Novel molecular markers of Chlamydia pecorum genetic diversity in the koala (Phascolarctos cinereus)

Background Chlamydia pecorum is an obligate intracellular bacterium and the causative agent of reproductive and ocular disease in several animal hosts including koalas, sheep, cattle and goats. C. pecorum strains detected in koalas are genetically diverse, raising interesting questions about the origin and transmission of this species within koala hosts. While the ompA gene remains the most widely-used target in C. pecorum typing studies, it is generally recognised that surface protein encoding genes are not suited for phylogenetic analysis and it is becoming increasingly apparent that the ompA gene locus is not congruent with the phylogeny of the C. pecorum genome. Using the recently sequenced C. pecorum genome sequence (E58), we analysed 10 genes, including ompA, to evaluate the use of ompA as a molecular marker in the study of koala C. pecorum genetic diversity. Results Three genes (incA, ORF663, tarP) were found to contain sufficient nucleotide diversity and discriminatory power for detailed analysis and were used, with ompA, to genotype 24 C. pecorum PCR-positive koala samples from four populations. The most robust representation of the phylogeny of these samples was achieved through concatenation of all four gene sequences, enabling the recreation of a "true" phylogenetic signal. OmpA and incA were of limited value as fine-detailed genetic markers as they were unable to confer accurate phylogenetic distinctions between samples. On the other hand, the tarP and ORF663 genes were identified as useful "neutral" and "contingency" markers respectively, to represent the broad evolutionary history and intra-species genetic diversity of koala C. pecorum. Furthermore, the concatenation of ompA, incA and ORF663 sequences highlighted the monophyletic nature of koala C. pecorum infections by demonstrating a single evolutionary trajectory for koala hosts that is distinct from that seen in non-koala hosts. Conclusions While the continued use of ompA as a fine-detailed molecular marker for epidemiological analysis appears justified, the tarP and ORF663 genes also appear to be valuable markers of phylogenetic or biogeographic divisions at the C. pecorum intra-species level. This research has significant implications for future typing studies to understand the phylogeny, genetic diversity, and epidemiology of C. pecorum infections in the koala and other animal species.

Spatio-temporal patterns of Barmah Forest virus disease in Queensland, Australia

Background Barmah Forest virus (BFV) disease is a common and wide-spread mosquito-borne disease in Australia. This study investigated the spatio-temporal patterns of BFV disease in Queensland, Australia using geographical information system (GIS) tools and geostatistical analysis. Methods/Principal Findings We calculated the incidence rates and standardised incidence rates of BFV disease. Moran's I statistic was used to assess the spatial autocorrelation of BFV incidences. Spatial dynamics of BFV disease was examined using semi-variogram analysis. Interpolation techniques were applied to visualise and display the spatial distribution of BFV disease in statistical local areas (SLAs) throughout Queensland. Mapping of BFV disease by SLAs reveals the presence of substantial spatio-temporal variation over time. Statistically significant differences in BFV incidence rates were identified among age groups (χ2 = 7587, df = 7327,p<0.01). There was a significant positive spatial autocorrelation of BFV incidence for all four periods, with the Moran's I statistic ranging from 0.1506 to 0.2901 (p<0.01). Semi-variogram analysis and smoothed maps created from interpolation techniques indicate that the pattern of spatial autocorrelation was not homogeneous across the state. Conclusions/Significance This is the first study to examine spatial and temporal variation in the incidence rates of BFV disease across Queensland using GIS and geostatistics. The BFV transmission varied with age and gender, which may be due to exposure rates or behavioural risk factors. There are differences in the spatio-temporal patterns of BFV disease which may be related to local socio-ecological and environmental factors. These research findings may have implications in the BFV disease control and prevention programs in Queensland.

