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.

Combining ganglion cell topology and data of patients with glaucoma to determine a structure-function map

PURPOSE: To introduce techniques for deriving a map that relates visual field locations to optic nerve head (ONH) sectors and to use the techniques to derive a map relating Medmont perimetric data to data from the Heidelberg Retinal Tomograph. METHODS: Spearman correlation coefficients were calculated relating each visual field location (Medmont M700) to rim area and volume measures for 10 degrees ONH sectors (HRT III software) for 57 participants: 34 with glaucoma, 18 with suspected glaucoma, and 5 with ocular hypertension. Correlations were constrained to be anatomically plausible with a computational model of the axon growth of retinal ganglion cells (Algorithm GROW). GROW generated a map relating field locations to sectors of the ONH. The sector with the maximum statistically significant (P < 0.05) correlation coefficient within 40 degrees of the angle predicted by GROW for each location was computed. Before correlation, both functional and structural data were normalized by either normative data or the fellow eye in each participant. RESULTS: The model of axon growth produced a 24-2 map that is qualitatively similar to existing maps derived from empiric data. When GROW was used in conjunction with normative data, 31% of field locations exhibited a statistically significant relationship. This significance increased to 67% (z-test, z = 4.84; P < 0.001) when both field and rim area data were normalized with the fellow eye. CONCLUSIONS: A computational model of axon growth and normalizing data by the fellow eye can assist in constructing an anatomically plausible map connecting visual field data and sectoral ONH data.

Sound radiation characteristics of a box-type structure

The finite element and boundary element methods are employed in this study to investigate the sound radiation characteristics of a box-type structure. It has been shown [T.R. Lin, J. Pan, Vibration characteristics of a box-type structure, Journal of Vibration and Acoustics, Transactions of ASME 131 (2009) 031004-1–031004-9] that modes of natural vibration of a box-type structure can be classified into six groups according to the symmetry properties of the three panel pairs forming the box. In this paper, we demonstrate that such properties also reveal information about sound radiation effectiveness of each group of modes. The changes of radiation efficiencies and directivity patterns with the wavenumber ratio (the ratio between the acoustic and the plate bending wavenumbers) are examined for typical modes from each group. Similar characteristics of modal radiation efficiencies between a box structure and a corresponding simply supported panel are observed. The change of sound radiation patterns as a function of the wavenumber ratio is also illustrated. It is found that the sound radiation directivity of each box mode can be correlated to that of elementary sound sources (monopole, dipole, etc.) at frequencies well below the critical frequency of the plates of the box. The sound radiation pattern on the box surface also closely related to the vibration amplitude distribution of the box structure at frequencies above the critical frequency. In the medium frequency range, the radiated sound field is dominated by the edge vibration pattern of the box. The radiation efficiency of all box modes reaches a peak at frequencies above the critical frequency, and gradually approaches unity at higher frequencies.

Contrast sensitivity changes due to glaucoma and normal aging: low-spatial-frequency losses in both magnocellular and parvocellular pathways

PURPOSE: To explore the effects of glaucoma and aging on low-spatial-frequency contrast sensitivity by using tests designed to assess performance of either the magnocellular (M) or parvocellular (P) visual pathways. METHODS: Contrast sensitivity was measured for spatial frequencies of 0.25 to 2 cyc/deg by using a published steady- and pulsed-pedestal approach. Sixteen patients with glaucoma and 16 approximately age-matched control subjects participated. Patients with glaucoma were tested foveally and at two midperipheral locations: (1) an area of early visual field loss, and (2) an area of normal visual field. Control subjects were assessed in matched locations. An additional group of 12 younger control subjects (aged 20-35 years) were also tested. RESULTS: Older control subjects demonstrated reduced sensitivity relative to the younger group for the steady (presumed M)- and pulsed (presumed P)-pedestal conditions. Sensitivity was reduced foveally and in the midperiphery across the spatial frequency range. In the area of early visual field loss, the glaucoma group demonstrated further sensitivity reduction relative to older control subjects across the spatial frequency range for both the steady- and pulsed-pedestal tasks. Sensitivity was also reduced in the midperipheral location of "normal" visual field for the pulsed condition. CONCLUSIONS: Normal aging results in a reduction of contrast sensitivity for the low-spatial-frequency-sensitive components of both the M and P pathways. Glaucoma results in a further reduction of sensitivity that is not selective for M or P function. The low-spatial-frequency-sensitive channels of both pathways, which are presumably mediated by cells with larger receptive fields, are approximately equivalently impaired in early glaucoma.

