Functional genomics of motile commensal intestinal bacteria

Flagella confer upon bacteria the ability to move and are therefore organelles of significant bacteriological importance. The innate immune system has evolved to recognise flagellin, (the major protein component of the bacterial flagellar filament). Flagellate microbes can potentially stimulate the immune systems of mammals, and thus have significant immunomodulatory potential. The flagellum-biogenesis genotype and phenotype of Lactobacillus ruminis, an autochthonous intestinal commensal, was studied. The flagellum-biogenesis genotypes of motile enteric Eubacterium and Roseburia species were also investigated. Flagellin proteins were recovered from these commensal species, their amino-termini were sequenced and the proteins were found to be pro-inflammatory, as assessed by measurement of interleukin-8 (IL-8) secretion from human intestinal epithelial cell lines. For L. ruminis, this IL-8 secretion required signalling through Toll Like Receptor 5. A model for the regulation of flagellum-biogenesis in L. ruminis was inferred from transcriptomics data and bioinformatics analyses. Motility gene expression in this species may be under the control of a novel regulator, LRC_15730. Potential promoters for genes encoding flagellin proteins in the Eubacterium and Roseburia genomes analysed were inferred in silico. Relative abundances of the target Eubacterium and Roseburia species in the intestinal microbiota of 25 elderly individuals were determined. These species were found to be variably abundant in these individuals. Motility genes from these species were variably detected in the shotgun metagenome databases generated by the ELDERMET project. This suggested that a greater depth of sequencing, or improved evenness of sequencing, would be required to capture the full diversity of microbial functions for specific target or low abundance species in microbial communities by metagenomics. In summary, this thesis used a functional genomics approach to describe flagellum-mediated motility in selected Gram-positive commensal bacteria. The regulation of flagellum biosynthesis in these species, and the consequences of flagella expression from a host-interaction perspective were also considered.

AuxAg1-x alloy seeds: A way to control growth, morphology and defect formation in Ge nanowires

Germanium (Ge) nanowires are of current research interest for high speed nanoelectronic devices due to the lower band gap and high carrier mobility compatible with high K-dielectrics and larger excitonic Bohr radius ensuing a more pronounced quantum confinement effect [1-6]. A general way for the growth of Ge nanowires is to use liquid or a solid growth promoters in a bottom-up approach which allow control of the aspect ratio, diameter, and structure of 1D crystals via external parameters, such as precursor feedstock, temperature, operating pressure, precursor flow rate etc [3, 7-11]. The Solid-phase seeding is preferred for more control processing of the nanomaterials and potential suppression of the unintentional incorporation of high dopant concentrations in semiconductor nanowires and unrequired compositional tailing of the seed-nanowire interface [2, 5, 9, 12]. There are therefore distinct features of the solid phase seeding mechanism that potentially offer opportunities for the controlled processing of nanomaterials with new physical properties. A superior control over the growth kinetics of nanowires could be achieved by controlling the inherent growth constraints instead of external parameters which always account for instrumental inaccuracy. The high dopant concentrations in semiconductor nanowires can result from unintentional incorporation of atoms from the metal seed material, as described for the Al catalyzed VLS growth of Si nanowires [13] which can in turn be depressed by solid-phase seeding. In addition, the creation of very sharp interfaces between group IV semiconductor segments has been achieved by solid seeds [14], whereas the traditionally used liquid Au particles often leads to compositional tailing of the interface [15] . Korgel et al. also described the superior size retention of metal seeds in a SFSS nanowire growth process, when compared to a SFLS process using Au colloids [12]. Here in this work we have used silver and alloy seed particle with different compositions to manipulate the growth of nanowires in sub-eutectic regime. The solid seeding approach also gives an opportunity to influence the crystallinity of the nanowires independent of the substrate. Taking advantage of the readily formation of stacking faults in metal nanoparticles, lamellar twins in nanowires could be formed.

Analysis of expression quantitative trait loci in D. melanogaster

Expression Quantitative Trait Loci (eQTL) analysis allows for the identification of genetic variation associated with variation in gene expression. It is often unclear however, which of the associated variants are causal, and by what mechanism. Integrating functional genomic data with eQTL data can provide insight into the impact of natural variation in the population, and the nature of the transcriptional machinery itself. In this thesis, I integrate functional genomic data with eQTL data derived from both 5’ CAGE and 3’ TagXseq expression assays, in developing embryos. I first use both datasets to analyse the transcription landscape in embryonic D., melanogaster, and then carry out an analysis of sequence motifs associated with transcription factor binding sites, promoters, and 3’ polyadenylation sites. Finally, I integrate functional genomic data, including these novel sequence motifs, to shed light on the mechanisms of gene expression variation in D.,melanogaster. I am able to demonstrate that some variants effecting gene regulation in Drosophila are found within haplotypes which buffer their effects.