Membrane associated transporter protein gene (SLC45A2) and the genetic basis of normal human pigmentation variation

This work is concerned with the genetic basis of normal human pigmentation variation. Specifically, the role of polymorphisms within the solute carrier family 45 member 2 (SLC45A2 or membrane associated transporter protein; MATP) gene were investigated with respect to variation in hair, skin and eye colour ― both between and within populations. SLC45A2 is an important regulator of melanin production and mutations in the gene underly the most recently identified form of oculocutaneous albinism. There is evidence to suggest that non-synonymous polymorphisms in SLC45A2 are associated with normal pigmentation variation between populations. Therefore, the underlying hypothesis of this thesis is that polymorphisms in SLC45A2 will alter the function or regulation of the protein, thereby altering the important role it plays in melanogenesis and providing a mechanism for normal pigmentation variation. In order to investigate the role that SLC45A2 polymorphisms play in human pigmentation variation, a DNA database was established which collected pigmentation phenotypic information and blood samples of more than 700 individuals. This database was used as the foundation for two association studies outlined in this thesis, the first of which involved genotyping two previously-described non-synonymous polymorphisms, p.Glu272Lys and p.Phe374Leu, in four different population groups. For both polymorphisms, allele frequencies were significantly different between population groups and the 272Lys and 374Leu alleles were strongly associated with black hair, brown eyes and olive skin colour in Caucasians. This was the first report to show that SLC45A2 polymorphisms were associated with normal human intra-population pigmentation variation. The second association study involved genotyping several SLC45A2 promoter polymorphisms to determine if they also played a role in pigmentation variation. Firstly, the transcription start site (TSS), and hence putative proximal promoter region, was identified using 5' RNA ligase mediated rapid amplification of cDNA ends (RLM-RACE). Two alternate TSSs were identified and the putative promoter region was screened for novel polymorphisms using denaturing high performance liquid chromatography (dHPLC). A novel duplication (c.–1176_–1174dupAAT) was identified along with other previously described single nucleotide polymorphisms (c.–1721C>G and c.–1169G>A). Strong linkage disequilibrium ensured that all three polymorphisms were associated with skin colour such that the –1721G, +dup and –1169A alleles were associated with olive skin in Caucasians. No linkage disequilibrium was observed between the promoter and coding region polymorphisms, suggesting independent effects. The association analyses were complemented with functional data, showing that the –1721G, +dup and –1169A alleles significantly decreased SLC45A2 transcriptional activity. Based on in silico bioinformatic analysis that showed these alleles remove a microphthalmia-associated transcription factor (MITF) binding site, and that MITF is a known regulator of SLC45A2 (Baxter and Pavan, 2002; Du and Fisher, 2002), it was postulated that SLC45A2 promoter polymorphisms could contribute to the regulation of pigmentation by altering MITF binding affinity. Further characterisation of the SLC45A2 promoter was carried out using luciferase reporter assays to determine the transcriptional activity of different regions of the promoter. Five constructs were designed of increasing length and their promoter activity evaluated. Constitutive promoter activity was observed within the first ~200 bp and promoter activity increased as the construct size increased. The functional impact of the –1721G, +dup and –1169A alleles, which removed a MITF consensus binding site, were assessed using electrophoretic mobility shift assays (EMSA) and expression analysis of genotyped melanoblast and melanocyte cell lines. EMSA results confirmed that the promoter polymorphisms affected DNA-protein binding. Interestingly, however, the protein/s involved were not MITF, or at least MITF was not the protein directly binding to the DNA. In an effort to more thoroughly characterise the functional consequences of SLC45A2 promoter polymorphisms, the mRNA expression levels of SLC45A2 and MITF were determined in melanocyte/melanoblast cell lines. Based on SLC45A2’s role in processing and trafficking TYRP1 from the trans-Golgi network to stage 2 melanosmes, the mRNA expression of TYRP1 was also investigated. Expression results suggested a coordinated expression of pigmentation genes. This thesis has substantially contributed to the field of pigmentation by showing that SLC45A2 polymorphisms not only show allele frequency differences between population groups, but also contribute to normal pigmentation variation within a Caucasian population. In addition, promoter polymorphisms have been shown to have functional consequences for SLC45A2 transcription and the expression of other pigmentation genes. Combined, the data presented in this work supports the notion that SLC45A2 is an important contributor to normal pigmentation variation and should be the target of further research to elucidate its role in determining pigmentation phenotypes. Understanding SLC45A2’s function may lead to the development of therapeutic interventions for oculocutaneous albinism and other disorders of pigmentation. It may also help in our understanding of skin cancer susceptibility and evolutionary adaptation to different UV environments, and contribute to the forensic application of pigmentation phenotype prediction.

