by Chow Wing Kuen. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1993. / Includes bibliographical references (leaves 94-109). / Abstract --- p.i / Acknowledgements --- p.iii / Table of contents --- p.v / List of Tables --- p.viii / List of Figures --- p.ix / Abbreviations --- p.xi / Chapter Chapter 1 --- General Introduction --- p.1 / Chapter Chapter 2 --- Literature review / Chapter 2.1 --- Hypersensitivity to Crustacea --- p.3 / Chapter 2.2 --- Characterization of allergens of shrimp --- p.10 / Chapter 2.3 --- Cross reactivity of crustacean allergens --- p.18 / Chapter 2.4 --- Molecular cloning and expression of allergens --- p.22 / Chapter Chapter 3 --- Immunological characterization of shrimp allergens / Chapter 3.1 --- Introduction --- p.26 / Chapter 3.2 --- Material and Methods / Chapter 3.2.1 --- Animals --- p.28 / Chapter 3.2.2 --- Sera --- p.28 / Chapter 3.2.3 --- Shrimp tissue extract --- p.29 / Chapter 3.2.4 --- Dot blotting --- p.29 / Chapter 3.2.5 --- Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) --- p.30 / Chapter 3.2.6 --- Immunoblotting --- p.32 / Chapter 3.3.7 --- Immunological detection of IgE binding proteins --- p.32 / Chapter 3.3 --- Results / Chapter 3.3.1 --- Detection of allergens in raw and cooked shrimp muscle extract --- p.35 / Chapter 3.3.2 --- Detection of allergens in hepatopancreas and ovary of the shrimp --- p.38 / Chapter 3.3.3 --- Detection of allergens in boiling shrimp fluid --- p.42 / Chapter 3.3.4 --- Detection of allergens in dried shrimp --- p.48 / Chapter 3.3.5 --- Reactivity of IgE from the shrimp- sensitive subjects with extracts from different species of penaeid shrimp --- p.48 / Chapter 3.3.6 --- Reactivity of IgE from the shrimp- sensitive subjects with muscle extracts of crustaceans and mollusks --- p.52 / Chapter 3.4 --- Discussion --- p.55 / Chapter Chapter 4 --- "Construction and immunoscreening of the cDNA library from muscle of the shrimp, Metapenaeus ensis" / Chapter 4.1 --- Introduction --- p.63 / Chapter 4.2 --- Materials and Methods / Chapter 4.2.1 --- Animals --- p.66 / Chapter 4.2.2 --- Sera --- p.66 / Chapter 4.2.3 --- Controlling ribonuclease activity --- p.66 / Chapter 4.2.4 --- Isolation of total RNA --- p.67 / Chapter 4.2.5 --- Isolation of mRNA / Chapter 4.2.5.1 --- Oligo-d(T) cellulose chromatography --- p.68 / Chapter 4.2.5.2 --- Magnetic separation --- p.70 / Chapter 4.2.6 --- Synthesis of double stranded cDNA --- p.71 / Chapter 4.2.7 --- Generation of EcoRI cohesive ends on cDNA --- p.72 / Chapter 4.2.8 --- Ligation of cDNA with λgtll vector --- p.74 / Chapter 4.2.9 --- In vitro packaging --- p.74 / Chapter 4.2.10 --- Titration of phage library --- p.75 / Chapter 4.2.11 --- Absorption of anti-E.coli antibodies --- p.76 / Chapter 4.2.12 --- Immunoscreening of the shrimp muscle cDNA library --- p.77 / Chapter 4.3 --- Results --- p.80 / Chapter 4.4 --- Discussion --- p.89 / Chapter Chapter 5 --- General conclusion --- p.92 / References --- p.94

