Detection of viable bacteria in environmental water samples using DNase I and PCR method. International Journal of Environmental Studies

In this study, we tested the potential application of a previously developed method in detecting Escherichia coli in environmental water samples. To increase the sensitivity of the method, and the recovery of microbial cells, water samples were filtered before being subjected to DNase treatment and polymerase chain reaction amplification. Results showed that DNase I treatment and PCR reaction were not affected by inhibitors as the expected amplicon was successfully amplified in autoclaved environmental waters spiked with E. coli. Then, we applied this method to naturally contaminated environmental water samples. We firstly confirmed the presence of coliforms and E. coli in these water samples by plating in eosin methylene blue agar. Simultaneous PCR amplification targeting Lac Z and uidR gene of total coliforms and E. coli respectively demonstrated that this developed method is potentially applicable for routine microbial assessment of health risks related to viable microorganisms in environmental or drinking waters

Coefficient shifts in geographical ecology: an empirical evaluation of spatial and non-spatial regression

Copyright © 2009 The Authors. Copyright © ECOGRAPHY 2009.A major focus of geographical ecology and macro ecology is to understand the causes of spatially structured ecological patterns. However, achieving this understanding can be complicated when using multiple regressions, because the relative importance of explanatory variables, as measured by regression coefficients, can shift depending on whether spatially explicit or non-spatial modelling is used. However, the extent to which coefficients may shift and why shifts occur are unclear. Here, we analyze the relationship between environmental predictors and the geographical distribution of species richness, body size, range size and abundance in 97 multi-factorial data sets. Our goal was to compare standardized partial regression coefficients of non-spatial ordinary least squares regressions (i.e. models fitted using ordinary least squares without taking autocorrelation into account; “OLS models” hereafter) and eight spatial methods to evaluate the frequency of coefficient shifts and identify characteristics of data that might predict when shifts are likely. We generated three metrics of coefficient shifts and eight characteristics of the data sets as predictors of shifts. Typical of ecological data, spatial autocorrelation in the residuals of OLS models was found in most data sets. The spatial models varied in the extent to which they minimized residual spatial autocorrelation. Patterns of coefficient shifts also varied among methods and datasets, although the magnitudes of shifts tended to be small in all cases. We were unable to identify strong predictors of shifts, including the levels of autocorrelation in either explanatory variables or model residuals. Thus, changes in coefficients between spatial and non-spatial methods depend on the method used and are largely idiosyncratic, making it difficult to predict when or why shifts occur. We conclude that the ecological importance of regression coefficients cannot be evaluated with confidence irrespective of whether spatially explicit modelling is used or not. Researchers may have little choice but to be more explicit about the uncertainty of models and more cautious in their interpretation

AIDS Vaccine for Asia Network (AVAN): Expanding the Regional Role in Developing HIV Vaccines

Yiming Shao and colleagues describe the work of AVAN, the AIDS Vaccine for Asia Network, which aims to strengthen its regional efforts in finding an AIDS vaccine

Variable responses of individual species to tropical forest degradation

The functional stability of ecosystems depends greatly on interspecific differences in responses to environmental perturbation. However, responses to perturbation are not necessarily invariant among populations of the same species, so intraspecific variation in responses might also contribute. Such inter-population response diversity has recently been shown to occur spatially across species ranges, but we lack estimates of the extent to which individual populations across an entire community might have perturbation responses that vary through time. We assess this using 524 taxa that have been repeatedly surveyed for the effects of tropical forest logging at a focal landscape in Sabah, Malaysia. Just 39 % of taxa – all with non-significant responses to forest degradation – had invariant responses. All other taxa (61 %) showed significantly different responses to the same forest degradation gradient across surveys, with 6 % of taxa responding to forest degradation in opposite directions across multiple surveys. Individual surveys had low power (< 80 %) to determine the correct direction of response to forest degradation for one-fifth of all taxa. Recurrent rounds of logging disturbance increased the prevalence of intra-population response diversity, while uncontrollable environmental variation and/or turnover of intraspecific phenotypes generated variable responses in at least 44 % of taxa. Our results show that the responses of individual species to local environmental perturbations are remarkably flexible, likely providing an unrealised boost to the stability of disturbed habitats such as logged tropical forests

Is Malaysia’s banded langur, Presbytis femoralis femoralis, actually Presbytis neglectus neglectus? Taxonomic revision with new insights on the radiation history of the Presbytis species group in Southeast Asia

The disjunct distribution of Presbytis femoralis subspecies across Sumatra (P. f. percura), southern (P. f. femoralis) and northern (P. f. robinsoni) Peninsular Malaysia marks the unique vicariance events in the Sunda Shelf. However, the taxonomic positions and evolutionary history of P. f. femoralis are unresolved after decades of research. To elucidate this evolutionary history, we analyzed 501 base pairs of the mitochondrial HVSI gene from 25 individuals representing Malaysia’s banded langur, with the addition of 29 sequences of Asian Presbytis from Genbank. Our results revealed closer affinity of P. f. femoralis to P. m. mitrata and P. m. sumatrana while maintaining the monophyletic state of P. f. femoralis as compared to P. f. robinsoni. Two central theses were inferred from the results; (1) P. f. femoralis does not belong in the same species classification as P. f. robinsoni, and (2) P. f. femoralis is the basal lineage of the Presbytis in Peninsular Malaysia. Proving the first hypothesis through genetic analysis, we reassigned P. f. femoralis of Malaysia to Presbytis neglectus (Schlegel’s banded langur) (Schlegel in Revue Methodique, Museum d’Histoire Naturelle des Pays-Bas 7:1, 1876) following the International Code of Zoological Nomenclature (article 23.3). The ancestors of P. neglectus are hypothesized to have reached southern Peninsular Malaysia during the Pleistocene and survived in refugium along the western coast. Consequently, they radiated upward, forming P. f. robinsoni and P. siamensis resulting in the highly allopatric distribution in Peninsular Malaysia. This study has successfully resolved the taxonomic position of P. neglectus in Peninsular Malaysia while providing an alternative biogeographic theory for the Asian Presbytis

