Die Deregulation des Transkriptionsfaktors Myc ist ein charakteristisches Merkmal für eine Vielzahl von humanen Tumoren. Durch die transkriptionelle Aktivierung von Genen, die im Zusammenhang mit Metabolismus, Translation und Proliferation stehen, wird dadurch das Tumorwachstum begünstigt. Myc bildet zudem mit dem Zinkfinger-Protein Miz1 einen Komplex, der hemmend auf die Transkription von Zielgenen wirkt. Bisher sind nur wenige Myc/Miz1-reprimierte Zielgene bekannt. In der vorliegenden Arbeit konnten genomweit die DNA-Bindestellen von Myc und Miz1 durch Chromatin-Immunpräzipitationen gefolgt von Hochdurchsatzsequenzierung in einer Zervixkarzinomzelllinie bestimmt werden. Es konnte gezeigt werden, dass Myc an Promotoren aller drei RNA-Polymerasen sowie in enhancer-Regionen bindet, während Miz1 Kernpromotoren von RNA-Polymerase II- und III-transkribierten Genen besetzt. reChIP-Experimente zeigten, dass Myc und Miz1 als Komplex an Promotoren von Zielgenen binden. Zudem wurde ein Miz1-DNA-Bindemotiv identifiziert und der transaktivierende Einfluss von Miz1 auf Gene mit diesem Motiv nachgewiesen. Das überwiegende Vorhandensein von Myc/Max-Komplexen führt zu einer Transaktivierung von E-Box-haltigen Promotoren. Andererseits erfolgt die transkriptionelle Repression von Myc/Miz1-Zielgenen an Promotoren, an denen der Myc/Miz1-Komplex vorherrscht. In aktuellen Publikationen konnte gezeigt werden, dass nach mitogener Stimulation von Lymphozyten es zu einer Erhöhung der Myc-Expression kommt, wodurch Myc als ein genereller Transkriptionsaktivator fungiert, der alle Gene gleichermaßen induziert. Trotz hoher Myc-Mengen in Tumorzellen konnte die generelle Myc-vermittelte Transaktivierung nicht nachgewiesen werden. Zusätzlich zur Myc-abhängigen Transaktivierung von E-Box-haltigen Genen, z. B. beteiligt an Translation und RNA-Prozessierung, und der Miz1-vermittelten transkriptionellen Aktivierung von Genen mit Miz1-Motiv (z. B. involviert in Autophagie), konnte entgegen dem Modell der generellen Genamplifikation durch Myc eine Myc/Miz1-abhängige Repression von Zielgenen belegt werden. Die neu gewonnenen Erkenntnisse des Bindeverhaltens des Myc/Miz1-Komplexes und der daraus resultierenden transkriptionellen Regulation von Myc/Miz1-Zielgenen ermöglichen ein besseres Verständnis der Myc-Funktion in Tumorzellen und könnte zur Verbesserung von Tumortherapien führen. / Deregulation of the transcription factor Myc is a characteristic feature of a variety of human tumors. The Myc-dependent transcriptional activation of genes involved in metabolism, translation and proliferation therefor promotes tumor growth. Additionally, Myc forms a complex with the zinc finger protein Miz1, which represses transcription of target genes. So far, only a limited number of Myc/Miz1-repressed genes is known. Within the present thesis DNA binding sites of Myc and Miz1 were mapped genome-wide using chromatin immunoprecipitations followed by high-throughput sequencing in a cervical cancer cell line. It could be shown that Myc binds to promoters of all three RNA polymerases as well as to enhancer regions, whereas Miz1 binding sites could be found only in core promoters of RNA polymerase II and III transcribed genes. reChIP experiments illustrated binding of Myc and Miz1 as a complex on DNA. Additionally, a DNA binding motif of Miz1 was identified and furthermore it was possible to verify the transctivating influence of Miz1 on genes carrying that motif in the promoter. On E-box containing promoters the predominantly existence of Myc/Max complexes resulted in transactivation of the respective genes. Otherwise, transcriptional repression of Myc/Miz1 target genes occured at promoters where the Myc/Miz1 complex dominates. Recent publications have illustrated that after mitogenic stimulation of primary lymphocytes, Myc expression is enhanced, whereby Myc serves as a general transcriptional activator that induces the expression of virtually all genes. Although Myc levels are high in tumor cells that general mechanism of Myc-mediated transactivation could not be verified. Additionally to the Myc-dependent transactivation of E-box-containing genes, e. g. involved in translation and RNA processing, and Miz1-mediated transcriptional activation of genes containing a Miz1 binding motif (e. g. autophagy-related genes), and in opposition to the general amplifier model a Myc/Miz1-dependent repression of target genes could be proven. The obtained evidences concerning DNA binding properties of the Myc/Miz1 complex as well as the resulting transcriptional regulation of Myc/Miz1 target genes facilitates a better understanding of Myc function in tumor cells and could leed to better anti-tumor therapies.

