<p>Today’s rapid development of powerful tools for geneexpression analysis provides unprecedented resources forelucidating complex molecular events.</p><p>The objective of this workhas been to apply, combine andevaluate tools for analysis of differential gene expressionusing atherosclerosis as a model system. First, an optimisedsolid-phase protocol for representational difference analysis(RDA) was applied to two<i>in vitro</i>model systems. Initially, The RDA enrichmentprocedure was investigated by shotgun cloning and sequencing ofsuccessive difference products. In the subsequent steps,combinations of RDA and microarray analysis were used tocombine the selectivity and sensitivity of RDA with thehigh-throughput nature of microarrays. This was achieved byimmobilization of RDA clones onto microarrays dedicated forgene expression analysis in atherosclerosis as well ashybridisation of labelled RDA products onto global microarrayscontaining more than 32,000 human clones. Finally, RDA wasapplied for the investigation of the focal localisation ofatherosclerotic plaques in mice using<i>in vivo</i>tissue samples as starting material.</p><p>A large number of differentially expressed clones wereisolated and confirmed by real time PCR. A very diverse rangeof gene fragments was identified in the RDA products especiallywhen they were screened with global microarrays. However, themicroarray data also seem to contain some noise which is ageneral problem using microarrays and should be compensated forby careful verification of the results.</p><p>Quite a large number of candidate genes related to theatherosclerotic process were found by these studies. Inparticular several nuclear receptors with altered expression inresponse to oxidized LDL were identified and deserve furtherinvestigation. Extended functional annotation does not liewithin the scope of this thesis but raw data in the form ofnovel sequences and accession numbers of known sequences havebeen made publicly available in GenBank. Parts of the data arealso available for interactive exploration on-line through aninteractive software tool. The data generated thus constitute abase for new hypotheses to be tested in the field ofatherosclerosis.</p><p><b>Keywords:</b>representational difference analysis, geneexpression profiling, microarray analysis, atherosclerosis,foam cell formation</p>

<p>Renewable fibers produced by forest trees provide excellentraw material of high economic value for industrialapplications. Despite this, the genes and corresponding enzymesinvolved in wood fiber biosynthesis in trees are poorlycharacterized. This thesis describes a functional genomicsapproach for the identification of carbohydrate-active enzymesinvolved in secondary cell wall (wood) formation in hybridaspen.</p><p>First, a 3' target amplification method was developed toenable microarray-based gene expression analysis on minuteamounts of RNA. The amplification method was evaluated usingboth a smaller microarray containing 192 cDNA clones and alarger microarray containing 2995 cDNA clones that werehybridized with targets isolated from xylem and phloem.Moreover, a gene expression study of phloem differentiation wasperformed to show the usefulness of the amplificationmethod.</p><p>A microarray containing 2995 cDNA clones representing aunigene set of a cambial region EST library was used to studygene expression during wood formation. Transcript populationsfrom thin tissue sections representing different stages ofxylem development were hybridized onto the microarrays. It wasdemonstrated that genes encoding lignin and cellulosebiosynthetic enzymes, as well as a number of genes withoutassigned function, were differentially expressed across thedevelopmental gradient.</p><p>Microarrays were also used to track changes in geneexpression in the developing xylem of transgenic, GA-20 oxidaseoverexpressing hybrid aspens that had increased secondarygrowth. The study revealed that a number of genes encoding cellwall related enzymes were upregulated in the transgenic trees.Moreover, most genes with high transcript changes could beassigned a role in the early events of xylogenesis.</p><p>Ten genes encoding putative cellulose synthases (CesAs) wereidentified in our own<i>Populus</i>ESTdatabase. Full length cDNA sequences wereobtained for five of them. Expression analyses performed withreal-time PCR and microarrays in normal wood undergoingxylogenesis and in tension wood revealed xylem specificexpression of four putative CesA isoenzymes.</p><p>Finally, an approach combining expressionprofiling,bioinformatics as well as EST and full length sequencing wasadopted to identify secondary cell wall related genes encodingcarbohydrate-active enzymes, such as glycosyltransferases andglycoside hydrolases. As expected, glycosyltransferasesinvolved in the carbohydrate biosynthesis dominated thecollection of the secondary cell wall related enzymes that wereidentified.</p><p><b>Key words:</b>Populus, xylogenesis, secondary cell wall,cellulose, hemicellulose, microarrays, transcript profiling,carbohydrate-active enzyme, glycosyltransferase, glycosidehydrolase</p>

<p>Forest biotechnology is a fast emerging field of research. The application of biotechnological tools will enhance the quality of the forest products. The resultant value added and environmentally sustainable products are an absolute necessity in the future. The study of wood biosynthesis and degradation will result in enormous knowledge resources, which can be used for exploiting wood properties. This thesis addresses questions representing both wood degradation and biosynthesis.</p><p>The wood degrading fungus <i>Phanerochaete chrysosporium</i> is expression profiled with the microarray technology. The objective is to understand the expression pattern of the extracellular carbohydrate active enzymes (CAZymes) secreted by the organism. The data obtained increases our understanding of gene expression upon growth on cellulose.</p><p>Wood biosynthesis is studied with the model wood forming tree species, <i>Populus</i>. The plentiful data resources from the expression profiling during wood formation in Populus are used as the platform of this work. One of the wood specific genes, <i>PttMAP20</i>, previously with an unknown function is studied in this thesis. The immunolocalisation of PttMAP20 with specific antibodies is demonstrated. The putative microtubule-targeting domain of the protein is demonstrated microscopically and by using a biochemical binding assay. </p>

Diss. (sammanfattning) Stockholm : Karolinska institutet, 2009.

