Real-time detection of DNA hybridization and melting on oligonucleotide arrays by using optical wave guides.

The challenge of the Human Genome Project is to increase the rate of DNA sequence acquisition by two orders of magnitude to complete sequencing of the human genome by the year 2000. The present work describes a rapid detection method using a two-dimensional optical wave guide that allows measurement of real-time binding or melting of a light-scattering label on a DNA array. A particulate label on the target DNA acts as a light-scattering source when illuminated by the evanescent wave of the wave guide and only the label bound to the surface generates a signal. Imaging/visual examination of the scattered light permits interrogation of the entire array simultaneously. Hybridization specificity is equivalent to that obtained with a conventional system using autoradiography. Wave guide melting curves are consistent with those obtained in the liquid phase and single-base discrimination is facile. Dilution experiments showed an apparent lower limit of detection at 0.4 nM oligonucleotide. This performance is comparable to the best currently known fluorescence-based systems. In addition, wave guide detection allows manipulation of hybridization stringency during detection and thereby reduces DNA chip complexity. It is anticipated that this methodology will provide a powerful tool for diagnostic applications that require rapid cost-effective detection of variations from known sequences.

Desenvolvimento e caracterização do filtro óptico de interferência variável para detectores de alta resolução espectral e biossensores.

O presente trabalho está fundamentado no desenvolvimento de uma metodologia e/ou uma tecnologia de obtenção e caracterização de filtros ópticos de interferência de banda passante variável [C.M. da Silva, 2010] e de banda de corte variáveis, constituídos por refletores dielétricos multicamadas de filmes finos intercalados por cavidades de Fabry-Perot não planares com espessuras linearmente variáveis, que apresentam a propriedade do deslocamento linear da transmitância máxima espectral em função da posição, isto é, um Filtro de Interferência Variável (FIV). Este método apresenta novas e abrangentes possibilidades de confecção de filtros ópticos de interferência variável: lineares ou em outras formas desejadas, de comprimento de onda de corte variável (passa baixa ou alta) e filtros de densidade neutra variável, através da deposição de metais, além de aplicações em uma promissora e nova área de pesquisa na deposição de filmes finos não uniformes. A etapa inicial deste desenvolvimento foi o estudo da teoria dos filtros ópticos dielétricos de interferência para projetar e construir um filtro óptico banda passante convencional de um comprimento de onda central com camadas homogêneas. A etapa seguinte, com base na teoria óptica dos filmes finos já estabelecida, foi desenvolver a extensão destes conhecimentos para determinar que a variação da espessura em um perfil inclinado e linear da cavidade entre os refletores de Bragg é o principal parâmetro para produzir o deslocamento espacial da transmitância espectral, possibilitando o uso de técnicas especiais para se obter uma variação em faixas de bandas de grande amplitude, em um único filtro. Um trabalho de modelagem analítica e análise de tolerância de espessuras dos filmes depositados foram necessários para a seleção da estratégia do \"mascaramento\" seletivo do material evaporado formado na câmara e-Beam (elétron-Beam) com o objetivo da obtenção do filtro espectral linear variável de características desejadas. Para tanto, de acordo com os requisitos de projeto, foram necessárias adaptações em uma evaporadora por e-Beam para receber um obliterador mecânico especialmente projetado para compatibilizar os parâmetros das técnicas convencionais de deposição com o objetivo de se obter um perfil inclinado, perfil este previsto em processos de simulação para ajustar e calibrar a geometria do obliterador e se obter um filme depositado na espessura, conformação e disposição pretendidos. Ao final destas etapas de modelagem analítica, simulação e refinamento recorrente, foram determinados os parâmetros de projeto para obtenção de um determinado FIV (Filtro de Interferência Variável) especificado. Baseadas nos FIVs muitas aplicações são emergentes: dispositivos multi, hiper e ultra espectral para sensoriamento remoto e análise ambiental, sistemas Lab-on-Chip, biossensores, detectores chip-sized, espectrofotometria de fluorescência on-chip, detectores de deslocamento de comprimento de onda, sistemas de interrogação, sistemas de imageamento espectral, microespectrofotômetros e etc. No escopo deste trabalho se pretende abranger um estudo de uma referência básica do emprego do (FIV) filtro de interferência variável como detector de varredura de comprimento de ondas em sensores biológicos e químicos compatível com pós processamento CMOS. Um sistema básico que é constituído por um FIV montado sobre uma matriz de sensores ópticos conectada a um módulo eletrônico dedicado a medir a intensidade da radiação incidente e as bandas de absorção das moléculas presentes em uma câmara de detecção de um sistema próprio de canais de microfluidos, configurando-se em um sistema de aquisição e armazenamento de dados (DAS), é proposto para demonstrar as possibilidades do FIV e para servir de base para estudos exploratórios das suas diversas potencialidades que, entre tantas, algumas são mencionadas ao longo deste trabalho. O protótipo obtido é capaz de analisar fluidos químicos ou biológicos e pode ser confrontado com os resultados obtidos por equipamentos homologados de uso corrente.

