Saliva-derived DNA performs well in large-scale, high-density single-nucleotide polymorphism microarray studies

As of June 2009, 361 genome-wide association studies (GWAS) had been referenced by the HuGE database. GWAS require DNA from many thousands of individuals, relying on suitable DNA collections. We recently performed a multiple sclerosis (MS) GWAS where a substantial component of the cases (24%) had DNA derived from saliva. Genotyping was done on the Illumina genotyping platform using the Infinium Hap370CNV DUO microarray. Additionally, we genotyped 10 individuals in duplicate using both saliva- and blood-derived DNA. The performance of blood- versus saliva-derived DNA was compared using genotyping call rate, which reflects both the quantity and quality of genotyping per sample and the “GCScore,” an Illumina genotyping quality score, which is a measure of DNA quality. We also compared genotype calls and GCScores for the 10 sample pairs. Call rates were assessed for each sample individually. For the GWAS samples, we compared data according to source of DNA and center of origin. We observed high concordance in genotyping quality and quantity between the paired samples and minimal loss of quality and quantity of DNA in the saliva samples in the large GWAS sample, with the blood samples showing greater variation between centers of origin. This large data set highlights the usefulness of saliva DNA for genotyping, especially in high-density single-nucleotide polymorphism microarray studies such as GWAS.

Incorporating spatial correlations into multispecies mean-field models

In biology, we frequently observe different species existing within the same environment. For example, there are many cell types in a tumour, or different animal species may occupy a given habitat. In modelling interactions between such species, we often make use of the mean field approximation, whereby spatial correlations between the locations of individuals are neglected. Whilst this approximation holds in certain situations, this is not always the case, and care must be taken to ensure the mean field approximation is only used in appropriate settings. In circumstances where the mean field approximation is unsuitable we need to include information on the spatial distributions of individuals, which is not a simple task. In this paper we provide a method that overcomes many of the failures of the mean field approximation for an on-lattice volume-excluding birth-death-movement process with multiple species. We explicitly take into account spatial information on the distribution of individuals by including partial differential equation descriptions of lattice site occupancy correlations. We demonstrate how to derive these equations for the multi-species case, and show results specific to a two-species problem. We compare averaged discrete results to both the mean field approximation and our improved method which incorporates spatial correlations. We note that the mean field approximation fails dramatically in some cases, predicting very different behaviour from that seen upon averaging multiple realisations of the discrete system. In contrast, our improved method provides excellent agreement with the averaged discrete behaviour in all cases, thus providing a more reliable modelling framework. Furthermore, our method is tractable as the resulting partial differential equations can be solved efficiently using standard numerical techniques.

Exploiting Web 2.0 technologies to forge live connectedness in class

The economics of supporting learning has seen institutional encouragement of a wide range of blended learning initiatives in face to face and online teaching and learning. This has become one of the key drivers for the adoption of technology in teaching, in a manner occassionally guilty of putting the cart before the horse. Learning spaces are increasingly equipped with a dizzying array of technological options testifying to institutional and governmental investment and commitment in supporting face to face blended learning (QUT, 2011, C/4.2). Yet innovation within traditional learning and teaching models faces a number of challenges both at an institutional level and at the teaching coal face. Web 2.0 technologies present a vast array of opportunities to harness and capture the attention of students in engaging learning opportunitites. This presentation will explore technologies supportive of active learning pedagogies.

A new era : personal technology challenges educational technology

As we race towards a new era, rapid change of conventional models has become the norm. Just as technology has etched itself to the core of society, the sheer quantity of student devices connecting to university networks presents a sector wide challenge coinciding almost perfectly with many universities creating technology rich learning spaces. New fears include future proofing. It is not just a matter of technology becoming outdated. In seeking to accommodate the teaching styles and experience of staff across diverse faculties, is this technology simply too vanilla to meet their needs as they become increasingly skilled and inspired by technology’s potential? Through the early findings of a study into staff use of technology within Queensland University of Technology's next generation collaborative learning spaces, this paper explores whether the answers lie in a model presented by students equipping themselves with the tools they need to learn in the 21st century.

