mRNA-Seq and microarray development for the Grooved carpet shell clam, Ruditapes decussatus: a functional approach to unravel host -parasite interaction

Background The Grooved Carpet shell clam Ruditapes decussatus is the autochthonous European clam and the most appreciated from a gastronomic and economic point of view. The production is in decline due to several factors such as Perkinsiosis and habitat invasion and competition by the introduced exotic species, the manila clam Ruditapes philippinarum. After we sequenced R. decussatus transcriptome we have designed an oligo microarray capable of contributing to provide some clues on molecular response of the clam to Perkinsiosis. Results A database consisting of 41,119 unique transcripts was constructed, of which 12,479 (30.3%) were annotated by similarity. An oligo-DNA microarray platform was then designed and applied to profile gene expression in R. decussatus heavily infected by Perkinsus olseni. Functional annotation of differentially expressed genes between those two conditionswas performed by gene set enrichment analysis. As expected, microarrays unveil genes related with stress/infectious agents such as hydrolases, proteases and others. The extensive role of innate immune system was also analyzed and effect of parasitosis upon expression of important molecules such as lectins reviewed. Conclusions This study represents a first attempt to characterize Ruditapes decussatus transcriptome, an important marine resource for the European aquaculture. The trancriptome sequencing and consequent annotation will increase the available tools and resources for this specie, introducing the possibility of high throughput experiments such as microarrays analysis. In this specific case microarray approach was used to unveil some important aspects of host-parasite interaction between the Carpet shell clam and Perkinsus, two non-model species, highlighting some genes associated with this interaction. Ample information was obtained to identify biological processes significantly enriched among differentially expressed genes in Perkinsus infected versus non-infected gills. An overview on the genes related with the immune system on R. decussatus transcriptome is also reported.

Vision, functional and cognitive determinants of motor vehicle incidents in older drivers

