DNA microarrays are widely used techniques in molecular biology and DNA computing area. Before performing the microarray experiment, a set of subsequences of DNA called probes which are complementary to the target genes of interest must be found. And its reliability seriously depends on the quality of the probe sequences. Therefore, one must carefully choose the probe set in target sequences. A new method for probe design strategy using multi-objective genetic algorithm is proposed. The proposed algorithm is able to find a set of suitable probes more efficient and uses a model based on suffix tree to speed up the specificity constraint checking. The dry dock experimental results show that the proposed algorithm finds several probes for DNA microarray that not only obey the design properties, but also have specificity.

Part I: Low complexity regions (LCRs) are common motifs in eukaryotic proteins, despite the fact that they are also mutationally unstable. For LCRs to be widely used and tolerated there must be regulatory mechanisms which compensate for their presence. I have endeavored to characterize the relationships and co-evolution of LCRs with the abundance of the proteins that host them as well as the transcripts which encode them. As the abundance of a gene product is ultimately responsible for its associated phenotype, any relationships have implications for the many neurodegenerative diseases associated with LCR expansion. I found that there are indeed relationships. LCRs are more associated with low abundance proteins, but the opposite is true at the RNA level: LCRs encoding transcripts have higher abundance. Investigating the co-evolution of LCRs and transcript abundance revealed that on short evolutionary timescales indels in LCRs influence the selective pressures on TAb. Viewing LCRs through the previously unexplored lens of abundance has generated new results. Results which, together with explorations of information flow and low-complexity in untranslated regions, expand our knowledge of the functional impacts of LCRs evolution. Part II: A commonly encountered problem in DNA sequencing is a situation where the DNA of interest makes up a small proportion of the DNA in a sample. This challenge can be compounded when the DNA of interest may come from many different organisms. Targeted metagenomics is a set of techniques which aim to bias sequencing results towards the DNA of interest. Many of these techniques rely on carefully designed probes which are specific to targets of interest. I have developed a bioinformatic tool, HUBDesign, to design oligonucleotide probes to capture identifying sequences from a given set of targets of interest. Using HUBDesign, and other methods, I have contributed to projects ranging in context from clinical to ancient DNA. / Thesis / Doctor of Science (PhD) / This thesis describes research in two fields: repetitive protein sequences and methods for sequencing the portions of a sample in which one is most interested. In the first part I describe the general properties of repetitive proteins, establish a connection between the presence of repeats in a protein and the amount of that protein which a cell maintains, and show that these two quantities evolve together. This informs our understanding of evolution and regulation with implications for repeat related diseases and further evolutionary research. In the second part I describe a method for selecting short nucleotide sequences which can be used to capture specifically the DNA of organisms of interest, as well as applications of this and other methods. These contributions are widely applicable as targeted sequencing is useful in fields as far apart as clinical sepsis diagnosis and determining the colour of ancient animals.

Doctor of Education / Department of Special Education, Counseling and Student Affairs / James Teagarden / This study investigated the effectiveness of an early literacy program for first grade students classified as at-risk for emotional and behavioral disorders, who were nonresponsive to previous schoolwide interventions, and who performed in the bottom one-third of their class on a standardized reading assessment. This study, which consisted of a multiple-probe across intervention groups experimental design aimed to produce literacy and behavior results previously obtained by other well-known researchers. Results indicated growth in oral reading fluency for all five participants, in nonsense word fluency for four out of the five participants, and a decreased display of total disruptive behaviors for all. Findings reaffirm outcomes obtained in previous investigations; specifically, improved early literacy skills are concomitant with ongoing decreases in disruptive classroom behavior. Limitations are discussed and suggestions for future research are provided.

