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.

Impacts of traditional husbandry practices on exploitable levels of genetic diversity in cultured 'Tra' catfish (Pangasianodon hypophthalmus) in the Mekong Delta, Vietnam

Sutchi catfish (Pangasianodon hypophthalmus) – known more universally by the Vietnamese name ‘Tra’ is an economically important freshwater fish in the Mekong Delta in Vietnam that constitutes an important food resource. Artificial propagation technology for Tra catfish has only recently been developed along the main branches of the Mekong River where more than 60% of the local human population participate in fishing or aquaculture. Extensive support for catfish culture in general, and that of Tra (P. hypophthalmus) in particular, has been provided by the Vietnamese government to increase both the scale of production and to develop international export markets. In 2006, total Vietnamese catfish exports reached approximately 286,602 metric tons (MT) and were valued at 736.87 $M with a number of large new export destinations being developed. Total value of production from catfish culture has been predicted to increase to approximately USD 1 billion by 2020. While freshwater catfish culture in Vietnam has a promising future, concerns have been raised about long-term quality of fry and the effectiveness of current brood stock management practices, issues that have been largely neglected to date. In this study, four DNA markers (microsatellite loci: CB4, CB7, CB12 and CB13) that were developed specifically for Tra (P. hypophthalmus) in an earlier study were applied to examine the genetic quality of artificially propagated Tra fry in the Mekong Delta in Vietnam. The goals of the study were to assess: (i) how well available levels of genetic variation in Tra brood stock used for artificial propagation in the Mekong Delta of Vietnam (breeders from three private hatcheries and Research Institute of Aquaculture No2 (RIA2) founders) has been conserved; and (ii) whether or not genetic diversity had declined significantly over time in a stock improvement program for Tra catfish at RIA2. A secondary issue addressed was how genetic markers could best be used to assist industry development. DNA was extracted from fins of catfish collected from the two main branches of the Mekong River inf Vietnam, three private hatcheries and samples from the Tra improvement program at RIA2. Study outcomes: i) Genetic diversity estimates for Tra brood stock samples were similar to, and slightly higher than, wild reference samples. In addition, the relative contribution by breeders to fry in commercial private hatcheries strongly suggest that the true Ne is likely to be significantly less than the breeder numbers used; ii) in a stock improvement program for Tra catfish at RIA2, no significant differences were detected in gene frequencies among generations (FST=0.021, P=0.036>0.002 after Bonferroni correction); and only small differences were observed in alleles frequencies among sample populations. To date, genetic markers have not been applied in the Tra catfish industry, but in the current project they were used to evaluate the levels of genetic variation in the Tra catfish selective breeding program at RIA2 and to undertake genetic correlations between genetic marker and trait variation. While no associations were detected using only four loci, they analysis provided training in the practical applications of the use of molecular markers in aquaculture in general, and in Tra culture, in particular.

Modelling risk at low exposure railway level crossings : supporting an argument for low-cost level crossing warning devices with lower levels of safety integrity

This paper describes a risk model for estimating the likelihood of collisions at low-exposure railway level crossings, demonstrating the effect that differences in safety integrity can have on the likelihood of a collision. The model facilitates the comparison of safety benefits between level crossings with passive controls (stop or give-way signs) and level crossings that have been hypothetically upgraded with conventional or low-cost warning devices. The scenario presented illustrates how treatment of a cross-section of level crossings with low cost devices can provide a greater safety benefit compared to treatment with conventional warning devices for the same budget.

Levels of social trust among men from refugee backgrounds after the 2011 Queensland floods

Purpose This paper examines the relationship between flood exposure and levels of social trust among a cohort of adult men from refugee backgrounds who were affected by the 2011 Queensland floods in Australia. Design/methodology/approach A quantitative questionnaire was administered to 141 men from refugee backgrounds almost two years after the 2011 Queensland floods. The survey was administered in person by trained peer in-terviewers, and included a number of standardised instruments assessing respondents’ so-cio-demographic characteristics, levels of social trust towards and from neighbours, the police, the wider Australian community, and the media, and exposure to and impact of the floods. Multiple logistic regression analyses were used to assess the relationship between flood exposure and social trust adjusting for pre-disaster levels of trust and other potentially confounding variables. Findings Participants with higher levels of flood exposure were significantly more likely to report greater levels of trust both towards and from their neighbours, the wider Australian community, and the media, and they were also more likely to believe that most people can be trusted. Research limitations/implications Although the study reports on data collected two years after the floods, the analysis has adjusted for pre-disaster measures of social trust and other socio-demographic variables. Originality/value Our paper has highlighted the important place of social trust and social capital for refugee communities in a post-disaster setting. Disaster responses that support social capital among marginalised populations are critical to increasing community resilience and supporting recovery.