Background: The proportion of older individuals in the driving population is predicted to increase in the next 50 years. This has important implications for driving safety as abilities which are important for safe driving, such as vision (which accounts for the majority of the sensory input required for driving), processing ability and cognition have been shown to decline with age. The current methods employed for screening older drivers upon re-licensure are also vision based. This study, which investigated social, behavioural and professional aspects involved with older drivers, aimed to determine: (i) if the current visual standards in place for testing upon re-licensure are effective in reducing the older driver fatality rate in Australia; (ii) if the recommended visual standards are actually implemented as part of the testing procedures by Australian optometrists; and (iii) if there are other non-standardised tests which may be better at predicting the on-road incident-risk (including near misses and minor incidents) in older drivers than those tests recommended in the standards. Methods: For the first phase of the study, state-based age- and gender-stratified numbers of older driver fatalities for 2000-2003 were obtained from the Australian Transportation Safety Bureau database. Poisson regression analyses of fatality rates were considered by renewal frequency and jurisdiction (as separate models), adjusting for possible confounding variables of age, gender and year. For the second phase, all practising optometrists in Australia were surveyed on the vision tests they conduct in consultations relating to driving and their knowledge of vision requirements for older drivers. Finally, for the third phase of the study to investigate determinants of on-road incident risk, a stratified random sample of 600 Brisbane residents aged 60 years and were selected and invited to participate using an introductory letter explaining the project requirements. In order to capture the number and type of road incidents which occurred for each participant over 12 months (including near misses and minor incidents), an important component of the prospective research study was the development and validation of a driving diary. The diary was a tool in which incidents that occurred could be logged at that time (or very close in time to which they occurred) and thus, in comparison with relying on participant memory over time, recall bias of incident occurrence was minimised. Association between all visual tests, cognition and scores obtained for non-standard functional tests with retrospective and prospective incident occurrence was investigated. Results: In the first phase,rivers aged 60-69 years had a 33% lower fatality risk (Rate Ratio [RR] = 0.75, 95% CI 0.32-1.77) in states with vision testing upon re-licensure compared with states with no vision testing upon re-licensure, however, because the CIs are wide, crossing 1.00, this result should be regarded with caution. However, overall fatality rates and fatality rates for those aged 70 years and older (RR=1.17, CI 0.64-2.13) did not differ between states with and without license renewal procedures, indicating no apparent benefit in vision testing legislation. For the second phase of the study, nearly all optometrists measured visual acuity (VA) as part of a vision assessment for re-licensing, however, 20% of optometrists did not perform any visual field (VF) testing and only 20% routinely performed automated VF on older drivers, despite the standards for licensing advocating automated VF as part of the vision standard. This demonstrates the need for more effective communication between the policy makers and those responsible for carrying out the standards. It may also indicate that the overall higher driver fatality rate in jurisdictions with vision testing requirements is resultant as the tests recommended by the standards are only partially being conducted by optometrists. Hence a standardised protocol for the screening of older drivers for re-licensure across the nation must be established. The opinions of Australian optometrists with regard to the responsibility of reporting older drivers who fail to meet the licensing standards highlighted the conflict between maintaining patient confidentiality or upholding public safety. Mandatory reporting requirements of those drivers who fail to reach the standards necessary for driving would minimise potential conflict between the patient and their practitioner, and help maintain patient trust and goodwill. The final phase of the PhD program investigated the efficacy of vision, functional and cognitive tests to discriminate between at-risk and safe older drivers. Nearly 80% of the participants experienced an incident of some form over the prospective 12 months, with the total incident rate being 4.65/10 000 km. Sixty-three percent reported having a near miss and 28% had a minor incident. The results from the prospective diary study indicate that the current vision screening tests (VA and VF) used for re-licensure do not accurately predict older drivers who are at increased odds of having an on-road incident. However, the variation in visual measurements of the cohort was narrow, also affecting the results seen with the visual functon questionnaires. Hence a larger cohort with greater variability should be considered for a future study. A slightly lower cognitive level (as measured with the Mini-Mental State Examination [MMSE]) did show an association with incident involvement as did slower reaction time (RT), however the Useful-Field-of-View (UFOV) provided the most compelling results of the study. Cut-off values of UFOV processing (>23.3ms), divided attention (>113ms), selective attention (>258ms) and overall score (moderate/ high/ very high risk) were effective in determining older drivers at increased odds of having any on-road incident and the occurrence of minor incidents. Discussion: The results have shown that for the 60-69 year age-group, there is a potential benefit in testing vision upon licence renewal. However, overall fatality rates and fatality rates for those aged 70 years and older indicated no benefit in vision testing legislation and suggests a need for inclusion of screening tests which better predict on-road incidents. Although VA is routinely performed by Australian optometrists on older drivers renewing their licence, VF is not. Therefore there is a need for a protocol to be developed and administered which would result in standardised methods conducted throughout the nation for the screening of older drivers upon re-licensure. Communication between the community, policy makers and those conducting the protocol should be maximised. By implementing a standardised screening protocol which incorporates a level of mandatory reporting by the practitioner, the ethical dilemma of breaching patient confidentiality would also be resolved. The tests which should be included in this screening protocol, however, cannot solely be ones which have been implemented in the past. In this investigation, RT, MMSE and UFOV were shown to be better determinants of on-road incidents in older drivers than VA and VF, however, as previously mentioned, there was a lack of variability in visual status within the cohort. Nevertheless, it is the recommendation from this investigation, that subject to appropriate sensitivity and specificity being demonstrated in the future using a cohort with wider variation in vision, functional performance and cognition, these tests of cognition and information processing should be added to the current protocol for the screening of older drivers which may be conducted at licensing centres across the nation.

What determines the health-related quality of life among regional and rural breast cancer survivors?

Objective: To assess the health-related quality of life (HRQoL) of regional and rural breast cancer survivors at 12 months post-diagnosis and to identify correlates of HRQoL. Methods: 323 (202 regional and 121 rural) Queensland women diagnosed with unilateral breast cancer in 2006/2007 participated in a population-based, cross-sectional study. HRQoL was measured using the Functional Assessment of Cancer Therapy, Breast plus arm morbidity (FACT-B+4) self-administered questionnaire. Results: In age-adjusted analyses, mean HRQoL scores of regional breast cancer survivors were comparable to their rural counterparts 12 months post-diagnosis (122.9, 95% CI: 119.8, 126.0 vs. 123.7, 95% CI: 119.7, 127.8; p>0.05). Irrespective of residence, younger (<50 years) women reported lower HRQoL than older (50+ years) women (113.5, 95% CI: 109.3, 117.8 vs. 128.2, 95%CI: 125.1, 131.2; p<0.05). Those women who received chemotherapy, reported two complications post-surgery, had poorer upper-body function than most, reported more stress, reduced coping, who were socially isolated, had no confidante for social-emotional support, had unmet healthcare needs, and low health self-efficacy reported lower HRQoL scores. Together, these factors explained 66% of the variance in overall HRQoL. The pattern of results remained similar for younger and older age groups. Conclusions and Implications: The results underscore the importance of supporting and promoting regional and rural breast cancer programs that are designed to improve physical functioning, reduce stress and provide psychosocial support following diagnosis. Further, the information can be used by general practitioners and other allied health professionals for identifying women at risk of poorer HRQoL.