Lei Ho Chee. / Thesis submitted in: December 2006. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2007. / Includes bibliographical references (leaves 140-153). / Abstracts in English and Chinese. / Abstract --- p.i / Abstract (Chinese) --- p.iii / Acknowledgements --- p.v / Contents --- p.vi / List of Tables --- p.x / List of Figures --- p.xii / Chapter 1 General Introduction --- p.1 / Chapter 2 Literature Review --- p.4 / Chapter 2.1 --- DNA taxonomy --- p.4 / Chapter 2.1.1 --- Definitions --- p.4 / Chapter 2.1.2 --- Significance of DNA taxonomy --- p.5 / Chapter 2.1.3 --- DNA taxonomy in different animals --- p.5 / Chapter 2.1.4 --- Studying DNA taxonomy on Crustacea with different gene markers --- p.6 / Chapter 2.1.4.1 --- Mitochondrial gene makers --- p.6 / Chapter 2.1.4.2 --- Nuclear gene marker --- p.9 / Chapter 2.1.5 --- Phylogenetic construction methods --- p.10 / Chapter 2.2 --- Taxonomy of infraorder Caridea based on morphologies --- p.13 / Chapter 2.3 --- DNA barcodes --- p.29 / Chapter 2.3.1 --- Idea of barcodes --- p.29 / Chapter 2.3.2 --- Significance of DNA barcode --- p.29 / Chapter 2.3.3 --- Mitochondrial COI gene as DNA barcode --- p.30 / Chapter 2.3.3.1 --- Species identification with COI gene --- p.31 / Chapter 2.3.3.2 --- Revealing cryptic species with COI gene --- p.31 / Chapter 2.3.4 --- Limitations of DNA barcodes --- p.32 / Chapter 2.4 --- Species Diagnosis with hybridization methods --- p.34 / Chapter 2.4.1 --- Species diagnosis with mircoarray --- p.35 / Chapter 2.4.2 --- Species diagnosis with dot blot hybridization --- p.35 / Chapter Chapter 3 --- DNA Taxonomy of Infraorder Caridea --- p.39 / Chapter 3.1 --- Introduction --- p.39 / Chapter 3.2 --- Materials and Methods --- p.40 / Chapter 3.2.1 --- Sample collection --- p.40 / Chapter 3.2.2 --- DNA extraction and PCR amplification --- p.41 / Chapter 3.2.3 --- DNA sequencing --- p.48 / Chapter 3.2.4 --- Phylogenetic analysis --- p.49 / Chapter 3.3 --- Results --- p.50 / Chapter 3.3.1 --- Sequence composition --- p.50 / Chapter 3.3.2 --- Comparisons of sequences divergence --- p.52 / Chapter 3.3.3 --- Phylogenetic analysis using the four gene regions --- p.76 / Chapter 3.3.3.1 --- COI --- p.76 / Chapter 3.3.3.2 --- 16S rRNA --- p.95 / Chapter 3.3.3.3 --- 12S rRNA --- p.96 / Chapter 3.3.3.4 --- 18S rRNA --- p.97 / Chapter 3.3.3.5 --- Combined analysis of 16S rRNA and 18S rRNA --- p.98 / Chapter 3.3.3.6 --- Composition vector analysis of 18S rRNA --- p.99 / Chapter 3.3.4 --- Saturation analysis --- p.99 / Chapter 3.4 --- Discussion --- p.105 / Chapter 3.4.1 --- Evaluation of the four DNA markers --- p.105 / Chapter 3.4.1.1 --- COI --- p.105 / Chapter 3.4.1.2 --- 16S rRNA and 12S rRNA --- p.107 / Chapter 3.4.1.3 --- 18SrRNA --- p.109 / Chapter 3.4.2 --- Comparison with morphological classification schemes --- p.111 / Chapter 3.4.2.1 --- Relationships at family level --- p.111 / Chapter 3.4.2.2 --- Relationships at superfamily level --- p.116 / Chapter 3.4.2.3 --- Relationship among superfamilies --- p.121 / Chapter Chapter 4 --- Development of specific probes for caridean family identification --- p.122 / Chapter 4.1 --- Introduction --- p.122 / Chapter 4.2 --- Methods and Materials --- p.123 / Chapter 4.2.1 --- Probe design --- p.123 / Chapter 4.2.2 --- Probe labeling and checking yield --- p.125 / Chapter 4.2.3 --- Preparation of target DNA and dot-blot --- p.126 / Chapter 4.2.4 --- Pre-hybridization and hybridization --- p.128 / Chapter 4.2.5 --- Stripping of membrane --- p.129 / Chapter 4.2.6 --- Preparation of chemicals and reagents --- p.129 / Chapter 4.3 --- Results --- p.131 / Chapter 4.4 --- Discussion --- p.135 / Chapter Chapter 5 --- General Conclusion --- p.138 / Literature cited --- p.140 / Appendices 1. Aligned sequences of mitochondrial COI gene --- p.154 / 2. Aligned sequences of mitochondrial 16S rRNA gene --- p.162 / 3. Aligned sequences of mitochondrial 12S rRNA gene --- p.168 / 4. Aligned sequences of nuclear 18S rRNA gene --- p.172

Chu Wai-ling. / Thesis submitted in: December 2003. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2004. / Includes bibliographical references (leaves 106-114). / Abstracts in English and Chinese. / Abstract --- p.i / Abstract (Chinese) --- p.iii / Acknowledgments --- p.v / Contents --- p.vi / List of Tables --- p.ix / List of Figures --- p.x / Chapter Chapter 1 --- General Introduction --- p.1 / Chapter Chapter 2 --- Literature Review --- p.8 / Chapter 2.1 --- Introduction to phylogenetic biology --- p.8 / Chapter 2.1.1 --- Definition of phylogenetics --- p.8 / Chapter 2.1.2 --- Why employ molecular genetic markers in phylogenetics? --- p.8 / Chapter 2.2 --- DNA analysis and the contributions to phylogenetics --- p.10 / Chapter 2.2.1 --- Historical development of DNA analysis in phylogenetics --- p.10 / Chapter 2.2.2 --- Nuclear ribosomal DNA (rDNA) --- p.12 / Chapter 2.2.3 --- Animal mitochondrial DNA (mt DNA) --- p.14 / Chapter 2.3 --- Molecular phylogeny of crustaceans --- p.16 / Chapter 2.3.1 --- Phylogenetic studies of crustaceans using nuclear ribosomal DNA --- p.16 / Chapter 2.3.2 --- Phylogenetic studies of crustaceans using mitochondrial DNA --- p.17 / Chapter 2.4 --- Taxonomy of the genus Heterocarpus --- p.22 / Chapter Chapter 3 --- Materials and Methods --- p.36 / Chapter 3.1 --- Collection and storage of specimens --- p.36 / Chapter 3.2 --- DNA extraction --- p.36 / Chapter 3.3 --- Amplification of mitochondrial genes --- p.38 / Chapter 3.3.1 --- PCR profile --- p.39 / Chapter 3.3.1.1 --- 16SrRNA gene --- p.39 / Chapter 3.3.1.2 --- COI gene --- p.42 / Chapter 3.3.1.2.1 --- Amplification of COI gene segments using primers LCD1490/HCO2198 --- p.42 / Chapter 3.3.1.2.2 --- Amplification of COI gene segments using primers COIf/COIa and COIp3/COIa --- p.43 / Chapter 3.4 --- DNA sequencing --- p.44 / Chapter 3.4.1 --- Purification of extension products --- p.45 / Chapter 3.4.2 --- Electrophoresis and data collection --- p.46 / Chapter 3.5 --- Data analysis --- p.47 / Chapter Chapter 4 --- Results --- p.50 / Chapter 4.1 --- PCR products of 16S rRNA and COI genes --- p.50 / Chapter 4.2 --- Genetic variability in Heterocarpus based on partial DNA sequence of 16S rRNA gene --- p.52 / Chapter 4.3 --- Genetic variability in Heterocarpus based on COI gene --- p.61 / Chapter 4.3.1 --- Genetic variability in Heterocarpus based on partial DNA sequence of COI gene --- p.61 / Chapter 4.3.2 --- Genetic variability in Heterocarpus based on amino acid sequence of COI --- p.69 / Chapter 4.4 --- Phylogenetic analysis --- p.75 / Chapter 4.4.1 --- Phylogenetic analysis based on 16S rDNA sequence --- p.75 / Chapter 4.4.2 --- Phylogenetic analysis based on DNA sequence of COI gene --- p.80 / Chapter 4.4.3 --- Phylogenetic analysis based on amino acid sequence of COI --- p.84 / Chapter 4.5 --- Kishino-Hasegawa and Shimodaira-Hasegawa tests --- p.86 / Chapter Chapter 5 --- Discussion --- p.90 / Chapter 5.1 --- Examination on the validity of the four Heterocarpus complexes --- p.90 / Chapter 5.2 --- Phylogenetic relationship of Heterocarpus species within each complex --- p.91 / Chapter 5.2.1 --- Phylogenetic relationship of Heterocarpus species within H.gibbosus complex --- p.92 / Chapter 5.2.2 --- Phylogenetic relationship of Heterocarpus species within H.woodmasoni complex --- p.94 / Chapter 5.2.3 --- Phylogenetic relationship of Heterocarpus species within H. ensifer and H. sibogae complexes --- p.96 / Chapter 5.3 --- Phylogenetic relationship among Heterocarpus complexes --- p.98 / Chapter 5.4 --- "Comparisons of phylogenetic resolving power of 16S rRNA, COI and 28S rRNA genes" --- p.100 / Chapter Chapter 6 --- Conclusions --- p.104 / Literature Cited --- p.106

A quantitative study of the decapod crustacean community commensal with the coral Pocillopora meandrina var. nobilis Verrill was undertaken and was accomplished through an analysis of communities collected in coral heads in Kaneohe Bay, Oahu. The coral head microhabitat was described and analyzed. The community was described and its relationship to the coral head habitat defined. It was found that community composition was affected by coral head size and that relative composition of the communities changed as the coral heads increased in size. Through stomach contents analysis and trophic behavior experiments the commensals were found to utilize the coral as a source of food, primarily by feeding on material caught on the coral. A correlation between the total biomass of the crustacean community and the surface area of the coral heads in which they were collected was found, suggesting that the com- munity is limited by the amount of surface area of a coralhead This may reflect the amount of food available to the symbionts. There was no good correlation between surface area of the corals and the biomass of the individual components of the community, indicating that other factors, such as the behavioral peculiarity of pairing and interspecific competition probably determine the exact composition of the community that a coral head can support. It was concluded that the crustaceans studied were true commensals with the coral, and that the commensal association involves the host providing a source of food as well as protection for the symbionts. / Typescript. Bibliography: leaves 62-64.

Univ., Diss.--Hamburg, 2004. / Die Vorlage enthält insgesamt 4 Werke. Leicht veränderte Fassung einer kumulativen Dissertation.

Thesis (M.S.)--Marshall University, 2004. / Title from document title page. Document formatted into pages; contains ix, 88 p. including illustrations. Includes abstract. Includes bibliographical references (p. 72-76).

Thesis (Ph. D.)--Rijksuniversiteit, Groningen, The Netherlands, 1937. / Bibliography: p. [109]-110.

