There are around 20.000 genes in the human genome all of which could potentially be expressed. However, it is obvious that not all of them can be active at the same time. Thus, there is a need for coordination achieved through the regulation of transcription. Transcriptional regulation is a crucial multi-component process involving genetic and epigenetic factors, which determine when and how genes are expressed. The aim of this thesis was to study two of these components, the transcription factors and the DNA sequence elements with which they interact. In papers I and II, we tried to characterize the regulatory role of repeated elements in the regulatory sequences of nitric oxide synthase 2 gene. We found that this type of repeat is able to adopt non B-DNA conformations in vitro and that it binds nuclear factors, in addition to RNA polymerase II. Therefore it is probable that these types of repeats can participate in the regulation of genes. In papers III-V, we intended to analyze the genome-wide binding sites for six transcription factors involved in fatty acid and cholesterol metabolism and the sites of an epigenetic mark in a human liver cell line. For this, we applied the chromatin immunoprecipitation (ChIP) method together with detection on microarrays (ChIP-chip) or by detection with the new generation massively parallel sequencers (ChIP-seq). We found that all of these transcription factors are involved in other liver-specific processes than metabolism, for example cell proliferation. We were also able to define two sets of transcription factors depending on the position of their binding relative to gene promoters. Finally, we demonstrated that the patterns of the epigenetic mark reflect the structure and transcriptional activity of the promoters. In conclusion, this thesis presents experiments, which moves our view from genetics to genomics, from in vitro to in vivo, and from low resolution to high resolution analysis of transcriptional regulation.

Regulation of transcription is a central mechanism in all living cells that now can be investigated with high-throughput technologies. Data produced from such experiments give new insights to how transcription factors (TFs) coordinate the gene transcription and thereby regulate the amounts of proteins produced. These studies are also important from a medical perspective since TF proteins are often involved in disease. To learn more about transcriptional regulation, we have developed strategies for analysis of data from microarray and massively parallel sequencing (MPS) experiments. Our computational results consist of methods to handle the steadily increasing amount of data from high-throughput technologies. Microarray data analysis tools have been assembled in the LCB-Data Warehouse (LCB-DWH) (paper I), and other analysis strategies have been developed for MPS data (paper V). We have also developed a de novo motif search algorithm called BCRANK (paper IV). The analysis has lead to interesting biological findings in human liver cells (papers II-V). The investigated TFs appeared to bind at several thousand sites in the genome, that we have identified at base pair resolution. The investigated histone modifications are mainly found downstream of transcription start sites, and correlated to transcriptional activity. These histone marks are frequently found for pairs of genes in a bidirectional conformation. Our results suggest that a TF can bind in the shared promoter of two genes and regulate both of them. From a medical perspective, the genes bound by the investigated TFs are candidates to be involved in metabolic disorders. Moreover, we have developed a new strategy to detect single nucleotide polymorphisms (SNPs) that disrupt the binding of a TF (paper IV). We further demonstrated that SNPs can affect transcription in the immediate vicinity. Ultimately, our method may prove helpful to find disease-causing regulatory SNPs.

Within manufacturing of metallic components, machining plays an important role and is of vital significance to ensure process reliability. From a cutting tool design perspective,  tool macro geometry  design  based on physics based  numerical modelling  is highly needed  that can predict chip morphology.  The chip morphology describes the chip shape geometry and the chip curl geometry. The prediction of chip flow and chip shape is vital in predicting chip breakage, ensuring good chip evacuation and lower surface roughness.  To this end, a platform where such a  numerical model’s chip morphology prediction  can be compared with experimental investigation is needed and is the focus of this work. The studied cutting processes are orthogonal cutting process and nose turning process. Numerical models that simulate the chip formation process are employed to predict the chip morphology and are accompanied by machining experiments. Computed tomography is used  to scan the chips obtained from machining experiments and its ability to capture the variation in  chip morphology  is evaluated.  For nose turning process,  chip  curl parameters during the cutting process are to be calculated. Kharkevich model is utilized in this regard to calculate the  ‘chip in process’ chip curl parameters. High speed videography is used to measure the chip side flow angle during the cutting process experiments and are directly compared to physics based model predictions. The results show that the methodology developed provides  the framework where advances in numerical models can be evaluated reliably from a chip morphology prediction capability view point for nose turning process. The numerical modeling results show that the chip morphology variation for varying cutting conditions is predicted qualitatively. The results of quantitative evaluation of chip morphology prediction shows that the error in prediction is too large to be used for predictive modelling purposes.

