Compilation of somatic mutations of the CDKN2 gene in human cancers : non-random distribution of base substitutions

The CDKN2 gene, encoding the cyclin-dependent kinase inhibitor p16, is a tumour suppressor gene that maps to chromosome band 9p21-p22. The most common mechanism of inactivation of this gene in human cancers is through homozygous deletion; however, in a smaller proportion of tumours and tumour cell lines intragenic mutations occur. In this study we have compiled a database of over 120 published point mutations in the CDKN2 gene from a wide variety of tumour types. A further 50 deletions, insertions, and splice mutations in CDKN2 have also been compiled. Furthermore, we have standardised the numbering of all mutations according to the full-length 156 amino acid form of p16. From this study we are able to define several hot spots, some of which occur at conserved residues within the ankyrin domains of p16. While many of the hotspots are shared by a number of cancers, the relative importance of each position varies, possibly reflecting the role of different carcinogens in the development of certain tumours. As reported previously, the mutational spectrum of CDKN2 in melanomas differs from that of internal malignancies and supports the involvement of UV in melanoma tumorigenesis. Notably, 52% of all substitutions in melanoma-derived samples occurred at just six nucleotide positions. Nonsense mutations comprise a comparatively high proportion of mutations present in the CDKN2 gene, and possible explanations for this are discussed.

Haplotype analysis of two recurrent CDKN2A mutations in 10 melanoma families : evidence for common founders and independent mutations

Germ-line mutations in CDKN2A have been shown to predispose to cutaneous malignant melanoma. We have identified 2 new melanoma kindreds which carry a duplication of a 24bp repeat present in the 5' region of CDKN2A previously identified in melanoma families from Australia and the United States. This mutation has now been reported in 5 melanoma families from 3 continents: Europe, North America, and Australasia. The M53I mutation in exon 2 of CDKN2A has also been documented in 5 melanoma families from Australia and North America. The aim of this study was to determine whether the occurrence of the mutations in these families from geographically diverse populations represented mutation hotspots within CDKN2A or were due to common ancestors. Haplotypes of 11 microsatellite markers flanking CDKN2A were constructed in 5 families carrying the M53I mutation and 5 families carrying the 24bp duplication. There were some differences in the segregating haplotypes due primarily to recombinations and mutations within the short tandem-repeat markers; however, the data provide evidence to indicate that there were at least 3 independent 24bp duplication events and possibly only 1 original M53I mutation. This is the first study to date which indicates common founders in melanoma families from different continents.

Stochastic models and simulation of ion channel dynamics

The behaviour of ion channels within cardiac and neuronal cells is intrinsically stochastic in nature. When the number of channels is small this stochastic noise is large and can have an impact on the dynamics of the system which is potentially an issue when modelling small neurons and drug block in cardiac cells. While exact methods correctly capture the stochastic dynamics of a system they are computationally expensive, restricting their inclusion into tissue level models and so approximations to exact methods are often used instead. The other issue in modelling ion channel dynamics is that the transition rates are voltage dependent, adding a level of complexity as the channel dynamics are coupled to the membrane potential. By assuming that such transition rates are constant over each time step, it is possible to derive a stochastic differential equation (SDE), in the same manner as for biochemical reaction networks, that describes the stochastic dynamics of ion channels. While such a model is more computationally efficient than exact methods we show that there are analytical problems with the resulting SDE as well as issues in using current numerical schemes to solve such an equation. We therefore make two contributions: develop a different model to describe the stochastic ion channel dynamics that analytically behaves in the correct manner and also discuss numerical methods that preserve the analytical properties of the model.

Preliminary development of a sewerage infrastructure buffer assessment tool for engineering risk and strategic land use planning

Urban expansion continues to encroach on once isolated sewerage infrastructure. In this context,legislation and guidelines provide limited direction to the amenity allocation of appropriate buffer distances for land use planners and infrastructure providers. Topography, wind speed and direction,temperature, humidity, existing land uses and vegetation profiles are some of the factors that require investigation in analytically determining a basis for buffer separations. This paper discusses the compilation and analysis of six years of Logan sewerage odour complaint data. Graphically,relationships between the complaints, topographical features and meteorological data are presented. Application of a buffer sizing process could assist planners and infrastructure designers alike, whilst automatically providing extra green spaces. Establishing a justifiable criterion for buffer zone allocations can only assist in promoting manageable growth for healthier and more sustainable communities.