Alterations in energy metabolism, neuroprotection and visual signal transduction in the retina of parkinsonian, MPTP-treated monkeys

Parkinson disease is mainly characterized by the degeneration of dopaminergic neurons in the central nervous system, including the retina. Different interrelated molecular mechanisms underlying Parkinson disease-associated neuronal death have been put forward in the brain, including oxidative stress and mitochondrial dysfunction. Systemic injection of the proneurotoxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) to monkeys elicits the appearance of a parkinsonian syndrome, including morphological and functional impairments in the retina. However, the intracellular events leading to derangement of dopaminergic and other retinal neurons in MPTP-treated animal models have not been so far investigated. Here we have used a comparative proteomics approach to identify proteins differentially expressed in the retina of MPTP-treated monkeys. Proteins were solubilized from the neural retinas of control and MPTP-treated animals, labelled separately with two different cyanine fluorophores and run pairwise on 2D DIGE gels. Out of >700 protein spots resolved and quantified, 36 were found to exhibit statistically significant differences in their expression levels, of at least ±1.4-fold, in the parkinsonian monkey retina compared with controls. Most of these spots were excised from preparative 2D gels, trypsinized and subjected to MALDI-TOF MS and LC-MS/MS analyses. Data obtained were used for protein sequence database interrogation, and 15 different proteins were successfully identified, of which 13 were underexpressed and 2 overexpressed. These proteins were involved in key cellular functional pathways such as glycolysis and mitochondrial electron transport, neuronal protection against stress and survival, and phototransduction processes. These functional categories underscore that alterations in energy metabolism, neuroprotective mechanisms and signal transduction are involved in MPTPinduced neuronal degeneration in the retina, in similarity to mechanisms thought to underlie neuronal death in the Parkinson’s diseased brain and neurodegenerative diseases of the retina proper.

TENDENCIA THATCHERITIS OR ENGLISHNESS REMADE: The Fictions of Julian Barnes, Hanif Kureishi and Pat Barker

Julian Barnes, Pat Barker, and Hanif Kureishi are all canonical authors whose fictions are widely believed to reflect the cultural and political state of a nation that is post-war, post-imperial and post-modern. While much has been written on how Barker’s and Kureishi’s early works in particular respond to and intervene in the presiding political narrative of the 1980s – Thatcherism – treatment of how revenants of Thatcherism have shaped these writers’ works from 1990 on has remained cursory. Thatcherism is more than an obvious historical reference point for Barker, Barnes, and Kureishi; their works demonstrate a sophisticated understanding of how Thatcher’s reworkings of the repertoires of Englishness – a representational as well as political and cultural endeavour – persist beyond her time in office. Barnes, Barker, and Kureishi seem to have reached the same conclusion as political and cultural critics: Thatcher and Thatcherism have remade not only the contemporary political and cultural landscapes but also the electorate and consequently the English themselves. Tony Blair’s conception of the New Britain proved less than satisfactory because contemporary repertoires of Englishness repeat and rework historical and not incidentally imperial formulations of England and Englishness rather than envision civic and populist formulations of renewal. Barnes’s England, England and Arthur & George confront the discourse of inevitability that has come to be attached to contemporary formulations of both political and cultural Englishness – both in terms of its predictable demise and its belated celebration. Kureishi’s The Buddha of Suburbia and “The Body” speak to an alteration that has taken place in which historical Englishness and Thatcherism have become complementary rather than contrasting discourses. What Barker’s Border Crossing and Double Vision offer against this backdrop is a subtle interrogation of how renewal itself comes to be a presiding mode of cultural reflection that absorbs revolutionary possibility.

