This thesis documents the contribution of my bioinformatics research activities, including
novel software development, to a range of research projects aimed at investigating the
interactions between bacterial and viral pathogens and their hosts. The focus is largely on
farm animal species and their pathogens, although some of the research has a wider
scientific impact.
RNA interference (RNAi) refers to a variety of related regulatory pathways present in
animals, plants and insects. The major pathways are microRNAs (miRNAs), small-interfering
RNAs (siRNAs) and PIWI-interacting RNAs (piRNAs). Marek’s disease virus is an important
pathogen of poultry, causing T-cell lymphoma. We identified the presence and expression
patterns of several MDV-encoded microRNAs, including the identification of 5 novel
microRNAs. We also showed that not only do virus-encoded microRNAs dominate the
mirNome within chicken cells, but also that specific host-microRNAs are down-regulated.
We also identify novel virus-encoded microRNAs in other Herpesviridae and provide the
first evidence of miRNA evolution by duplication in viruses. In related work, we present a
novel microRNA generated by the canonical miRNA biogenesis pathway in Avian Leukosis
Virus, another avian oncogenic virus, and publish data showing the expression pattern of
known chicken microRNAs across a range of important avian cells. Two of the other RNAi
pathways (siRNA and piRNA) form an important part of the antiviral response in
arthropods. We have published work demonstrating an siRNA antiviral response to
bluetongue virus and Schmallenberg virus in cells from the Culicoides midge, an important
insect vector, as well as work demonstrating the importance of the piRNA pathway in the
antiviral response to Semliki forest virus (SFV). Further work on flaviviruses in ticks
demonstrates the active suppression of the siRNA response by Langat Virus, as well as a key
difference between the siRNA responses in Mosquitos compared to ticks.
Salmonella is one of the most important zoonoses, with an estimated 1.4 million cases of
human salmonellosis per annum in the USA alone. Salmonella infections of farm animals
are an important route into the human food chain. This thesis presents work on the
comparative structure and function of 13 fimbrial operons within Salmonella enterica
serovar Enteritidis as well as a genomic comparison of that serovar with Salmonella
enterica serovar Gallinarum, a chicken-specific serovar. We characterised the global
expression profile of Salmonella enterica serovar Typhimurium during colonization of the
chicken intestine, and we have published the genomes of four strains of Salmonella
eneterica serovars of well-defined virulence in food-producing animals. Our work in this
area led to us publishing an important and comprehensive review of the automatic
annotation of bacterial genomes.
Finally, I present work on novel software development. ProGenExpress, a software tool
that allows the easy and accurate integration and visualisation of quantitative data with the
genome annotation of bacteria; Meta4 is a web application that allows data sharing of
bacterial genome annotations from metagenomes; CORNA, a software tool that allows
scientists to link together microRNA targets, gene expression and functional annotation;
viRome, a software tool for the analysis of siRNA and piRNA responses in virus-infection
studies; DetectiV, a software tool for the analysis of pathogen-detection microarray data;
and poRe, a software tool that enables users to organise and analyse nanopore sequencing
dat