Congo Red adsorption by ball-milled sugarcane bagasse

The adsorption of Congo Red (CR) by ball-milled sugarcane bagasse was evaluated in an aqueous batch system. CR adsorption capacity increased significantly with small changes in bagasse surface area. CR removal decreased with increasing solution pH from 5.0 to 10.0. Maximum adsorption capacity was 38.2 mg/g bagasse at a CR concentration of 500 mg/L. The equilibrium isotherm fitted the Freundlich model and the adsorption kinetics obeyed pseudo-second order equation. CR adsorption obeyed the intra-particle diffusion model very well with bagasse surface area in the range of 0.58–0.66 m2/g, whereas it was controlled by multi-adsorption stages with bagasse surface area in the range of 1.31–1.82 m2/g. Thermodynamic analysis indicated that the adsorption process is an exothermic and spontaneous process. Fourier transform infrared analysis of bagasse containing adsorbed CR indicated interactions between the carboxyl and hydroxyl groups of bagasse and CR function groups.

Lingodroids : studies in spatial cognition and language

The Lingodroids are a pair of mobile robots that evolve a language for places and relationships between places (based on distance and direction). Each robot in these studies has its own understanding of the layout of the world, based on its unique experiences and exploration of the environment. Despite having different internal representations of the world, the robots are able to develop a common lexicon for places, and then use simple sentences to explain and understand relationships between places even places that they could not physically experience, such as areas behind closed doors. By learning the language, the robots are able to develop representations for places that are inaccessible to them, and later, when the doors are opened, use those representations to perform goal-directed behavior.

Design and implementation of a virtual world training simulation of ICU first hour handover processes

Nursing training for an Intensive Care Unit (ICU) is a resource intensive process. High demands are made on staff, students and physical resources. Interactive, 3D computer simulations, known as virtual worlds, are increasingly being used to supplement training regimes in the health sciences; especially in areas such as complex hospital ward processes. Such worlds have been found to be very useful in maximising the utilisation of training resources. Our aim is to design and develop a novel virtual world application for teaching and training Intensive Care nurses in the approach and method for shift handover, to provide an independent, but rigorous approach to teaching these important skills. In this paper we present a virtual world simulator for students to practice key steps in handing over the 24/7 care requirements of intensive care patients during the commencing first hour of a shift. We describe the modelling process to provide a convincing interactive simulation of the handover steps involved. The virtual world provides a practice tool for students to test their analytical skills with scenarios previously provided by simple physical simulations, and live on the job training. Additional educational benefits include facilitation of remote learning, high flexibility in study hours and the automatic recording of a reviewable log from the session. To the best of our knowledge, we believe this is a novel and original application of virtual worlds to an ICU handover process. The major outcome of the work was a virtual world environment for training nurses in the shift handover process, designed and developed for use by postgraduate nurses in training.

Sensitivity of building cooling loads to future weather predictions

The interaction and relationship between the global warming and the thermal performance buildings are dynamic in nature. In order to model and understand this behavior, different approaches, including keeping weather variable unchanged, morphing approach and diurnal modelling method, have been used to project and generate future weather data. Among these approaches, various assumptions on the change of solar radiation, air humidity and/or wind characteristics may be adopted. In this paper, an example to illustrate the generation of future weather data for the different global warming scenarios in Australia is presented. The sensitivity of building cooling loads to the possible changes of assumed values used in the future weather data generation is investigated. It is shown that with ± 10% change of the proposed future values for solar radiation, air humidity or wind characteristics, the corresponding change in the cooling load of the modeled sample office building at different Australian capital cities would not exceed 6%, 4% and 1.5% respectively. It is also found that with ±10% changes on the proposed weather variables for both the 2070-high future scenario and the current weather scenario, the corresponding change in the cooling loads at different locations may be weaker (up to 2% difference in Hobart for ±10% change in global solar radiation), similar (less than 0.6%) difference in Hobart for ±10% change in wind speed), or stronger (up to 1.6% difference in Hobart for ±10% change in relative humidity) in the 2070-high future scenario than in the current weather scenario.

