Exploring the function and evolution of proteins using domain families

Proteins are frequently composed of multiple domains which fold independently. These are often evolutionarily distinct units which can be adapted and reused in other proteins. The classification of protein domains into evolutionary families facilitates the study of their evolution and function. In this thesis such classifications are used firstly to examine methods for identifying evolutionary relationships (homology) between protein domains. Secondly a specific approach for predicting their function is developed. Lastly they are used in studying the evolution of protein complexes. Tools for identifying evolutionary relationships between proteins are central to computational biology. They aid in classifying families of proteins, giving clues about the function of proteins and the study of molecular evolution. The first chapter of this thesis concerns the effectiveness of cutting edge methods in identifying evolutionary relationships between protein domains. The identification of evolutionary relationships between proteins can give clues as to their function. The second chapter of this thesis concerns the development of a method to identify proteins involved in the same biological process. This method is based on the concept of domain fusion whereby pairs of proteins from one organism with a concerted function are sometimes found fused into single proteins in a different organism. Using protein domain classifications it is possible to identify these relationships. Most proteins do not act in isolation but carry out their function by binding to other proteins in complexes; little is understood about the evolution of such complexes. In the third chapter of this thesis the evolution of complexes is examined in two representative model organisms using protein domain families. In this work, protein domain superfamilies allow distantly related parts of complexes to be identified in order to determine how homologous units are reused

Partial discharge behavior under operational and anomalous conditions in HVDC systems

Power cables undergo various types of overstressing conditions during their operation that influence the integrity of their insulation systems. This causes accelerated ageing and might lead to their premature failure in severe cases. This paper presents an investigation of the impacts of various dynamic electric fields produced by ripples, polarity reversal and transient switching impulses on partial discharge (PD) activity within solid dielectrics with the aim of considering such phenomena in high voltage direct current (HVDC) cable systems. Appropriate terminal voltages of a generic HVDC converter were reproduced - with different harmonic contaminations - and applied to the test samples. The effects of systematic operational polarity reversal and superimposed switching impulses with the possibility of transient polarity reversal were also studied in this investigation. The experimental results show that the PD is greatly affected by the dynamic changes of electric field represented by polarity reversal, ripples and switching. The findings of this study will assist in understanding the behaviour of PDs under HVDC conditions and would be of interest to asset managers considering the effects of such conditions on the insulation diagnostics

Monitoring contamination level on insulator materials under dry condition with a microwave reflectometer

Current techniques used for monitoring the levels of contamination on high voltage insulators, such as leakage current and infrared, are not effective in dry conditions since they require the surface of the insulator to be wetted by fog, rain or snow. If a buildup of contamination occurs during a prolonged dry period prior to a weather change there will be a significant risk that flashover may occur before there is time to implement preventative maintenance. Previous work has demonstrated the use of microwave radiometry to determine the levels of contamination on an insulator material under dry conditions, however practical applications are limited by low sensitivity. This paper reports the development of a novel technique based on microwave reflectometry to detect the power levels reflected from the surface of the insulator material. The level of contamination is then determined as a function of received power. A theoretical model establishes the relationship between equivalent salt deposit density levels on insulator surface and the dielectric properties of the contamination layer. A Finite Difference Time Domain (FDTD) model is used to simulate the total loss as a function of the contamination level. Experimental results verify the FDTD model and demonstrate the sensitivity of the reflectometer system to be approximately 100 times greater than the radiometer system. Therefore, the reflectometry system has considerably greater potential for practical applications to provide advance warning of the future failure of insulators under dry conditions for both HVDC and HVAC systems

Feasibility study on application of microwave radiometry to monitor contamination level on insulator materials

This paper introduces a novel method for monitoring contamination levels on high voltage insulators based on microwave radiometry. Present contamination monitoring solutions for high voltage insulators are only effective in predicting flashover risk when the contamination layer has been wetted by rain, fog or condensation. The challenge comes where the pollution occurs during a dry period prior to a weather change. Under these conditions, flashover can often occur within a short time period after wetting and is not predicted by measurements taken in the dry period. The microwave radiometer system described in this paper measures energy emitted from the contamination layer and could provide a safe, reliable, contactless monitoring method that is effective under dry conditions. The relationship between equivalent salt deposit density and radiometer output is described using a theoretical model and experimentally verified using a specially designed X-band radiometer. Results demonstrate that the output from the radiometer is able to clearly distinguish between different levels of contamination on insulator materials under dry conditions. This novel contamination monitoring method could potentially provide advance warning of the future failure of wet insulators in climates where insulators can experience dry conditions for extended periods

Tourniquet Test for Dengue Diagnosis: Systematic Review and Meta-analysis of Diagnostic Test Accuracy.

BACKGROUND: Dengue fever is a ubiquitous arboviral infection in tropical and sub-tropical regions, whose incidence has increased over recent decades. In the absence of a rapid point of care test, the clinical diagnosis of dengue is complex. The World Health Organisation has outlined diagnostic criteria for making the diagnosis of dengue infection, which includes the use of the tourniquet test (TT). PURPOSE: To assess the quality of the evidence supporting the use of the TT and perform a diagnostic accuracy meta-analysis comparing the TT to antibody response measured by ELISA. DATA SOURCES: A comprehensive literature search was conducted in the following databases to April, 2016: MEDLINE (PubMed), EMBASE, Cochrane Central Register of Controlled Trials, BIOSIS, Web of Science, SCOPUS. STUDY SELECTION: Studies comparing the diagnostic accuracy of the tourniquet test with ELISA for the diagnosis of dengue were included. DATA EXTRACTION: Two independent authors extracted data using a standardized form. DATA SYNTHESIS: A total of 16 studies with 28,739 participants were included in the meta-analysis. Pooled sensitivity for dengue diagnosis by TT was 58% (95% Confidence Interval (CI), 43%-71%) and the specificity was 71% (95% CI, 60%-80%). In the subgroup analysis sensitivity for non-severe dengue diagnosis was 55% (95% CI, 52%-59%) and the specificity was 63% (95% CI, 60%-66%), whilst sensitivity for dengue hemorrhagic fever diagnosis was 62% (95% CI, 53%-71%) and the specificity was 60% (95% CI, 48%-70%). Receiver-operator characteristics demonstrated a test accuracy (AUC) of 0.70 (95% CI, 0.66-0.74). CONCLUSION: The tourniquet test is widely used in resource poor settings despite currently available evidence demonstrating only a marginal benefit in making a diagnosis of dengue infection alone. REGISTRATION: The protocol for this systematic review was registered at PROSPERO: CRD42015020323