Cette thèse a pour objectif de développer une méthode électrochimique permettant de cribler à haut débit des inhibiteurs d'enzymes. Pour cela, une enzyme cible a été sélectionnée pour son intérêt thérapeutique, la transcétolase (TK) : elle est impliquée dans de nombreuses pathologies (cancer, maladies neurodégénératives, diabète…) et dans la survie de certains parasites pathogènes. Afin de mesurer l'activité de la TK, deux systèmes rapporteurs ont été développés, à l'aide de plaques de criblage électrochimique (PCE) constituées de 96 électrodes indépendantes. Le premier système rapporteur repose sur un système bienzymatique nécessitant l'intervention d'une enzyme auxiliaire, la galactose oxydase (GAOx) sous forme libre ou immobilisée dans la laponite. Cette enzyme est capable d'oxyder les produits de réaction de la TK et de produire du peroxyde d'hydrogène. Le format 96 des PCE a permis d'optimiser rapidement la détection électrochimique par ampérométrie pulsée par intermittence (IPA) d'activité oxydase et seulement 10 minutes sont nécessaires pour réaliser 96 mesures simultanées. Parallèlement, afin d'exploiter au maximum le système à 96 électrodes, cette détection d'activité oxydase a également été réalisée, en 10 minutes par électrochimiluminescence. Cette méthode offre l'avantage d'être plus sensible et moins variable que par IPA, mais limite l'utilisation de matrice d'immobilisation d'enzymes. La GAOx a ensuite été utilisée pour mesurer l'activité TK, cependant, les conditions réactionnelles n'étant pas optimales en présence du système bienzymatique (TK-GAOx), des temps d'incubation longs sont nécessaires et sont peu adaptées au criblage d'inhibiteurs de la TK. Un second système rapporteur ne nécessitant plus d'enzyme auxiliaire et faisant intervenir uniquement un seul substrat de la TK a été optimisé. Ce système repose sur l'oxydation de l'intermédiaire réactionnel formé par la fixation du cofacteur (la thiamine pyrophosphate) et du substrat sur l'enzyme par le ferricyanure. Cette méthode permet de mesurer 96 activités TK en seulement 7 minutes et a aisément été utilisée pour cribler une bibliothèque de molécules. Le criblage de 1360 molécules a permis d'identifier un nouvel inhibiteur de cet enzyme, présentant une CI50 de 63 μM. Le système électrochimique a également été utilisé pour déterminer le mécanisme d'inhibition (non compétitive pure partielle) et la constante d'inhibition associée (3,4 μM). Ces résultats sont inédits dans le domaine de l'électrochimie et offrent un large éventail d'applications que ce soit pour le criblage d'activité enzymatiques ou d'inhibiteurs d'enzymes / This thesis focuses on the development of a new electrochemical method allowing the high throughputscreening of enzyme inhibitors. For this purpose, a target enzyme has been selected for its therapeutic interest,transketolase (TK): this enzyme is involved in many diseases (cancer, neurodegenerative diseases, diabetes ...) and inthe survival of pathogenic parasites. To measure TK activity, two reporter systems have been developed by usingelectrochemical plates, composed of 96 independent electrodes.The first one is based on a bienzymatic system, requiring the use of an auxiliary enzyme, galactose oxidase(GAOx), in its soluble form or immobilized in laponite. This enzyme is able to oxidize TK products and producehydrogen peroxide. The 96-well format allowed to quickly optimize the electrochemical detection of oxidase activityby intermittent pulse amperometry (IPA) of oxidase activity and only 10 minutes are required to perform 96simultaneous measurements. In parallel, in order to harness the 96-well electrochemical system, this detection ofoxidase activity was also carried out in 10 minutes using electrochemiluminescence. This method is more sensitiveand less variable than IPA but is limited to the use of soluble enzymes. However, the reaction conditions are notoptimal for the bienzymatic system (TK-GAOx): long incubation times are required and are poorly adapted for thescreening of TK inhibitors.A second reporter system no longer requiring an auxiliary enzyme and involving only one TK substrate hasbeen optimized. This system relies on the oxidation by ferricyanide of the reactional intermediate resulted of thebinding of the cofactor (thiamine pyrophosphate) and the substrate. This method allows to measure 96 TK activitiesin only 7 minutes and was easily used to screen an in-house chemical library. The screening of 1360 molecules leadto the identification of a new TK inhibitor with an IC50 of 63 μM. This electrochemical system was also used todetermine the mechanism of inhibition (partial non-competitive mechanism) and the associated inhibition constant(3.4 μM). These results are innovative in the field of electrochemistry and offer a wide range of applications forenzymatic activity screening or the screening of enzymes inhibitors

