Thesis (Ph. D.)--University of Hong Kong, 2010. / Includes bibliographical references (p. 169-186). Also available in print.

Prokaryotes are single-cell microorganisms. These creatures can be further classified to bacteria and archaea. Their DNA genetic meterials are spread around the cytoplasm rather than residing in the nucleus. Unlike eukaryotes, a high percentage of prokaryotic genome is composed of genes. The evolution of prokaryotes is different from that of the eukaryotes. Prokaryotes are found almost everywhere including the harshest environments on Earth. Understanding the whole pictures of their genomes will benefit us a lot in terms of new enzyme discovery, decoding drug resistance, biofuel development, etc. 　High-throughput sequencing technology is becoming increasingly popular in various sequencing projects. With different platforms, scientists are able to achieve millions ~ billions of sequences within days. In the last two years, there are a lot of prokaryotic genomes being sequenced under these platforms. However, there are only 1,542 complete chromosomes available in NCBI GenBank (September 2011) since the first complete genome of Bacillus subtilis was published in 1997. The most difficult step in finishing a complete genome is closing all gaps among different contigs. In this thesis, a series of comprehensive simulation studies based on 1,542 complete chromosomes have been performed in search of a cost-effective way to achieve complete prokaryotic genomes. Solutions to both draft and complete genome sequencing were provided by computer simulation. Moreover, classification studies have been performed to identify special prokaryotic phyla/orders (if any) dissatisfying our proposed strategies. 　Our results indicate that: 1) low coverage (6x-10x) pyrosequencing with long reads (400 bp) is sufficient to produce highly continuous and complete assemblies, presenting a tiny proportion of false gene duplication/loss. High quality draft genomes could be generated by this strategy; 2) Long repeats to some extent influence the assembly quality, especially for the genome coverage and contig number. The number of contigs and genome coverage rate are significantly correlated with the total size of repeat regions; 3) With a combination of one run of single-end reads (10x, 400bp read length) and one run of paired end reads (10x, 8kb library, 400bp read length), ~90% of chromosome assemblies are less than 10 scaffolds and ~95% of chromosome assemblies are less than 150 contigs. Most of the chromosomes can be assembled into high quality draft chromosomes (<50 contigs, ~4 scaffolds, >370kb contig N50 size, >99.99% single base accuracy and <0.5% false gene duplication/loss rate in average); 4) Similar patterns found in both simulated and real reads imply that our simulation analysis is not overestimated; 5) Greater attention is needed regarding the orders Thiotrichales, Enterobacteriales and Nostocales, when applying the above strategies for complete genome sequencing; 6) For prokaryotic species with multiple chromosomes, Pulse Field Gel Electrophoresis is needed to separate all their chromosomes which will be individually collected by electroelution prior to draft/complete genome sequencing. A comprehensive computer simulation study based on 1,542 chromosomes (all availabe prokaryotic complete chromosomes, September 2011) has been performed in this thesis. The sequencing strategies for both prokaryotic draft and complete genome proposed by the simulation study could facilitate the ongoing prokaryotic complete genome sequencing projects. / published_or_final_version / Biological Sciences / Doctoral / Doctor of Philosophy

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This thesis work presents a simple and practical technique for seamlessly texturing quadrilateral meshes. Using this technique, an isotropic homogeneous texture can be mapped to any quadrilateral mesh without any discontinuity or singularity in the resultant texturing. The method involves organizing a set of square texture tiles that satisfy specific boundary conditions into one texture image file which is called a tiled texture. Based on the tiled textures, we have developed an extremely simple texture mapping algorithm that randomly assigns one tile to every patch in any given quadrilateral mesh. The mapping technique developed yields singularity free textures, regardless of the singularities existing in the quadrilateral mesh, gives seamless and continuous boundaries across textures and provides an aperiodic and interesting look to the entire textured surface.

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Let f be a mapping (i.e., continuous transformation) of a topological space X onto a topological space Y. It is of interest to investigate the properties of X which are inherited by Y under the mapping f. In particular, if f is a homeomorphism, X and Y are topologically equivalent, so that Y will share all the topological properties of X. Hovever, under 1ess restricted oonditions on f , many of the properties such as connectedness, compactness, separability, local separability (i.e., first countability) and strong separability (i.e., second countability), etc., will be inherited by Y. In this work, we are interested in investigating some important classes of mappings: open mappings, closed mappings and perfect mappings, and in determining how the image space is affected under such mappings. These mappings play fundamental role in many studies, e.g., the theory of function of one or several complex variables. Work along these lines have been initiated by G. T. Whyburn, S. Stoilow, H. Grauert, B. Remmert and K. Stein.

As a specific reading disability with a neurobiological origin, developmental dyslexia is distinct from reading difficulties due to sensory impairments in vision or hearing. The disability is commonly attributed to a core deficit in phonological processing, the understanding of how phonemes, syllables and words are used in a language. Dyslexia is a complex genetic disorder with a strong genetic component; nine susceptibility loci (DYX1-9) have been identified with eight other dyslexia linkages lacking gene symbols also reported. The statistical methods of linkage and association were employed to investigate the genetic susceptibility for phonological coding dyslexia (PCD), a common form of dyslexia characterized by difficulties in single word decoding and resulting from deficits in phonological processing. A genome-wide non-parametric linkage (NPL) study and four targeted fine-mapping family-based association studies were performed to locate the genes predisposing to PCD in 101 Canadian families with multiple affected members. The NPL scan identified suggestive evidence for linkage with PCD at the two novel regions 16p12 and 4q12-q13, and provided independent confirmation of linkage to the well-replicated DYX3 locus (at 2p21). Some support for linkage was noted at a further five regions previously linked to dyslexia, while no linkage was detected at five other reportedly-linked regions, in particular, no linkage to DYX2 (6p22.2). Four regions (16p12, 2p21, 4q12-q13 and 6p22.2) were tested for association with PCD in 83 trios, a subset of the 101 families, using the transmission disequilibrium test (TDT) and the affected family-based controls (AFBAC) test. Association was detected in each of the three PCD-linked regions in the NPL scan; none of the tested marker alleles was associated with PCD in the 6p22.2 region. Four candidate genes were identified, two of which belong to the same gene family, with a possible role in the neurodevelopmental mechanisms underlying reading.

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