The effect of exercise intensity on fat oxidation and non-exercise activity thermogenesis in overweight/obese men

It is frequently reported that the actual weight loss achieved through exercise interventions is less than theoretically expected. Amongst other compensatory adjustments that accompany exercise training (e.g., increases in resting metabolic rate and energy intake), a possible cause of the less than expected weight loss is a failure to produce a marked increase in total daily energy expenditure due to a compensatory reduction in non-exercise activity thermogenesis (NEAT). Therefore, there is a need to understand how behaviour is modified in response to exercise interventions. The proposed benefits of exercise training are numerous, including changes to fat oxidation. Given that a diminished capacity to oxidise fat could be a factor in the aetiology of obesity, an exercise training intensity that optimises fat oxidation in overweight/obese individuals would improve impaired fat oxidation, and potentially reduce health risks that are associated with obesity. To improve our understanding of the effectiveness of exercise for weight management, it is important to ensure exercise intensity is appropriately prescribed, and to identify and monitor potential compensatory behavioural changes consequent to exercise training. In line with the gaps in the literature, three studies were performed. The aim of Study 1 was to determine the effect of acute bouts of moderate- and high-intensity walking exercise on NEAT in overweight and obese men. Sixteen participants performed a single bout of either moderate-intensity walking exercise (MIE) or high-intensity walking exercise (HIE) on two separate occasions. The MIE consisted of walking for 60-min on a motorised treadmill at 6 km.h-1. The 60-min HIE session consisted of walking in 5-min intervals at 6 km.h-1 and 10% grade followed by 5-min at 0% grade. NEAT was assessed by accelerometer three days before, on the day of, and three days after the exercise sessions. There was no significant difference in NEAT vector magnitude (counts.min-1) between the pre-exercise period (days 1-3) and the exercise day (day 4) for either protocol. In addition, there was no change in NEAT during the three days following the MIE session, however NEAT increased by 16% on day 7 (post-exercise) compared with the exercise day (P = 0.32). During the post-exercise period following the HIE session, NEAT was increased by 25% on day 7 compared with the exercise day (P = 0.08), and by 30-33% compared with the pre-exercise period (day 1, day 2 and day 3); P = 0.03, 0.03, 0.02, respectively. To conclude, a single bout of either MIE or HIE did not alter NEAT on the exercise day or on the first two days following the exercise session. However, extending the monitoring of NEAT allowed the detection of a 48 hour delay in increased NEAT after performing HIE. A longer-term intervention is needed to determine the effect of accumulated exercise sessions over a week on NEAT. In Study 2, there were two primary aims. The first aim was to test the reliability of a discontinuous incremental exercise protocol (DISCON-FATmax) to identify the workload at which fat oxidation is maximised (FATmax). Ten overweight and obese sedentary male men (mean BMI of 29.5 ¡Ó 4.5 kg/m2 and mean age of 28.0 ¡Ó 5.3 y) participated in this study and performed two identical DISCON-FATmax tests one week apart. Each test consisted of alternate 4-min exercise and 2-min rest intervals on a cycle ergometer. The starting work load of 28 W was increased every 4-min using 14 W increments followed by 2-min rest intervals. When the respiratory exchange ratio was consistently >1.0, the workload was increased by 14 W every 2-min until volitional exhaustion. Fat oxidation was measured by indirect calorimetry. The mean FATmax, ƒtV O2peak, %ƒtV O2peak and %Wmax at which FATmax occurred during the two tests were 0.23 ¡Ó 0.09 and 0.18 ¡Ó 0.08 (g.min-1); 29.7 ¡Ó 7.8 and 28.3 ¡Ó 7.5 (ml.kg-1.min-1); 42.3 ¡Ó 7.2 and 42.6 ¡Ó 10.2 (%ƒtV O2max) and 36.4 ¡Ó 8.5 and 35.4 ¡Ó 10.9 (%), respectively. A paired-samples T-test revealed a significant difference in FATmax (g.min-1) between the tests (t = 2.65, P = 0.03). The mean difference in FATmax was 0.05 (g.min-1) with the 95% confidence interval ranging from 0.01 to 0.18. Paired-samples T-test, however, revealed no significant difference in the workloads (i.e. W) between the tests, t (9) = 0.70, P = 0.4. The intra-class correlation coefficient for FATmax (g.min-1) between the tests was 0.84 (95% confidence interval: 0.36-0.96, P < 0.01). However, Bland-Altman analysis revealed a large disagreement in FATmax (g.min-1) related to W between the two tests; 11 ¡Ó 14 (W) (4.1 ¡Ó 5.3 ƒtV O2peak (%)).These data demonstrate two important phenomena associated