service (DoS) attack, ensures forward privacy and impersonation attack.

L’essor considérable de la RFID s’accompagne actuellement par le développement de nombreuses technologies qui viennent compléter l’offre déjà présente tout en cherchant à répondre à de nouvelles problématiques. La RFID sans puce (ou chipless) en est un exemple ; l’objectif affiché est de réduire considérablement le prix du tag ainsi que d’augmenter significativement la quantité d’information qu’il contient de manière à pouvoir concurrencer le code à barres tout en conservant les bénéfices d’une approche de lecture flexible basée sur une communication par ondes radio. Pour répondre à la problématique de la quantité d’information d’un tag, ce travail de thèse propose une nouvelle méthode de codage basée sur la forme globale du RCS du tag. Pour ce faire, il faut être capable de réaliser des tags dont le RCS est donné, ce qui consiste à résoudre un problème inverse. Une méthode de conception basée sur l’assemblage de motifs résonants est proposée. Les principales caractéristiques de ces éléments de base (amplitude, fréquence, coefficient de qualités) sont contrôlées par des paramètres géométriques. / The important growth of RFID goes along with the development of many technologies which complement the current offer by adding new possibilities. The chipless RFID is a perfect example of such technology. The purpose of the approach is to considerably reduce the price of the tag while increasing the data encoding capacity in order to compete with the barcode. The RF link between the tag and the reader also permit a flexible reading. In order to increase the coding capacity of a chipless tag, this PHD work proposes a new coding method based on the overall shape of the electromagnetic signature. To do this, we must be able design tags for which the RCS is given in advance, which amounts to the resolution of an inverse problem. A method based on the decomposition of the RCS on a base of resonators is proposed. The main characteristics of these base elements (amplitude, frequency, quality factor) are controlled by geometric parameters.

La RFID sans puce, en raison du très faible coût des tags, a ouvert une nouvelle voie pour les systèmes d'identification. Les étiquettes RFID sans puce fonctionnant dans le domaine temporel ont l'avantage d'être compatibles avec de grandes distances de lecture, de l'ordre de quelques mètres, et de pouvoir fonctionner dans les bandes de fréquence ISM. Cependant, les tags de ce type développés jusqu'à lors n'offraient qu'une faible capacité de codage. Cette thèse propose une nouvelle méthode pour augmenter la capacité de codage des tags fonctionnant dans le domaine temporel en utilisant des C-sections, c'est-à-dire des lignes de transmission repliées de manière à avoir des zones fortement couplées, ce qui leur donne un caractère dispersif. Une autre approche basée sur une technique multi-couches a également été introduite de façon à augmenter considérablement la capacité de codage. Pour terminer, la preuve de concept d'un tag-capteur d'humidité, basé sur l'utilisation de nano fils de silicium, est également présentée. / Chipless RFID tags, owing to their low cost, have opened a new way to the identification systems. Chipless RFID tags operating in the time domain have the advantage of being compatible with large reading distances of the order of a few meters, and also can operate in the ISM frequency bands. However, time domain tags developed until now offer poor coding capacity. This thesis proposes a new method to increase the coding capacity of tags operating in time domain by using C-sections, i.e. the transmission lines are folded so as to have tightly coupled zones that give them a dispersive nature. Another approach based on a multi-layer technique was also introduced, in order to increase the coding capacity considerably. Finally, the proof of concept of a humidity sensor tag based on silicon nanowires is also presented.

Presented diploma work represents a further development of my bachelor-degree diploma work, dealing with new technologies in retail business. In contrast of said bachelor diploma work, which extent was limited to theoretical part of the problem, practical application of the objective new technologies has been analyzed within TESCO stores buiseness environment. Therefore, this diploma work deals with specific technologies, which are really used in the TESCO retail network. The technologies analyzed in this work were chosen on the basis of Retail Summit 2011 topics. Application potential of m-commerce and e-commerce is analyzed and EDI technology innovation, which makes this option available for small companies, is described. Beside self-service cash desks, which are currently widely used, the RFID, NFC and LCD price tags, which are still in the testing process, are dealt with.

Doctor of Philosophy / Biochemistry and Molecular Biophysics Interdepartmental Program / Timothy P. Durrett / The direct use of vegetable oils as a biofuel suffers from problems such as high viscosity, low volatility and poor cold temperature properties. 3-acetyl-1,2-diacyl-sn-glycerols (acetyl-TAGs) have lower viscosity and freezing temperature than regular vegetable oils. However, by modifying their fatty acid composition, further improvement in their fuel properties is possible. Our goal was to develop plants that synthesize seed oils with further improved fuel properties. Euonymus alatus diacylglycerol acetyltransferase (EaDAcT) synthesizes acetyl-TAGs by the acetyl-CoA dependent acylation of diacylglycerol (DAG). Knowledge of the substrate specificity of EaDAcT for its acetyl-CoA donor and DAG acceptor substrates is important to generate the required acetyl-TAG composition in seed oil. A rapid method to quantify acetyl-TAGs was developed based on electrospray ionization mass spectrometry to gain information about the substrate specificity of EaDAcT. This method is as accurate and more rapid than the traditional radiolabeled substrate based assay and additionally provides information on acetyl-TAG molecular species present. Using this assay, EaDAcT specificity for different chain length acyl-CoA and DAGs was tested. It was found that although EaDAcT can use other short chain length acyl-CoAs as acyl donors, it has high preference for acetyl-CoA. Further, EaDAcT can acetylate a variety of DAGs with short, medium and long chain length fatty acids with high preference for DAGs containing unsaturated fatty acids. To generate acetyl-TAGs with lower molecular mass, EaDAcT was transformed into transgenic Camelina sativa lines producing high amounts of medium chain fatty acids (MCFAs). EaDAcT expression was also combined with the knockdown of DGAT1 and PDAT enzymes, which compete with EaDAcT for their common DAG substrate. High acetyl-TAG yielding homozygous T3 transgenic lines were generated but the incorporation of MCFAs into acetyl-TAGs was inefficient. A small increase in the viscosity of acetyl-TAGs from these lines was observed compared to acetyl-TAGs produced in wild type Camelina plant. The combined effect of insufficient lowering of molecular mass and increased fatty acid saturation levels of acetyl-TAGs might be responsible for this increased viscosity. Overall, it was concluded that the molecular mass and the saturation levels of fatty acids of acetyl-TAGs need to be considered at the same time in future attempts to further decrease their viscosity.