Genetic analysis of bacteriophages from clinical and environmental samples

Bacteriophages, viruses infecting bacteria, are uniformly present in any location where there are high numbers of bacteria, both in the external environment and the human body. Knowledge of their diversity is limited by the difficulty to culture the host species and by the lack of the universal marker gene present in all viruses. Metagenomics is a powerful tool that can be used to analyse viral communities in their natural environments. The aim of this study was to investigate diverse populations of uncultured viruses from clinical (a sputum of patient with cystic fibrosis, CF) and environmental samples (a sludge from a dairy food wastewater treatment plant) containing rich bacterial populations using genetic and metagenomic analyses. Metagenomic sequencing of viruses obtained from these samples revealed that the majority of the metagenomic reads (97-99%) were novel when compared to the NCBI protein database using BLAST. A large proportion of assembled contigs were assignable as novel phages or uncharacterised prophages, the next largest assignable group being single-stranded eukaryotic virus genomes. Sputum from a cystic fibrosis patient contained DNA typical of phages of bacteria that are traditionally involved in CF lung infections and other bacteria that are part of the normal oral flora. The only eukaryotic virus detected in the CF sputum was Torque Teno virus (TTV). A substantial number of assigned sequences from dairy wastewater could be affiliated with phages of bacteria that are typically found in the soil and aquatic environments, including wastewater. Eukaryotic viral sequences were dominated by plant pathogens from the Geminiviridae and Nanoviridae families, and animal pathogens from the Circoviridae family. Antibiotic resistance genes were detected in both metagenomes suggesting phages could be a source for transmissible antimicrobial resistance. Overall, diversity of viruses in the CF sputum was low, with 89 distinct viral genotypes predicted, and higher (409 genotypes) in the wastewater. Function-based screening of a metagenomic library constructed from DNA extracted from dairy food wastewater viruses revealed candidate promoter sequences that have ability to drive expression of GFP in a promoter-trap vector in Escherichia coli. The majority of the cloned DNA sequences selected by the assay were related to ssDNA circular eukaryotic viruses and phages which formed a minority of the metagenome assembly, and many lacked any significant homology to known database sequences. Natural diversity of bacteriophages in wastewater samples was also examined by PCR amplification of the major capsid protein sequences, conserved within T4-type bacteriophages from Myoviridae family. Phylogenetic analysis of capsid sequences revealed that dairy wastewater contained mainly diverse and uncharacterized phages, while some showed a high level of similarity with phages from geographically distant environments.

Electrical machine characterisation and analysis for renewable energy applications

There has been an increased use of the Doubly-Fed Induction Machine (DFIM) in ac drive applications in recent times, particularly in the field of renewable energy systems and other high power variable-speed drives. The DFIM is widely regarded as the optimal generation system for both onshore and offshore wind turbines and has also been considered in wave power applications. Wind power generation is the most mature renewable technology. However, wave energy has attracted a large interest recently as the potential for power extraction is very significant. Various wave energy converter (WEC) technologies currently exist with the oscillating water column (OWC) type converter being one of the most advanced. There are fundemental differences in the power profile of the pneumatic power supplied by the OWC WEC and that of a wind turbine and this causes significant challenges in the selection and rating of electrical generators for the OWC devises. The thesis initially aims to provide an accurate per-phase equivalent circuit model of the DFIM by investigating various characterisation testing procedures. Novel testing methodologies based on the series-coupling tests is employed and is found to provide a more accurate representation of the DFIM than the standard IEEE testing methods because the series-coupling tests provide a direct method of determining the equivalent-circuit resistances and inductances of the machine. A second novel method known as the extended short-circuit test is also presented and investigated as an alternative characterisation method. Experimental results on a 1.1 kW DFIM and a 30 kW DFIM utilising the various characterisation procedures are presented in the thesis. The various test methods are analysed and validated through comparison of model predictions and torque-versus-speed curves for each induction machine. Sensitivity analysis is also used as a means of quantifying the effect of experimental error on the results taken from each of the testing procedures and is used to determine the suitability of the test procedures for characterising each of the devices. The series-coupling differential test is demonstrated to be the optimum test. The research then focuses on the OWC WEC and the modelling of this device. A software model is implemented based on data obtained from a scaled prototype device situated at the Irish test site. Test data from the electrical system of the device is analysed and this data is used to develop a performance curve for the air turbine utilised in the WEC. This performance curve was applied in a software model to represent the turbine in the electro-mechanical system and the software results are validated by the measured electrical output data from the prototype test device. Finally, once both the DFIM and OWC WEC power take-off system have been modeled succesfully, an investigation of the application of the DFIM to the OWC WEC model is carried out to determine the electrical machine rating required for the pulsating power derived from OWC WEC device. Thermal analysis of a 30 kW induction machine is carried out using a first-order thermal model. The simulations quantify the limits of operation of the machine and enable thedevelopment of rating requirements for the electrical generation system of the OWC WEC. The thesis can be considered to have three sections. The first section of the thesis contains Chapters 2 and 3 and focuses on the accurate characterisation of the doubly-fed induction machine using various testing procedures. The second section, containing Chapter 4, concentrates on the modelling of the OWC WEC power-takeoff with particular focus on the Wells turbine. Validation of this model is carried out through comparision of simulations and experimental measurements. The third section of the thesis utilises the OWC WEC model from Chapter 4 with a 30 kW induction machine model to determine the optimum device rating for the specified machine. Simulations are carried out to perform thermal analysis of the machine to give a general insight into electrical machine rating for an OWC WEC device.

Design and analysis of a compliant parallel pan-tilt platform

In combination of the advantages of both parallel mechanisms and compliant mechanisms, a compliant parallel mechanism with two rotational DOFs (degrees of freedom) is designed to meet the requirement of a lightweight and compact pan-tilt platform. Firstly, two commonly-used design methods i.e. direct substitution and FACT (Freedom and Constraint Topology) are applied to design the configuration of the pan-tilt system, and similarities and differences of the two design alternatives are compared. Then inverse kinematic analysis of the candidate mechanism is implemented by using the pseudo-rigid-body model (PRBM), and the Jacobian related to its differential kinematics is further derived to help designer realize dynamic analysis of the 8R compliant mechanism. In addition, the mechanism’s maximum stress existing within its workspace is tested by finite element analysis. Finally, a method to determine joint damping of the flexure hinge is presented, which aims at exploring the effect of joint damping on actuator selection and real-time control. To the authors’ knowledge, almost no existing literature concerns with this issue.