Resumo: Os crustáceos da ordem Decapoda são muito importantes na produção pesqueira marinha do estado de Santa Catarina. Os estudos sobre a composição, abundância e distribuição das larvas desses animais podem informar sobre locais e épocas de reprodução dos adultos. A composição e densidade das fases larvais dos crustáceos podem ser afetadas pelas características oceanográficas como massas de água e circulação. É fundamental compreender como os fatores bióticos e abióticos afetam o ciclo de vida dos decápodes. Assim, este estudo avaliou a composição, a distribuição, e a dinâmica sazonal das larvas de decápodes na plataforma interna (<50 m) de Santa Catarina, bem como os fatores oceanográficos que podem influenciar a disponibilidade das mesmas. Para isso, foram analisadas amostras de zooplâncton coletadas em cinco cruzeiros, realizados entre novembro de 2005 e junho de 2006, em um transecto transversal à costa. As larvas encontradas foram classificadas em 32 táxons das infraordens Penaeidea, Caridea, Thalassinidea, Anomura e Brachyura. Penaeidea foi a infraordem mais abundante, com densidade média de 10 ind.m-3 e a Anomura foi a menos abundante com densidade média de 1 ind.m-3. O Lucifer faxoni foi a espécie mais abundante do estudo, com densidade máxima de 51 ind.m-3. Dentre os meses estudados, as larvas foram mais abundantes em novembro e janeiro e se distribuíram sem um padrão definido por toda a plataforma interna. A análise de correspondência canônica indicou que não houve influencia dos fatores ambientais na densidade das larvas.

Os crustáceos do gênero Aegla, endêmicos da América do Sul, são os únicos decápodes anomuros que vivem em ambientes de água doce. A descoberta de fósseis em sedimentos marinhos deixou poucas dúvidas sobre a origem do grupo. Diversos estudos taxonômicos, morfológicos e de distribuição geográfica têm sido realizados sobre os eglídeos. Entretanto, informações filogenéticas baseadas na morfologia do grupo limitam-se, basicamente, aos trabalhos sobre a posição da família Aeglidae na infraordem Anomura e a um trabalho pioneiro, no qual os autores propuseram um cladograma para sete espécies com ocorrência no Chile. A partir de revisões taxonômicas e de uma análise cladística, com base em caracteres morfológicos, das espécies de Aegla que ocorrem nas bacias hidrográficas do Alto Paraná e Alto Uruguai, obteve-se: 1. O não-monofiletismo do clado Alto Paraná-Alto Uruguai; 2. Aegla leptochela relacionada filogeneticamente com outras espécies do Alto Ribeira; 3. Aegla marginata é uma espécie parafilética e forma um complexo com Aegla quilombola n. sp.; 4. Aegla franca e A. perobae são espécies irmãs; 5. Aegla lata, entre outras espécies, aparecem relacionadas com populações de diferentes bacias hidrográficas demonstrando tanto a falta de caracteres derivados dentro de Aeglidae, bem como a possibilidade de existirem mais complexos de diferentes espécies nessa família; 6. A invasão ao ambiente subterrâneo ocorreu mais de uma vez ao longo do tempo e espécies estigobiontes não são irmãs recíprocas exclusivas; 7. Aegla paulensis trata-se de um complexo de sete espécies distintas: Aegla paulensis s. str., A. rosanae, A. lancinhas, A. japi n. sp., A. jaragua n. sp., A. jundiai n. sp. e A. vanini n. sp. Além disso, análises em microscopia eletrônica de varredura dos tubos sexuais de machos de 39 espécies de Aegla, revelaram dois principais tipos, o longo estreito e o curto largo e, ainda, que cada espécie possui um conjunto de características específicas para essa estrutura, podendo, então, ser utilizada como caráter diagnóstico em descrições taxonômicas / The South American endemic genus Aegla represents the only anomuran decapod crustaceans strictly living in freshwaters. Marine fossil records left no doubts regarding the origin of the group. A number of studies on taxonomy, morphology and geographical distribution of aeglid have been carried out. Nevertheless, morphology based phylogenetic information about the group is limited to studies of the positioning of Aeglidae into the Anomuran infraorder and one pioneer work which presented a cladogram for seven species from Chile. Through cladistic analysis based on morphological characters of Aegla species occurring in the upper Paraná and upper Uruguay hydrographic basins the following results were obtained: 1. The non-monophyletic condition of the upper Paraná-upper Uruguay clade; 2. Aegla leptochela phylogenetically related to other species from Alto Ribeira; 3. Aegla marginata is paraphyletic, constituting a complex with Aegla quilombola n. sp.; 4. Aegla franca and A. perobae are sister