Assessment of quantitative polymerase chain reaction for BCR-ABL1 transcripts in chronic myeloid leukaemia: Are improved outcomes in patients with e14a2 transcripts an artefact of technology?

The clinical outcome of chronic myeloid leukaemia patients has vastly improved since the introduction of tyrosine kinase inhibitor treatment, with a significant proportion of patients able to achieve treatment-free remission. However, studies have shown that patients with the e13a2 transcript were less likely to achieve major molecular response compared to those with e14a2 transcripts. Most quantitative polymerase chain reaction (PCR) assays for detection of the BCR-ABL1 fusion gene do not differentiate between the two transcripts and we therefore hypothesised that technical bias linked to the qPCR assay could partially explain the discrepancy in outcomes. We designed an e14a2-specific assay and identified no difference in results compared to an e13a2 standard assay. We then demonstrated that the commercial e14a2 standards were causing a significant overestimation of the e13a2 transcripts. Finally, we reviewed patient management after the qPCR values were corrected, using our new evaluation. We concluded that despite statistically significant differences in qPCR results, there was no impact on patient management or outcome. We conclude that, at least in our institution, it would be inappropriate to perform separate assays for patients with e13a2 or e14a2.

Xpert MRSA screening in surgical patient flow; time for a rethink for hub-and-spoke laboratory models?

The move towards pathology networks and hub-and-spoke models of medical laboratory service provision has significantly changed the flow of samples, and the impact of results on patients, over recent years. At the same time advances in technology, including rapid, simple to use molecular platforms, are changing the way microbiology results can be utilized. Like many other medical microbiology laboratories, we struggle with this balance for many different sample types and test requests. Work published by Neilson et al. in Journal of Medical Microbiology last year looked at this balance for methicillin-resistant Staphylococcus aureus (MRSA) genotypic diagnostics and suggested significant cost savings when a whole-healthcare economy perspective was adopted. However, as with all changes, implementing MRSA molecular diagnostics in different clinical settings must be considered carefully. We add to this discussion in our accompanying letter, detailing our experience (in a hub-and-spoke medical microbiology laboratory setting) of 'rapid' MRSA molecular diagnostics for day-case surgery where pre-operative assessment had been missed, exploring the impact and costs of these tests. We find no impact on patient care, but at considerable additional cost. We hope this will add a cautionary note to those considering implementing molecular microbiology diagnostics, and reopen the debate on where, in hub-and-spoke laboratory models, such devices should be situated.

Responses of Aquatic Plants to Eutrophication in Rivers: A Revised Conceptual Model.

Compared to research on eutrophication in lakes, there has been significantly less work carried out on rivers despite the importance of the topic. However, over the last decade, there has been a surge of interest in the response of aquatic plants to eutrophication in rivers. This is an area of applied research and the work has been driven by the widespread nature of the impacts and the significant opportunities for system remediation. A conceptual model has been put forward to describe how aquatic plants respond to eutrophication. Since the model was created, there have been substantial increases in our understanding of a number of the underlying processes. For example, we now know the threshold nutrient concentrations at which nutrients no longer limit algal growth. We also now know that the physical habitat template of rivers is a primary selector of aquatic plant communities. As such, nutrient enrichment impacts on aquatic plant communities are strongly influenced, both directly and indirectly, by physical habitat. A new conceptual model is proposed that incorporates these findings. The application of the model to management, system remediation, target setting, and our understanding of multi-stressor systems is discussed. We also look to the future and the potential for new numerical models to guide management.

Herbivore regulation of plant abundance in aquatic ecosystems.

Herbivory is a fundamental process that controls primary producer abundance and regulates energy and nutrient flows to higher trophic levels. Despite the recent proliferation of small-scale studies on herbivore effects on aquatic plants, there remains limited understanding of the factors that control consumer regulation of vascular plants in aquatic ecosystems. Our current knowledge of the regulation of primary producers has hindered efforts to understand the structure and functioning of aquatic ecosystems, and to manage such ecosystems effectively. We conducted a global meta-analysis of the outcomes of plant-herbivore interactions using a data set comprised of 326 values from 163 studies, in order to test two mechanistic hypotheses: first, that greater negative changes in plant abundance would be associated with higher herbivore biomass densities; second, that the magnitude of changes in plant abundance would vary with herbivore taxonomic identity. We found evidence that plant abundance declined with increased herbivore density, with plants eliminated at high densities. Significant between-taxa differences in impact were detected, with insects associated with smaller reductions in plant abundance than all other taxa. Similarly, birds caused smaller reductions in plant abundance than echinoderms, fish, or molluscs. Furthermore, larger reductions in plant abundance were detected for fish relative to crustaceans. We found a positive relationship between herbivore species richness and change in plant abundance, with the strongest reductions in plant abundance reported for low herbivore species richness, suggesting that greater herbivore diversity may protect against large reductions in plant abundance. Finally, we found that herbivore-plant nativeness was a key factor affecting the magnitude of herbivore impacts on plant abundance across a wide range of species assemblages. Assemblages comprised of invasive herbivores and native plant assemblages were associated with greater reductions in plant abundance compared with invasive herbivores and invasive plants, native herbivores and invasive plants, native herbivores and mixed-nativeness plants, and native herbivores and native plants. By contrast, assemblages comprised of native herbivores and invasive plants were associated with lower reductions in plant abundance compared with both mixed-nativeness herbivores and native plants, and native herbivores and native plants. However, the effects of herbivore-plant nativeness on changes in plant abundance were reduced at high herbivore densities. Our mean reductions in aquatic plant abundance are greater than those reported in the literature for terrestrial plants, but lower than aquatic algae. Our findings highlight the need for a substantial shift in how biologists incorporate plant-herbivore interactions into theories of aquatic ecosystem structure and functioning. Currently, the failure to incorporate top-down effects continues to hinder our capacity to understand and manage the ecological dynamics of habitats that contain aquatic plants.