The increasing activity of a vascular ultrasound service

Objectives:To examine the change in activity of a vascular ultrasound service over 7 years.Design:Retrospective review.Setting:Vascular studies unit, University hospital.Method:Audit of the number of vascular ultrasound tests carried out over the last 7 years using a prospective computerised database.Results:Data shows that the overall workload has tripled over the 7-year period. In addition the complexity of investigations has increased during this time. The number of carotid scans has increased four-fold while the number of graft surveillance scans and vein scans has increased seven-fold. Assessment of lower limb arteries has developed from simple pressure measurements to detailed ultrasound scans and, as a consequence, the number of diagnostic angiograms has fallen by 75%. The factors that have influenced these changes are discussed.Conclusion:There has been an important increase in the role of colour Doppler ultrasound as it becomes the “first line” vascular diagnostic test. However this trend can only continue if vascular ultrasound services are appropriately resourced. It is therefore essential to maintain an efficient audit system

Mafic dykes of the southeastern Gawler Craton: ca 1564 Ma magmatism with an enriched mantle source

Published online: 20 Jan 2022This study investigates the age and composition of a suite of mafic dykes in the southeastern Gawler Craton. Mafic dykes intrude the gneissic fabric of the ca 1850 Ma Donington Suite and were previously interpreted to have been emplaced at ca 1845 Ma. However, sensitive high-resolution ion microprobe U–Pb dating of zircon within one of these mafic dykes shows it was emplaced at 1564 ± 4 Ma. The sampled dyke also contains a population of inherited zircon cores with an age of 1770 ± 6 Ma, and one grain with an age of ca 1860 Ma, likely derived from country rock. Whole-rock geochemistry from this dyke and nearby dykes with similar structural and mineralogical features show that there is a suite of dykes in the region with gabbroic, low SiO2 and TiO2 contents and tholeiitic characteristics. The dykes are enriched in Ba, K and Rb, with low to moderate MgO, Ni and Cr contents, and moderate light rare earth element enrichment. Negative Nb and Ta anomalies with subtle negative Ti anomalies suggest some interaction with continental crust. Sm–Nd isotopic data have εNd(1560 Ma) between −6.8 and −2.9, and depleted mantle model ages >2.5 Ga. Th/Nb ratios are 0.21–0.73 consistent with a metasomatised, subduction modified lithospheric mantle source. The relatively primitive nature of the tholeiites suggests the crustal-like signatures are inherited from the source region, which likely represents an enriched continental lithospheric mantle in the eastern Gawler Craton. This ca 1564 Ma mafic magmatism is newly named the Daly Head Metadolerite. In addition, narrow high-strain zones overprint the dated mafic dyke and locally the Donington Suite wall rocks. A syn-kinematic granitic dyke intrusion within one high-strain zone has been dated via laser ablation-inductively coupled plasma mass spectrometry U–Pb zircon methods and was emplaced at ca 1555 Ma. This localised ca 1555 Ma deformation is a previously unrecognised tectonic event in the southern Gawler Craton. This study adds to the growing database showing magmatism and deformation in the Gawler Craton continued after the voluminous Gawler Range Volcanics and Hiltaba Suite magmatism (ca 1596–1575 Ma). These younger tectono-magmatic events typically occur around the margins of the Gawler Craton, suggesting the internal ‘core’ of the craton may have been substantially less fertile for melting during these younger thermal/structural events, likely because of the high-temperature nature of the early Mesoproterozoic Gawler Range Volcanics and Hiltaba Suite magmatism.A. J. Reid, C. E. Wade and E. A. Jagodzinsk

Environment-induced dynamical chaos

We examine the interplay of nonlinearity of a dynamical system and thermal fluctuation of its environment in the ``physical limit'' of small damping and slow diffusion in a semiclassical context and show that the trajectories of c-number variables exhibit dynamical chaos due to the thermal fluctuations of the bath.Comment: Revtex, 4 pages and 4 figure

Exposure to boat noise in the field yields minimal stress response in wild reef fish

Aquatic anthropogenic noise is on the rise, with growing concern about its impact on species that are sensitive to low-frequency sounds (e.g. most fish and invertebrates). We investigated whether the reef fish Halichoeres bivittatus living in both noisy and quiet areas had differing levels of baseline stress (measured as whole-body cortisol) and whether they would exhibit a physiological stress response when exposed to boat noise playbacks. While the playback experiments significantly increased cortisol levels in fish from our experiment compared to baseline levels, there were minimal pairwise differences across treatments and no difference in baseline stress for fish living in noisy vs. quiet areas. These results may be explained by low overall auditory sensitivity, habituation to a fairly noisy environment (due to biological sounds), or that boat noise simply may not represent an immediate threat to survival in this species. These findings contrast recent studies that have shown elevated stress responses in fishes when exposed to boat noise and highlights that inter-specific differences must be considered when evaluating potential impacts of anthropogenic noise on marine life