The association between social support and levels of psychological distress in pregnant women in Australia

The purpose of this study was to explore associations between forms of social support and levels of psychological distress during pregnancy. Methods: A cross-sectional analysis of 2,743 pregnant women from south-east Queensland, Australia, was conducted utilising data collected between 2007-2011 as part of the Environments for Healthy Living (EFHL) project, Griffith University. Psychological distress was measured using the Kessler 6; social support was measured using the following four factors: living with a partner, living with parents or in-laws, self-perceived social network, and area satisfaction. Data were analysed using an ordered logistic regression model controlling for a range of socio-demographic factors. Results: There was an inverse association between self-perceived strength of social networks and levels of psychological distress (OR = 0.77; 95%CI: 0.70, 0.85) and between area satisfaction and levels of psychological distress (OR = 0.77; 95%CI: 0.69, 0.87). There was a direct association between living with parents or in-laws and levels of psychological distress (OR = 1.50; 95%CI: 1.16, 1.96). There was no statistically significant association between living with a partner and the level of psychological distress of the pregnant woman after accounting for household income. Conclusion: Living with parents or in-laws is a strong marker for psychological distress. Strategies aiming to build social support networks for women during pregnancy have the potential to provide a significant benefit. Policies promoting stable family relationships and networks through community development could also be effective in promoting the welfare of pregnant women.

Elevated levels of PFOS and PFHxS in firefighters exposed to aqueous film forming foam (AFFF)

Exposure to aqueous film forming foam (AFFF) was evaluated in 149 firefighters working at AFFF training facilities in Australia by analysis of PFOS and related compounds in serum. A questionnaire was designed to capture information about basic demographic factors, lifestyle factors and potential occupational exposure (such as work history and self-reported skin contact with foam). The results showed that a number of factors were associated with PFAA serum concentrations. Blood donation was found to be linked to low PFAA levels, and the concentrations of PFOS and PFHxS were found to be positively associated with years of jobs with AFFF contact. The highest levels of PFOS and PFHxS were one order of magnitude higher compared to the general population in Australia and Canada. Study participants who had worked ten years or less had levels of PFOS that were similar to or only slightly above those of the general population. This coincides with the phase out of 3M AFFF from all training facilities in 2003, and suggests that the exposures to PFOS and PFHxS in AFFF have declined in recent years. Self-reporting of skin contact and frequency of contact were used as an index of exposure. Using this index, there was no relationship between PFOS levels and skin exposure. This index of exposure is limited as it relies on self-report and it only considers skin exposure to AFFF, and does not capture other routes of potential exposure. Possible associations between serum PFAA concentrations and five biochemical outcomes were assessed. The outcomes were serum cholesterol, triglycerides, high-density lipoproteins, low density lipoproteins, and uric acid. No statistical associations between any of these endpoints and serum PFAA concentrations were observed.

Abnormal levels of heterogeneous nuclear ribonucleoprotein A2B1 (hnRNPA2B1) in tumour tissue and blood samples from patients diagnosed with lung cancer

Lung cancer is the second most common type of cancer in the world and is the most common cause of cancer-related death in both men and women. Research into causes, prevention and treatment of lung cancer is ongoing and much progress has been made recently in these areas, however survival rates have not significantly improved. Therefore, it is essential to develop biomarkers for early diagnosis of lung cancer, prediction of metastasis and evaluation of treatment efficiency, as well as using these molecules to provide some understanding about tumour biology and translate highly promising findings in basic science research to clinical application. In this investigation, two-dimensional difference gel electrophoresis and mass spectrometry were initially used to analyse conditioned media from a panel of lung cancer and normal bronchial epithelial cell lines. Significant proteins were identified with heterogeneous nuclear ribonucleoprotein A2B1 (hnRNPA2B1), pyruvate kinase M2 isoform (PKM2), Hsc-70 interacting protein and lactate dehydrogenase A (LDHA) selected for analysis in serum from healthy individuals and lung cancer patients. hnRNPA2B1, PKM2 and LDHA were found to be statistically significant in all comparisons. Tissue analysis and knockdown of hnRNPA2B1 using siRNA subsequently demonstrated both the overexpression and potential role for this molecule in lung tumorigenesis. The data presented highlights a number of in vitro derived candidate biomarkers subsequently verified in patient samples and also provides some insight into their roles in the complex intracellular mechanisms associated with tumour progression.