A framework for fully decentralised cycle stealing

Ordinary desktop computers continue to obtain ever more resources – in-creased processing power, memory, network speed and bandwidth – yet these resources spend much of their time underutilised. Cycle stealing frameworks harness these resources so they can be used for high-performance computing. Traditionally cycle stealing systems have used client-server based architectures which place significant limits on their ability to scale and the range of applica-tions they can support. By applying a fully decentralised network model to cycle stealing the limits of centralised models can be overcome. Using decentralised networks in this manner presents some difficulties which have not been encountered in their previous uses. Generally decentralised ap-plications do not require any significant fault tolerance guarantees. High-performance computing on the other hand requires very stringent guarantees to ensure correct results are obtained. Unfortunately mechanisms developed for traditional high-performance computing cannot be simply translated because of their reliance on a reliable storage mechanism. In the highly dynamic world of P2P computing this reliable storage is not available. As part of this research a fault tolerance system has been created which provides considerable reliability without the need for a persistent storage. As well as increased scalability, fully decentralised networks offer the ability for volunteers to communicate directly. This ability provides the possibility of supporting applications whose tasks require direct, message passing style communication. Previous cycle stealing systems have only supported embarrassingly parallel applications and applications with limited forms of communication so a new programming model has been developed which can support this style of communication within a cycle stealing context. In this thesis I present a fully decentralised cycle stealing framework. The framework addresses the problems of providing a reliable fault tolerance sys-tem and supporting direct communication between parallel tasks. The thesis includes a programming model for developing cycle stealing applications with direct inter-process communication and methods for optimising object locality on decentralised networks.

Experimental study of Australian sugarcane bagasse pulp permeability

In this experimental study the permeability of Australian bagasse chemical pulps obtained from different bagasse fractions were measured in a simple permeability cell and the results compared to one another as well as to eucalypt, Argentinean bagasse and pine pulps. The pulps were characterised in terms of the permeability parameters, the specific surface area, Sv, and the swelling factor, α. It was found that the bagasse fraction used affects these parameters. Fractionation of whole bagasse prior to pulping produced pulps that have permeability properties that compare favourably with eucalypt pulp. The values of Sv and α for bagasse pulp also depend on whether a constant or a variable Kozeny factor is used.

Initial CFD investigation of an MR fluid in a bicycle ergometer

A bicycle ergometer is a scientific device used by exercise physiologists which attempts to mimic on-road cycling characteristics such as foot technique, EMG activity, VO2, VCO2 and rider cardiology in a laboratory environment. Presently there are no known useful scientific ergometers that mimic these characteristics and are able to provide a satisfactory controlled resistance that is independent of speed. Previous research has suggested the use of a Magneto-Rheological (MR) Fluid as part of the ergometer design, as when used in a rotary brake application it is able to be controlled electronically to increase resistance instantly and independent of speed. In the target application, MR fluids are subject to immense tribological wear and temperature during viscous shearing, and will eventually show some degree of deterioration which is usually manifested as an increase in off-state viscosity. It is not known exactly how the fluid fails, however the amount of deterioration is related to the shear rate, temperature and duration and directly related to the power dissipation. Currently, there is very little literature that investigates the flow and thermal characteristics of MR fluid tribology using CFD. In this paper, we present initial work that aims to improve understanding of MR fluid wear via CFD modelling using Fluent, and results from the model are compared with those obtained from a experimental test rig of an MR fluid-based bicycle ergometer.

Washout hole for bi-ventricular assist device (BVAD) centrifugal blood pump

The shortage of donor hearts for patients with end stage heart failure has accelerated the development of ventricular assist devices (VAD) that act as a replacement heart. Mechanical devices involving pulsatile, axial and centrifugal devices have been proposed. Recent clinical developments indicate that centrifugal devices are not only beneficial for bridge to transplantation applications, but may also aid myocardial recovery. The results of a recent study have shown that patients who received a VAD have extended lives and improved quality of life compared to recipients of drug therapy. Unfortunately 25% of these patients develop right heart failure syndrome, sepsis and multi-organ failure. It was reported that 17% of patients initially receiving an LVAD later required a right ventricular assist device (RVAD). Hence, current research focus is in the development of a bi-ventricular assist device (BVAD). Current BVAD technology is either too bulky or necessitates having to implant two pumps working independently. The latter requires two different controllers for each pump leading to the potential complication of uneven flow dynamics and the requirements for a large amount of body space. This paper illustrates the combination of the LVAD and RVAD as one complete device to augment the function of both the left and right cardiac chambers with double impellers. The proposed device has two impellers rotating in counter directions, hence eliminating the necessity of the body muscles and tubing/heart connection to restrain the pump. The device will also have two separate chambers with independent rotating impeller for the left and right chambers. A problem with centrifugal impellers is the fluid stagnation underneath the impeller. This leads to thrombosis and blood clots.This paper presents the design, construction and location of washout hole to prevent thrombus for a Bi-VAD centrifugal pump. Results using CFD will be used to illustrate the superiority of our design concept in terms of preventing thrombus formation and hemolysis.

Computational fluid dynamics of a centrifugal heart pump as biventricular assist device(BVAD)

The results of a recent study have shown that there is a severe shortage of donor hearts to meet the demand of patients suffering from acute heart failures, and patients who received a left ventricular assist device (LVAD) have extended lives. However, some of them develop right heart failure syndrome, and these patients required a right ventricular assist device (RVAD). Hence, current research focus is in the development of a bi-ventricular assist device (Bi-VAD). Computational Fluid Dynamics (CFD) is useful for estimating blood damage for design of a Bi-VAD centrifugal heart pump to meet the demand of the left and right ventricles of a normal hearts with a flow rate of 5 lit/min and the supply pressure of 100 mmHg for the left ventricle and 20 mmHg for the right ventricle. Numerical studies have been conducted to predict pressure, flow rate, the velocity profiles, and streamlines in a continuous flow Bi-VAD using. Based on the predictions of numerical simulations, only few flow regions in the Bi-VAD exhibited signs of velocity profiles and stagnation points, thereby signifying potentially low levels of thrombogenesis.

Indoor environments : design, productivity and health

In a typical large office block, by far the largest lifetime expense is the salaries of the workers - 84% for salaries compared with : office rent (14%), total energy (1%), and maintenance (1%). The key drive for business is therefore the maximisation of the productivity of the employees as this is the largest cost. Reducing total energy use by 50% will not produce the same financial return as 1% productivity improvement? The aim of the project which led to this review of the literature was to understand as far as possible the state of knowledge internationally about how the indoor environment of buildings does influence occupants and the impact this influence may have on the total cost of ownership of buildings. Therefore one of the main focus areas for the literature has been identifying whether there is a link between productivity and health of building occupants and the indoor environment. Productivity is both easy to define - the ratio of output to input - but at the same time very hard to measure in a relatively small environment where individual contributions can influence the results, in particular social interactions. Health impacts from a building environment are also difficult to measure well, as establishing casual links between the indoor environment and a particular health issue can be very difficult. All of those issues are canvassed in the literature reported here. Humans are surprisingly adaptive to different physical environments, but the workplace should not test the limits of human adaptability. Physiological models of stress, for example, accept that the body has a finite amount of adaptive energy available to cope with stress. The importance of, and this projects' focus on, the physical setting within the integrated system of high performance workplaces, means this literature survey explores research which has been undertaken on both physical and social aspects of the built environment. The literature has been largely classified in several different ways, according to the classification scheme shown below. There is still some inconsistency in the use of keywords, which is being addressed and greater uniformity will be developed for a CD version of this literature, enabling searching using this classification scheme.

ARCS collaboration tools

The Australian Research Collaboration Service (ARCS) has been supporting a wide range of Collaboration Services and Tools which have been allowing researchers, groups and research communities to share ideas and collaborate across organisational boundaries.----- This talk will give an introduction to a number of exciting technologies which are now available. Focus will be on two main areas of Video Collaboration Tools, allowing researchers to talk face-to-face and share data in real-time, and Web Collaboration Tools, allowing researchers to share information and ideas with other like-minded researchers irrespective of distance or organisational structure. A number of examples will also be shown of how these technologies have been used with in various research communities.----- A brief introduction will be given to a number of services which ARCS is now operating and/or supporting such as:--- * EVO – A video conferencing application, which is particularly suited to desktop or low bandwidth applications.--- * AccessGrid – An open source video conferencing and collaboration tool kit, which is great for room to room meetings.--- * Sakai – An online collaboration and learning environment, support teaching and learning, ad hoc group collaboration, support for portfolios and research collaboration.--- * Plone – A ready-to-run content management system, that provides you with a system for managing web content that is ideal for project groups, communities, web sites, extranets and intranets.--- * Wikis – A way to easily create, edit, and link pages together, to create collaborative websites.