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Ho, Ka Chai. / Thesis submitted in: November 2006. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2007. / Includes bibliographical references (leaves 127-145). / Abstracts in English and Chinese. / Abstract --- p.i / Abstract (Chinese) --- p.iii / Acknowledgements --- p.v / Table of Contents --- p.vi / List of Tables --- p.ix / List of Figures --- p.x / Chapter Chapter 1 --- General Introduction --- p.1 / Chapter 1.1 --- Molecular phylogeny of Metanephrops --- p.1 / Chapter 1.2 --- Identification of Nephropidae using DNA barcodes --- p.3 / Chapter Chapter 2 --- Literature Review --- p.5 / Chapter 2.1 --- Molecular phylogenetic studies of crustaceans --- p.5 / Chapter 2.1.1 --- Molecular phylogeny and reasons of using molecular markers in phylogenetic studies --- p.5 / Chapter 2.1.2 --- Characteristics of animal mitochondrial genome --- p.7 / Chapter 2.1.3 --- Examples of crustacean phylogenetic studies derived from mitochondrial DNA --- p.8 / Chapter 2.2 --- Identification of species based on DNA barcode --- p.17 / Chapter 2.2.1 --- Traditional taxonomy and its current practice --- p.17 / Chapter 2.2.2 --- Needs for DNA barcode --- p.18 / Chapter 2.2.3 --- Molecular identification based on DNA barcodes --- p.21 / Chapter 2.3 --- Taxonomy of Nephropidae --- p.28 / Chapter 2.3.1 --- Classification and phylogenetic relationship of Nephropidae --- p.28 / Chapter 2.3.2 --- Classification and distribution of Metanephrops --- p.31 / Chapter 2.3.3 --- Evolutionary history of Metanephrops --- p.36 / Chapter Chapter 3 --- Molecular Phylogeny of Metanephrops --- p.38 / Chapter 3.1 --- Introduction --- p.38 / Chapter 3.2.1 --- Species studied and sample collection --- p.41 / Chapter 3.2.2 --- DNA extraction --- p.43 / Chapter 3.2.3 --- Amplification of mitochondrial genes --- p.43 / Chapter 3.2.4 --- Nucleotide sequencing --- p.46 / Chapter 3.2.4.1 --- Asymmetric PCR --- p.46 / Chapter 3.2.4.2 --- Purification of asymmetric PCR products --- p.47 / Chapter 3.2.5 --- Sequence alignment --- p.47 / Chapter 3.2.6 --- Phylogenetic analyses --- p.48 / Chapter 3.3 --- Results --- p.50 / Chapter 3.3.1 --- PCR products of 16S rRNA and COI genes --- p.50 / Chapter 3.3.2 --- Nucleotide composition of 16S rRNA gene alignments --- p.52 / Chapter 3.3.3 --- Nucleotide composition of COI gene alignments --- p.54 / Chapter 3.3.4 --- Intraspecific and interspecific genetic variation --- p.56 / Chapter 3.3.5 --- Phylogenetic analysis based on 16S rRNA gene sequences --- p.61 / Chapter 3.3.6 --- Phylogenetic analysis based on COI gene sequences --- p.68 / Chapter 3.3.7 --- Phylogenetic analysis based on combined data set --- p.74 / Chapter 3.4 --- Discussion --- p.80 / Chapter 3.4.1 --- Interspecific genetic divergence --- p.80 / Chapter 3.4.2 --- Monophyly of the four species groups --- p.81 / Chapter 3.4.3 --- Phylogenetic relationship in Metanephrops --- p.84 / Chapter 3.4.4 --- Evolutionary history of Metanephrops --- p.90 / Chapter Chapter 4 --- Molecular Identification of Nephropidae --- p.92 / Chapter 4.1 --- Introduction --- p.92 / Chapter 4.2 --- Materials and methods --- p.93 / Chapter 4.2.1 --- Species studied and sample collection --- p.93 / Chapter 4.2.2 --- DNA extraction --- p.95 / Chapter 4.2.3 --- Amplification of genes --- p.95 / Chapter 4.2.4 --- PCR profiles for mitochondrial genes --- p.97 / Chapter 4.2.5 --- Nucleotide sequencing --- p.97 / Chapter 4.2.6 --- Purification of asymmetric PCR products --- p.97 / Chapter 4.2.7 --- Sequence alignment --- p.97 / Chapter 4.2.8 --- Cluster analysis --- p.97 / Chapter 4.2.9 --- Graphical summary of species similarity --- p.98 / Chapter 4.2.10 --- Testing of molecular identification system in Nephropidae --- p.98 / Chapter 4.3 --- Results --- p.100 / Chapter 4.3.1 --- PCR products and sequence alignments of 16S rRNA and COI genes --- p.100 / Chapter 4.3.2 --- Species identification for clawed lobsters --- p.100 / Chapter 4.3.2.1 --- 16S rRNA profile --- p.100 / Chapter 4.3.2.2 --- COI profile --- p.108 / Chapter 4.4 --- Discussion --- p.116 / General Conclusion --- p.124 / Literature Cited --- p.127 / Appendices --- p.146