Uncritical framing : lesson and knowledge structure in school science

There is clearly contention over the shape and formation of science curriculum and over, ultimately, what will count as scientific knowledge, skill, capacity and world view. The Cold War set the policy context for an ongoing focus on science education across Western nations. Sputnik-era US and UK educational policy offered a broad premise for the purpose of school science: in a risky geopolitical environment, high levels of advanced scientific expertise were central to the national interest and necessary for the maintenance of military/industrial and technological power. Half a century on, in the context of global economic and environmental crisis, as a justification for digital, industrial and biomedical innovation, the rationale for the production of scientific capital is central to curriculum settlements and educational policy in Europe, Asia and the Americas.

The effects of habitat fragmentation on the demography and population genetic structure of Uromys Caudimaculatus

Habitat fragmentation can have an impact on a wide variety of biological processes including abundance, life history strategies, mating system, inbreeding and genetic diversity levels of individual species. Although fragmented populations have received much attention, ecological and genetic responses of species to fragmentation have still not been fully resolved. The current study investigated the ecological factors that may influence the demographic and genetic structure of the giant white-tailed rat (Uromys caudimaculatus) within fragmented tropical rainforests. It is the first study to examine relationships between food resources, vegetation attributes and Uromys demography in a quantitative manner. Giant white-tailed rat densities were strongly correlated with specific suites of food resources rather than forest structure or other factors linked to fragmentation (i.e. fragment size). Several demographic parameters including the density of resident adults and juvenile recruitment showed similar patterns. Although data were limited, high quality food resources appear to initiate breeding in female Uromys. Where data were sufficient, influx of juveniles was significantly related to the density of high quality food resources that had fallen in the previous three months. Thus, availability of high quality food resources appear to be more important than either vegetation structure or fragment size in influencing giant white-tailed rat demography. These results support the suggestion that a species’ response to fragmentation can be related to their specific habitat requirements and can vary in response to local ecological conditions. In contrast to demographic data, genetic data revealed a significant negative effect of habitat fragmentation on genetic diversity and effective population size in U. caudimaculatus. All three fragments showed lower levels of allelic richness, number of private alleles and expected heterozygosity compared with the unfragmented continuous rainforest site. Populations at all sites were significantly differentiated, suggesting restricted among population gene flow. The combined effects of reduced genetic diversity, lower effective population size and restricted gene flow suggest that long-term viability of small fragmented populations may be at risk, unless effective management is employed in the future. A diverse range of genetic reproductive behaviours and sex-biased dispersal patterns were evident within U. caudimaculatus populations. Genetic paternity analyses revealed that the major mating system in U. caudimaculatus appeared to be polygyny at sites P1, P3 and C1. Evidence of genetic monogamy, however, was also found in the three fragmented sites, and was the dominant mating system in the remaining low density, small fragment (P2). High variability in reproductive skew and reproductive success was also found but was less pronounced when only resident Uromys were considered. Male body condition predicted which males sired offspring, however, neither body condition nor heterozygosity levels were accurate predictors of the number of offspring assigned to individual males or females. Genetic spatial autocorrelation analyses provided evidence for increased philopatry among females at site P1, but increased philopatry among males at site P3. This suggests that male-biased dispersal occurs at site P1 and female-biased dispersal at site P3, implying that in addition to mating systems, Uromys may also be able to adjust their dispersal behaviour to suit local ecological conditions. This study highlights the importance of examining the mechanisms that underlie population-level responses to habitat fragmentation using a combined ecological and genetic approach. The ecological data suggested that habitat quality (i.e. high quality food resources) rather than habitat quantity (i.e. fragment size) was relatively more important in influencing giant white-tailed rat demographics, at least for the populations studied here . Conversely, genetic data showed strong evidence that Uromys populations were affected adversely by habitat fragmentation and that management of isolated populations may be required for long-term viability of populations within isolated rainforest fragments.