with exercise-induced substrate oxidation; firstly, that maximal fat oxidation derived from a discontinuous FATmax protocol differed statistically between repeated tests, and secondly, there was large variability in the workload corresponding with FATmax. The second aim of Study 2 was to test the validity of a DISCON-FATmax protocol by comparing maximal fat oxidation (g.min-1) determined by DISCON-FATmax with fat oxidation (g.min-1) during a continuous exercise protocol using a constant load (CONEX). Ten overweight and obese sedentary males (BMI = 29.5 ¡Ó 4.5 kg/m2; age = 28.0 ¡Ó 4.5 y) with a ƒtV O2max of 29.1 ¡Ó 7.5 ml.kg-1.min-1 performed a DISCON-FATmax test consisting of alternate 4-min exercise and 2-min rest intervals on a cycle ergometer. The 1-h CONEX protocol used the workload from the DISCON-FATmax to determine FATmax. The mean FATmax, ƒtV O2max, %ƒtV O2max and workload at which FATmax occurred during the DISCON-FATmax were 0.23 ¡Ó 0.09 (g.min-1); 29.1 ¡Ó 7.5 (ml.kg-1.min-1); 43.8 ¡Ó 7.3 (%ƒtV O2max) and 58.8 ¡Ó 19.6 (W), respectively. The mean fat oxidation during the 1-h CONEX protocol was 0.19 ¡Ó 0.07 (g.min-1). A paired-samples T-test revealed no significant difference in fat oxidation (g.min-1) between DISCON-FATmax and CONEX, t (9) = 1.85, P = 0.097 (two-tailed). There was also no significant correlation in fat oxidation between the DISCON-FATmax and CONEX (R=0.51, P = 0.14). Bland- Altman analysis revealed a large disagreement in fat oxidation between the DISCONFATmax and CONEX; the upper limit of agreement was 0.13 (g.min-1) and the lower limit of agreement was ¡V0.03 (g.min-1). These data suggest that the CONEX and DISCONFATmax protocols did not elicit different rates of fat oxidation (g.min-1). However, the individual variability in fat oxidation was large, particularly in the DISCON-FATmax test. Further research is needed to ascertain the validity of graded exercise tests for predicting fat oxidation during constant load exercise sessions. The aim of Study 3 was to compare the impact of two different intensities of four weeks of exercise training on fat oxidation, NEAT, and appetite in overweight and obese men. Using a cross-over design 11 participants (BMI = 29 ¡Ó 4 kg/m2; age = 27 ¡Ó 4 y) participated in a training study and were randomly assigned initially to: [1] a lowintensity (45%ƒtV O2max) exercise (LIT) or [2] a high-intensity interval (alternate 30 s at 90%ƒtV O2max followed by 30 s rest) exercise (HIIT) 40-min duration, three times a week. Participants completed four weeks of supervised training and between cross-over had a two week washout period. At baseline and the end of each exercise intervention,ƒtV O2max, fat oxidation, and NEAT were measured. Fat oxidation was determined during a standard 30-min continuous exercise bout at 45%ƒtV O2max. During the steady state exercise expired gases were measured intermittently for 5-min periods and HR was monitored continuously. In each training period, NEAT was measured for seven consecutive days using an accelerometer (RT3) the week before, at week 3 and the week after training. Subjective appetite sensations and food preferences were measured immediately before and after the first exercise session every week for four weeks during both LIT and HIIT. The mean fat oxidation rate during the standard continuous exercise bout at baseline for both LIT and HIIT was 0.14 ¡Ó 0.08 (g.min-1). After four weeks of exercise training, the mean fat oxidation was 0.178 ¡Ó 0.04 and 0.183 ¡Ó 0.04 g.min-1 for LIT and HIIT, respectively. The mean NEAT (counts.min-1) was 45 ¡Ó 18 at baseline, 55 ¡Ó 22 and 44 ¡Ó 16 during training, and 51 ¡Ó 14 and 50 ¡Ó 21 after training for LIT and HIIT, respectively. There was no significant difference in fat oxidation between LIT and HIIT. Moreover, although not statistically significant, there was some evidence to suggest that LIT and HIIT tend to increase fat oxidation during exercise at 45% ƒtV O2max (P = 0.14 and 0.08, respectively). The order of training treatment did not significantly influence changes in fat oxidation, NEAT, and appetite. NEAT (counts.min-1) was not significantly different in the week following training for either LIT or HIIT. Although not statistically significant (P = 0.08), NEAT was 20% lower during week 3 of exercise training in HIIT compared with LIT. Examination of appetite sensations revealed differences in the intensity of hunger, with higher ratings after LIT compared with HIIT. No differences were found in preferences for high-fat sweet foods between LIT and HIIT. In conclusion, the results of this thesis suggest that while fat oxidation during steady state exercise was not affected by the level of exercise intensity, there is strong evidence to suggest that intense exercise could have a debilitative effect on NEAT.