The heterogenous nature and the demand for extensive parallel processing in modern applications have resulted in widespread use of Multicore System-on-Chip (SoC) architectures. The emerging Network-on-Chip (NoC) architecture provides an energy-efficient and scalable communication solution for Multicore SoCs, serving as a powerful replacement for traditional bus-based solutions. The key to successful realization of such architectures is a flexible, fast and robust emulation platform for fast design space exploration. In this research, we present the design and evaluation of a highly configurable NoC used in AcENoCs (Accelerated Emulation platform for NoCs), a flexible and cycle accurate field programmable gate array (FPGA) emulation platform for validating NoC architectures. Along with the implementation details, we also discuss the various design optimizations and tradeoffs, and assess the performance improvements of AcENoCs over existing simulators and emulators. We design a hardware library consisting of routers and links using verilog hardware description language (HDL). The router is parameterized and has a configurable number of physical ports, virtual channels (VCs) and pipeline depth. A packet switched NoC is constructed by connecting the routers in either 2D-Mesh or 2D-Torus topology. The NoC is integrated in the AcENoCs platform and prototyped on Xilinx Virtex-5 FPGA. The NoC was evaluated under various synthetic and realistic workloads generated by AcENoCs' traffic generators implemented on the Xilinx MicroBlaze embedded processor. In order to validate the NoC design, performance metrics like average latency and throughput were measured and compared against the results obtained using standard network simulators. FPGA implementation of the NoC using Xilinx tools indicated a 76% LUT utilization for a 5x5 2D-Mesh network. A VC allocator was found to be the single largest consumer of hardware resources within a router. The router design synthesized at a frequency of 135MHz, 124MHz and 109MHz for 3-port, 4-port and 5-port configurations, respectively. The operational frequency of the router in the AcENoCs environment was limited only by the software execution latency even though the hardware itself could be clocked at a much higher rate. An AcENoCs emulator showed speedup improvements of 10000-12000X over HDL simulators and 5-15X over software simulators, without sacrificing cycle accuracy.

Dieser Vortrag stellt einen neuartigen Prüfstand vor, mit welchem das Chip & Cut Verhalten von Elastomeren charakterisiert werden kann. Sowohl theoretischer Hintergrund als auch praktische Erkenntnisse werden diskutiert. Die Vorstellung der Praxisrelevanz dieser Untersuchungen steht im Fokus des Vortrags.

Indiana University-Purdue University Indianapolis (IUPUI) / Immune response enables the body to resist foreign invasions. The Inflammatory response is an important aspect in the immune response which is articulated by elements such as cytokines, APC, T-cell and B-cell, effector cell or natural killer. Of these elements, T-cells especially T-helper cells; a sub class of T-cells plays a pivotal role in stimulating the immune response by participating in various biological reactions such as, the transcription regulatory network. Transcriptional regulatory mechanisms are mediated by a set of transcription factors (TFs), that bind to a specific region (motifs or transcription factor binding sites, TFBS), on the target gene(s) controlling the expression of genes that are involved in T-helper cell mediated immune response. Eukaryotic regulatory motifs, referred to as cis regulatory modules (CRMs) or cistrome, co-occur with the regulated gene’s transcription start site (TSS) thus, providing all the essential components for building the transcriptional regulatory networks that depends on the relevant TF-TFBS interactions. Here, we study IL-12 stimulated transcriptional regulators in STAT4 mediated T helper 1 (Th1) cell development by focusing on the identification of TFBS and CRMs using a set of Stat4 ChIP-on-chip target genes. A region containing 2000 bases of Mus musculus sequences with the Stat4 binding site, derived from the ChIP-on-chip data, has been characterized for enrichment of other motifs and, thus CRMs. Our experiments identify some potential motifs, (such as NF-κB and PPARγ/RXR) being enriched in the Stat4 binding sequences compared to neighboring background sequences. Furthermore, these predicted CRMs were observed to be associated with biologically relevant target genes in the ChIP-on-chip data set by meaningful gene ontology annotations. These analyses will enable us to comprehend the complicated transcription regulatory network and at the same time categorically analyze the IL-12 stimulated Stat4 mediated Th1 cell differentiation.

No description available.

No description available.

