<p>Abstract</p><p>Crimean-Congo Hemorrhagic Fever virus (CCHF) and Lassa virus are giving sources illness to humans. In addition to zoonotic transmission, CCHF and Lassa virus can spread from person to person. After a short incubation period, CCHF and Lassa virus infections are characterized by a sudden onset of high fever, chills, headache and cough just like flu. Even some people are vomiting and have diarrhoea. After a few days of illness hemorrhagic manifestations occur. Treatment options for CCHF and Lassa viruses are limited, and there is no vaccine available for use in humans. The purpose of the present study was to produce recombinant nucleocapsid protein of Lassavirus and CCHF virus including an aminoterminal His-tag by a Semliki Forest Virus Replicon (pSFV 4.2). The recombinant proteins are planned to be used in future development of diagnostic methods.</p>

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.

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. 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. 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. <b>Keywords:</b>functional genomics, 3´-end signaturetags, pyrosequencing, amplification, PrEST, chromosome 21,polyclonal antibodies, dual expression, affinitypurification.

Questions have been raised about the genomic complexity of the human genome, since it was reported that it only consisted of 32,000 genes. Alternative splicing is considered the explanation of the enormous difference between the number of genes and the number of proteins. Aligning expressed sequence tags (ESTs) to the genomic sequence has become a popular approach for gene prediction, revealing alternative splice variants. The aim in this thesis is to identify and analyse splice variants of the adhesion family of G protein-coupled receptors using EST data. 75% of the genes in the data set of 33 sequences were found to have a total of 51 splice variants. About half of the variants were considered functional.

Abstract Crimean-Congo Hemorrhagic Fever virus (CCHF) and Lassa virus are giving sources illness to humans. In addition to zoonotic transmission, CCHF and Lassa virus can spread from person to person. After a short incubation period, CCHF and Lassa virus infections are characterized by a sudden onset of high fever, chills, headache and cough just like flu. Even some people are vomiting and have diarrhoea. After a few days of illness hemorrhagic manifestations occur. Treatment options for CCHF and Lassa viruses are limited, and there is no vaccine available for use in humans. The purpose of the present study was to produce recombinant nucleocapsid protein of Lassavirus and CCHF virus including an aminoterminal His-tag by a Semliki Forest Virus Replicon (pSFV 4.2). The recombinant proteins are planned to be used in future development of diagnostic methods.

Aujourd'hui, l'énergie nucléaire représente une partie non-négligeable du marché énergétique mondial, très probablement vouée à croître dans les prochaines décennies. Les réacteurs du futur devront notamment répondre à des critères supplémentaires économiques mais surtout de sûreté, de non-prolifération, de gestion optimisée du combustible et d'une gestion responsable des déchets nucléaires. Dans le cadre de cette thèse, des études concernant la non-prolifération des armes nucléaires sont abordées, dans le cadre de la recherche et développement d'un nouvel outil potentiel de surveillance des réacteurs nucléaires ; la détection des antineutrinos des réacteurs. En effet, les propriétés de ces particules pourraient intéresser l'Agence Internationale de l'Energie Atomique (AIEA) en charge de l'application du Traité de non-prolifération des armes nucléaires. L'AIEA encourage ainsi ses états membres à mener une étude de faisabilité. Une première étude de non-prolifération est réalisée avec la simulation d'un scénario proliférant utilisant un réacteur de type CANDU et de l'émission en antineutrinos associée. Nous en déduisons une prédiction de la sensibilité d'un détecteur d'antineutrinos de taille modeste à la diversion d'une quantité significative de plutonium. Une seconde étude est réalisée dans le cadre du projet Nucifer, détecteur d'antineutrinos placé auprès du réacteur de recherche OSIRIS. Nucifer est un détecteur d'antineutrinos dédié à la non-prolifération à l'efficacité optimisée conçu pour être un démonstrateur pour l'AIEA. La simulation du réacteur OSIRIS est développée ici pour le calcul de l'émission d'antineutrinos qui sera comparée aux données mesurées par le détecteur ainsi que pour caractériser le bruit de fond important émis par le réacteur détecté dans Nucifer. De façon générale, les antineutrinos des réacteurs sont émis lors des décroissances radioactives des produits de fission. Ces décroissances radioactives sont également à l'origine de la puissance résiduelle émise après l'arrêt d'un réacteur nucléaire, dont l'estimation est un enjeu de sûreté. Nous présenterons dans cette thèse un travail expérimental dont le but est de mesurer les propriétés de décroissance bêta de produits de fission importants pour la non-prolifération et la puissance résiduelle des réacteurs. Des premières mesures utilisant la technique de Spectroscopie par Absorption Totale (TAGS) ont été réalisées auprès du dispositif de l'Université de Jyväskylä. Nous présenterons la technique employée, le dispositif expérimental ainsi qu'une partie de l'analyse de cette expérience.

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.

Personal document management systems provide good support for storing and organizing digital documents. However, there are no computer tools that support organization of paper documents on our desks. We ran a study of people's organization of their office desk space with respect to their digital workspace. This study resulted in a set of requirements for a media bridging tool. Based on these requirements, we built a prototype media bridging tool called PaperSpace that uses computer vision to link paper and digital documents. The system also tracks piles of paper documents on the real desktop, and links those papers to digital documents stored in the computer. Digital documents can be sorted and grouped according to the physical layout of the corresponding papers on the desk. The system automatically creates digital piles of documents in a simulated desktop that reflect the paper piles on the real desktop. The user can access valuable information through the system, such as printing statistics, location of a printed document on the desk, and past projects and their documents. A two week user evaluation of the system showed interesting usage scenarios and future trends for improving user interaction.

Personal document management systems provide good support for storing and organizing digital documents. However, there are no computer tools that support organization of paper documents on our desks. We ran a study of people's organization of their office desk space with respect to their digital workspace. This study resulted in a set of requirements for a media bridging tool. Based on these requirements, we built a prototype media bridging tool called PaperSpace that uses computer vision to link paper and digital documents. The system also tracks piles of paper documents on the real desktop, and links those papers to digital documents stored in the computer. Digital documents can be sorted and grouped according to the physical layout of the corresponding papers on the desk. The system automatically creates digital piles of documents in a simulated desktop that reflect the paper piles on the real desktop. The user can access valuable information through the system, such as printing statistics, location of a printed document on the desk, and past projects and their documents. A two week user evaluation of the system showed interesting usage scenarios and future trends for improving user interaction.

<p>Questions have been raised about the genomic complexity of the human genome, since it was reported that it only consisted of 32,000 genes. Alternative splicing is considered the explanation of the enormous difference between the number of genes and the number of proteins. Aligning expressed sequence tags (ESTs) to the genomic sequence has become a popular approach for gene prediction, revealing alternative splice variants. The aim in this thesis is to identify and analyse splice variants of the adhesion family of G protein-coupled receptors using EST data. 75% of the genes in the data set of 33 sequences were found to have a total of 51 splice variants. About half of the variants were considered functional.</p>