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It is well known that the mitochondrial genome has a much higher spontaneous mutation rate than the nuclear genome. mtDNA mutations have been identified in association with many diseases and aging. mtDNA replication continues throughout the cell cycle, even in post-mitotic cells. Therefore, a constant supply of nucleotides is required for replication and maintenance of the mitochondrial genome. However, it is not clear how dNTPs arise within mitochondria nor how mitochondrial dNTP pools are regulated. Recent evidence suggests that abnormal mitochondrial nucleoside and nucleotide metabolism is associated with several human diseases. Clearly, to uncover the pathogenesis of these diseases and the mechanisms of mitochondrial mutagenesis, information is needed regarding dNTP biosynthesis and maintenance within mitochondria, and biochemical consequences of disordered mitochondrial dNTP metabolism. The studies described in this thesis provide important insight into these questions. First, we found that a distinctive form of ribonucleotide reductase is associated with mammalian liver mitochondria, indicating the presence of de novo pathway for dNTP synthesis within mitochondria. Second, we found that long term thymidine treatment could induce mtDNA deletions and the mitochondrial dNTP pool changes resulting from thymidine treatment could account for the spectrum of mtDNA point mutations found in Mitochondrial neurogastrointestinal encephalomyopathy (MNGIE) patients. These results support the proposed pathogenesis of this disease. Third, we found that normal intramitochondrial dNTP pools in rat tissues are highly asymmetric, and in vitro fidelity studies show that these imbalanced pools can stimulate base substitution and frameshift mutations, with a substitution pattern that correlates with mitochondrial substitution mutations in vivo. These findings suggest that normal intramitochondrial dNTP pool asymmetries could contribute to mitochondrial mutagenesis and mitochondrial diseases. Last, Amish lethal microcephaly (MCPHA) has been proposed to be caused by insufficient transport of dNTPs into mitochondria resulting from a loss-of-function mutation in the gene encoding a mitochondrial deoxynucleotide carrier (DNC). We found that there are no significant changes of intramitochondrial dNTP levels in both a MCPHA patient's lymphoblasts with a missense point mutation in Dnc gene and the homozygous mutant cells extracted from Dnc gene knockout mouse embryos. These results do not support the proposed pathogenesis of this disease and indicate that the DNC protein does not play a crucial role in the maintenance of intramitochondrial dNTP pools. / Graduation date: 2005

Caenorhabditis elegans is arguably the best understood animal on the planet. Used for over 50 years to study development, we have a vast amount of knowledge of the inner workings of this worm. Our knowledge is incomplete, however, without placing this organism in its evolutionary and ecological context. In this body of work, I focused on examining the evolutionary forces shaping Caenorhabditis nematodes, with a particular emphasis on C. briggsae. In the first part, I examined the evolution of mitochondrial genomes throughout the genus. I tested for signatures of selection and examined the evolution of mitochondrial genome architecture. Through this, I have shown that the mitochondrial genomes of Caenorhabditis nematodes appear to be primarily influenced by purifying selection and that molecular evolutionary inference is greatly limited by mutational saturation. The evolutionary forces acting on mitochondrial genomes have been examined before, however, this study, extensively examining this within a single genus, provides a much better characterization than any of the studies to date. In the second part, I characterized the evolutionary dynamics of mitochondrial pseudogenes in C. briggsae and its closest relatives. I showed that these elements, while they might not evolve under strictly neutral terms, are still quite useful in uncovering cryptic diversity and population structure. I also observed that they appear/disappear in a manner that appears inconsistent with one commonly held model for mitochondrial pseudogene evolution. In the final part, I examined the evolution of C. briggsae in response to a biotic environment. I showed that fitness in a parasite-containing environment incurs a trade-off with fitness in the absence of parasites. Together, the chapters of this dissertation demonstrate the strength of Caenorhabditis, and in particular C. briggsae, for examining evolutionary questions and advances this system as a tool for evolutionary biology research. / Graduation date: 2013