How to Support Toddlers' Autonomy: A Qualitative Study with Childcare Educators

Essai doctoral d’intégration présenté à la Faculté des études supérieures et postdoctorales en vue de l’obtention du grade Psychologiae Doctor (D.Psy) en psychologie clinique, option clinique.

How to Support Toddlers' Autonomy: A Qualitative Study with Childcare Educators

Essai doctoral d’intégration présenté à la Faculté des études supérieures et postdoctorales en vue de l’obtention du grade Psychologiae Doctor (D.Psy) en psychologie clinique, option clinique.

Spectacular Disappearances : Celebrity and Privacy, 1696-1801 /

How can the modern individual control his or her self-representation when the whole world seems to be watching? This question is a familiar one amid the the twenty-first century's architecture of 24-hour newsrooms, chat rooms and interrogation rooms, but this book traces this question back to the stages, the pages, and the streets of eighteenth-century London--and to the strange and spectacular self-representations performed there by England's first modern celebrities. These self-representations include the enormous wig that the actor, manager, and playwright Colley Cibber donned in his most famous comic role as Lord Foppington--and that later reappeared on the head of Cibber's cross-dressing daughter, Charlotte Charke. They include the black page of 'Tristram Shandy,' a memorial to the parson Yorick (and his author Laurence Sterne), a page so full of ink that it cannot be read. And they include the puffs and prologues that David Garrick used to hiehgten his publicity while protecting his privacy; the epistolary autobiography, modeled on the sentimental novel, of Garrick's protégée George Anne Bellamy; and the elliptical poems and portraits of the poet, actress, and royal courtesan Mary Robinson, known throughout her life as Perdita. Linking all of these representations is a quality that Fawcett terms "over-expression." 'Spectacular Disappearances' theorizes over-expression as the unique quality that allows celebrities to meet their spectators' demands for disclosure without giving themselves away. Like a spotlight so brilliant it is blinding, these exaggerated but illegible self-representations suggest a new way of understanding some of the key aspects of celebrity culture, both in the eighteenth century and today. They also challenge many of the disciplinary divides between theatrical character and novelistic character in eighteenth-century studies, or between performance studies and literary studies today. Drawing on a wide variety of materials and methodologies, 'Spectacular Disappearances' provides an overlooked but indispensable history for scholars and students of celebrity studies, performance studies, and autobiography--as well as to anyone curious about the origins of the eighteenth-century self.

Historie van het leven en sterven van Heer Johan van Oldenbarnevelt ... Waerachtelijek beschreven door een liefhebber der waarheydt.

Contains also"Eenige opmerckingen, memorien, notitien, ende consideratien, tegens den inhouldt van de pretense, ende gansch ongesondeerde, sententie, op den 13 May, 1619, tegens den Heere Iohan van Olden-Barnevelt..."