Modelling the interaction of keratinocytes and fibroblasts during normal and abnormal wound healing processes

The crosstalk between fibroblasts and keratinocytes is a vital component of the wound healing process, and involves the activity of a number of growth factors and cytokines. In this work, we develop a mathematical model of this crosstalk in order to elucidate the effects of these interactions on the regeneration of collagen in a wound that heals by second intention. We consider the role of four components that strongly affect this process: transforming growth factor-beta, platelet-derived growth factor, interleukin-1 and keratinocyte growth factor. The impact of this network of interactions on the degradation of an initial fibrin clot, as well as its subsequent replacement by a matrix that is mainly comprised of collagen, is described through an eight-component system of nonlinear partial differential equations. Numerical results, obtained in a two-dimensional domain, highlight key aspects of this multifarious process such as reepithelialisation. The model is shown to reproduce many of the important features of normal wound healing. In addition, we use the model to simulate the treatment of two pathological cases: chronic hypoxia, which can lead to chronic wounds; and prolonged inflammation, which has been shown to lead to hypertrophic scarring. We find that our model predictions are qualitatively in agreement with previously reported observations, and provide an alternative pathway for gaining insight into this complex biological process.

Indigenous knowledge and effective parent–school partnerships : issues and insights

Towards the last decade of the last millennium, Indigenous knowledge was central to international scholarly debates relating to decolonising knowledge. Indigenous scholars, particularly those from Australia, New Zealand, Canada, and the United States, advanced many of these debates. They argued for Indigenous knowledge to be used as the epistemological standpoint for intellectual engagements and the methodology for resisting colonial constructions of the colonised other (Rigney 1997; Smith 1999, 2005). However, the challenge of engaging Indigenous knowledge to inform research and educational processes, in many respects, is still a contested debate in Western-oriented universities and institutions of higher education. This chapter discusses findings of the Parent–School Partnership Initiative (hereafter referred to as PSPI) project conducted by the Oodgeroo Unit staff and the Aboriginal and Torres Strait Islander Education Focus Group for the Caboolture Shire, in South East Queensland. The state government sponsored initiative examined factors that promote and enhance parent–school engagement with students’ schooling, and contributed to Aboriginal and Torres Strait Islander students’ learning and completion of secondary schooling within the participating schools. We argue in this chapter for the importance of recognising Indigenous knowledge and its place in enhancing parent–school partnerships.

Models of collective cell behaviour with crowding effects : comparing lattice-based and lattice-free approaches

Individual-based models describing the migration and proliferation of a population of cells frequently restrict the cells to a predefined lattice. An implicit assumption of this type of lattice based model is that a proliferative population will always eventually fill the lattice. Here we develop a new lattice-free individual-based model that incorporates cell-to-cell crowding effects. We also derive approximate mean-field descriptions for the lattice-free model in two special cases motivated by commonly used experimental setups. Lattice-free simulation results are compared to these mean-field descriptions and to a corresponding lattice-based model. Data from a proliferation experiment is used to estimate the parameters for the new model, including the cell proliferation rate, showing that the model fits the data well. An important aspect of the lattice-free model is that the confluent cell density is not predefined, as with lattice-based models, but an emergent model property. As a consequence of the more realistic, irregular configuration of cells in the lattice-free model, the population growth rate is much slower at high cell densities and the population cannot reach the same confluent density as an equivalent lattice-based model.

