Spatial population genetic structure reveals strong natal site fidelity in Echinocladius martini (Diptera: Chironomidae) in northeast Queensland, Australia

1. A diverse array of patterns has been reported regarding the spatial extent of population genetic structure and effective dispersal in freshwater macroinvertebrates. In river systems, the movements of many taxa can be restricted to varying degrees by the natural stream channel hierarchy. 2. In this study, we sampled populations of the non-biting freshwater midge Echinocladius martini in the Paluma bioregion of tropical northeast Queensland to investigate fine scale patterns of within- and among-stream dispersal and gene flow within a purported historical refuge. We amplified a 639 bp fragment of mitochondrial COI and analysed genetic structure using pairwise ΦST, hierarchical AMOVA, Mantel tests and a parsimony network. Genetic variation was partitioned among stream sections using Streamtree to investigate the effect of potential instream dispersal barriers. 3. The data revealed strong natal site fidelity and significant differentiation among neighbouring, geographically proximate streams. We found evidence for only episodic adult flight among sites on separate stream reaches. Overall, however, our data suggested that both larval and adult dispersal was largely limited to within a stream channel. 4. This may arise from a combination of the high density of riparian vegetation physically restricting dispersal and from the joint effects of habitat stability and large population sizes. Together these may mitigate the requirement for movement among streams to avoid inbreeding and local extinction due to habitat change and may thus enable persistence of upstream populations in the absence of regular compensatory upstream flight. Taken together, these data suggest that dispersal of E. martini is highly restricted, to the scale of only a few kilometres, and hence occurs predominantly within the natal stream.

Numerical simulation for the variable-order Galilei invariant advection diffusion equation with a nonlinear source term

In this paper, we consider the variable-order Galilei advection diffusion equation with a nonlinear source term. A numerical scheme with first order temporal accuracy and second order spatial accuracy is developed to simulate the equation. The stability and convergence of the numerical scheme are analyzed. Besides, another numerical scheme for improving temporal accuracy is also developed. Finally, some numerical examples are given and the results demonstrate the effectiveness of theoretical analysis. Keywords: The variable-order Galilei invariant advection diffusion equation with a nonlinear source term; The variable-order Riemann–Liouville fractional partial derivative; Stability; Convergence; Numerical scheme improving temporal accuracy

Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer

Background Phylogeographic reconstruction of some bacterial populations is hindered by low diversity coupled with high levels of lateral gene transfer. A comparison of recombination levels and diversity at seven housekeeping genes for eleven bacterial species, most of which are commonly cited as having high levels of lateral gene transfer shows that the relative contributions of homologous recombination versus mutation for Burkholderia pseudomallei is over two times higher than for Streptococcus pneumoniae and is thus the highest value yet reported in bacteria. Despite the potential for homologous recombination to increase diversity, B. pseudomallei exhibits a relative lack of diversity at these loci. In these situations, whole genome genotyping of orthologous shared single nucleotide polymorphism loci, discovered using next generation sequencing technologies, can provide very large data sets capable of estimating core phylogenetic relationships. We compared and searched 43 whole genome sequences of B. pseudomallei and its closest relatives for single nucleotide polymorphisms in orthologous shared regions to use in phylogenetic reconstruction. Results Bayesian phylogenetic analyses of >14,000 single nucleotide polymorphisms yielded completely resolved trees for these 43 strains with high levels of statistical support. These results enable a better understanding of a separate analysis of population differentiation among >1,700 B. pseudomallei isolates as defined by sequence data from seven housekeeping genes. We analyzed this larger data set for population structure and allele sharing that can be attributed to lateral gene transfer. Our results suggest that despite an almost panmictic population, we can detect two distinct populations of B. pseudomallei that conform to biogeographic patterns found in many plant and animal species. That is, separation along Wallace's Line, a biogeographic boundary between Southeast Asia and Australia. Conclusion We describe an Australian origin for B. pseudomallei, characterized by a single introduction event into Southeast Asia during a recent glacial period, and variable levels of lateral gene transfer within populations. These patterns provide insights into mechanisms of genetic diversification in B. pseudomallei and its closest relatives, and provide a framework for integrating the traditionally separate fields of population genetics and phylogenetics for other bacterial species with high levels of lateral gene transfer.

Laser doppler imaging in a paediatric burns population

Objective Laser Doppler imaging (LDI) was compared to wound outcomes in children's burns, to determine if the technology could be used to predict these outcomes. Methods Forty-eight patients with a total of 85 burns were included in the study. Patient median age was 4 years 10 months and scans were taken 0–186 h post-burn using the fast, low-resolution setting on the Moor LDI2 laser Doppler imager. Wounds were managed by standard practice, without taking into account the scan results. Time until complete re-epithelialisation and whether or not grafting and scar management were required were recorded for each wound. If wounds were treated with Silvazine™ or Acticoat™ prior to the scan, this was also recorded. Results The predominant colour of the scan was found to be significantly related to the re-epithelialisation, grafting and scar management outcomes and could be used to predict those outcomes. The prior use of Acticoat™ did not affect the scan relationship to outcomes, however, the use of Silvazine™ did complicate the relationship for light blue and green scanned partial thickness wounds. Scans taken within the 24-h window after-burn also appeared to be accurate predictors of wound outcome. Conclusion Laser Doppler imaging is accurate and effective in a paediatric population with a low-resolution fast-scan.