Air Gondwana and Mosswood Manor : blended learning environments utilising second life machinima to teach negotiation skills

Seminal reports into higher education in Australia and overseas have recognised negotiation as an essential skill of a practising lawyer and have recommended that all law schools include instruction in negotiation theory and practice in their curricula. Effective negotiation training includes the elements of instruction, modelling, practice and feedback. Ideally such training takes place in the context of small groups. However, this does not necessarily mean that negotiation cannot be taught effectively in the context of large groups. This paper discusses two related blended learning environments that provide instruction in negotiation theory and practice as part of the graduate capabilities program of the undergraduate law degree in the School of Law at the Queensland University of Technology in Brisbane, Australia. Air Gondwana, which forms part of the curriculum of the two first year Contract Law subjects, and Mosswood Manor, which forms part of the curriculum of the second year Trusts subject, utilise a common narrative concerning the family of a wealthy industrialist to facilitate learning of negotiation skills. The programs both combine online and in-class components, the online components utilising machinima (computer graphics created without the need for professional software) to depict the narrative. This strategy has enabled the creation of effective, engaging and challenging learning experiences for large cohorts of students studying by different modes (full-time, part-time and distance external). The use of a common narrative, including the same characters and settings, in the two programs also provides a familiar environment in which students advance their learning from one level of attainment to the next.

Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma

We characterized the mutational landscape of melanoma, the form of skin cancer with the highest mortality rate, by sequencing the exomes of 147 melanomas. Sun-exposed melanomas had markedly more ultraviolet (UV)-like C>T somatic mutations compared to sun-shielded acral, mucosal and uveal melanomas. Among the newly identified cancer genes was PPP6C, encoding a serine/threonine phosphatase, which harbored mutations that clustered in the active site in 12% of sun-exposed melanomas, exclusively in tumors with mutations in BRAF or NRAS. Notably, we identified a recurrent UV-signature, an activating mutation in RAC1 in 9.2% of sun-exposed melanomas. This activating mutation, the third most frequent in our cohort of sun-exposed melanoma after those of BRAF and NRAS, changes Pro29 to serine (RAC1P29S) in the highly conserved switch I domain. Crystal structures, and biochemical and functional studies of RAC1P29S showed that the alteration releases the conformational restraint conferred by the conserved proline, causes an increased binding of the protein to downstream effectors, and promotes melanocyte proliferation and migration. These findings raise the possibility that pharmacological inhibition of downstream effectors of RAC1 signaling could be of therapeutic benefit.

A simplified approach for calculating the moments of action for linear reaction-diffusion equations

The mean action time is the mean of a probability density function that can be interpreted as a critical time, which is a finite estimate of the time taken for the transient solution of a reaction-diffusion equation to effectively reach steady state. For high-variance distributions, the mean action time under-approximates the critical time since it neglects to account for the spread about the mean. We can improve our estimate of the critical time by calculating the higher moments of the probability density function, called the moments of action, which provide additional information regarding the spread about the mean. Existing methods for calculating the nth moment of action require the solution of n nonhomogeneous boundary value problems which can be difficult and tedious to solve exactly. Here we present a simplified approach using Laplace transforms which allows us to calculate the nth moment of action without solving this family of boundary value problems and also without solving for the transient solution of the underlying reaction-diffusion problem. We demonstrate the generality of our method by calculating exact expressions for the moments of action for three problems from the biophysics literature. While the first problem we consider can be solved using existing methods, the second problem, which is readily solved using our approach, is intractable using previous techniques. The third problem illustrates how the Laplace transform approach can be used to study coupled linear reaction-diffusion equations.

Identification of a serine protease inhibitor which causes inclusion vacuole reduction and is lethal to Chlamydia trachomatis

The mechanistic details of the pathogenesis of Chlamydia, an obligate intracellular pathogen of global importance, have eluded scientists due to the scarcity of traditional molecular genetic tools to investigate this organism. Here we report a chemical biology strategy that has uncovered the first essential protease for this organism. Identification and application of a unique CtHtrA inhibitor (JO146) to cultures of Chlamydia resulted in a complete loss of viable elementary body formation. JO146 treatment during the replicative phase of development resulted in a loss of Chlamydia cell morphology, diminishing inclusion size, and ultimate loss of inclusions from the host cells. This completely prevented the formation of viable Chlamydia elementary bodies. In addition to its effect on the human C. trachomatis strain, JO146 inhibited the viability of the mouse strain, Chlamydia muridarum, both in vitro and in vivo. Thus, we report a chemical biology approach to establish an essential role for Chlamydia CtHtrA. The function of CtHtrA for Chlamydia appears to be essential for maintenance of cell morphology during replicative the phase and these findings provide proof of concept that proteases can be targetted for anti-microbial therapy for intracellular pathogens.