Persistence of multiple genetic lineages within intra-host populations of Ross River virus

We examined the structure and extent of genetic diversity in intrahost populations of Ross River virus (RRV) in samples from six human patients, focusing on the nonstructural (nsP3) and structural (E2) protein genes. Strikingly, although the samples were collected from contrasting ecological settings 3,000 kilometers apart in Australia, we observed multiple viral lineages in four of the six individuals, which is indicative of widespread mixed infections. In addition, a comparison with previously published RRV sequences revealed that these distinct lineages have been in circulation for at least 5 years, and we were able to document their long-term persistence over extensive geographical distances

Correlation-based damage detection for complicated truss bridges using multi-layer genetic algorithms

The study presents a multi-layer genetic algorithm (GA) approach using correlation-based methods to facilitate damage determination for through-truss bridge structures. To begin, the structure’s damage-suspicious elements are divided into several groups. In the first GA layer, the damage is initially optimised for all groups using correlation objective function. In the second layer, the groups are combined to larger groups and the optimisation starts over at the normalised point of the first layer result. Then the identification process repeats until reaching the final layer where one group includes all structural elements and only minor optimisations are required to fine tune the final result. Several damage scenarios on a complicated through-truss bridge example are nominated to address the proposed approach’s effectiveness. Structural modal strain energy has been employed as the variable vector in the correlation function for damage determination. Simulations and comparison with the traditional single-layer optimisation shows that the proposed approach is efficient and feasible for complicated truss bridge structures when the measurement noise is taken into account.

Genetic algorithms to schedule container transfers at multimodal terminals

Optimising the container transfer schedule at the multimodal terminals is known to be NP-hard, which implies that the best solution becomes computationally infeasible as problem sizes increase. Genetic Algorithm (GA) techniques are used to reduce container handling/transfer times and ships' time at the port by speeding up handling operations. The GA is chosen due to the relatively good results that have been reported even with the simplest GA implementations to obtain near-optimal solutions in reasonable time. Also discussed, is the application of the model to assess the consequences of increased scheduled throughput time as well as different strategies such as the alternative plant layouts, storage policies and number of yard machines. A real data set used for the solution and subsequent sensitivity analysis is applied to the alternative plant layouts, storage policies and number of yard machines.

Excess power circulation in distribution networks containing distributed energy resources

The presence of large number of single-phase distributed energy resources (DERs) can cause severe power quality problems in distribution networks. The DERs can be installed in random locations. This may cause the generation in a particular phase exceeds the load demand in that phase. Therefore the excess power in that phase will be fed back to the transmission network. To avoid this problem, the paper proposes the use of distribution static compensator (DSTATCOM) that needs to be connected at the first bus following a substation. When operated properly, the DSTATCOM can facilitate a set of balanced current flow from the substation, even when excess power is generated by DERs. The proposals are validated through extensive digital computer simulation studies using PSCAD and MATLAB.

Energy-efficient virtual machine placement in data centers by genetic algorithm

Server consolidation using virtualization technology has become an important technology to improve the energy efficiency of data centers. Virtual machine placement is the key in the server consolidation. In the past few years, many approaches to the virtual machine placement have been proposed. However, existing virtual machine placement approaches to the virtual machine placement problem consider the energy consumption by physical machines in a data center only, but do not consider the energy consumption in communication network in the data center. However, the energy consumption in the communication network in a data center is not trivial, and therefore should be considered in the virtual machine placement in order to make the data center more energy-efficient. In this paper, we propose a genetic algorithm for a new virtual machine placement problem that considers the energy consumption in both the servers and the communication network in the data center. Experimental results show that the genetic algorithm performs well when tackling test problems of different kinds, and scales up well when the problem size increases.

An expressed sequence tag (EST) library for Drosophila serrata, a model system for sexual selection and climatic adaptation studies

The native Australian fly Drosophila serrata belongs to the highly speciose montium subgroup of the melanogaster species group. It has recently emerged as an excellent model system with which to address a number of important questions, including the evolution of traits under sexual selection and traits involved in climatic adaptation along latitudinal gradients. Understanding the molecular genetic basis of such traits has been limited by a lack of genomic resources for this species. Here, we present the first expressed sequence tag (EST) collection for D. serrata that will enable the identification of genes underlying sexually-selected phenotypes and physiological responses to environmental change and may help resolve controversial phylogenetic relationships within the montium subgroup.

