Ph. D., Faculty of Health Sciences, University of the Witwatersrand, 2008. / The human chromosome complement contains nonrandom genomic regions that are prone to breaks and recurrently altered in tumors. These chromosomal “hot spots” are preferentially involved in early events of genomic instability and point to genes in their vicinity that may participate to carcinogenesis. Amplicons and deletions are frequently generated at “hot spots”, including common fragile sites (CFS), and are thought to host cancer genes whose rearrangements drive cell proliferation and promote the initiation and progression of cancer. Chromosomal “hot spots” in South African cancer patients, were investigated in this study with a view to characterizing underlying gene alterations. A chromosome 12p amplicon was mapped and array comparative genomic hybridization (aCGH) was pioneered to identify candidate genes in the amplicon. Genes of the 12p stem cell gene cluster (NANOG, STELLAR and GDF3) were involved in striking similarity to what has been reported in testicular germ cell tumors and suggest that they may be more commonly involved in different types of cancer. Two tumor suppressor genes, FHIT and WWOX, are located at the two most commonly expressed fragile sites, FRA3B and FRA16D respectively. Alterations in these fragile site associated genes have been reported in a variety of tumors including lung, esophageal, gastric, breast and cervical cancers most frequently as a result of submicroscopic deletions. Genomic deletions at CFS have been mostly investigated using loss of heterozygosity assays that do not necessarily inform on gene exon deletions. A new method was developed based on multiplex ligation-dependent probe amplification (MLPA) that screens for exon deletions/amplifications of genes at CFS. The assay was validated on five esophageal squamous carcinoma cell lines and showed deletions in the FRA3B-associated gene FHIT in four of the cell lines. Two geographically distinct South African cohorts of esophageal squamous cell carcinoma were then screened for FHIT/WWOX exon deletions and a visual basic (VBA) encoded program was written to automate MPLA products analysis. A high frequency of intragenic deletions in FHIT and/or WWOX (73%) was observed in the Eastern Cape cohort. FHIT deletions were seen in 27% of specimens from the Gauteng cohort, which by contrast did not show WWOX deletions. This difference may however reflect a difference in sampling collection. The breakpoints of a translocation t(3;11)(p14;p15.1) present in an ovarian carcinoma cell line was characterized using the above MLPA assay, aCGH and the polymerase chain reaction. The translocation was found to interrupt the FHIT gene making it the 5th cancer associated translocation involving FHIT. The evaluation of gene relative copy number by aCGH and MLPA were highly correlated further validating the power of the MLPA assay in fresh tissue. The involvement of critical genes at “hot spots” in SA cancer patients was high in the context of this study raising questions about the possible role of environmental exposure. The new MLPA assay may assist to expand the screening of critical genes at fragile sites in the future.

Thesis (Ph. D.)--University of Wisconsin--Madison, 1943. / Typescript. Vita. eContent provider-neutral record in process. Description based on print version record. Includes bibliographical references (leaf 27).

Presented as Thesis (Ph. D.)--University of Wisconsin--Madison, 1917. / Reprinted from Journal of agricultural research, vol. XV, no. 3 (21 Oct. 1918). Contribution from Bureau of Plant Industry (G--160). "Literature cited": p. 220.

Thesis (Ph. D.)--University of Wisconsin--Madison, 1964. / Typescript. Vita. eContent provider-neutral record in process. Description based on print version record. Includes bibliographical references.

Thesis (Ph. D.)--University of Wisconsin--Madison, 1965. / Typescript. Vita. eContent provider-neutral record in process. Description based on print version record. Includes bibliographical references.

Thesis (Ph. D.)--University of Wisconsin--Madison, 1963. / Typescript. Vita. eContent provider-neutral record in process. Description based on print version record. Includes bibliographical references (leaves 67-70).

Two isolates (A and B) of apple chlorotic leafspot virus (ACLSV) associated with line pattern symptoms in Prunus, glandulosa were isolated in Chenopodium quinoa and purified by a simple method using bentonite clarification, polyethylene glycol precipitation, and caesium sulphate isopycnic centrifugation. Symptoms on herbaceous hosts were as previously reported for ACLSV. No symptoms were observed on a range of ACLSV woody host indicators. Isolates A and B had a coat protein MW of 26 and 24.5 kilodaltons respectively, ssRNA of MW 2.6 x 10⁶ daltons, and dsRNA of MW 5.6 x 10⁶, 4.9 x 10⁶, and 4.5 x 10⁶ daltons. The particle widths were 12 nm and lengths were 782 nm (A) and 732 nm (B). Buoyant density in caesium sulphate was 1.27 g/cc³. In thin sections of C. quinoa, flexuous rods were seen in the cytoplasm and nucleus of young sieve-tube members. Polyclonal antisera prepared against the A and B isolates had high background reactions and required cross-adsorption with host sap. Three monoclonal antibodies (MAB) against isolate A detected Prunus strains while a fourth detected both Malus and Prunus strains in C. quinoa with low background reactions. The broad spectrum MAB could not be used as a trapping antibody but could be directly conjugated with alkaline phosphatase or used in an indirect triple-antibody sandwich ELISA. Tobacco mosaic virus (TMV) recovered from P. glandulosa was identical in serological and physical properties to the TMV-U1 type strain. / Land and Food Systems, Faculty of / Graduate