Virtual worlds in Australian and New Zealand higher education : remembering the past, understanding the present and imagining the future

3D virtual reality, including the current generation of multi-user virtual worlds, has had a long history of use in education and training, and it experienced a surge of renewed interest with the advent of Second Life in 2003. What followed shortly after were several years marked by considerable hype around the use of virtual worlds for teaching, learning and research in higher education. For the moment, uptake of the technology seems to have plateaued, with academics either maintaining the status quo and continuing to use virtual worlds as they have previously done or choosing to opt out altogether. This paper presents a brief review of the use of virtual worlds in the Australian and New Zealand higher education sector in the past and reports on its use in the sector at the present time, based on input from members of the Australian and New Zealand Virtual Worlds Working Group. It then adopts a forward-looking perspective amid the current climate of uncertainty, musing on future directions and offering suggestions for potential new applications in light of recent technological developments and innovations in the area.

Effect of aerobic interval training and caffeine on blood platelet function

Purpose: Hyperactive platelets contribute to the thrombotic response in humans, and exercise transiently increases platelet function. Caffeine is routinely used by athletes as an ergogenic aid, but the combined effect of exercise and caffeine on platelet function has not been investigated. Methods: Twelve healthy males were randomly assigned to one of four groups and undertook four experimental trials of a high-intensity aerobic interval training (AIT) bout or rest with ingestion of caffeine (3 mg·kg-1) or placebo. AIT was 8 × 5 min at approximately 75% peak power output (approximately 80% V?O2peak) and 1-min recovery (approximately 40% peak power output, approximately 50% V?O2peak) intervals. Blood/urine was collected before, 60, and 90 min after capsule ingestion and analyzed for platelet aggregation/activation. Results: AIT increased platelet reactivity to adenosine diphosphate (placebo 30.3%, caffeine 13.4%, P < 0.05) and collagen (placebo 10.8%, caffeine 5.1%, P < 0.05) compared with rest. Exercise placebo increased adenosine diphosphate-induced aggregation 90 min postingestion compared with baseline (40.5%, P < 0.05), but the increase when exercise was combined with caffeine was small (6.6%). During the resting caffeine protocol, collagen-induced aggregation was reduced (-4.3%, P < 0.05). AIT increased expression of platelet activation marker PAC-1 with exercise placebo (P < 0.05) but not when combined with caffeine. Conclusion: A single bout of AIT increases platelet function, but caffeine ingestion (3 mg·kg) does not exacerbate platelet function at rest or in response to AIT. Our results provide new information showing caffeine at a dose that can elicit ergogenic effects on performance has no detrimental effect on platelet function and may have the potential to attenuate increases in platelet activation and aggregation when undertaking strenuous exercise.

Fresh ideas : services thinking for social marketing

Purpose The social marketing literature tends to focus on upstream marketing (policy) and downstream (individual behaviour change) and has a limited view on midstream (working with partners and community groups) social marketing. The paper proposes midstream social marketing should also include an understanding of how services and service employees influence and support individual behaviour change goals. The paper presents four key services marketing principles - derived from services theory and thinking - which the paper believes to be essential for implementing effective midstream social marketing. Design/methodology/approach This is a conceptual paper that uses service theory and case-examples to show how service thinking can be used as a midstream social marketing approach. Findings For effective uptake and impact of social marketing services amongst people and populations, social marketers need to design programs that consider the service experience, the service employee, service quality/customer value and the active role of the customer in value creation. Research limitations/implications Services marketing is a well-established sub-discipline of marketing which, until recently, has not interacted with social marketing. The extension and application of services theory for social marketing can enrich and propel the social marketing discipline forward. Further research is recommended to evaluate how service principles can be applied in practice. Social implications Given that social marketing services tend not to be accessed in sufficient numbers by the people who most need them, social marketers need to think beyond the technical, cognitive, and organisational-focused goals when designing social services. Originality/value This paper identifies key service theories that social marketers should understand and use and is thus a source of fresh ideas for theory and practice.