Images of a Broken World

Thesis (Master's)--University of Washington, 2016-08

California Calling

Thesis (Master's)--University of Washington, 2016-06

Intersectionality in the Language and Writing Classroom

Thesis (Ph.D.)--University of Washington, 2016-06

A comprehensive analysis of sexual dimorphism in the midbrain dopamine system

Thesis (Ph.D.)--University of Washington, 2016-06

Echocardiographic parameters in 14 healthy English Bull Terriers

Objective To determine the range of various cardiac parameters using echocardiography in apparently normal, healthy English Bull Terriers. Design Fourteen English Bull Terriers were selected for study. Cardiac auscultation of the parents of these dogs was normal. Echocardiographic examination of one parent of each animal showed: no mitral or aortic valve abnormalities; no myocardial lesions; no two dimensional evidence of fixed or dynamic left ventricular outflow tract obstruction; and no systolic aortic or left ventricular outflow tract turbulence on colour flow Doppler examination. The 14 selected dogs did not have arrhythmias or murmurs, and on echocardiographic examination had similar findings to their parents. Systolic blood pressure was measured in all dogs and they had no clinical evidence of Bull Terrier polycystic kidney disease or Bull Terrier hereditary nephritis. Procedure All dogs were auscultated and subjected to a sequential global echocardiographic assessment of the heart, including two dimensional long and short axis, and colour flow Doppler interrogation of the mitral and aortic valves. Dimensional measurements, including those from the left atrium, aortic annulus and left ventricle, were taken from a right parasternal window, and derived values such as fractional shortening, stroke volume and left atrial to aortic annulus ratio were calculated. Peak systolic aortic velocity was measured from the left parasternal window using two dimensional-guided pulsed wave Doppler with angle correction. Systolic blood pressure was measured using a Doppler monitor. The absence of Bull Terrier polycystic kidney disease was determined using renal ultrasonography, and of Bull Terrier hereditary nephritis using urinary protein to creatinine ratio. Results These 14 dogs had greater left ventricular wall thickness and smaller aortic root diameters than those reported as normal for other breeds of comparable body size. Left atrial dimensions were also larger, however this may have been due to the maximising method of measurement. These apparently normal English Bull Terriers also had higher aortic velocities than those reported for other breeds, possibly due to a smaller aortic root diameter or other anatomic substrate of the left ventricular outflow tract, lower systemic vascular resistance, or breed-specific normal left ventricular hypertrophy. While these dogs were selected to be as close to normal as possible, the breed may have a particular anatomy that produces abnormal left ventricular echocardiographic parameters. Conclusion These echocardiographic parameters may be used to diagnose left ventricular outflow tract obstruction and left ventricular hypertrophy, and inaccurate diagnoses may result if breed-specific values are not used.

mecA locus diversity in methicillin-resistant Staphylococcus aureus isolates in Brisbane, Australia, and the development of a novel diagnostic procedure for the Western Samoan phage pattern clone

An emerging public health phenomenon is the increasing incidence of methicillin-resistant Staphylococcus aureus (MRSA) infections that are acquired outside of health care facilities. One lineage of community-acquired MRSA (CA-MRSA) is known as the Western Samoan phage pattern (WSPP) clone. The central aim of this study was to develop an efficient genotyping procedure for the identification of WSPP isolates. The approach taken was to make use of the highly variable region downstream of mecA in combination with a single nucleotide polymorphism (SNP) defined by the S. aureus multilocus sequence typing (MLST) database. The premise was that a combinatorial genotyping method that interrogated both a highly variable region and the genomic backbone would deliver a high degree of informative power relative to the number of genetic polymorphisms-interrogated. Thirty-five MRSA isolates were used for this study, and their gene contents and order downstream of mecA were determined. The CA-MRSA isolates were found to contain a truncated mecA downstream region consisting of mecA-HVR-IS431 mec-dcs-Ins117, and a PCR-based method for identifying this structure was developed. The hospital-acquired isolates were found to contain eight different mecA downstream regions, three of which were novel. The Minimum SNPs computer software program was used to mine the S. aureus MLST database, and the arcC 2726 polymorph was identified as 82% discriminatory for ST-30. A real-time PCR assay was developed to interrogate this SNP. We found that the assay for the truncated mecA downstream region in combination with the interrogation of arcC position 272 provided an unambiguous identification of WSPP isolates.

Transcriptome analysis of Neotyphodium and Epichloë grass endophytes

Large-scale gene discovery has been performed for the grass fungal endophytes Neotyphodium coenophialum, Neotyphodium lolii, and Epichloe festucae. The resulting sequences have been annotated by comparison with public DNA and protein sequence databases and using intermediate gene ontology annotation tools. Endophyte sequences have also been analysed for the presence of simple sequence repeat and single nucleotide polymorphism molecular genetic markers. Sequences and annotation are maintained within a MySQL database that may be queried using a custom web interface. Two cDNA-based microarrays have been generated from this genome resource, They permit the interrogation of 3806 Neotyphodium genes (Nchip (TM) rnicroarray), and 4195 Neotyphodium and 920 Epichloe genes (EndoChip (TM) microarray), respectively. These microarrays provide tools for high-throughput transcriptome analysis, including genome-specific gene expression studies, profiling of novel endophyte genes, and investigation of the host grass-symbiont interaction. Comparative transcriptome analysis in Neotyphodium and Epichloe was performed. (c) 2006 Elsevier