Focusing on the needs of users, design can leverage new product development process by offering insightful knowledge of those needs. This research investigates the technology development of smart homes. Design is utilised as a product research tool to identify key insights of the home life of the older adults living in the UK, and for the purpose of informing the front-end of the new product development process. The review of the literature in the field of smart homes suggests that the developments have lagged by a technology-push approach, the lack of appropriate concepts from users’ perspectives as well as the lack of development strategy, which has consequently been reflected in consumers’ reluctance towards smart homes. As a result, this doctoral research aimed to ‘develop a user-oriented product design research tool that improves the understanding of the home life of older adults.’ To achieve the aim, this research employs qualitative methodology to develop a research process that utilises the cultural probe, semi-structured interview and video tour. Informed by ethnographic tradition, this research establishes its trustworthiness and credibility by employing a thorough process of analysis (qualitative analysis with computer-assisted software NVivo 8 and peers debriefing) and evaluation (creative workshop and evaluative interview) with practitioners from the field of product design, design management and design education. The result of the field investigation is presented as ten personas and taxonomy of nodes, which form the contribution of this research, a sensitising tool and process. This research contributes a sensitising tool - a design-led, user-inspired and participatory product design research that the offers insightful knowledge of those older adults and their relationships with their homes living in the UK. This sensitising tool is developed for the smart home designers for the purpose of generating new product ideas and challenges designers’ preconception of users and smart homes, and provokes reflections on the practices of user-centred and user-participatory design, as examined in the creative workshop. In addition, this research also contributes to the growing debate surrounding the issues relating to ethnographic user research and the use of cultural probe for the design of new smart homes.

Les microorganismes, par leurs fascinantes capacités d’adaptation liées à l’extraordinaire diversité de leurs capacités métaboliques, jouent un rôle fondamental dans les tous les processus biologiques. Ils interviennent notamment au niveau des changements globaux, comme le réchauffement climatique, en partie occasionné par les émissions croissantes de méthane dans l’atmosphère, mais également par les pollutions résultant de la dispersion de molécules comme les Hydrocarbures Aromatiques Polycycliques. Ainsi, les communautés microbiennes vont participer à réduire ou à augmenter les effets délétères de l’anthropisation des écosystèmes. La régulation des changements globaux passe donc par une meilleure connaissance de ces communautés qui doivent être explorées dans leur globalité au sein des environnements. Néanmoins en raison de leur forte complexité, une telle exploration n’est possible qu’en utilisant des outils d’analyse haut-débit. Cependant, l’emploi d’outils moléculaires à haut-débit comme les biopuces à ADN passe par la détermination de sondes combinant à la fois une forte sensibilité, une très bonne spécificité et un caractère exploratoire. Pour concevoir de telles sondes un nouveau logiciel KASpOD a donc été développé. De même, en utilisant des sondes présentant les mêmes caractéristiques, le développement d’une nouvelle approche innovante en écologie microbienne de capture de gènes en solution été entrepris. Cette nouvelle méthode d’enrichissement de gènes d’intérêt couplée à du séquençage haut-débit a été appliquée pour l’exploration des communautés méthanogènes du lac Pavin. Les résultats obtenus montrent la pertinence de l’approche qui assure une meilleure évaluation de diversité de l’écosystème avec notamment l’identification de populations appartenant à la biosphère rare. L’autre ajout majeur de cette approche est qu’elle autorise l’identification de grandes régions d’ADN génomique exploitable pour caractériser de nouveaux gènes ou de nouveaux processus adaptatifs. / Microorganisms play a crucial role in all biological processes related to their huge metabolic potentialities. They are involved in global changes such as global warming partially caused by the growing methane emissions in the atmosphere, but also by the release of pollutants such as Polycyclic Aromatic Hydrocarbons. Thus, microbial communities will contribute to reduce or increase the negative effects of human impacts on ecosystems. The regulation of global changes needs a better knowledge of the microbial communities involved in complex environments functioning. Nevertheless, a complete exploration of such environments requires the use of high-throughput tools, due to the extraordinary diversity of microorganisms within the ecosystems. The use of DNA microarrays requires a probe design step allowing the selection of highly sensitive, specific and explorative oligonucleotides. For this purpose, we have developed KASpOD, a new software, allowing the generation of efficient probes dedicated to environmental applications. Using high quality probe sets, an innovative in solution-based gene capture method combined with Next Generation Sequencing, was developed and applied for the exploration of the methanogen communities in lake Pavin, Results showed the relevance of this approach that allows a better evaluation of the methanogen diversity with an efficient detection of populations belonging to the rare biosphere. The other main advantage of this approach is the identification of large regions of genomic DNA, useful for the characterization of new genes or adaptive processes.