species; 5. Aegla lata and other species were related with populations from different hydrographic basins, showing the lack of derived characters in Aeglidae and the possibility of existence of other species complexes in this family; 6. Invasion to the underground environments occurred more than once and the stygobiont species are not exclusive reciprocal sisters; 7. Aegla paulensis is a species complex encompassing seven species: Aegla paulensis s. str., A. rosanae, A. lancinhas, A. japi n. sp., A. jaragua n. sp., A. jundiai n. sp. e A. vanini n. sp.. In addition, scanning electron microscopy revealed two main types of sexual tubes (long and narrow; short and wide) in males from 39 Aegla species. Each species has a specific set of characters for this structure, hence indicating it can be used as diagnostic character in taxonomic descriptions

Finally, the gene tree of the true crabs, Brachyura, confirms that the basal "Podotremata" is paraphyletic, with the Raninoidea and Cyclodorippoidea more closely related to Eubrachyura than to the other podotremes. Within the monophyletic Eubrachyura, the analysis supports the reciprical monophyly of the two subsections, Heterotremata and Thoracotremata. All of the Old World freshwater crabs cluster together, representing an early diverged lineage in the Heterotremata. / From the inferred phylogeny, we have obtained new insights on the evolution of decapods. First, the spiny lobster from the family Palinuridae is found to be paraphyletic with the polyphyletic Synaxidae nested within it. The Stridentes forms a monophyletic assemblage, indicating that the stridulating sound producing organ evolved only once in the spiny lobsters. Moreover, the spiny lobsters originated in the shallower water rocky reefs of the Southern Hemisphere and then invaded deep sea habitats and diversified. / In sum, I demonstrate the utility of the nuclear protein-coding gene markers in decapod phylogeny and they are informative across a wide range of taxonomic levels. I propose that nuclear protein-coding genes should constitute core markers for future phylogenetic studies of decapods, especially for higher systematics. / Second, we show that hermit crabs have a single origin, but surprisingly, that almost all other major clades and body forms within the Anomura, are derived from within the hermit crabs. The crab-like form and squat lobster form have each evolved at least twice from separate symmetrical hermit crab ancestors. These remarkable cases of multiple parallelism suggest considerable phenotypic flexibility within the hermit crab ground plan, with a general tendency towards carcinization. Rather than having a separate origin from other major clades, hermit crabs have given rise to most other major anomuran body types. / The high diversity of decapods has attracted the interest of carcinologists but there is no consensus on decapod phylogeny in spite of the endeavors using both morphological and molecular approaches. New sources of information are necessary to elucidate the phylogenetic relationships among decapods. In the present study, I attempted to develop and apply the nuclear protein-coding gene markers on decapod phylogeny. Using only two protein-coding genes, we have successfully resolved most of the infraordinal relationships with good statistical support, indicating the superior efficiency of these markers compared to nuclear ribosomal RNA and mitochondrial genes commonly used in phylogenetic reconstruction of decapods. Apparently these two types of markers suffer from the problems of alignment ambiguities and rapid saturation, respectively. Subsequently, I tried to apply the nuclear protein-coding genes in revealing interfamilial and intergeneric evolutionary history in three selected decapod groups, the spiny lobster (family Palinuridae), the infraorder Anomura and the true crabs of the infraorder Brachyura to further evaluate the utility of these markers and reconstruct the evolutionary history the groups. Trees with robust support can be obtained using sequences of three to five genes for the infraorders and families tested including the most speciose Brachyura. The genes are shown to be informative in elucidating interspecific phylogeny as well. / Tsang, Ling Ming. / Adviser: Ka Hou Chu. / Source: Dissertation Abstracts International, Volume: 73-02, Section: B, page: . / Thesis (Ph.D.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 127-153). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. [Ann Arbor, MI] : ProQuest Information and Learning, [201-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese.