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.

Designing to maintain human agency in context-aware systems

This paper describes a series of design games, specifically aimed at exploring shifts in human agency, how they are managed, and the impact this will have on the design of future context-aware applications. The games focussed on understanding information handling issues in dental practice with participants from the University of Queensland Dental School playing an active role in the activities. Participatory design activities reveal how technology solution impact on dental practices. By finding methods of representing technological possibilities in ways which can easily be understood we enhance the contribution that dentists can make to the design process.

The proximal first exon architecture of the murine ghrelin gene is highly similar to its human orthologue

BACKGROUND: The murine ghrelin gene (Ghrl), originally sequenced from stomach tissue, contains five exons and a single transcription start site in a short, 19 bp first exon (exon 0). We recently isolated several novel first exons of the human ghrelin gene and found evidence of a complex transcriptional repertoire. In this report, we examined the 5' exons of the murine ghrelin orthologue in a range of tissues using 5' RACE. -----FINDINGS: 5' RACE revealed two transcription start sites (TSSs) in exon 0 and four TSSs in intron 0, which correspond to 5' extensions of exon 1. Using quantitative, real-time RT-PCR (qRT-PCR), we demonstrated that extended exon 1 containing Ghrl transcripts are largely confined to the spleen, adrenal gland, stomach, and skin. -----CONCLUSION: We demonstrate that multiple transcription start sites are present in exon 0 and an extended exon 1 of the murine ghrelin gene, similar to the proximal first exon organisation of its human orthologue. The identification of several transcription start sites in intron 0 of mouse ghrelin (resulting in an extension of exon 1) raises the possibility that developmental-, cell- and tissue-specific Ghrl mRNA species are created by employing alternative promoters and further studies of the murine ghrelin gene are warranted.

Lesser-known worlds : bridging the telematic flows with located human experience through game design

This paper represents a new theorization of the role of location-based games (LBGs) as potentially playing specific roles in peoples’ access to the culture of cities [22]. A LBG is a game that employs mobile technologies as tools for game play in real world environments. We argue that as a new genre in the field of mobile entertainment, research in this area tends to be preoccupied with the newness of the technology and its commercial possibilities. However, this overlooks its potential to contribute to cultural production. We argue that the potential to contribute to cultural production lies in the capacity of these experiences to enhance relationships between specific groups and new urban spaces. Given that developers can design LBGs to be played with everyday devices in everyday environments, what new creative opportunities are available to everyday people?

Maintaining human agency in the design on context-aware systems : Design games in a dental surgery

This paper describes a series of design games, specifically aimed at exploring shifts in human agency in order to inform the design of context-aware applications. The games focused on understanding information handling issues in dental practice with participants from a university dental school playing an active role in the activities. Participatory design activities help participants to reveal potential implicit technical resources that can be presented explicitly in technologies in order to assist humans in managing their interactions with and amidst technical systems gracefully.

Rural and remote road safety study : final report

• Introduction: Concern and action for rural road safety is relatively new in Australia in comparison to the field of traffic safety as a whole. In 2003, a program of research was begun by the Centre for Accident Research and Road Safety - Queensland (CARRS-Q) and the Rural Health Research Unit (RHRU) at James Cook University to investigate factors contributing to serious rural road crashes in the North Queensland region. This project was funded by the Premier’s Department, Main Roads Department, Queensland Transport, QFleet, Queensland Rail, Queensland Ambulance Service, Department of Natural Resources and Queensland Police Service. Additional funding was provided by NRMA Insurance for a PhD scholarship. In-kind support was provided through the four hospitals used for data collection, namely Cairns Base Hospital, The Townsville Hospital, Mount Isa Hospital and Atherton Hospital.----- The primary aim of the project was to: Identify human factors related to the occurrence of serious traffic incidents in rural and remote areas of Australia, and to the trauma suffered by persons as a result of these incidents, using a sample drawn from a rural and remote area in North Queensland.----- The data and analyses presented in this report are the core findings from two broad studies: a general examination of fatalities and casualties from rural and remote crashes for the period 1 March 2004 until 30 June 2007, and a further linked case-comparison study of hospitalised patients compared with a sample of non-crash-involved drivers.----- • Method: The study was undertaken in rural North Queensland, as defined by the Australian Bureau of Statistics (ABS) statistical divisions of North Queensland, Far North Queensland and North-West Queensland. Urban areas surrounding Townsville, Thuringowa and Cairns were not included. The study methodology was centred on serious crashes, as defined by a resulting hospitalisation for 24 hours or more and/or a fatality. Crashes meeting this criteria within the North Queensland region between 1 March 2004 and 30 June 2007 were identified through hospital records and interviewed where possible. Additional data was sourced from coroner’s reports, the Queensland Transport road crash database, the Queensland Ambulance Service and the study hospitals in the region.----- This report is divided into chapters corresponding to analyses conducted on the collected crash and casualty data.----- Chapter 3 presents an overview of all crashes and casualties identified during the study period. Details are presented in regard to the demographics and road user types of casualties; the locations, times, types, and circumstances of crashes; along with the contributing circumstances of crashes.----- Chapter 4 presents the results of summary statistics for all casualties for which an interview was able to be conducted. Statistics are presented separately for drivers and riders, passengers, pedestrians and cyclists. Details are also presented separately for drivers and riders crashing in off-road and on-road settings. Results from questionnaire data are presented in relation to demographics; the experience of the crash in narrative form; vehicle characteristics and maintenance; trip characteristics (e.g. purpose and length of journey; periods of fatigue and monotony; distractions from driving task); driving history; alcohol and drug use; medical history; driving attitudes, intentions and behaviour; attitudes to enforcement; and experience of road safety advertising.----- Chapter 5 compares the above-listed questionnaire results between on-road crash-involved casualties and interviews conducted in the region with non-crash-involved persons. Direct comparisons as well as age and sex adjusted comparisons are presented.----- Chapter 6 presents information on those casualties who were admitted to one of the study hospitals during the study period. Brief information is given regarding the demographic characteristics of these casualties. Emergency services’ data is used to highlight the characteristics of patient retrieval and transport to and between hospitals. The major injuries resulting from the crashes are presented for each region of the body and analysed by vehicle type, occupant type, seatbelt status, helmet status, alcohol involvement and nature of crash. Estimates are provided of the costs associated with in-hospital treatment and retrieval.----- Chapter 7 describes the characteristics of the fatal casualties and the nature and circumstances of the crashes. Demographics, road user types, licence status, crash type and contributing factors for crashes are presented. Coronial data is provided in regard to contributing circumstances (including alcohol, drugs and medical conditions), cause of death, resulting injuries, and restraint and helmet use.----- Chapter 8 presents the results of a comparison between casualties’ crash descriptions and police-attributed crash circumstances. The relative frequency of contributing circumstances are compared both broadly within the categories of behavioural, environmental, vehicle related, medical and other groupings and specifically for circumstances within these groups.----- Chapter 9 reports on the associated research projects which have been undertaken on specific topics related to rural road safety.----- Finally, Chapter 10 reports on the conclusions and recommendations made from the program of research.---- • Major Recommendations : From the findings of these analyses, a number of major recommendations were made: + Male drivers and riders - Male drivers and riders should continue to be the focus of interventions, given their very high representation among rural and remote road crash fatalities and serious injuries.----- - The group of males aged between 30 and 50 years comprised the largest number of casualties and must also be targeted for change if there is to be a meaningful improvement in rural and remote road safety.