How green is my river? A new paradigm of eutrophication in rivers.

Although the process of eutrophication is reasonably well understood in lakes, there is currently no conceptual understanding of how eutrophication develops in rivers. This issue is addressed here. A review of the main processes controlling the development of eutrophication in lakes has been carried out as a precursor to considering the effect in rivers. The importance of hydraulic flushing in controlling algal growth suggests that short-retention-time rivers will show different effects compared to long retention-time, impounded rivers. The latter are likely to operate like lakes, moving from macrophyte domination to phytoplankton domination whereas the former move to benthic and filamentous algal domination. Subsequently, a conceptual model of the development of eutrophic conditions in short-retention-time rivers is developed. Although there is general agreement in the literature that an increase in nutrients, particularly phosphorus, is a pre-requisite for the eutrophic conditions to develop, there is little evidence in short-retention-time rivers that the plant (macro and micro) biomass is limited by nutrients and a good case can be made that the interaction of hydraulic drag with light limitation is the main controlling factor. The light limitation is brought about by the development of epiphytic algal films on the macrophyte leaves. The implications of this conceptual model are discussed and a series of observable effects are predicted, which should result if the model is correct.

Functional trait composition of aquatic plants can serve to disentangle multiple interacting stressors in lowland streams.

Historically, close attention has been paid to negative impacts associated with nutrient loads to streams and rivers, but today hydromorphological alterations are considered increasingly implicated when lowland streams do not achieve good ecological status. Here, we explore if trait-abundance patterns of aquatic plants change along gradients in hydromorphological degradation and eutrophication in lowland stream sites located in Denmark. Specifically, we hypothesised that: i) changes in trait-abundance patterns occur along gradients in hydromorphological degradation and ii) trait-abundance patterns can serve to disentangle effects of eutrophication and hydromorphological degradation in lowland streams reflecting that the mechanisms behind changes differ. We used monitoring data from a total of 147 stream reaches with combined data on aquatic plant species abundance, catchment land use, hydromorphological alterations (i.e. planform, cross section, weed cutting) and water chemistry parameters. Traits related to life form, dispersal, reproduction and survival together with ecological preference values for nutrients and light (Ellenberg N and L) were allocated to 41 species representing 79% of the total species pool. We found clear evidence that habitat degradation (hydromorphological alterations and eutrophication) mediated selective changes in the trait-abundance patterns of the plant community. Specific traits could distinguish hydromorphological degradation (free-floating, surface; anchored floating leaves; anchored heterophylly) from eutrophication (free-floating, submerged; leaf area). We provide a conceptual framework for interpretation of how eutrophication and hydromorphological degradation interact and how this is reflected in trait-abundance patterns in aquatic plant communities in lowland streams. Our findings support the merit of trait-based approaches in biomonitoring as they shed light on mechanisms controlling structural changes under environmental stress. The ability to disentangle several stressors is particularly important in lowland stream environments where several stressors act in concert since the impact of the most important stressor can be targeted first, which is essential to improve the ecological status.

Plant trait characteristics vary with size and eutrophication in European lowland streams.