As the area of nucleic acid based technologies develops, so will our understanding of how structural variations in DNA and RNA pathogens are associated with disease. The overall goal of this thesis is the development of broadly targeted measurement techniques for variable viral RNA by Real-Time PCR (here referred to as quantitative reverse transcriptase PCR, QRT-PCR). In papers I & II, broadly targeted and specific QRT-PCRs were used to study expression of endogenous and exogenous betaretrovirus sequences in human tissues. Results from human tissues demonstrated endogenous betaretrovirus expression in a tissue-specific manner, highest in reproductive tissues. Despite the high sensitivity, no exogenous betaretrovirus was found in human breast cancer samples. The limits of primer and probe degeneracy for detection of a diverse set of retroviral sequences was evaluated. These methods are useful for further investigations on the pathophysiological contribution(s) of endogenous betaretrovirus and to investigate whether an exogenous betaretrovirus is involved in human breast cancer. In papers III & IV, we developed and applied broadly targeted one-step QRT-PCRs for influenza viruses and coronaviruses. In addition to the generic primers, two novel probe design strategies were used in order to be able to broadly amplify these diverse sets of viruses: A triplex system for simultaneous detection and quantification of influenza A, B and C (3QRT-PCR and further developed 3QRT-PCR-MegB; where MegB stands for MegaBeacon) based on TaqMan® and MegB probes, and a pan-CoV QRT-PCR, based on three TaqMan® probes i.e., degeneracy was distributed on three probes. Probe fault tolerance was thus increased in two ways, either with short probes with/without locked nucleic acid (LNA) nucleotides concentrated to conserved stretches, or with long probes (MegB), compensating mismatching positions with many matching ones. Clinical samples, negative by antigen detection with immunofluorescence (IFA), were influenza A positive with 3QPCR-MegB. Avian pooled samples, negative with an earlier pan-CoV QPCR, came out positive with the triple-probe system. Assay evaluation with clinical samples and reference strains revealed good clinical diagnostic potential. Thus, the thesis describes several strategies to counteract sequence variation of RNA viruses and describes a set of broadly targeted QRT-PCRs useful for scientific screening or diagnostics of betaretroviruses and respiratory viruses.

This study was done to evaluate the simultaneous prompting procedure when teaching math skills during play time to young children with disabilities. The research included 5 students who participated in a special education resource classroom and general education classroom. The researcher used a design similar to a multiple probe design. The study found all participants who began intervention met criterion. The research also found students who participated in maintenance and generalization met criterion during those stages.

Five elementary age students with moderate to severe intellectual disabilities were taught shape identification. A multiple probe design across behaviors, replicated across participants, was used to determine the effectiveness of constant time delay to determine the effectiveness of Constant Time Delay to teach shapes. Nontarget information was included in praise statements. All students met criterion on target information of shape identification. All students increased their ability to identify shape words, spell shape words, tell the number of sides of the shapes when presented and tell the number of angles of shapes presented. Generalization occurred during daily walks through the school and community as well as during the probe sessions.

This thesis deals with design of an eddy current transducer which enables non-destructive inspection of composite aircraft structures primarily carbon fiber reinforced plastic (CFRP) in areas of manufacture and maintenance. The design of the transducer is based on analytical-experimental approach and its electrical and mechanical parameters were optimized to ensure a good signal to noise ratio at the six composite samples. These samples contain artificial discontinuities in the form of various types of defects. These defects are simulating the various types of damage created in the aircraft structure, especially delamination or thickness changes of composite materials. The experimental measurements, data collection and non-destructive evaluation were performed during the period. The result of this work is functional eddy current probe, which is reliably able to detect some damage of the carbon composite structures to the depth of 3,9 mm.

This thesis deals with design of an eddy current transducer which enables non-destructive inspection of composite aircraft structures primarily carbon fiber reinforced plastic (CFRP) in areas of manufacture and maintenance. The design of the transducer is based on analytical-experimental approach and its electrical and mechanical parameters were optimized to ensure a good signal to noise ratio at the six composite samples. These samples contain artificial discontinuities in the form of various types of defects. These defects are simulating the various types of damage created in the aircraft structure, especially delamination or thickness changes of composite materials. The experimental measurements, data collection and non-destructive evaluation were performed during the period. The result of this work is functional eddy current probe, which is reliably able to detect some damage of the carbon composite structures to the depth of 3,9 mm.