Troubling Empowerment : A feminist critique of a rural women and communication technology project

Participatory research methodologies and interactive communication technologies (ICTs) are increasingly seen as offering ways of enhancing women’s empowerment and rural community development. However, some researchers suggest the need for caution about such claims. This book details findings from an evaluation of a feminist action research project that explored the impacts of ICTs for rural women in Queensland, Australia, in terms of personal, business and community development. Using praxis and poststructuralist feminist theories and methodologies, this innovative study presents a rigorous analysis and critique of women's empowerment and participation. This study demonstrates the value of adopting a critical yet pragmatic approach that takes diversity and difference, power-knowledge relations, and the contradictory effects of participation into account. This is argued to enable the development of more effective strategies for women’s empowerment, participation and inclusion. This book should be of particular interest to researchers, postgraduate students, and others working in the fields of communication, gender, and rural development, and feminist evaluation and ethnography.

Social enterprise and regional development : a pilot study

This preliminary study is an early attempt to explicitly explore the role of social enterprises in regional development. Focusing on North West Tasmania, an isolated and predominately rural region, this study examines three social enterprises based in the region and the nature of their social and economic impacts.

Evidence-based practice and rural nursing : A literature review

This literature review is an exploration of issues related to evidence-based practice and rural nursing. Given the contribution that nursing research can make to improved client care in rural areas, it is important that nurses’ awareness and understanding of evidence-based practice be enhanced, and that strategies for fostering the development of clinically relevant programs of nursing research be identified for rural health services. The review highlights the deficiencies in the current metropolitan-based approaches to evidence-based practice that may disadvantage rural clients and nursing practitioners, because they do not accommodate the inherent differences in rural and metropolitan healthcare cultures. It emphasises the need to seek approaches to research-based practice that arise from the specific needs of the rural setting.

A pilot study exploring Australian general practice nurses roles, responsibilities and professional development needs in well and sick child care

Aim Explore practice nurses' (PNs) role in child health and development, and advising parents about child health issues. Background Introduction of the four-year-old child health check into general practice in 2008 placed additional responsibilities on PNs in child health and wellness. This study explores their readiness to expand their practice into this area. Design Integrated mixed method design, self-report survey. Method A purpose-developed questionnaire explored demographics, child health roles and responsibilities, difficulties encountered, professional development needs, barriers and facilitators, and professional development activities undertaken in the past year. Surveys were posted to 218 PNs in one rural Division of General Practice (DGP) in Queensland, Australia; 29 responded. Results PNs reported a significant role in well and sick child care (93.1%) though few had a paediatric/child health background (14.3%). Roles included immunisations (92.3%), child health checks (65.4%), general child health and development (26.9%), asthma (23.1%), feeding (15.4%), fever (11.5%), settling/sleeping (11.5%). PNs were interested in learning more about (81.5%) and incorporating more child health into their practice (81.5%). Professional development in childhood growth and development (80.0%), health and illness (60.0%) and advising new mothers (20.0%) was needed. Conclusions PNs play a substantial role in child health, are unprepared for the complexities of this role and have preferred methods for undertaking professional development to address knowledge deficits. Implications for practice PNs are unprepared for an advanced role in child health and wellness. Significant gaps in their knowledge to support this role were identified. This ever-expanding role requires close monitoring to ensure knowledge precedes expectations to practice.

Secure and safe water supplies in remote Australian and rural Sri Lankan regions : common issues and emerging responses

Most urban dwelling Australians take secure and safe water supplies for granted. That is, they have an adequate quantity of water at a quality that can be used by people without harm from human and animal wastes, salinity and hardness or pollutants from agriculture and manufacturing industries. Australia wide urban and peri-urban dwellers use safe water for all domestic as well as industrial purposes. However, this is not the situation remote regions in Australia where availability and poor quality water can be a development constraint. Nor is it the case in Sri Lanka where people in rural regions are struggling to obtain a secure supply of water, irrespective of it being safe because of the impact of faecal and other contaminants. The purposes of this paper are to overview: the population and environmental health challenges arising from the lack of safe water in rural and remote communities; response pathways to address water quality issues; and the status of and need for integrated catchment management (ICM) in selected remote regions of Australia and vulnerable and lagging rural regions in Sri Lanka. Conclusions are drawn that focus on the opportunity for inter-regional collaborations between Australia and Sri Lanka for the delivery of safe water through ICM.

