No description available.

No description available.

No description available.

No description available.

Sex determination in mammals is regulated by the sex-determining region on the Y chromosome (SRY); the presence of SRY activates the male developmental pathway and suppresses the gene network necessary for female gonad development. Mutations in sex determination genes lead to various abnormal sexual phenotypes, including sex reversal syndrome in which the genetic and phenotypic sex do not match. Sex reversal syndrome has been reported in humans, mouse, and several domestic species. In horses, SRY-negative XY sex reversal syndrome has been well described and is caused by deletions on the Y chromosome. However, the molecular causes of the SRY-positive condition in horses and other mammals are not known. This research investigated five horses affected with SRY-positive XY sex reversal syndrome. Sequencing of the coding exon region of the SRY gene in the five cases showed 99-100% alignment with the sequences of normal males. Genotyping of two closely related individuals with 46 normal male controls on an equine SNP50 Beadchip identified two statistically significant SNPs in a ~16 Mb region on the long arm of horse chromosome 3 (ECA3q). The region was analyzed using Gene Ontology (GO) and Gene Relationships Across Implicated Loci (GRAIL) to select functionally relevant candidate genes for sequencing. Further analysis of the entire horse genome was done through array comparative genomic hybridization (aCGH), which investigated possible structural rearrangements, such as copy number variants (CNVs). Deletions of olfactory receptor genes were detected on multiple chromosomes and confirmed through quantitative real-time PCR (qPCR). A homozygous deletion on ECA29 in a region containing genes of the aldo-keto reductase gene family, known to play a role in interconverting sex hormones between active forms and inactive forms, was discovered in two sex reversed animals. The findings were confirmed through qPCR and fluorescence in situ hybridization (FISH), and experiments to define the specific breakpoints of the deletion through PCR have been initiated. This research represents the first systematic search in the horse genome for mutations and CNVs related to sex determination. The findings contribute to better understanding of the molecular mechanisms of sex determination in horses and other mammals, including humans.

Graduate

This thesis examines a series of near-field antenna arrays used to perform subwavelength focusing and subwavelength imaging outside the extreme near field. For this purpose, slot and dipole arrays have been designed to produce a subwavelength focal spot at a distance of a quarter wavelength from the array. The dipole arrays are then used as scanning probes to produce images with subwavelength resolution based on perturbations in the scattered field. Unlike negative-refractive-index metamaterial superlenses, the imaging resolution is not affected by losses in the array. Furthermore, the arrays are simple to fabricate and are frequency scalable up to Terahertz frequencies and beyond. A near-field analogue to classic antenna-array theory called ``shifted beam theory'' is presented as a design tool. Based on the linear independence of element field patterns in the near field, this theory is very intuitive and provides a simplified way to calculate the element current weights necessary to generate a given target near-field pattern. Two-dimensional near-field subwavelength focusing is demonstrated using a slotted transmission-screen, or ``meta-screen'', under plane-wave incidence. At a distance of a quarter wavelength, the transverse electric field was measured in experiment to have a full-width half-maximum beamwidth of 0.40 by 0.27 wavelengths. This is compared to a single slot transmission-screen which had a beamwidth of 0.60 by 0.58 wavelengths. Broadside and end-fire dipole arrays are used to perform subwavelength imaging in one and two dimensions, respectively. The experimental minimum resolvable separation between two objects at a quarter-wavelength distance was 0.26 wavelengths using the end-fire array probe, as compared to 0.43 wavelengths for a single monopole probe. For an experiment using eight objects scattered over a one-square-wavelength area, however, the array probe imaging resolution remained around 0.25 wavelengths while the baseline monopole probe was no longer able to resolve any of the objects. Experiments were also conducted using objects buried behind a dielectric barrier as well as objects immersed within a dielectric. These results were consistent with the resolution improvements observed in the free-space resolution experiments.