Bayesian methodology for genetics of complex diseases

Genetic research of complex diseases is a challenging, but exciting, area of research. The early development of the research was limited, however, until the completion of the Human Genome and HapMap projects, along with the reduction in the cost of genotyping, which paves the way for understanding the genetic composition of complex diseases. In this thesis, we focus on the statistical methods for two aspects of genetic research: phenotype definition for diseases with complex etiology and methods for identifying potentially associated Single Nucleotide Polymorphisms (SNPs) and SNP-SNP interactions. With regard to phenotype definition for diseases with complex etiology, we firstly investigated the effects of different statistical phenotyping approaches on the subsequent analysis. In light of the findings, and the difficulties in validating the estimated phenotype, we proposed two different methods for reconciling phenotypes of different models using Bayesian model averaging as a coherent mechanism for accounting for model uncertainty. In the second part of the thesis, the focus is turned to the methods for identifying associated SNPs and SNP interactions. We review the use of Bayesian logistic regression with variable selection for SNP identification and extended the model for detecting the interaction effects for population based case-control studies. In this part of study, we also develop a machine learning algorithm to cope with the large scale data analysis, namely modified Logic Regression with Genetic Program (MLR-GEP), which is then compared with the Bayesian model, Random Forests and other variants of logic regression.

Psychometric properties of the parents' fever management scale in a Turkish population

Aim: This paper reports a study designed to assess the psychometric properties (validity and reliability) of a Turkish version of the Australian Parents’ Fever Management Scale (PFMS). Background: Little is known about childhood fever management among Turkish parents. No scales to measure parents’ fever management practices in Turkey are available. Design: This is a methodological study. Methods: Eighty parents, of febrile children aged six months to five years, were randomly selected from the paedaitric hospital and two community family health centers in Sakarya, Turkey. The PFMS was back translated; language equivalence and content validity were validated. PFMS and socio-demographic data were collected in 2009. Means and standard deviations were calculated for interval level data and p values greater than 0.05 were considered statistically significant. Unrotated principal component analysis was used to determine construct validity and Cronbach’s coefficient alpha determined the internal consistency reliability. Results: The PFMS was psychometrically sound in this population. Construct validity, confirmed by confirmatory factor analysis [KMO 0.812, Bartlett’s Specificity (χ² = 182.799, df=28, P < 0·001)] revealed the Turkish version to be comprised of the eight original PFMS items. Internal consistency reliability coefficient was 0.80 and the scale’s total-item correlation coefficients ranged from 0.15 to 0.66 and were significant (p<0.001). Interestingly parents reported high scores on the PFMS 34.52±4.60 (range 8-40 with 40 indicating a high burden of care for febrile children). Conclusion: The PFMS was as psychometrically robust in a Turkish population as in an Australian population and is, therefore, a useful tool for health professionals to identify parents’ practices, provide targeted education thereby in reducing the unnecessary burden of care they place on themselves when caring for a febrile child. Relevance to clinical practice. Testing in different populations, cultures and healthcare systems will further assist in reporting the PFMS usefulness in clinical practice and research.

Use of first nucleotide change technology to determine the frequency of factor V Leiden in a population of Australian blood donors

Activated protein C resistance (APCR), the most common risk factor for venous thrombosis, is the result of a G to A base substitution at nucleotide 1691 (R506Q) in the factor V gene. Current techniques to detect the factor V Leiden mutation, such as determination of restriction length polymorphisms, do not have the capacity to screen large numbers of samples in a rapid, cost- effective test. The aim of this study was to apply the first nucleotide change (FNC) technology, to the detection of the factor V Leiden mutation. After preliminary amplification of genomic DNA by polymerase chain reaction (PCR), an allele-specific primer was hybridised to the PCR product and extended using fluorescent terminating dideoxynucleotides which were detected by colorimetric assay. Using this ELISA-based assay, the prevalence of the factor V Leiden mutation was determined in an Australian blood donor population (n = 500). A total of 18 heterozygotes were identified (3.6%) and all of these were confirmed with conventional MnlI restriction digest. No homozygotes for the variant allele were detected. We conclude from this study that the frequency of 3.6% is compatible with others published for Caucasian populations. In addition, the FNC technology shows promise as the basis for a rapid, automated DNA based test for factor V Leiden.

Queue protection parameters’ fine-tuning for variable speed limits

Any incident on motorways potentially can be followed by secondary crashes. Rear-end crashes also could happen as a result of queue formation downstream of high speed platoons. To decrease the occurrence of secondary crashes and rear-end crashes, Variable Speed Limits (VSL) can be applied to protect queue formed downstream. This paper focuses on fine tuning the Queue Protection algorithm of VSL. Three performance indicators: activation time, deactivation time and number of false alarms are selected to optimise the Queue Protection algorithm. A calibrated microscopic traffic simulation model of Pacific Motorway in Brisbane is used for the optimisation. Performance of VSL during an incident and heavy congestion and the benefit of VSL will be presented in the paper.