Open Specification for BIM : Sydney Opera House Case Study

Executive Summary The objective of this report was to use the Sydney Opera House as a case study of the application of Building Information Modelling (BIM). The Sydney opera House is a complex, large building with very irregular building configuration, that makes it a challenging test. A number of key concerns are evident at SOH: • the building structure is complex, and building service systems - already the major cost of ongoing maintenance - are undergoing technology change, with new computer based services becoming increasingly important. • the current “documentation” of the facility is comprised of several independent systems, some overlapping and is inadequate to service current and future services required • the building has reached a milestone age in terms of the condition and maintainability of key public areas and service systems, functionality of spaces and longer term strategic management. • many business functions such as space or event management require up-to-date information of the facility that are currently inadequately delivered, expensive and time consuming to update and deliver to customers. • major building upgrades are being planned that will put considerable strain on existing Facilities Portfolio services, and their capacity to manage them effectively While some of these concerns are unique to the House, many will be common to larger commercial and institutional portfolios. The work described here supported a complementary task which sought to identify if a building information model – an integrated building database – could be created, that would support asset & facility management functions (see Sydney Opera House – FM Exemplar Project, Report Number: 2005-001-C-4 Building Information Modelling for FM at Sydney Opera House), a business strategy that has been well demonstrated. The development of the BIMSS - Open Specification for BIM has been surprisingly straightforward. The lack of technical difficulties in converting the House’s existing conventions and standards to the new model based environment can be related to three key factors: • SOH Facilities Portfolio – the internal group responsible for asset and facility management - have already well established building and documentation policies in place. The setting and adherence to well thought out operational standards has been based on the need to create an environment that is understood by all users and that addresses the major business needs of the House. • The second factor is the nature of the IFC Model Specification used to define the BIM protocol. The IFC standard is based on building practice and nomenclature, widely used in the construction industries across the globe. For example the nomenclature of building parts – eg ifcWall, corresponds to our normal terminology, but extends the traditional drawing environment currently used for design and documentation. This demonstrates that the international IFC model accurately represents local practice for building data representation and management. • a BIM environment sets up opportunities for innovative processes that can exploit the rich data in the model and improve services and functions for the House: for example several high-level processes have been identified that could benefit from standardized Building Information Models such as maintenance processes using engineering data, business processes using scheduling, venue access, security data and benchmarking processes using building performance data. The new technology matches business needs for current and new services. The adoption of IFC compliant applications opens the way forward for shared building model collaboration and new processes, a significant new focus of the BIM standards. In summary, SOH current building standards have been successfully drafted for a BIM environment and are confidently expected to be fully developed when BIM is adopted operationally by SOH. These BIM standards and their application to the Opera House are intended as a template for other organisations to adopt for the own procurement and facility management activities. Appendices provide an overview of the IFC Integrated Object Model and an understanding IFC Model Data.

Damage propagation in reinforced concrete frames under external blast loading

Iconic and significant buildings are the common target of bombings by terrorists causing large numbers of casualties and extensive property damage. Recent incidents were external bomb attacks on multi-storey buildings with reinforced concrete frames. Under a blast load circumstance, crucial damage initiates at low level storeys in a building and may then lead to a progressive collapse of whole or part of the structure. It is therefore important to identify the critical initial influence regions along the height, width and depth of the building exposed to blast effects and the structure response in order to assess the vulnerability of the structure to disproportionate and progressive collapse. This paper discusses the blast response and the propagation of its effects on a two dimensional reinforced concrete (RC) frame, designed to withstand normal gravity loads. The explicit finite element code, LS DYNA is used for the analysis. A complete RC portal frame seven storeys by six bays is modelled with reinforcement details and appropriate materials to simulate strain rate effects. Explosion loads derived from standard manuals are applied as idealized triangular pressures on the column faces of the numerical models. The analysis reports the influence of blast propagation as displacements and material yielding of the structural elements in the RC frame. The effected regions are identified and classified according to the load cases. This information can be used to determine the vulnerability of multi-storey RC buildings to various external explosion scenarios and designing buildings to resist blast loads.