<p>^{Ethernet functionality testing as a generic term used for checking connectivity,throughput and capability to transfer packets over the network. Especially in the packet-switchenvironment, Ethernet testing has become an essential part for deploying a reliable network.Over a long distance Ethernet testing parameter for analyzing network performance must havetwo devices attached and synchronized.}</p><p>Saab Microwave Systems is among the leading suppliers of radar systems developing groundbased,naval and air-borne radar systems. To ensure the correct functionality, the developerwants to verify the performance of computer network and looking for a suitable solution.</p><p>A software application is required to verify and test the functionality of the Ethernet network andto verify the functionality and performance of the TCP/IP stack of newly added node. Theprograms shall be easily ported to different operating systems and must not depend on specificproduct properties.A software application, <em>“NetBurst”</em>, is developed for Ethernet functionality testing. Theapplication is vendor and platform independent.</p><p><strong> </strong></p>

<p>We are very thirsty in terms of everything to fulfil our needs in a sophisticated way, and this leads me choose the so called master thesis titled “Multihop Concept in Cellular Systems”.</p><p>This thesis introduces an approach towards the integration of relaying or multihop scheme in the next generation of cellular networks. In a multihop cellular architecture, the users send their data to the base station via relay station or with direct communication to the base station. These relay stations can either be the nomadic, fixed at specific location or users’ mobile station (i.e. mobile relay station). The main objective of this paper is to compare the difference between the relaying network architecture with different channel bandwidth as well as their performance gain. For this we integrate the relay station into conventional cellular networks using IEEE 802.16j (One of the standard introduced relay station concept in WiMAX) OFDMA (Orthogonal Frequency Division Multiple Access is a transmission technique that is based on many orthogonal subchannels (set of carriers) that transmits simultaneously). The results show that under certain conditions the throughput and coverage of the system has been increased with the introduction of the relay station in to cellular base station zone.</p>

<p>The main objective of the reported study was to investigate how biomedical ontologies, logically structured representations of various aspects of the biomedical reality, can help researchers in analyzing experimental data. The dissertation reports two attempts to construct tools for the analysis of high-throughput experimental results using explicit domain knowledge representations. Furthermore, integrative efforts made by the community of Open Biomedical Ontologies (OBO), in which the author has participated, are reported, and a framework for consistently connecting the Gene Ontology (GO) with the Taxonomy of Species is proposed and discussed.</p>

Physical-Layer Network Coding (PNC) is a promising technique that has great potentials for improving the achievable data rates of end-to-end flows through higher packet transmission rates, thereby increasing the overall network throughput. In this thesis, we study the performance of the PNC transmission techniques for unidirectional end-to-end flows in multi-hop wireless networks, and compare it with that of the traditional transmission techniques. We first derive the bit-error rate (BER) that the PNC transmission technique achieves. Then, using the derived BER, we evaluate and quantify the achievable network throughput under both the PNC transmission technique and the traditional technique, where the network throughput is measured as the aggregate/sum of all end-to-end flows' achievable data rates in the wireless network. Using extensive simulations, we show that PNC increases the overall achievable end-to-end flow throughput in multi-hop wireless networks, especially under medium to high signal-to-noise ratios. / Graduation date: 2012