Levels of cardiac knowledge and cardiopulmonary resuscitation training among older people in Queensland

Objectives: The current study was conducted to determine levels of cardiac knowledge and cardiopulmonary resuscitation (CPR) training in older people in Queensland, Australia.---------- Methods: A telephone survey of 4490 Queensland adults examined respondents’ knowledge of coronary heart disease (CHD) risk factors, knowledge of heart attack symptoms, knowledge of the local emergency telephone number, as well as respondents’ rates and recency of training in CPR.---------- Results: Older participants, aged 60 years and over, were approximately one and a half times more likely than the 30–39 year-old reference group to have limited knowledge of heart disease risk factors (OR = 1.53), and low knowledge of heart attack symptoms (OR = 1.60). Knowledge of the local emergency telephone number also decreased with age. Older participants had significantly lower rates of training in CPR, with almost three quarters (71.7%) reporting that they had never been trained. Older people who had completed CPR training were significantly less likely to have done so recently.---------- Conclusions: Cardiac knowledge levels and CPR training rates in older Queensland persons were lower than those found in the younger population.

Research productivity levels of Chinese TEFL academics

Since China’s Economic Reform and its Open Door Policy, China has entered a new era of education (Adamson, 2002; Hu, 2005a). English has gained status as a language for international relations (Graddol, 1997) and international trade (Qu, 2007). Hence, in 2001, China’s Ministry of Education (MOE) required universities to offer 5-10% of their course units in English, particularly in the fields of information technology, biotechnology, finance and law (Jen, 2001; MOE, 2001). However, “the upgrading of national English proficiency, then, is predicted largely on the professional competence of the teaching force” (Hu, 2005b, p. 655). For TEFL academics, one component of this competence is the capacity to conduct research (Day, 1991; Shu, 2002). Indeed, research productivity has become essential for university success, and academics’ employment and promotional prospects. This study aims to investigate 182 Chinese TEFL academics’ research outputs across three Chinese higher education institutions through the research question: What are the research productivity levels of Chinese TEFL academics? A survey instrument was devised to gather TEFL academics’ calculations of research productivity and, in particular, the quality and quantity of research outputs over a five-year period (2004-2008). Descriptive statistics through SPSS were used to analyse data across research output fields (e.g., journal articles, conference papers). Academic status varied (n=182; teaching assistants 23.6%, lecturers 47.3%, associate professors 22.5%, and professors 6.6%) as did years of teaching (1-5 years 27.4%, 6-10 years 24.7%, 11-15 18.1%, 16-20 years 13.7%, > 21 years 15.9%). Results (n=182, male=27%, females=73%) indicated 18% had not produced any research in the five-year period. Indeed, more than 70% had produced no research in all categories except non-core journal articles and provincial projects. An overwhelming majority of TEFL academics had zero productivity in 10 of the 12 categories. Nevertheless, there were highly-productive TEFL academics, who had produced five or more pieces of research across the 12 categories. In addition, there was not much difference between sole and co-authored research outputs, except non-core journal articles where sole authored work was 20% higher than co-authored work. China’s desire for international competitiveness in education will require measures that facilitate higher levels of research productivity. These measures must include professional development, support and mentoring programs, and employment of personnel who can guide these processes. Research performance is an outcome, hence there is a need to understand Chinese TEFL academics’ perceptions about research, and experiences that may hinder and facilitate higher research productivity.

Homework for refugee middle school students with backgrounds marked by low levels of engagement with English school literacy

Homework presents many challenges for refugees from Africa who are arriving in Australian schools with histories of little, no or severely interrupted schooling. This is evident in the emergence of school- and community-based homework help, clubs and tutoring programs for the students. The aim of this article is to describe the homework support options accessed by eight students from Burundi, Rwanda, Eritrea and Sudan who participated in a study of pedagogy for middle school-aged African refugees, and the views on homework of their parents and teachers. The article shows some tensions between family and school expectations and the dilemmas that arise for teachers in a broader context of public concern about and official policy statement on excessive and repetitive homework. It is argued that application of policy guidelines needs to account for disadvantages that potentially accrue to students who cannot design their own independent study programs. Further, it is suggested that integration of skills and meaning-based pedagogy inherent in recent approaches to literacy education has potential for ensuring that students receive the forms of homework they require.

Developing a conceptual model for measuring the satisfaction levels of Malaysian contractors

The evaluation of satisfaction levels related to performance is an important aspect in increasing market share, improving profitability and enlarging opportunities for repeat business and can lead to the determination of areas to be improved, improving harmonious working relationships and conflict avoidance. In the construction industry, this can also result in improved project quality, enhanced reputation and increased competitiveness. Many conceptual models have been developed to measure satisfaction levels - typically to gauge client satisfaction, customer satisfaction and home buyer satisfaction - but limited empirical research has been carried out, especially in investigating the satisfaction of construction contractors. In addressing this, this paper provides a unique conceptual model or framework for contractor satisfaction based on attributes identified by interviews with practitioners in Malaysia. In addition to progressing research in this topic and being of potential benefit to Malaysian contractors, it is anticipated that the framework will also be useful for other parties - clients, designers, subcontractors and suppliers - in enhancing the quality of products and/or services generally.

The effect of graded levels of exercise on energy intake and balance in free-living men, consuming their normal diet

Objective: To assess the effect of graded increases in exercised-induced energy expenditure (EE) on appetite, energy intake (EI), total daily EE and body weight in men living in their normal environment and consuming their usual diets. Design: Within-subject, repeated measures design. Six men (mean (s.d.) age 31.0 (5.0) y; weight 75.1 (15.96) kg; height 1.79 (0.10) m; body mass index (BMI) 23.3(2.4) kg/m2), were each studied three times during a 9 day protocol, corresponding to prescriptions of no exercise, (control) (Nex; 0 MJ/day), medium exercise level (Mex; ~1.6 MJ/day) and high exercise level (Hex; ~3.2 MJ/day). On days 1-2 subjects were given a medium fat (MF) maintenance diet (1.6 ´ resting metabolic rate (RMR)). Measurements: On days 3-9 subjects self-recorded dietary intake using a food diary and self-weighed intake. EE was assessed by continual heart rate monitoring, using the modified FLEX method. Subjects' HR (heart rate) was individually calibrated against submaximal VO2 during incremental exercise tests at the beginning and end of each 9 day study period. Respiratory exchange was measured by indirect calorimetry. Subjects completed hourly hunger ratings during waking hours to record subjective sensations of hunger and appetite. Body weight was measured daily. Results: EE amounted to 11.7, 12.9 and 16.8 MJ/day (F(2,10)=48.26; P<0.001 (s.e.d=0.55)) on the Nex, Mex and Hex treatments, respectively. The corresponding values for EI were 11.6, 11.8 and 11.8 MJ/day (F(2,10)=0.10; P=0.910 (s.e.d.=0.10)), respectively. There were no treatment effects on hunger, appetite or body weight, but there was evidence of weight loss on the Hex treatment. Conclusion: Increasing EE did not lead to compensation of EI over 7 days. However, total daily EE tended to decrease over time on the two exercise treatments. Lean men appear able to tolerate a considerable negative energy balance, induced by exercise, over 7 days without invoking compensatory increases in EI.

Reducing high levels of communication apprehension among primary school students

This study focused on a group of primary school teachers as they implemented a variety of intervention actions within their class programs aimed towards supporting the reduction of high levels of communication apprehension (CA) among students.Six teachers and nine students, located across three primary schools, four year levels,and six classes, participated in this study. For reasons of confidentiality the schools,principals, parents, teachers, teacher assistants, and students who were involved in this study were given fictitious names. The following research question was explored in this study: What intervention actions can primary school teachers implement within their class programs that support the reduction of high CA levels among students? Throughout this study the term CA referred to "an individual's level of fear or anxiety associated with either real or anticipated (oral) communication with another person or persons" (McCroskey, 1984, p. 13). The sources of CA were explained with reference to McCroskey's state-trait continuum. The distinctions between high and appropriate levels of CA were determined conceptually and empirically. The education system within which this study was conducted promoted the philosophy of inclusion and the practices of inclusive schooling. Teachers employed in this system were encouraged to create class programs inclusive of and successful for all students. Consequently the conceptual framework within which this study was conducted was based around the notion of inclusion. Action research and case study research were the methodologies used in the study. Case studies described teachers' action research as they responded to the challenge of executing intervention actions within their class programs directed towards supporting the reduction of high CA levels among students. Consequently the teachers and not the researcher were the central characters in each of the case studies. Three principal data collection instruments were used in this study: Personal Report of Communication Fear (PRCF) scale, semistructured interviews, and dialogue journals. The PRCF scale was the screening tool used to identify a pool of students eligible for the study. Data relevant to the students involved in the study were gathered during semistructured interviews and throughout the dialogue journaling process. Dialogue journaling provided the opportunity for regular contact between teachers and the researcher, a sequence to teacher and student intervention behaviours, and a permanent record of teacher and student growth and development. The majority of teachers involved in this study endeavoured to develop class programs inclusive of all students.These teachers acknowledged the importance of modifying aspects of their class programs in response to the diverse and often multiple needs of individual students with high levels of CA. Numerous conclusions were drawn regarding practical ways that the teachers in this study supported the reduction of high CA levels among students. What this study has shown is that teachers can incorporate intervention actions within their class programs aimed towards supporting students lower their high levels of CA. Whilst no teacher developed an identical approach to intervention, similarities and differences were evident among teachers regarding their selection, interpretation, and implementation of intervention actions. Actions that teachers enacted within their class programs emerged from numerous fields of research including CA, inclusion, social skills, behaviour teaching, co-operative learning, and quality schools. Each teacher's knowledge of and familiarity with these research fields influenced their preference for and commitment to particular intervention actions. Additional factors including each teacher's paradigm of inclusion and exclusion contributed towards their choice of intervention actions. Possible implications of these conclusions were noted with reference to teachers,school administrators, support personnel, system personnel, teacher educators, parents, and researchers.