A new model to analyze metaphyseal bone healing in mice

Background: Despite the increasing clinical problems with metaphyseal fractures, most experimental studies investigate the healing of diaphyseal fractures. Although the mouse would be the preferable species to study the molecular and genetic aspects of metaphyseal fracture healing, a murine model does not exist yet. Using a special locking plate system, we herein introduce a new model, which allows the analysis of metaphyseal bone healing in mice. Methods: In 24 CD-1 mice the distal metaphysis of the femur was osteotomized. After stabilization with the locking plate, bone repair was analyzed radiologically, biomechanically, and histologically after 2 (n = 12) and 5 wk (n = 12). Additionally, the stiffness of the bone-implant construct was tested biomechanically ex vivo. Results: The torsional stiffness of the bone-implant construct was low compared with nonfractured control femora (0.23 ± 0.1 Nmm/°versus 1.78 ± 0.15 Nmm/°, P < 0.05). The cause of failure was a pullout of the distal screw. At 2 wk after stabilization, radiological analysis showed that most bones were partly bridged. At 5 wk, all bones showed radiological union. Accordingly, biomechanical analyses revealed a significantly higher torsional stiffness after 5 wk compared with that after 2 wk. Successful healing was indicated by a torsional stiffness of 90% of the contralateral control femora. Histological analyses showed new woven bone bridging the osteotomy without external callus formation and in absence of any cartilaginous tissue, indicating intramembranous healing. Conclusion: With the model introduced herein we report, for the first time, successful metaphyseal bone repair in mice. The model may be used to obtain deeper insights into the molecular mechanisms of metaphyseal fracture healing. © 2012 Elsevier Inc. All rights reserved.

Tear film surface quality with rigid and soft contact lenses

Objectives: To measure tear film surface quality (TFSQ) using dynamic high-speed videokeratoscopy during short-term (8 hours) use of rigid and soft contact lenses. Methods: A group of fourteen subjects wore 3 different types of contact lenses on 3 different non-consecutive days (order randomized) in one eye only. Subjects were screened to exclude those with dry eye. The lenses included a PMMA hard, an RGP (Boston XO) and a soft silicone hydrogel lens. Three 30 second long high speed videokeratoscopy recordings were taken with contact lenses in-situ, in the morning and again after 8 hours of contact lens wear, both in normal and suppressed blinking conditions. Recordings were also made on a baseline day with no contact lens wear. Results: The presence of a contact lens in the eye had a significant effect on the mean TFSQ in both natural and suppressed blinking conditions (p=0.001 and p=0.01 respectively, repeated measures ANOVA). TFSQ was worse with all the lenses compared to no lens in the eye (in the afternoon during both normal and suppressed blinking conditions (all p<0.05). In natural blinking conditions, the mean TFSQ for the PMMA and RGP lenses was significantly worse than the baseline day (no lens) for both morning and afternoon measures (p<0.05). Conclusions: This study shows that both rigid and soft contact lenses adversely affect the TFSQ in both natural and suppressed blinking conditions. No significant differences were found between the lens types and materials. Keywords: Tear film surface quality, rigid contact lens, soft contact lens, dynamic high-speed videokeratoscopy

Synthesizing and databasing fossil calibrations: divergence dating and beyond

Divergence dating studies, which combine temporal data from the fossil record with branch length data from molecular phylogenetic trees, represent a rapidly expanding approach to understanding the history of life. National Evolutionary Synthesis Center hosted the first Fossil Calibrations Working Group (3–6 March, 2011, Durham, NC, USA), bringing together palaeontologists, molecular evolutionists and bioinformatics experts to present perspectives from disciplines that generate, model and use fossil calibration data. Presentations and discussions focused on channels for interdisciplinary collaboration, best practices for justifying, reporting and using fossil calibrations and roadblocks to synthesis of palaeontological and molecular data. Bioinformatics solutions were proposed, with the primary objective being a new database for vetted fossil calibrations with linkages to existing resources, targeted for a 2012 launch.