This thesis investigates how the discourses and governance of human embryonic stem cell (hESC) research operated in South Korea. Comparing South Korea to the UK in three fields (government, newspapers, and public responses) and reflecting scientific misconduct in the South Korean scientists' community, the study tries to identify hidden variables that influenced the national trajectory. To capture dynamic yet underrepresented national and cultural characteristics, the author has analysed microscopic interactions including actors' utterances, media framing, human relations and strategies. By using the methodology to pursue sociological approaches with semantic and social network analysis, concepts usually inferred and narrated by the researcher gain a visual and measurable representation in terms of Actor-Networks. The study concludes that the failure to institutionalise a sustainably cooperative research environment and (bio)ethical regulation in South Korea is an outcome of the lack of reflexive social discourse and deliberative governance. The national characteristics mainly derived from the subdued status of experts, scientists, in the government and the predominant media framing to represent life science as a mere tool to economic development. More crucially, people in general accepted the economy-oriented discourse. From the outcome of the semantic network analysis, it turns out that the public attitude was mainly constructed from people's limited objective and desire to utilise science to pursue social status and economic development. South Korean people largely disregarded the possible threat of hESC research to women's bodies that was related to human rights. A new scientific leadership should recognise this culturally embedded atmosphere and more effectively mediate government, mass media, lay public and scientific community by reconstituting expert role, critical media framing of science, and broader deliberation on the social function of scientific knowledge.

Advances in DNA sequencing technologies, particularly the advent of next generation sequencing (NGS) platforms, have revolutionised the field of metagenomics and allowed great progress to be made in the way that microbial communities are analysed. However, the wealth of data now available thanks to these advancements has made the possibilities far more numerous than just the obvious applications, with a wide variety of novel and diverse studies conceivable. The technologies themselves have also created further areas for research as better methods of handling the, often overwhelming in quantity and misleading in content, data are sought. The analysis carried out in this thesis demonstrates the wide range of study possible stemming from two experiments involving the sequencing of meiofauna DNA. The first of these involves community analysis of marine benthic meiofauna with particular emphasis on diversity and distribution. The second experiment involves the sequencing of pooled nematode samples in order to investigate the effects of sample richness and species relatedness on the generation of chimeric reads in sequencing data. It is shown that the data generated from these two experiments can be used to help formulate an algorithm to simulate PCR and therefore assist the generation of realistic noisy NGS data. These data can, in turn, be used to generate a simulated in silico microbial community for analysis, the results of which reveal insights into the accuracy of chimera detection software and the reliability of metagenetic community analyses. Worryingly, these results suggest that findings from similar in vitro studies are not as reliable as originally perceived. The same experimental data may also be used to investigate interactions between meiofauna species based on the incidental presence of prey species highlighted from the sequencing of individual meiofauna organisms. It is shown that these data can be used to accurately predict a nematode’s feeding type without having to examine the organism directly. It is also shown that there is no correlation between this method of inferring interactions between species and other methods which have been used in the past. This suggests that the earlier methods are inadequate when used for the detection of feeding interactions.