Thesis (Ph. D.)--University of Washington, 2003. / Vita. Includes bibliographical references (leaves 178-195).

Les nouvelles technologies introduisent de nouveaux problèmes et risques. Par exemple, les internautes sont constamment tracés et profilés sur l'Internet. Ce profilage permet aux divers sites de personaliser et ainsi d'améliorer le service qu'ils fournissent à chaque internaute. Cependant ce profilage introduit aussi des problèmes d'intimité et de protection de la vie privée. Il est d'ailleurs reconnu que ces données personnelles sont souvent échangées, voire vendues, et qu'il existe une vraie economie des données personnelles. Cet thèse étudie comment ces données personnelles, et en particulier les historique Web - c'est à dire la liste des sites Internet visités par un internaute-, sont collectées, échangées et vendues. Elle propose une analyse de la vie privée des systèmes de vente aux enchères des publicités ciblés. Elle montre comment les différents acteurs de la publicité en ligne collectent et s'echangent les données personnelles, et étudie les risques pour les Internautes. Elle propose également une analyse économique et montre, notamment, que les données sont bradées pour quelques millièmes de dollars. / New medias introduce new problems and risks. There are important security and privacy considerations related to online interactions. Users browsing the Web leave a constant trail of traces referring to their Web actions. A large number of entities take advantage of this data to constantly improve how the Web services function, often offering rich personalization capabilities -- to achieve this, user data is needed. To obtain user data, Web users are being tracked and profiled. Having user data may help enhancing functionality and usability, but it also has the potential of introducing complex privacy problems, related to data collection, storing and processing. The incentives to gather user data are of economical nature: user data is monetized. We start with a description of privacy problems and risks, highlighting their roots in technology changes; users must constantly struggle to adapt to changes. The legal frameworks relating to privacy are about to change: Web companies will have to adopt to new realities. First part of this thesis is devoted to measuring the consequences of private data leaks and tracking. We show how Web browsing history convey insight relating to user interests. We study the risks of Web browsing history leaks. We point out that browsing history is to large extent unique; we perform this basing on a dataset of more than 350k partial history fingerprints. The consequence here is that if browsing histories are personally identifiable information (PII), the upcoming European privacy legal frameworks could potentially result in strict guidelines for their collection, storing and processing. The tracking measurement of third-party resources confirms the popular notion that most of the tracking is carried by US-based companies. This creates interesting information asymmetries, which are of great importance, especially if user data could be simply equated to financial and economical benefits. Second part discusses value of privacy. We study the emerging technology of Real-Time Bidding (RTB), online real-time auctions of ad spaces. We highlight that during the auction phase, bidders in RTB obtain user information such as the visited Web site or user location and they pay for serving ads. In other words, user data flows are strictly related to financial flows. User data is thus monetized. We expose an interesting design characteristic of RTB which allows us to monitor a channel with winning bids -- dynamically established fees bidders pay for displaying their ads. We perform a detailed measurement of RTB and study how this price for user information varies according to such aspects like time of day, user location and type of visited Web site. Using data obtained from real users, we also study the effect of user profiles. Users are indeed treated differently, based on their previously visited Web sites (browsing history). We observed variability in prices of RTB ads, based on those traits. The price for user information in RTB is volatile and typically is in the range of $0.0001-$0.001. This study also had a decidedly important transparency part. We introduced a Web browser extension allowing to discover the price that bidders in RTB pay. This demonstrates how the user awareness could be improved. In part three, we continue the transparency trail. We point out that Web browsers allow every Web site (or third-party resources they include) to record the mouse movements of their visitors. We point out that recent advances in mouse movement analysis points to the notion that mouse movements can potentially be used to recognize and track Web users across the Web; mouse movement analysis can also be used to infer users' demographics data such as age. We highlight the existence of mouse movement analytics -- third-party scripts specializing in mouse movement collections. We also suggest that Web browser vendors should consider including permissions for accessing the API enabling these kind of recordings.