High rates of muscle glycogen resynthesis after exhaustive exercise when carbohydrate is coingested with caffeine

We determined the effect of coingestion of caffeine (Caff) with carbohydrate (CHO) on rates of muscle glycogen resynthesis during recovery from exhaustive exercise in seven trained subjects who completed two experimental trials in a randomized, double-blind crossover design. The evening before an experiment subjects performed intermittent exhaustive cycling and then consumed a low-CHO meal. The next morning subjects rode until volitional fatigue. On completion of this ride subjects consumed either CHO [4 g/kg body mass (BM)] or the same amount of CHO + Caff (8 mg/kg BM) during 4 h of passive recovery. Muscle biopsies and blood samples were taken at regular intervals throughout recovery. Muscle glycogen levels were similar at exhaustion [?75 mmol/kg dry wt (dw)] and increased by a similar amount (?80%) after 1 h of recovery (133 ± 37.8 vs. 149 ± 48 mmol/kg dw for CHO and Caff, respectively). After 4 h of recovery Caff resulted in higher glycogen accumulation (313 ± 69 vs. 234 ± 50 mmol/kg dw, P < 0.001). Accordingly, the overall rate of resynthesis for the 4-h recovery period was 66% higher in Caff compared with CHO (57.7 ± 18.5 vs. 38.0 ± 7.7 mmol·kg dw-1·h-1, P < 0.05). After 1 h of recovery plasma Caff levels had increased to 31 ± 11 ?M (P < 0.001) and at the end of the recovery reached 77 ± 11 ?M (P < 0.001) with Caff. Phosphorylation of CaMKThr286 was similar after exercise and after 1 h of recovery, but after 4 h CaMKThr286 phosphorylation was higher in Caff than CHO (P < 0.05). Phosphorylation of AMP-activated protein kinase (AMPK)Thr172 and AktSer473 was similar for both treatments at all time points. We provide the first evidence that in trained subjects coingestion of large amounts of Caff (8 mg/kg BM) with CHO has an additive effect on rates of postexercise muscle glycogen accumulation compared with consumption of CHO alone.

The anodized crystalline WO3 nanoporous network with enhanced electrochromic properties

We demonstrate that a three dimensional (3D) crystalline tungsten trioxide (WO3) nanoporous network, directly grown on a transparent conductive oxide (TCO) substrate, is a suitable working electrode material for high performance electrochromic devices. This nanostructure, with achievable thicknesses of up to 2 μm, is prepared at room temperature by the electrochemical anodization of a RF-sputtered tungsten film deposited on a fluoride doped tin oxide (FTO) conductive glass, under low applied anodic voltages and mild chemical dissolution conditions. For the crystalline nanoporous network with thicknesses ranging from 0.6 to 1 μm, impressive coloration efficiencies of up to 141.5 cm2 C−1 are achieved by applying a low coloration voltage of −0.25 V. It is also observed that there is no significant degradation of the electrochromic properties of the porous film after 2000 continuous coloration–bleaching cycles. The remarkable electrochromic characteristics of this crystalline and nanoporous WO3 are mainly ascribed to the combination of a large surface area, facilitating increased intercalation of protons, as well as excellent continuous and directional paths for charge transfer and proton migration in the highly crystalline material.

Anodic formation of a thick three-dimensional nanoporous WO3 film and its photocatalytic property

We report an efficient solar-light-driven photocatalyst based on three-dimensional nanoporous tungsten trioxide (WO3) films. These films are obtained by anodizing W foils in fluoride-containing electrolytes at room temperature and under low applied voltages with an efficient growth rate of 2 μm h− 1. The maximum thickness of the films is ~ 3 μm that exceeds those of previously reported anodized WO3 films in fluoride-containing electrolytes. By investigating the photocatalytic properties of the films with thicknesses ranging from ~ 0.5 to ~ 3 μm, the optimum thickness of the nanoporous film is found to be ~ 1 μm, which demonstrates an impressive 120% improvement in the photocatalytic performance compared to that of a RF-sputtered nanotextured film with similar weights. We mainly ascribe this to large surface area and smaller bandgap.

Aqueous phase synthesis of copper nanoparticles : a link between heavy metal resistance and nanoparticle synthesis ability in bacterial systems

We demonstrate aqueous phase biosynthesis of phase-pure metallic copper nanoparticles (CuNPs) using a silver resistant bacterium Morganella morganii. This is particularly important considering that there has been no report that demonstrates biosynthesis and stabilization of pure copper nanoparticles in the aqueous phase. Electrochemical analysis of bacterial cells exposed to Cu2+ ions provides new insights into the mechanistic aspect of Cu2+ ion reduction within the bacterial cell and indicates a strong link between the silver and copper resistance machinery of bacteria in the context of metal ion reduction. The outcomes of this study take us a step closer towards designing rational strategies for biosynthesis of different metal nanoparticles using microorganisms.