We present novel architectures for parallel-node low-density parity-check convolutional code (PN-LDPC-CC) encoders and decoders. Based on a recently introduced implementation-aware class of LDPC-CCs, these encoders and decoders take advantage of increased node-parallelization to simultaneously decrease the energy-per-bit and increase the decoded information throughput. A series of progressively improved encoder and decoder designs are presented and characterized using synthesis results with respect to power, area and throughput. The best of the encoder and decoder designs significantly advance the state-of-the-art in terms of both the energy-per-bit and throughput/area metrics. One of the presented decoders, for an Eb /N0 of 2.5 dB has a bit-error-rate of 106, takes 4.5 mm2 in a CMOS 90-nm process, and achieves an energy-per-decoded-information-bit of 65 pJ and a decoded information throughput of 4.8 Gbits/s. We implement an earlier non-parallel node LDPC-CC encoder, decoder and a channel emulator in silicon. We provide readers, via two sets of tables, the ability to look up our decoder hardware metrics, across four different process technologies, for over 1000 variations of our PN-LDPC-CC decoders. By imposing practical decoder implementation constraints on power or area, which in turn drives trade-offs in code size versus the number of decoder processors, we compare the code BER performance. An extensive comparison to known LDPC-BC/CC decoder implementations is provided.

Biological data derived from high-throughput microarrays can be transformed into finite, simple, undirected graphs and analyzed using tools first introduced by the Langston Lab at the University of Tennessee. Transforming raw data can be broken down into three main tasks: data normalization, generation of similarity metrics, and threshold selection. The choice of methods used in each of these steps effect the final outcome of the graph, with respect to size, density, and structure. A number of different algorithms are examined and analyzed to illustrate the magnitude of the effects. Graph-based tools are then used to extract putative gene networks. These tools are loosely based on the concept of clique, which generates clusters optimized for density. Innovative additions to the paraclique algorithm, developed at the Langston Lab, are introduced to generate results that have highest average correlation or highest density. A new suite of algorithms is then presented that exploits the use of a priori gene interactions. Aptly named the anchored analysis toolkit, these algorithms use known interactions as anchor points for generating subgraphs, which are then analyzed for their graph structure. This results in clusters that might have otherwise been lost in noise. A main product of this thesis is a novel collection of algorithms to generate exact solutions to the maximum clique problem for graphs that are too large to fit within core memory. No other algorithms are currently known that produce exact solutions to this problem for extremely large graphs. A combination of in-core and out-of-core techniques is used in conjunction with a distributed-memory programming model. These algorithms take into consideration such pitfalls as external disk I/O and hardware failure and recovery. Finally, a web-based tool is described that provides researchers access the aforementioned algorithms. The Graph Algorithms Pipeline for Pathway Analysis tool, GrAPPA, was previously developed by the Langston Lab and provides the software needed to take raw microarray data as input and preprocess, analyze, and post-process it in a single package. GrAPPA also provides access to high-performance computing resources, via the TeraGrid.

The concept of the gene has been constantly challenged by new discoveries in the life sciences. Recent challenging observations include the high frequency of alternative splicing events and the common transcription of non-protein-coding-RNAs (ncRNAs) from the genome. The latter has long been considered noise in biological systems. Multiple lines of evidence from genomic studies indicate that alternative splicing and ncRNA play important roles in expanding proteome diversity in eukaryotes. Here, the aim is to find the link between alternative splicing and ncRNAs by studying the expression profile of the spliceosomal snRNAs (U snRNA). Spliceosomal snRNAs are essential for pre-mRNA splicing in eukaryotes. They participate in splice site selection, recruitment of protein factors and catalyzing the splicing reaction. Because of this, both the abundance and diversity of U snRNAs were expected to be large. In our study we deeply analyzed the U snRNA population in primates using a combination of bioinformatical, biochemical and high throughput sequencing approaches. This transcriptome profiling has revealed that human, chimpanzee and rhesus have similar U snRNA populations, i.e. the vast majority of U snRNAs originate from few well-defined gene loci and the heterogeneity observed in U snRNA populations was largely due to the presence of SNPs at these loci. It seems that the gene loci that could potentially encode a significantly heterogeneous population of U snRNAs are mostly silent. Only few minority transcripts were detected in our study, and among them three U1-like snRNAs might play a role in the regulation of alternative splicing by recognizing non-canonical splicing sites. Mutations of U snRNA have been shown to impact the splicing process. Therefore, our study provides a reference to study the biological significance of SNPs in U snRNA genes and their association with diseases.

The main objective of the reported study was to investigate how biomedical ontologies, logically structured representations of various aspects of the biomedical reality, can help researchers in analyzing experimental data. The dissertation reports two attempts to construct tools for the analysis of high-throughput experimental results using explicit domain knowledge representations. Furthermore, integrative efforts made by the community of Open Biomedical Ontologies (OBO), in which the author has participated, are reported, and a framework for consistently connecting the Gene Ontology (GO) with the Taxonomy of Species is proposed and discussed.