The many meanings of evidence: a comparative analysis of the forms and roles of evidence within three health policy processes in Cambodia

Background Discussions within the health community routinely emphasise the importance of evidence in informing policy formulation and implementation. Much of the support for the evidence-based policy movement draws from concern that policy decisions are often based on inadequate engagement with high-quality evidence. In many such discussions, evidence is treated as differing only in quality, and assumed to improve decisions if it can only be used more. In contrast, political science scholars have described this as an overly simplistic view of the policy-making process, noting that research ‘use’ can mean a variety of things and rely on nuanced aspects of political systems. An approach more in recognition of how policy-making systems operate in practice can be to consider how institutions and ideas influence which pieces of evidence appear to be relevant for, and are used within, different policy processes. Methods Drawing on in-depth interviews undertaken in 2015/16 with key health sector stakeholders in Cambodia, we investigate the evidence perceived to be relevant to policy decisions for three contrasting health policy examples – tobacco control, HIV/AIDS and performance-based salary incentives. These cases allow us to examine the ways that policy relevant evidence may differ given the framing of the issue and the broader institutional context in which evidence is considered. Results The three health issues show few similarities in how pieces of evidence were used in various aspects of policy-making, despite all being discussed within a broad policy environment in which evidence-based policymaking is rhetorically championed. Instead, we find that evidence use can be better understood by mapping how these health policy issues differ in terms of the issue characteristics, and also in terms of the stakeholders structurally established as having dominant influence for each issue. Both of these have important implications for evidence use. Contrasting concerns of key stakeholders meant that evidence related to differing issues could be understood in terms of how it was policy relevant. The stakeholders involved, however, could further be seen to possess differing logics about how to go about achieving their various outcomes – logics that could further help explain the differences seen in evidence utilisation. Conclusion A comparative approach reiterates that evidence is not a uniform concept for which more is obviously better, but rather illustrates how different constructions and pieces of evidence become relevant in relation to the features of specific health policy decisions. An institutional approach that considers the structural position of stakeholders with differing core goals or objectives, as well as their logics related to evidence utilisation, can further help to understand some of the complexities of evidence use in health policymaking

Thresholds for adding degraded tropical forest to the conservation estate

Logged and disturbed forests are often viewed as degraded and depauperate environments compared with primary forest. However, they are dynamic ecosystems1 that provide refugia for large amounts of biodiversity2,3, so we cannot afford to underestimate their conservation value4. Here we present empirically defined thresholds for categorizing the conservation value of logged forests, using one of the most comprehensive assessments of taxon responses to habitat degradation in any tropical forest environment. We analysed the impact of logging intensity on the individual occurrence patterns of 1,681 taxa belonging to 86 taxonomic orders and 126 functional groups in Sabah, Malaysia. Our results demonstrate the existence of two conservation-relevant thresholds. First, lightly logged forests (68%) of their biomass removed, and these are likely to require more expensive measures to recover their biodiversity value. Overall, our data confirm that primary forests are irreplaceable5, but they also reinforce the message that logged forests retain considerable conservation value that should not be overlooked

Charting the Research Course for Sustainable Aquaculture in Sabah, Malaysia

Due to arising needs and demands, aquaculture is currently the fastest growing food production sector. In order to increase yield and yet to remain sustainable, the challenges would be to minimise impact on the environment and ecosystem services. Aquaculture activity contributes significantly to Malaysia and also the state of Sabah’s economy and food security. Hence, the future changes in the environment as a result of rapid population growth and development would pose as threats to this industry in terms of quality, quantity and sustainability. Unforeseen environmental changes such as environmental pollution from other sources, climate change and the changes in policies would jeopardize the sustainability of this industry. In order to anticipate such impacts to the aquaculture activities, this paper set to chart a sustainable course for its development. Four important research courses were proposed: establishment of a sustainable framework, assessment of impacts of climate change, viability and vulnerability assessment due to future environmental changes and food security. Such findings would eventually allow the stakeholders to plan and manage the resources and aquaculture activities in such a way that foster sustainable food security and resilient aquatic ecosystems

Charting the Research Course for Sustainable Aquaculture in Sabah, Malaysia

Due to arising needs and demands, aquaculture is currently the fastest growing food production sector. In order to increase yield and yet to remain sustainable, the challenges would be to minimise impact on the environment and ecosystem services. Aquaculture activity contributes significantly to Malaysia and also the state of Sabah’s economy and food security. Hence, the future changes in the environment as a result of rapid population growth and development would pose as threats to this industry in terms of quality, quantity and sustainability. Unforeseen environmental changes such as environmental pollution from other sources, climate change and the changes in policies would jeopardize the sustainability of this industry. In order to anticipate such impacts to the aquaculture activities, this paper set to chart a sustainable course for its development. Four important research courses were proposed: establishment of a sustainable framework, assessment of impacts of climate change, viability and vulnerability assessment due to future environmental changes and food security. Such findings would eventually allow the stakeholders to plan and manage the resources and aquaculture activities in such a way that foster sustainable food security and resilient aquatic ecosystems