Abstracts Capricornis swinhoei is one of the indangered wild animals in Taiwan. The objective of this study is using molecular biology and morphology methods to analyze the genetic diversity, observed population structure, differentiation and biogeographic relationships among the population of Capricornis swinhoei. Samples used in this study were collected from the Central Mountains located in Taiwan. DNA sequences (1099 bp) from the mitochondrial DNA (mtDNA) control region, D-loop, were used to test the phylogeographic relationships among the Capricornis swinhoei. A phylogenetic tree was constructed on the basis of GCG-Seq Web and MEGA softwares. In addition, distance analyses, neighbor-join, and maximum parsimony to resolve these phylogenetic relationships were performed. The C. sumatraensis and C. crispus sequence were also determined and used as the outgroups. Our findings clearly demonstrate that Capricornis swinhoei can be clustered into two groups, north and south groups, and consistent with the truth of geographic isolation. The data obtained from this study may facilitate the program of wildlife conservation in Taiwan.

Antrodia camphorata is a Taiwan-unique fungus which grows on the walls inside the core of decayed Cinnamomum kanehirae. Antrodia camphorata provides many bioactive substance and it is cultivated mainly via mycelium nowadays. First section of this research is focused on Antrodia camphorata (CCRC-35716) in liquid cultivation medium and the changes within extracellular polysaccharides, trierpenoids, pH and growth. It also uses HPLC to analyze the differences of mycelium triterpenoids. This experiment showed when Antrodia camphorata was cultivated in PDB liquid medium for 14 days; it had the highest extracellular polysaccharides (0.23

Complete DNA sequences were determined for the mitochondrial (mt) genomes of the sea anemones, Mesactinia genesis ¡]20,544 bp¡^, Heteractis aurora (19,800 bp) and partial mtDNA between cox2 and nad4 of the Calliactis sp. (3,713 bp). In addition, complete mtDNA sequences were determined for the sea squirt, Eudistoma gilboviride (14,203 bp). The circular, sea anemones genomes contain the genes for 13 energy pathway proteins and two ribosomal RNAs and two transfer RNAs. H. aurora contains a previously undescribed ORF between the cox2 and nad4 genes encoding a putative protein of 646 amino acids. In M. geneisis and Calliactis sp. encodes two separate smaller ORFs of 259 and 243 as well as 269 and 345 in the corresponding regions, respectively. Possible control region of the mitochondrial genomes of M. geneisis and H. aurora were identified in the intergenic region 13. The sea squirt genomes contain the genes for 11 energy pathway proteins and two rRNAs and 22 tRNAs. All genes are encoded by the heavy strand, except for trnM, trnK, and trnV, which are encoded by the light strand. The ascidians showed frequent and extensive gene rearrangement. The gene order in E. gilboviride are very much different from the other ascidians mt-genome. The E. gilboviride mtDNA does not encode the nad6 and a tpyical atp8. Molecular phylogenetic analyses based on nucleic acid and amino acid sequences of the deuterostome (echinoderms, chordate and Xenoturbella), and cnidaria coincide with the morphological characters.

Thesis (Ph. D.)--Ohio State University, 2003. / Title from first page of PDF file. Document formatted into pages; contains xiii, 164, p.: ill. (some col.). Includes abstract and vita. Advisor: Paul W. Sciulli, Dept. of Anthropology. Includes bibliographical references (leaves 145-160).