abstract: This dissertation describes a novel, low cost strategy of using particle streak (track) images for accurate micro-channel velocity field mapping. It is shown that 2-dimensional, 2-component fields can be efficiently obtained using the spatial variation of particle track lengths in micro-channels. The velocity field is a critical performance feature of many microfluidic devices. Since it is often the case that un-modeled micro-scale physics frustrates principled design methodologies, particle based velocity field estimation is an essential design and validation tool. Current technologies that achieve this goal use particle constellation correlation strategies and rely heavily on costly, high-speed imaging hardware. The proposed image/ video processing based method achieves comparable accuracy for fraction of the cost. In the context of micro-channel velocimetry, the usability of particle streaks has been poorly studied so far. Their use has remained restricted mostly to bulk flow measurements and occasional ad-hoc uses in microfluidics. A second look at the usability of particle streak lengths in this work reveals that they can be efficiently used, after approximately 15 years from their first use for micro-channel velocimetry. Particle tracks in steady, smooth microfluidic flows is mathematically modeled and a framework for using experimentally observed particle track lengths for local velocity field estimation is introduced here, followed by algorithm implementation and quantitative verification. Further, experimental considerations and image processing techniques that can facilitate the proposed methods are also discussed in this dissertation. Unavailability of benchmarked particle track image data motivated the implementation of a simulation framework with the capability to generate exposure time controlled particle track image sequence for velocity vector fields. This dissertation also describes this work and shows that arbitrary velocity fields designed in computational fluid dynamics software tools can be used to obtain such images. Apart from aiding gold-standard data generation, such images would find use for quick microfluidic flow field visualization and help improve device designs. / Dissertation/Thesis / Ph.D. Electrical Engineering 2011