This thesis examines a series of near-field antenna arrays used to perform subwavelength focusing and subwavelength imaging outside the extreme near field. For this purpose, slot and dipole arrays have been designed to produce a subwavelength focal spot at a distance of a quarter wavelength from the array. The dipole arrays are then used as scanning probes to produce images with subwavelength resolution based on perturbations in the scattered field. Unlike negative-refractive-index metamaterial superlenses, the imaging resolution is not affected by losses in the array. Furthermore, the arrays are simple to fabricate and are frequency scalable up to Terahertz frequencies and beyond. A near-field analogue to classic antenna-array theory called ``shifted beam theory'' is presented as a design tool. Based on the linear independence of element field patterns in the near field, this theory is very intuitive and provides a simplified way to calculate the element current weights necessary to generate a given target near-field pattern. Two-dimensional near-field subwavelength focusing is demonstrated using a slotted transmission-screen, or ``meta-screen'', under plane-wave incidence. At a distance of a quarter wavelength, the transverse electric field was measured in experiment to have a full-width half-maximum beamwidth of 0.40 by 0.27 wavelengths. This is compared to a single slot transmission-screen which had a beamwidth of 0.60 by 0.58 wavelengths. Broadside and end-fire dipole arrays are used to perform subwavelength imaging in one and two dimensions, respectively. The experimental minimum resolvable separation between two objects at a quarter-wavelength distance was 0.26 wavelengths using the end-fire array probe, as compared to 0.43 wavelengths for a single monopole probe. For an experiment using eight objects scattered over a one-square-wavelength area, however, the array probe imaging resolution remained around 0.25 wavelengths while the baseline monopole probe was no longer able to resolve any of the objects. Experiments were also conducted using objects buried behind a dielectric barrier as well as objects immersed within a dielectric. These results were consistent with the resolution improvements observed in the free-space resolution experiments.

During storage of grain, there may have significant damage to its quality due to unfavorable physical and biological interactions and thus requires continuous monitoring. Therefore, an easy, cost-effective and environmentally friendly method is necessary for efficient monitoring of stored-grain. Arrays of sensors are being used for classifying liquors, perfumes, quality of food products mimicking mammalian olfactory systems. Monitoring of stored grain is a new application of sensor arrays. The main objective was to fabricate a carbon black polymer sensor array which can easily monitor incipient grain spoilage by detecting spoiling stored grain volatiles (benzene derivatives and aliphatic hydrocarbon derivatives) with minimum interference from relative humidity. Various aspects of a good sensor were analyzed using statistical analysis (RSD, LDA, PCA, t-test). The developed sensor array can identify red flour beetle-infected and uninfected wheat and fungal volatiles at ambient conditions as well as some stored grain conditions (MC 16%, RH 52%).

<p>Promising applications in the design of various biological systems hold critical implications as heralded in the rising field of synthetic biology. But, to achieve these goals, the ability to synthesize in situ DNA constructs of any size or sequence rapidly, accurately and economically is crucial. Today, the process of DNA oligonucleotide synthesis has been automated but the overall development of gene and genome synthesis technology has far lagged behind that of gene and genome sequencing. This has meant that numerous ideas go unfulfilled due to scale, cost and impediments in the quality of DNA due to synthesis errors. </p><p>This thesis presents the development of a multi-tool ensemble platform targeted at gene synthesis. An inkjet oligonucleotide synthesizer is constructed to synthesize DNA microarrays onto silica functionalized cylic olefin copolymer substrates. The arrays are married to microfluidic wells that provide a chamber to for enzymatic amplification and assembly of the DNA from the microarrays into a larger construct. Harvested product is then amplified off-chip and error corrected using a mismatch endonuclease-based reaction. This platform has the potential to be particularly low-cost since it employs standard phosphoramidite reagents and parts that are cheaper than optical and electrochemical systems. Genes sized 160 bp to 993 bp were successfully harvested and, after error correction, achieved up to 94% of intended functionality.</p> / Dissertation