A theoretical framework describing the carbon nanotubes interaction, involving two distinct approaches, is presented. Based on the results obtained practical applications using carbon nanotubes are further proposed. First a classical approach is employed for different geometrical configurations, such as parallel or concentric carbon nanotubes. For all the cases analytical expressions for the systems potential energies are derived. The results obtained using the classical approach are used to propose a few practical applications. These applications include a non-contact device for profiling surfaces and a custom telescopic double wall carbon nanotube for nanolithography applications. It is expected that such devices can be effectively used with major advantages. Next the interaction between nanotubes is considered using a quantum electrodynamics approach suitable for dispersing and absorbing media. Each carbon nanotube is characterized by its individual full dielectric response. The method also allows taking into account the full carbon nanotube cylindrical geometry by imposing the appropriate boundary conditions at the nanotubes surfaces. It is found that at small nanotube separations, similar to their equilibrium distances, the interaction is dominated by the collective excitations in the electron energy loss spectra originating from interband transitions. Furthermore, it is shown that the collective surface excitations and their chirality dependent characteristics play a profound role in the interaction strength in double wall carbon nanotube systems. The obtained results are in good agreement with experimental measurements on determining the chirality of individual double wall carbon nanotubes

Polymeric waveguide-on-flex has the potential to replace complex and costly light-turning devices in optoelectronic applications. As light signals are propagated and confined through the definition of core-cladding interface, the light guiding structure is required to adhere well and ensure long term interfacial stability. This thesis addresses the gap that has emerged in the fundamental material issues such as the polymeric optical waveguide materials deposited on the flexible substrates. In addition, this thesis investigates the feasibility of a new approach using electrostatic-induced lithography in micro-patterning of polymer, in optical waveguide fabrication. Plasma treatment is applied to enhance interfacial adhesion between flex substrates and optical cladding layers. The modified flex surfaces of polyimide KaptonHNTM and liquid crystal polymer VecstarTM materials are characterised. In addition, sonochemical surface treatment is evaluated on these flexible substrates. ToF-SIMS depth profiling has confirmed the interface reaction mechanisms where it has shown that plasma treatment increases the interfacial interpenetration. The larger interfacial width increases the possible entanglement mechanism between the polymer chains. These results, together with the double cantilever beam testing, indicate the strengthening of the polymeric interface upon plasma treatment, which is essential for long term optical and mechanical stability of waveguide-on-flex applications. A new method of micro-pattering of polymer material has been adopted for fabricating multimode waveguide-on-flex. The method, using an electrostatic-induced lithography, is developed to produce 50 μm x 50 μm arrays of polysiloxane LightlinkTM waveguide on flex. This thesis looks at various process recipes of the technique and reports the pattern formation of polymeric optical core. By adjusting the spin-coated liquid core thickness, pre-bake condition, UV exposure and applied voltage, the aspect ratio and profile of the optical core microstructure can be varied. As the electrostatic pressure overcoming the surface tension of spin-coated waveguide material induces the optical core formation, the core structure is smooth, making it ideal for low scattering loss waveguide. The propagation loss of fabricated waveguide is measured at 1.97 dB/cm at 850 nm wavelength. The result shows that the use of electrostatic-induced lithography in optical polymer is a promising approach for low cost and low temperature (<150 °C) processing at back end optical-electrical integrated circuitry assembly.

The main approach to studying the proteome is a technique called data dependent acquisition (DDA). In DDA, peptides are analyzed by mass spectrometry to determine the protein composition of a biological isolate. However, DDA is limited in its ability to analyze the proteome, in that it only selects the most abundant ions for analysis, and different protein identifications can result even if the same sample is analyzed multiple times in succession. Data independent acquisition (DIA) is a newly developed method that should be able to solve these limitations and improve our ability to analyze the proteome. We used an implementation of DIA (SWATH) to perform relative protein quantitation in the model bacterial system, Clostridium stercorarium, using two different carbohydrate sources, and found that it was able to provide precise quantitation of proteins and was overall more consistent in its ability to identify components of the proteome than DDA. Relative quantitation of proteins is an important method that can determine which proteins are important to a biochemical process of interest. How we determine which proteins are differentially regulated between different conditions is an important question in proteomic analysis. We developed a new approach to analyzing differential protein expression using variation between biological replicates to determine which proteins are being differentially regulated between two conditions. This analysis showed that a large proportion of proteins identified by quantitative proteomic analysis can be differentially regulated and that these proteins are in fact related to biological processes. Analyzing changes in protein expression is a useful tool that can pinpoint many key processes in biological systems. However, these techniques fail to take into account that enzyme activity is regulated by other factors than controlling their level of expression. Activity based protein profiling (ABPP) is a method that can determine the activity state of an enzyme in whole cell proteomes. We found that enzyme activity can change in response to a number of different conditions and that these changes do not always correspond with compositional changes. Mass spectrometry techniques were also used to identify serine hydrolases and characterize their expression in this organism. / February 2016

This study examined how mainstream and black press newspapers framed the phenomena of "racial profiling" three years before and three years after the September 11 terrorist attacks. It looked particularly at frames, ethnic groups, source selection and article emphasis. Results indicate that even in the face of a tragedy, black press reporters did not waiver in their position and continued to cover issues from a "black perspective." On the other hand, mainstream newspapers altered their coverage during the high-stress period and began to portray racial profiling as an anti-Arab/terrorist tactic that is acceptable in some cases. This study helps answer the question of whether black press newspapers are necessary in today's society. The answer is yes. They still carry a unique viewpoint. Until the gap that divides African American and other readers ceases to exist, the black press will remain an important staple in the black community. / text