Submitted by Bruno Rossitto de Marchi (bruno_dmarchi@hotmail.com) on 2018-08-08T18:14:08Z No. of bitstreams: 1 Bruno De Marchi Tese Definitivo.pdf: 5408910 bytes, checksum: 6c7b13538e592fdcfc85ae1e3eb12212 (MD5) / Approved for entry into archive by Maria Lucia Martins Frederico null (mlucia@fca.unesp.br) on 2018-08-08T18:50:48Z (GMT) No. of bitstreams: 1 de marchi_ br_dr_botfca.pdf: 5386545 bytes, checksum: 8a0580cd031695c504bc6270ee8317c9 (MD5) / Made available in DSpace on 2018-08-08T18:50:48Z (GMT). No. of bitstreams: 1 de marchi_ br_dr_botfca.pdf: 5386545 bytes, checksum: 8a0580cd031695c504bc6270ee8317c9 (MD5) Previous issue date: 2018-07-31 / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / A mosca-branca, Bemisia tabaci (Gennadius) é uma praga de distribuição global que afeta centenas de diferentes plantas hospedeiras incluindo grandes culturas, olerícolas e ornamentais. B. tabaci causa danos principalmente através da transmissão de vírus de plantas como os begomovirus, crinivirus, ipomovirus, torradovirus e carlavirus. Atualmente, B. tabaci é considerada um complexo de pelo menos 40 espécies crípticas que apresentam diversidade genética, biológica e diferentes composições de bactérias endossimbiontes facultativas. No Brasil, tanto espécies nativas quanto exóticas de mosca-branca são encontradas e ainda há uma escassez de dados genômicos destas populações e das bactérias endossimbiontes. Na África Oriental, altas populações de moscas-brancas estão disseminando diferentes vírus de plantas que causam epidemias na cultura da mandioca (Manihot esculenta) e com perdas na produtividade. A principal forma de manejo desses vírus na África é através da utilização de variedades tolerantes. Portanto, é essencial a identificação de novos genes de resistência para o desenvolvimento de variedades e um manejo eficiente das doenças. O sequenciamento de transcriptomas é uma ferramenta que possibilita uma análise genômica da mosca-branca, dos vírus transmitidos por ela, das bactérias endossimbiontes e das plantas hospedeiras dessa praga. Portanto, os dados genômicos obtidos dão suporte para o desenvolvimento de novas técnicas que podem se tornar futuras alternativas de controle de mosca-branca e dos vírus associados. No Capítulo 1, dados de transcriptomas foram obtidos das diferentes espécies de B. tabaci encontradas no Brasil, tendo sido possível a obtenção de genomas mitocondriais completos de espécies exóticas e nativas de mosca-branca, além de genomas parciais do endossimbionte facultativo Hamiltonella. A análise filogenética revelou que as diferenças genéticas presentes no gene mtCOI entre as espécies nativas e as espécies exóticas se estendem ao genoma mitocondrial e ao endossimbionte facultativo Hamiltonella. Além disso, foi possível verificar uma deleção de aminoácidos somente no gene GroEL de Hamiltonella que está presente em populações de moscas-brancas nativas. Esse gene é conhecido por estar associado a transmissão de vírus de plantas. No Capítulo 2, foram sequenciados transcriptomas de plantas de mandioca naturalmente infectadas com vírus coletadas no campo em diferentes países da África. A partir desses dados, foi avaliada a diversidade de genes do cloroplasto e a relação com diferentes espécies de vírus. Há uma baixa diversidade dentre as cultivares de mandioca atualmente plantadas na África e não foi possível verificar nenhuma relação entre os genes de cloroplastos avaliados e as espécies de vírus detectadas ocorrendo naturalmente no campo. Os dados obtidos reforçam a necessidade da introdução de novos materiais genéticos para aumentar a diversidade genética das cultivares de mandioca plantadas nesses países, a fim de melhorar as alternativas de manejo das epidemias de vírus. / The whitefly, Bemisia tabaci (Gennadius) is a global pest that affects hundreds of different plant hosts including vegetable, fiber and ornamental crops. B. tabaci causes damage mainly by the transmission of plant viruses such as begomoviruses, criniviruses, ipomoviruses, torradoviruses, and carlaviruses. Currently, B. tabaci is known as a complex of at least 40 putative cryptic species that shows genetic and biological diversity and a different composition of bacterial facultative endosymbionts. In Brazil, both exotic and indigenous species of whiteflies are found and there is still a lack of genomic data available among these populations and also their bacterial endosymbionts. In East Africa, high populations of whiteflies are transmitting different plant viruses that are causing epidemics in cassava crops (Manihot esculenta) and leading to great yield losses. Currently, the management of these viral diseases in Africa is carried out mainly by growing cassava tolerant varieties. Therefore, is essential to identify new target genes for the development of new varieties for an efficient management of viral diseases. Transcriptome sequencing is a tool that allows a genomic analysis of the whitefly, whitefly-transmitted viruses, bacterial endosymbionts and plant hosts. Therefore, the genomic data obtained gives support for the development of new technics that might aid for future management alternatives of whiteflies and their associated viruses. In Chapter 1, transcriptome data were obtained from different B. tabaci species found in Brazil which allowed to obtain complete mitochondrial genomes from different whitefly species and draft genomes of the facultative endosymbiont Hamiltonella. The phylogenetic analysis revealed that the genetic differences among exotic and native populations present in the mtCOI gene extends to the mitochondrial genome and to the facultative endosymbiont Hamiltonella. In addition, it was verified an amino acid deletion in the GroEL gene from Hamiltonella present only in native populations of whiteflies. This gene is known to be associated with the transmission of plant viruses. In Chapter 2, transcriptome data were obtained from virus-infected cassava plants collected in the field in different African countries. The data allowed to evaluate the diversity of chloroplast genes and their relationship with different virus species. The data revealed a low genetic diversity among cassava currently grow in East Africa. In addition, there was no direct relationship between the evaluated chloroplast genes and the virus species detected. The obtained data reinforce the need of introduction of new genetic accession to increase the genetic diversity of the currently grown cassava in Africa in order to improve the alternatives of management of viral diseases. / CNPq 131324/2015-5 / CNPq 200826/2015-8