----- + Motorcyclists - Single vehicle motorcycle crashes constitute over 80% of serious, on-road rural motorcycle crashes and need particular attention in development of policy and infrastructure.----- - The motorcycle safety consultation process currently being undertaken by Queensland Transport (via the "Motorbike Safety in Queensland - Consultation Paper") is strongly endorsed. As part of this process, particular attention needs to be given to initiatives designed to reduce rural and single vehicle motorcycle crashes.----- - The safety of off-road riders is a serious problem that falls outside the direct responsibility of either Transport or Health departments. Responsibility for this issue needs to be attributed to develop appropriate policy, regulations and countermeasures.----- + Road safety for Indigenous people - Continued resourcing and expansion of The Queensland Aboriginal Peoples and Torres Strait Islander Peoples Driver Licensing Program to meet the needs of remote and Indigenous communities with significantly lower licence ownership levels.----- - Increased attention needs to focus on the contribution of geographic disadvantage (remoteness) factors to remote and Indigenous road trauma.----- + Road environment - Speed is the ‘final common pathway’ in determining the severity of rural and remote crashes and rural speed limits should be reduced to 90km/hr for sealed off-highway roads and 80km/hr for all unsealed roads as recommended in the Austroads review and in line with the current Tasmanian government trial.----- - The Department of Main Roads should monitor rural crash clusters and where appropriate work with local authorities to conduct relevant audits and take mitigating action. - The international experts at the workshop reviewed the data and identified the need to focus particular attention on road design management for dangerous curves. They also indicated the need to maximise the use of audio-tactile linemarking (audible lines) and rumble strips to alert drivers to dangerous conditions and behaviours.----- + Trauma costs - In accordance with Queensland Health priorities, recognition should be given to the substantial financial costs associated with acute management of trauma resulting from serious rural and remote crashes.----- - Efforts should be made to develop a comprehensive, regionally specific costing formula for road trauma that incorporates the pre-hospital, hospital and post-hospital phases of care. This would inform health resource allocation and facilitate the evaluation of interventions.----- - The commitment of funds to the development of preventive strategies to reduce rural and remote crashes should take into account the potential cost savings associated with trauma.----- - A dedicated study of the rehabilitation needs and associated personal and healthcare costs arising from rural and remote road crashes should be undertaken.----- + Emergency services - While the study has demonstrated considerable efficiency in the response and retrieval systems of rural and remote North Queensland, relevant Intelligent Transport Systems technologies (such as vehicle alarm systems) to improve crash notification should be both developed and evaluated.----- + Enforcement - Alcohol and speed enforcement programs should target the period between 2 and 6pm because of the high numbers of crashes in the afternoon period throughout the rural region.----- + Drink driving - Courtesy buses should be advocated and schemes such as the Skipper project promoted as local drink driving countermeasures in line with the very high levels of community support for these measures identified in the hospital study.------ - Programs should be developed to target the high levels of alcohol consumption identified in rural and remote areas and related involvement in crashes.----- - Referrals to drink driving rehabilitation programs should be mandated for recidivist offenders.----- + Data requirements - Rural and remote road crashes should receive the same quality of attention as urban crashes. As such, it is strongly recommended that increased resources be committed to enable dedicated Forensic Crash Units to investigate rural and remote fatal and serious injury crashes.----- - Transport department records of rural and remote crashes should record the crash location using the national ARIA area classifications used by health departments as a means to better identifying rural crashes.----- - Rural and remote crashes tend to be unnoticed except in relatively infrequent rural reviews. They should receive the same level of attention and this could be achieved if fatalities and fatal crashes were coded by the ARIA classification system and included in regular crash reporting.----- - Health, Transport and Police agencies should collect a common, minimal set of data relating to road crashes and injuries, including presentations to small rural and remote health facilities.----- + Media and community education programmes - Interventions seeking to highlight the human contribution to crashes should be prioritised. Driver distraction, alcohol and inappropriate speed for the road conditions are key examples of such behaviours.----- - Promotion of basic safety behaviours such as the use of seatbelts and helmets should be given a renewed focus.----- - Knowledge, attitude and behavioural factors that have been identified for the hospital Brief Intervention Trial should be considered in developing safety campaigns for rural and remote people. For example challenging the myth of the dangerous ‘other’ or ‘non-local’ driver.----- - Special educational initiatives on the issues involved in rural and remote driving should be undertaken. For example the material used by Main Roads, the Australian Defence Force and local initiatives.