Early visual processing is subject to binocular interactions because cells in striate cortex show binocular responses and ocular dominance (Hubel & Weisel, 1968). The work presented in this thesis suggests that these physiological interactions can be revealed in psychophysical experiments using normal human observers. In the region corresponding to the blind spot, where binocular interactions differ from areas of the visual field which are represented by two eyes, monocular contrast sensitivity is increased. This finding can be partially explained by an absence of normal binocular interactions in this location (Chapter 2). A hemianopic patient was studied in an attempt to discover whether the effect in normal observers was mediated by either a mechanism in striate cortex or via a subcortical pathway. However, the results were unable to distinguish between these two explanations (Chapter 3).In a visual search task, no difference in reaction time was observed for targets presented to the region corresponding to the blind spot compared with targets presented to adjacent binocularly represented areas of the visual field. Since performance was unaffected by the monocularity of the region corresponding to the blind, pop-out for orientation may be mediated beyond striate cortex where cells are binocularly balanced (Chapter 5). Further support for this contention was provided by studies of orientation pop-out in central vision which found that dichoptic presentation of stimuli did not affect the degree of pop-out obtained and that in general, visual search for a target based solely on eye of origin is impossible (Chapter 6). However, a task that measured orientation difference sensitivity more directly than the search experiments, found that thresholds were higher for dichoptically presented stimuli. This suggests the involvement of neurons that receive a weighted input from each eye. A model of orientation difference coding can account for the results by assuming that the range of inhibition across which orientation differences are coded is narrower for dichoptic stimuli leading to a greater resolvable orientation difference (Chapter 7).

The development, implementation, and performance evaluation of new techniques for the location of hot spots in proteins and exons in DNA using digital filters are presented. The application of bandpass notch (BPN) digital filters for locating hot spots in proteins is first investigated. A technique is proposed for designing the appropriate BPN filter for a specific protein sequence in which the area under the amplitude response is minimized to achieve maximum selectivity for a chosen stability margin. The minimization is performed using the golden-section search. A tuning technique is also proposed for improving the accuracy of the BPN filter. The tuning is carried out using a least-squares polynomial model. Several example protein sequences are used to illustrate these techniques. BPN filters are then employed for locating exons in DNA. An additional step of lowpass filtering is introduced in order to detect the strength of the bandpass filtered signal as a function of nucleotide location. For the character-to-numerical mapping, the application of the electron-ion interaction potentials (EIIPs) of the nucleotides as well as their binary sequences is investigated. The performance of the techniques is then evaluated using metrics such as sensitivity, specificity, accuracy, precision, and computational efficiency. These metrics are used in conjunction with the so-called receiver operating characteristic (ROC) technique to establish a reliable framework for the comparisons. For exon location, a technique based on the short-time discrete Fourier transform (STDFT) reported in the literature is also included in the comparison. The effect of using different window functions on the prediction accuracy of the technique is explored. Using a set of examples, it is shown that BPN filters predict short exons with better accuracy than the STDFT. The test dataset comprised 66 protein sequences and 160 DNA sequences obtained from the protein data bank and the HMR195 database, respectively. Results show that among the techniques considered, BPN filters perform best for the location of both protein hot spots and DNA exons in terms of accuracy and computational efficiency. User-friendly MATLAB implementations of the techniques incorporating graphical interfaces are also described. Optimized numerical mapping schemes are proposed for exon location using both EIIP as well as binary sequences. Characteristic numerical values are obtained for the four nucleotides using a training procedure in which the prediction accuracy is maximized using a quasi-Newton algorithm based on the Broyden-Fletcher-Goldfarb-Shanno updating formula. A training set of 80 DNA sequences is chosen from the HMR195 database and the objective function is formulated using the ROC technique. The procedure is initialized using EIIP values. Unbiased testing of the optimized values is carried out using a test set that has no overlap with the training set. Simulation results show that the optimized values yield more accurate exon locations than those obtained using the actual EIIP values. In addition, they perform significantly better than a set of existing optimized complex values. By employing a similar strategy to optimize the weights of the binary sequences, it is shown that, in practice, only three out of four binary sequences are necessary to obtain accurate estimates of exon locations. Consequently, a computational saving of 25% can be achieved, which is substantial considering that DNA sequences encountered in practice are very long in nature. / Graduate

Thesis(M.S.)--Auburn University, 2006. / Abstract. Vita. Includes bibliographic references (p.48-50).