Master of Science / Department of Plant Pathology / Erick D. DeWolf / Wheat streak mosaic (WSM) is a devastating disease of winter wheat (Triticum aestivum L.) in Kansas. Although WSM can cause heavy crop losses, the severity of regional and statewide losses varies by year and location. Wheat streak mosaic is caused primarily by the Wheat streak mosaic virus (WSMV) and is spread by the wheat curl mite, Aceria tosichella Keifer. To infect fall planted wheat, both the virus and mite require a living, grass host to survive the summer months. The first research objective was to determine the risk of different grass species to serve as a source of WSM. Published experiments and surveys were reviewed to determine the suitability of each host based on a set of criteria. An analysis of the reports from the reviewed literature found 39 species to host both pests. Categorical analysis of these observations suggested that well-studied grass species could be placed in four risk groupings with ten species at high risk of carrying both pests. Furthermore, results from controlled experimentation generally agrees with results from field survey results for both pests. The second objective was to determine the weather and cropping factors that are associated with regional epidemics of WSM in Kansas. Historic disease observations, weather summaries, soil moisture indices, and cropping statistics were collected from Kansas crop reporting districts from 1995-2013. Binary response variables (non-epidemic case vs epidemic cases) were developed from different thresholds of district losses attributed to WSM. Variables associated with WSM epidemics were identified by a combination of non-parametric correlation, classification trees, and logistic regression. This analysis indicates that the total acres of wheat planted per season was associated with the low frequency of epidemics in Eastern Kansas. Temperature during September appears to influence the yield losses caused by WSM. Wheat planting generally begins during September and continues through October in the state. Temperature during the winter months (December-February) was also identified as important with warm conditions favoring outbreaks of disease. Dry soil conditions in February was also associated with epidemics of WSM. Models combining these variables correctly classified 60 to 74% of the cases considered in this analysis.

Doctor of Philosophy / Plant Pathology / Frank F. White / Rice and wheat are two major crops that suffer losses from the diseases of bacterial blight and bacterial leaf streak, which are caused by Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas translucens pv. undulosa (Xtu), respectively. Transcriptional-Activator Like (TAL) effectors, a special family of type III effector proteins from Xanthomonas, have been demonstrated as critical virulence factors that act by inducing corresponding susceptibility (S) genes in several disease complexes of plants. In this study, I analyzed the contributions of TAL effectors from Xoo and Xtu to virulence and in modulating host gene expression to enhance susceptibility. Specifically, the TalC effector from the African Xoo strain AXO1947 was identified as a critical virulence factor, which functions by promoting expression of the gene OsSWEET14 in rice. TalC is interchangeable with other major TAL effectors from Asian strains of Xoo on the basis of functional complementation. The TAL effector PthXo2 from the Asian Xoo strain JXO1 is a major virulence factor and contains 21.5 repeats in the central repetitive region that targets OsSWEET13 in indica rice varieties but not in japonica rice varieties. A one repeat deletion in the PthXo2 effector enabled effector specificity to switch from indica rice to japonica rice. TAL effector genes from a genomic analysis of the Xtu strain XT4699 and related strains were characterized with regards to their involvement in virulence and the modulation of host gene expression in the Chinese Spring wheat cultivar. The identification of TAL effectors with virulence contributions and their target S genes is important for understanding the virulence mechanisms of Xanthomonas bacteria and promises to provide new strategies for disease control.

Abstract The thesis clearly demonstrates that photon migration measurements allow characterization of pulp and paper properties, especially the fines and filler content of pulp, and the basis weight, thickness and porosity of paper. Pulp and paper are materials with a worldwide significance. Their properties strongly depend on the manufacturing process used. For efficient process control, the employed monitoring and measuring has to be fast. Therefore it is worthwhile to try to develop new approaches and techniques for such measurements. Recent advancements in optics offer new possibilities for such development. If two samples have different optical properties their photon migration distributions are different. The measurement of a photon migration distribution allows some features between two optically slightly dissimilar samples to be distinguished. Some simple measurements, which only yielded the photons' average time of flight, were made with an oscilloscope and a time-of-flight lidar. More precise measurements yielding photon pathway distribution or some selected characteristics like light pulse rise time, broadening, or fall time were measured with a streak camera. Two methods to assess photon path length distribution were introduced: particle determination with simulation, and streak camera with deconvolution. The basic properties for pulp are consistency and fines content and for paper the basic properties are thickness, basis weight and porosity. The influence on photon migration caused by changes in these basic properties was determined. As pulp and paper are rarely very basic, an additional property was demonstrated for both materials. For pulp it was the content of filler talc, and for paper it was the use of beaten pulp as a raw material. These additional properties were also distinguishable.