The mechanisms controlling the transmission of bluetongue virus (DTV) by vector Culicoides species were studied using immunohistochemistry, virus titration assays, in vitro transmission tests, viral binding protein analyses and transmission electron microscopy. After infection with BTV by intrathoracic (IT) inoculation, 100% of C. variipennis individuals from a susceptible colony developed a fully disseminated infection and transmitted the virus through their saliva. However only 35.4% of midges were . persistently infected after ingestion of an infectious blood meal, while only 12.1 % of persistently infected midges transmitted the virus through their saliva. The titres of BTV were about 10,·oTCIDsJmidge [Standard error of means (SEM) of log-transformed data=0.15, n=1400] in IT inoculated midges and varied from 0.32 to lQs.oTCIDsJmidge in orally infected individuals. Only those midges containing ~1 03.oTCIDso of BTV could transmit the virus through their saliva. The following patterns were observed in orally (persistently) infected individuals: 1) virus was restricted to the anterior and posterior midgut, and the foregut-midgut junction; 2) virus replicated in the gut cells, disseminated into the haemocoel but could only be detected in a few sporadic fat body cells beyond the gut; 3) virus escaped from the gut cells into the haemocoel and replicated in some secondary organs/tissues but at low levels; 4) a fully disseminated infection was observed and virus replicated in the haemocoel and secondary organs/tissues, including the salivary glands, at high levels. The infection of the gut can be divided into two main types: 1) virus replication in gut cells ranging from very low to higher levels but with virus spread throughout the cytoplasm of the infected cells; 2) virus positive reaction restricted to endosome-like structures in the cytoplasm of some gut cells. BTV was detected in the anterior and posterior midgut, foregut-midgut junction, fat body, ganglia, salivary glands and ommatidia of the compound eyes of some infected midges. No virus was ever found in the hindgut cells, muscles, Malpighian tubes and oocytes/nurse cells of the ovaries. BTV infection of the salivary glands of C. l'ariipcnnis was shown to follow a typical pattern. Virus entered the acinar cells from the haemococl passing through the basement membrane, then localised and replicated in virus inclusion bodies (VIBs) in the cytoplasm of acinar cells. Mature progeny virus particles were released into acini, then transported through intermediate ducts and accumulated in crystalline arrays in the lumen of the major secretory ducts. No virus was released back into the haemocoel through the basement membrane; nor was virus released back into acinar cells from the acini. Nervous tissue of C. l'ariipennis is one of the most susceptible tissues to BTV. Ultrastructural observation showed characteristics ofBTV replication, including formation of VIBs, large amounts of progeny virus particles and tubules, in infected thoracic ganglia. A 60-kD viral protein adhered to both BHK-21 (mammalian) cells and a Culicoides cell line, KC cells. A 44-kD BTV viral protein, co-migrating with non structural protein NS2, adsorbed to BHK-21 cells but not to KC cells, while a 39.6 kD viral protein, co-migrating with major inner capsid protein VP7, adhered only to KC cells but not to BHK-21 cells.

No description available.

Thesis (Ph. D.) -- University of Texas Southwestern Medical Center at Dallas, 2004. / Vita. Bibliography: 291-299.

Thesis (M. Phil.)--University of Hong Kong, 2005. / Title proper from title frame. Also available in printed format.

Developmental disorders including: autism, intellectual disability, and congenital abnormalities are present in 3-8% of live births and display a huge amount of phenotypic and genetic heterogeneity. Traditionally, geneticists have identified individual monogenic diseases among these patients but a majority of patients fail to receive a clinical diagnosis. However, the genomes of these patients frequently harbour large copynumber variants (CNVs) but their interpretation remains challenging. Using pathway analysis I found significant functional associations for 329 individual phenotypes and show that 39% of these could explain the patients’ multiple co-morbid phenotypes; and multiple associated genes clustered within individual CNVs. I showed there was significantly more such clustering than expected by chance. In addition, the presence of a multiple functionally-related genes is a significant predictor of CNV pathogenicity beyond the presence of known disease genes and size of the CNV. This clustering of functionally-related genes was part of a broader pattern of functional clusters across the human genome. These genome-wide functional clusters showed tissuespecific expression and some evidence of chromatin-domain level regulation. Furthermore, many genome-wide functional clusters were enriched in segmental duplications making them prone to CNV-causing mutations and were frequently seen disrupted in healthy individuals. However, the majority of the time a pathogenic CNV affected the entire functional cluster, where as benign CNVs tended to affect only one or two genes. I also showed that patients with CNVs affecting the same functional cluster are significantly more phenotypically similar to each other than expected even if their CNVs do not affect any of the same genes. Lastly, I considered one of the major limitations in pathway analysis, namely ascertainment biases in functional information due to the prioritization of genes linked to human disease, and show how the modular nature of gene-networks can be used to identify and prioritize understudied genes.