Australian lungfish (Neoceratodus forsteri: Dipnoi) have low genetic variation at allozyme and mitochondrial DNA loci : a conservation alert?

Genetic variation at allozyme and mitochondrial DNA loci was investigated in the Australian lungfish, Neoceratodus forsteri Krefft 1870. Tissue samples for genetic analysis were taken non-lethally from 278 individuals representing two spatially distinct endemic populations (Mary and Burnett rivers), as well as one population thought to be derived from an anthropogenic translocation in the 1890's (Brisbane river). Two of 24 allozyme loci resolved from muscle tissue were polymorphic. Mitochondrial DNA nucleotide sequence diversity estimated across 2,235 base pairs in each of 40 individuals ranged between 0.000423 and 0.001470 per river. Low genetic variation at allozyme and mitochondrial loci could be attributed to population bottlenecks, possibly induced by Pleistocene aridity. Limited genetic differentiation was detected among rivers using nuclear and mitochondrial markers suggesting that admixture may have occurred between the endemic Mary and Burnett populations during periods of low sea level when the drainages may have converged before reaching the ocean. Genetic data was consistent with the explanation that lungfish were introduced to the Brisbane river from the Mary river. Further research using more variable genetic loci is needed before the conservation status of populations can be determined, particularly as anthropogenic demands on lungfish habitat are increasing. In the interim we recommend a management strategy aimed at conserving existing genetic variation within and between rivers.

Deforestation, REDD and international law

International environmental law governing conservation and management of forests has been largely limited to soft-law instruments. Nevertheless, increasing attention has been given to forest issues, most recently in the context of the climate change regime and the reducing emissions from deforestation and degradation (REDD) mechanism. The current law impacting upon the protection of forests and the contribution of emissions from deforestation will be considered in this chapter. The way forward will be explored, including the current options being considered for the post-Kyoto period.

Enabling access to and re-use of publicly funded research data as Open Educational Resources : a strategy for overcoming the legal barriers to data access and re-use

Open Educational Resources (OER) are teaching, learning and research materials that have been released under an open licence that permits online access and re-use by others. The 2012 Paris OER Declaration encourages the open licensing of educational materials produced with public funds. Digital data and data sets produced as a result of scientific and non-scientific research are an increasingly important category of educational materials. This paper discusses the legal challenges presented when publicly funded research data is made available as OER, arising from intellectual property rights, confidentiality and information privacy laws, and the lack of a legal duty to ensure data quality. If these legal challenges are not understood, addressed and effectively managed, they may impede and restrict access to and re-use of research data. This paper identifies some of the legal challenges that need to be addressed and describes 10 proposed best practices which are recommended for adoption to so that publicly funded research data can be made available for access and re-use as OER.

Kallikrein 14 is down-regulated by androgen receptor signalling and harbours genetic variation that is associated with prostate tumour aggressiveness

Kallikrein 14 (KLK14) has been proposed as a useful prognostic marker in prostate cancer, with expression reported to be associated with tumour characteristics such as higher stage and Gleason score. KLK14 tumour expression has also shown the potential to predict prostate cancer patients at risk of disease recurrence after radical prostatectomy. The KLKs are a remarkably hormone-responsive family of genes, although detailed studies of androgen regulation of KLK14 in prostate cancer have not been undertaken to date. Using in vitro studies, we have demonstrated that unlike many other prostatic KLK genes that are strictly androgen responsive, KLK14 is more broadly expressed and inversely androgen regulated in prostate cancer cells. Given these results and evidence that KLK14 may play a role in prostate cancer prognosis, we also investigated whether common genetic variants in the KLK14 locus are associated with risk and/or aggressiveness of prostate cancer in approximately 1200 prostate cancer cases and 1300 male controls. Of 41 single nucleotide polymorphisms assessed, three were associated with higher Gleason score (≥7): rs17728459 and rs4802765, both located upstream of KLK14, and rs35287116, which encodes a p.Gln33Arg substitution in the KLK14 signal peptide region. Our findings provide further support for KLK14 as a marker of prognosis in prostate cancer.