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Various research efforts have focused on Banana streak badnavirus (BSV), the causal agent of banana streak disease (BSD), since the discovery of endogenous sequences of the virus in the nuclear genome of several Musa (banana and plantain) species. In vitro propagation of Musa was identified as one of the main activation triggers of integrated BSV sequences to cause systemic (episomal) BSD. This was especially observed in B genome-containing tetraploid hybrids. Although, the South African banana industry is based on Cavendish varieties, some plantations with tetraploid hybrids have been established. In order to investigate the occurrence of episomally expressed BSV, a survey was done in the Kiepersol area of South Africa and episomal BSV was detected in six out of seven locations sampled. No episomal BSV was detected in the Cavendish cultivars sampled in close proximity to BSV infected cultivars. To determine the risk of vector-assisted spread of endogenous BSV, which has become episomally activated after tissue culture, transmission studies with local mealybug species (Planococcus citri (Risso), P. ficus (Signoret), Dysmicoccus brevipes (Cockerell) and Pseudococcus longispinus (Targioni-Tozzetti)) were conducted under controlled conditions. Virus-free FHIA-21 was multiplied in vitro and resulting progeny with, putatively episomally activated BSV, served as sources for mealybug-assisted transmissions to Cavendish. Activated, episomal BSV was transmitted by three mealybug species to Cavendish. Transmission with P. ficus was demonstrated for the first time. Limited antiserum stocks against BSV occur worldwide and detection of the virus remains crucial for the safe movement of Musa germplasm between continents. Antiserum is needed in order to detect the episomal form of the virus that causes BSD. Using conventional immunization methodology, antisera against a wide spectrum of BSV isolates were produced. Twenty diverse BSV isolates were characterized by IC-PCR and selected as sources for the production of the polyclonal antiserums in two animal species. An effective triple antibody sandwich (TAS) enzyme linked immunosorbent assay (ELISA) system; able to detect various serologically different species of BSV was developed. BSV was screened with a synthetically manufactured phage displayed antibody library; however, no satisfactory polyclonal or monoclonal antibodies were obtianed in using this approach. / Dissertation (MSc (Microbiology))--University of Pretoria, 2007. / Microbiology and Plant Pathology / unrestricted

In medical ophthalmology, refractive studies have become an integral part of a complete ophthalmic examination and second only to a slit-lamp biomicroscopic examination in determining visual function and ability. This study shows that the same ideology applies to refractive studies on dogs. The refraction technique has evolved in process, with refinement of the technology and methods used; with the development of handheld autorefractors utilised in paediatric refraction. Fifty guide dogs completed this study however five of the dogs were subsequently excluded and replaced because of poor compliance. Forty six of the dogs were Labrador Retrievers; one was a Golden Retriever, one a Great Dane cross, one a Labrador cross and one a cross breed. The median sample age was 17months with an interquartile range (IQR) of13 to 34months. We validated the agreement in refractive error measurement between the Welch Allyn ™ "SureSight" (WASS) autorefractor to the traditional Welch Allyn ™ handheld streak retinoscope (SR) by two experienced investigators, due to previous studies showing variability in measurement for both instruments. The refractive state for 60°/o of the guide dogs sampled at South African Guide Dogs Association (SAGDA) were emmetropic (-0.5 to +0.5D), 34% were hypermetropic (>+0.5D) with 6% myopic (<-0.5D). For agreement between the instruments, a wide range of differences using mean spherical equivalence (MSE) was observed between the 95% limits of agreement (-1.911 D to 1.698D). On average,measurements with the WASS were slightly lower compared to the SR (mean difference = 0.013). Both instruments showed a better average agreement in determining emmetropia with a tendency to underestimate refractive errors for greater negative and positive diopters. The WASS showed better agreement with the SR for refractive error measurement with higher reliability scale values (8 and above). Clinical astigmatism (>- 0.50 cylinder) was detected more readily on the WASS (37 dogs) than on the SR (9 dogs). Between investigators the MSE measurements differed significantly (P = 0.02), with the average agreement on the SR slightly better than the WASS. Overall, the handheld manual streak retinoscope remains the more practical, cost effective and efficient instrument for objective refraction in dogs. We can also conclude, that current subjective criteriae utilised in the selection of guide dogs at SAGA can be further improved by including objective methods of refraction. Copyright / Dissertation (MMedVet)--University of Pretoria, 2011. / Companion Animal Clinical Studies / unrestricted

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