Master of Science / Department of Civil Engineering / Mustaque A. Hossain / Pavement preservation by adopting low-cost maintenance techniques is increasing among transportation agencies day by day. Chip seal, also known as seal coat, is widely used as a low-cost, thin surface treatment in preventive maintenance of asphalt pavements in many states, including Kansas. Loosening of aggregate particles from chip-sealed pavement and associated windshield damage to vehicles is a common problem. Thus the Kansas Department of Transportation (KDOT) uses lightweight aggregates as cover materials for chip seals. Although this has decreased windshield damage problems extensive chip loss on seal-coated pavements in the state has been reported. In this study, lightweight aggregates along with polymer-modified asphalt emulsion were used to determine proper aggregate and emulsion application rates to minimize chip loss in chip seals. Again, lightweight aggregates were studied in the laboratory to determine the effect of moisture content and electrical charge on chip loss. Evaluation of chip seal was performed by statistical analysis based on rutting potential, chip embedment, and retention. Results show that aggregate retention and embedment depth depend on aggregate-emulsion interaction, whereas rutting depends on the type of aggregate. Proper selection of aggregate and asphalt emulsion is important to maximize aggregate retention in chip seal. Chip loss also results from a lack of compatibility between the aggregate and asphalt emulsion. Results indicate that retention of aggregate depends on the prevailing charges of aggregate and emulsion particles. Moisture condition of the aggregate does not have any effect on chip loss. A new sweep test machine has been developed to assess chip loss, and it was found to be better than the sweep test currently recommended by the American Society for Testing and Materials (ASTM).

Lors de la phase haploïde de la spermatogenèse (spermiogenèse) des mammifères, un important remodelage de la chromatine est nécessaire à la compaction de l'ADN. Au cours de ce remodelage, les histones sont remplacées successivement par les protéines de transition, puis finalement par les protamines. Ce processus implique une succession encore peu connue de modifications post-traductionnelles des histones telles que l'acétylation et la méthylation.Lors de récents travaux, notre laboratoire a montré des évidences suggérant que l'hyperacétylation de l'histone H4 (H4h) semble impliquée dans ce remaniement de la chromatine et fournirait un contexte favorable à l'apparition de cassures de l'ADN. Puisque le contexte chromatinien d'une spermatide diffère de celui d'une cellule somatique, la mise au point de techniques pouvant établir la distribution de H4h dans cette cellule germinale haploïde serait un atout précieux pour établir l'association de cette modification post-traductionnelle à la formation des cassures. Ce mémoire présente ainsi une démarche bipartite visant la mise au point d'approches microscopiques de même que le développement d'une approche d'immunoprécipitation de la chromatine pouvant s'appliquer à la chromatine particulière des spermatides. Grâce à la mise au point de la technique d'immunoprécipitation de la chromatine combinée à l'utilisation de biopuces d'ADN (ChIP-on-chip), nous tentons d'établir la cartographie de H4Ac sur une portion du chromosome X utilisé en guise de sentinelle. Avec la cartographie simultanée de [gamma]-H2AX (H2AFX) en tant que marqueur des cassures bicaténaires de l'ADN, nous tentons de vérifier, au niveau moléculaire, l'hypothèse d'une relation entre l'hyperacétylation des histones et l'apparition des cassures dans les spermatides allongeantes. La compréhension de la formation des cassures est importante puisque la réparation de l'ADN, dans cette cellule haploïde, ne peut compter sur la recombinaison homologue; l'instabilité génétique associée à ce phénomène pourrait fournir l'étiologie d'anomalies génétiques idiopathiques associées au développement de l'embryon. A l'aide d'anticorps couplés à des billes d'or, la microscopie électronique nous permet d'obtenir les premiers résultats d'une double détection de l'histone H4 hyperacétylée et des cassures de l'ADN au sein des noyaux des cellules germinales de la spermatogenèse. Les travaux d'immunoprécipitation de la chromatine dévoilent une répartition hétérogène de l'hyperacétylation de l'histone H4 au niveau du chromosome X, suggérant que l'hyperacétylation du génome lors de la spermiogenèse est progressive. Nous démontrons aussi qu'il existe une interaction entre cette chromatine et le variant d'histone [gamma]-H2AX. Les différences entre les patrons de distribution des deux histones ne permettent pas d'établir si l'hyperacétylation de la chromatine serait à l'origine du dépôt de [gamma]-H2AX, par le biais des cassures double brin.