The endangered population of Amur tigers (Panthera tigris altaica) in the Russian Far East (RFE) faces an increasing risk of extinction due to infection with canine distemper virus (CDV). Short-lasting CDV infections are unlikely to be maintained in small populations of species with limited connectivity like tigers, where viruses fade out as susceptible hosts are depleted. Multi-host pathogens can persist in more abundant host species that can act as reservoirs of infection for threatened populations. This study combines assessments of host demography, serology and viral phylogeny to establish the relative contribution of domestic dogs and small bodied wild mesocarnivores to the maintenance of CDV, and as sources of infection for tigers. No antibodies were detected among tigers sampled prior to 2000 (n=19), but were measured in 35.7% of tigers in subsequent years (n=56), with at least five discrete transmission events occurring in one well-monitored population. Viral sequences from three tigers and one Far Eastern leopard (P. pardus orientalis) aligned within the Arctic-like clade of CDV, and shared recent common ancestry with viruses from 22 other wild carnivores from the region. Extensive spatial mixing of wild carnivore lineages suggested long chains of transmission consistent with a maintenance population. The exposure of tigers following 2000 coincides with increases in sable (Martes zibellina) numbers and hunting pressure, which could lead to greater pathogen prevalence and potential for spill over from a wild reservoir. The ratio of humans to dogs in rural areas in the RFE are among the lowest in the world (1.73), but the overall number of dogs has been stable during the period of increased CDV exposure in tigers. The only CDV sequence obtained from dogs shared high identity with Asia-4 clade viruses from dogs in Thailand, and was distantly related to wildlife sequences from the RFE. Serum antibodies were detected in dogs in all 26 communities where households were surveyed, but seroprevalence was higher in remote, less densely populated areas, suggesting possible transmission from wildlife. Although the maintenance of CDV in Russian dogs remains unconfirmed, the strong support for a wildlife reservoir limits options for managing the impact of CDV on tiger populations. The high turnover of large and often inaccessible populations of mesocarnivores combines with limitations in vaccine safety, efficacy and delivery, to render the control of CDV in a wildlife reservoir untenable. Managing the impact of CDV on Amur tigers must therefore focus on restoring the size and integrity of remaining tiger populations to withstand future outbreaks. The safety and efficacy of vaccine products for tigers should also be investigated, for use in low coverage vaccination strategies that could enhance the long-term persistence of tiger populations.

No description available.

Recently, long non-coding RNAs (lncRNAs) emerged as important regulators of many cellular functions. Many nuclear lncRNAs regulate the expression of geomically proximal or overlapping protein coding genes. Less clear is whether intergenic lncRNAs can regulate transcription by modulating chromatin at genomically distant loci in an RNA-dependent manner. This thesis investigated molecular functions of Dali, an intergenic central nervous system expressed lncRNA conserved in therian mammals. Dali is transcribed from a locus 50 kb downstream of the Pou3f3 transcription factor gene and performs both genomically local and distal RNA-dependent roles. Its depletion disrupts the differentiation of neuroblastoma cells. Locally, Dali regulates transcription of the Pou3f3 locus. Distally, it preferentially binds near to and regulates active promoters across the genome, including by physically associating with the POU3F3 transcription factor. Dali also interacts with the DNMT1 DNA methyltransferase in mouse and human and regulates CpG island-associated promoters by modulating their DNA methylation levels in trans. This work is the first to demonstrate that a lncRNA can regulate the DNA methylation of CpG island-associated promoters in trans and one of the first large scale studies to identify direct transcriptional targets of a lncRNA genome-wide. It also provides a more detailed molecular dissection of the extended Pou3f3 locus and a framework for the prioritisation and comprehensive functional characterisation of nuclear lncRNAs.