Fostering digital participation in regional and rural Australia

The deployment of high speed broadband around Australia offers opportunities to extend digital participation among and between regional and rural communities. Full realisation of these opportunities requires a greater understanding about community members’ current digital participation and development needs, to underpin innovative community-driven initiatives. This paper outlines the Fostering Digital Participation Project’s initial undertakings to determine current digital participation and the future digital aspirations of a number of regional and rural communities.

Light environment and tree development of young Acacia melanoxylon in mixed-species regrowth forest, Tasmania, Australia

Blackwood (Acacia melanoxylon R. Br.) is a valuable leguminous cabinetwood species which is commonly found as a canopy or subcanopy tree in a broad range of mixed-species moist forests on tablelands and coastal escarpments in eastern Australia. This paper reports on the competitive light environment of a commercially valuable multi-species regrowth forest in NW Tasmania, in order to define some of the functional interactions and competitive dynamics of these stands. Comparative observations were made of the internal forest light environment in response to small-gap silvicultural treatments, in a young regenerative mix of three codominant tree species. Light measurements were made during periods of maximum external irradiance of the regrowth Eucalyptus obliqua/A. melanoxylon forest canopy at age 10.5 years. This was at a time of vigourous stand development, 4.5 years following the application of three experimental silvicultural treatments whose effects were observed in comparison with an untreated canopy sample designed as a control. Minimal irradiance was observed within and beneath the dense subcanopy of the native nurse species (Pomaderris apetala) which closely surrounds young blackwood regeneration. Unlike current plantation nurse systems, the dense foliage of the native broadleaved Pomaderris all but eliminated direct side-light and low-angle illumination of the young blackwood, from the beginning of tree establishment. The results demonstrated that retention of these densely stocked native codominants effectively suppressed both size and frequency of blackwood branches on the lower bole, through effective and persistent interception of sunlight. Vigorous young blackwood crowns later overtopped the codominant nurse species, achieving a predictable height of branch-free bole. This competitive outcome offers a valuable tool for management of blackwood crown dynamics, stem form and branch habit through manipulation of light environment in young native regrowth systems. Results demonstrate that effective self-pruning in the lower bole of blackwood is achieved through a marked reduction in direct and diffuse sunlight incident on the lower crown, notably to less than 10-15% of full sunlight intensity during conditions of maximum insolation. The results also contain insights for the improved design of mixed-species plantation nurse systems using these or functionally similar species' combinations. Based on evidence presented here for native regrowth forest, plantation nurse systems for blackwood will need to achieve 85-90% interception of external side-light during early years of tree development if self-pruning is to emulate the results achieved in the native nurse system.

Energy and rural buildings in India

This paper attempts to evaluate the energy inputs needed to produce rural buildings. Based on a survey, a comparison is carried out of traditional and innovative technologies with reference to their energy consumption. Some basic data regarding energies in transportation are also presented. The implications of this analysis for development objectives is discussed.

Stress and texture development during sputtering of yttria, zirconia, and yttria stabilized zirconia films on Si substrates

Understanding and controlling growth stress is a requisite for integrating oxides with Si. Yttria stabilized zirconia (YSZ) is both an important functional oxide and a buffer layer material needed for integrating other functional oxides. Stress evolution during the growth of (100) and (111) oriented YSZ on Si (100) by radio frequency and reactive direct current sputtering has been investigated with an in-situ monitor and correlated with texture evolution. Films nucleated at rates <5 nm/min are found to be (111) oriented and grow predominantly under a compressive steady state stress. Films nucleated at rates >20 nm/min are found to be (100) oriented and grow under tension. A change in growth rate following the nucleation stage does not change the orientation. The value of the final steady state stress varies from -4.7 GPa to 0.3 GPa. The in-situ studies show that the steady state stress generation is a dynamic phenomenon occurring at the growth surface and not decided at film nucleation. The combination of stress evolution and texture evolution data shows that the adatom injection into the grain boundaries is the predominant source of compressive stress and grain boundary formation at the growth surface is the source of tensile stress. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4757924]

Livelihood analysis and development of a planning support for the poor in aquaculture and aquatic resource management. Workshop proceedings. 13-15 February 2001, Thai Nguyen, Vietnam

The workshop was organized to understand and describe the livelihoods of poor people who manage aquatic resources for planning support. The purpose was to support field workers to carry out livelihood analysis and how to use this information. (PDF contains 13 pages)