Assessing the structure of learning outcomes from counselling using the SOLO taxonomy: an exploratory study

Thirty-five clients who had received counselling completed a letter to a friend describing in as much detail as possible what they had learned from counselling. The participants' written responses were analysed and classified using the Structure of Learning Outcomes (SOLO) taxonomy. The results suggested that an expanded SOLO offers a promising and exciting way to view the outcomes of counselling within a learning framework. If the SOLO taxonomy is found to be stable in subsequent research, and clients are easily able to be classified using the taxonomy, then this approach may have implications for the process of counselling. To maximise the learning outcomes, counsellors could use strategies and techniques to enhance their clients' learning.

Micro-structure differences in kaolinite suspensions

SEM observations of the aqueous suspensions of kaolinite from Birdwood (South Australia) and Georgia (USA) show noticeable differences in number of physical behaviour which has been explained by different microstructure constitution.. Birdwood kaolinite dispersion gels are observed at very low solid loadings in comparison with Georgia KGa-1 kaolinite dispersions which remain fluid at higher solids loading. To explain this behaviour, the specific particle interactions of Birdwood kaolinite, different from interaction in Georgia kaolinite have been proposed. These interactions may be brought about by the presence of nano-bubbles on clay crystal edges and may force clay particles to aggregate by bubble coalescence. This explains the predominance of stair step edge-edge like (EE) contacts in suspension of Birdwood kaolinite. Such EE linked particles build long strings that form a spacious cell structure. Hydrocarbon contamination of colloidal kaolinite particles and low aspect ratio are discussed as possible explanations of this unusual behaviour of Birdwood kaolinite. In Georgia KGa-1 kaolinite dispersions instead of EE contact between platelets displayed in Birdwood kaolinite, most particles have edge to face (EF) contacts building a cardhouse structure. Such an arrangement is much less voluminous in comparison with the Birdwood kaolinite cellular honeycomb structure observed previously in smectite aqueous suspensions. Such structural characteristics of KGa-1 kaolinite particles enable higher solid volume fractions pulps to form before significantly networked gel consistency is attained.

Polyurethane (PU) scaffolds prepared by solvent casting/particulate leaching (SCPL) combined with centrifugation

This article reports an enhanced solvent casting/particulate (salt) leaching (SCPL) method developed for preparing three-dimensional porous polyurethane (PU) scaffolds for cardiac tissue engineering. The solvent for the preparation of the PU scaffolds was a mixture of dimethylformamide (DFM) and tetrahydrofuran (THF). The enhanced method involved the combination of a conventional SCPL method and a step of centrifugation, with the centrifugation being employed to improve the pore uniformity and the pore interconnectivity of scaffolds. Highly porous three-dimensional scaffolds with a well interconnected porous structure could be achieved at the polymer solution concentration of up to 20% by air or vacuum drying to remove the solvent. When the salt particle sizes of 212-295, 295-425, or 425-531 µm and a 15% w/v polymer solution concentration were used, the porosity of the scaffolds was between 83-92% and the compression moduli of the scaffolds were between 13 kPa and 28 kPa. Type I collagen acidic solution was introduced into the pores of a PU scaffold to coat the collagen onto the pore walls throughout the whole PU scaffold. The human aortic endothelial cells (HAECs) cultured in the collagen-coated PU scaffold for 2 weeks were observed by scanning electron microscopy (SEM). It was shown that the enhanced SCPL method and the collagen coating resulted in a spatially uniform distribution of cells throughout the collagen-coated PU scaffold.

On feasibility of regional frequency-based emergency control plans

Decentralized and regional load-frequency control of power systems operating in normal and near-normal conditions has been well studied; and several analysis/synthesis approaches have been developed during the last few decades. However in contingency and off-normal conditions, the existing emergency control plans, such as under-frequency load shedding, are usually applied in a centralized structure using a different analysis model. This paper discusses the feasibility of using frequency-based emergency control schemes based on tie-line measurements and local information available within a control area. The conventional load-frequency control model is generalized by considering the dynamics of emergency control/protection schemes and an analytic approach to analyze the regional frequency response under normal and emergency conditions is presented.

Concepts of normal bereavement

This study used a 25-item questionnaire to examine the perceptions of 128 people with a close interest in bereavement and its literature. The study is part of a project to identify key aspects and the bereavement process. Subjects were asked to rate their perceptions of key bereavement phenomena with regards their frequency in the acute and later stages of bereavement. Descriptive results are presented and discussed, and a profile of phenomena perceived to be common to both stages is outlined.