Previous studies investigating community-level relationships between plant functional trait characteristics and stream environmental characteristics remain scarce. Here, we used community-weighted means to identify how plant traits link to lowland stream typology and how agricultural intensity in the catchment affects trait composition.We analysed plant trait characteristics in 772 European lowland streams to test the following two hypotheses: (i) trait characteristics differ between plant communities in small and medium-sized streams, reflecting adaptations to different habitat characteristics, and (ii) trait characteristics vary with the intensity of agricultural land use in the stream catchment, mediated either directly by an increase in productive species or indirectly by an increase in species that efficiently intercept and utilize light.We found that the communities in small streams were characterized by a higher abundance of light-demanding species growing from single apical meristems, reproducing by seeds and rooted to the bottom with floating and/or heterophyllous leaves, whereas the community in medium-sized streams was characterized by a higher abundance of productive species growing from multi-apical and basal growth meristems forming large canopies.We also found indications that community trait characteristics were affected by eutrophication. We did not find enhanced abundance of productive species with an increasing proportion of agriculture in the catchments. Instead, we found an increase in the abundance of species growing from apical and multi-apical growth meristems as well as in the abundance of species tolerant of low light availability. The increase in the abundance of species possessing these traits likely reflects different strategies to obtain greater efficiency in light interception and utilization in nutrient-enriched environments. Synthesis and applications. Our findings challenge the general assumption of the EU Water Framework Directive compliant assessment systems that plant community patterns in streams reflect the nutrient preference of the community. Instead, light availability and the ability to improve interception and utilization appeared to be of key importance for community composition in agricultural lowland streams. We therefore suggest moving from existing approaches building on species-specific preference values for nutrients to determine the level of nutrient impairment to trait-based approaches that provide insight into the biological mechanisms underlying the changes. We recommend that existing systems are critically appraised in the context of the findings of this study.

Can sacrificial feeding areas protect aquatic plants from herbivore grazing? Using behavioural ecology to inform wildlife management.

Effective wildlife management is needed for conservation, economic and human well-being objectives. However, traditional population control methods are frequently ineffective, unpopular with stakeholders, may affect non-target species, and can be both expensive and impractical to implement. New methods which address these issues and offer effective wildlife management are required. We used an individual-based model to predict the efficacy of a sacrificial feeding area in preventing grazing damage by mute swans (Cygnus olor) to adjacent river vegetation of high conservation and economic value. The accuracy of model predictions was assessed by a comparison with observed field data, whilst prediction robustness was evaluated using a sensitivity analysis. We used repeated simulations to evaluate how the efficacy of the sacrificial feeding area was regulated by (i) food quantity, (ii) food quality, and (iii) the functional response of the forager. Our model gave accurate predictions of aquatic plant biomass, carrying capacity, swan mortality, swan foraging effort, and river use. Our model predicted that increased sacrificial feeding area food quantity and quality would prevent the depletion of aquatic plant biomass by swans. When the functional response for vegetation in the sacrificial feeding area was increased, the food quantity and quality in the sacrificial feeding area required to protect adjacent aquatic plants were reduced. Our study demonstrates how the insights of behavioural ecology can be used to inform wildlife management. The principles that underpin our model predictions are likely to be valid across a range of different resource-consumer interactions, emphasising the generality of our approach to the evaluation of strategies for resolving wildlife management problems.

Evaluating the effects of population management on a herbivore grazing conflict.

Abundant herbivores can damage plants and so cause conflict with conservation, agricultural, and fisheries interests. Management of herbivore populations is a potential tool to alleviate such conflicts but may raise concerns about the economic and ethical costs of implementation, especially if the herbivores are 'charismatic' and popular with the public. Thus it is critical to evaluate the probability of achieving the desired ecological outcomes before proceeding to a field trial. Here we assessed the potential for population control to resolve a conflict of non-breeding swans grazing in river catchments. We used a mathematical model to evaluate the consequences of three population management strategies; (a) reductions in reproductive success, (b) removal of individuals, and (c) reduced reproductive success and removal of individuals combined. This model gave accurate projections of historical changes in population size for the two rivers for which data were available. Our model projected that the River Frome swan population would increase by 54%, from 257 to 397 individuals, over 17 years in the absence of population control. Removal of ≥60% of non-breeding individuals each year was projected to reduce the catchment population below the level for which grazing conflicts have been previously reported. Reducing reproductive success, even to 0 eggs per nest, failed to achieve the population reduction required. High adult and juvenile survival probabilities (>0.7) and immigration from outside of the catchment limited the effects of management on population size. Given the high, sustained effort required, population control does not represent an effective management option for preventing the grazing conflicts in river catchments. Our study highlights the need to evaluate the effects of different management techniques, both alone and in combination, prior to field trials. Population models, such as the one presented here, can provide a cost-effective and ethical means of such evaluations.

Understanding plant community responses to combinations of biotic and abiotic factors in different phases of the plant growth cycle.

Understanding plant community responses to combinations of biotic and abiotic factors is critical for predicting ecosystem response to environmental change. However, studies of plant community regulation have seldom considered how responses to such factors vary with the different phases of the plant growth cycle. To address this deficit we studied an aquatic plant community in an ecosystem subject to gradients in mute swan (Cygnus olor) herbivory, riparian shading, water temperature and distance downstream of the river source. We quantified abundance, species richness, evenness, flowering and dominance in relation to biotic and abiotic factors during the growth-, peak-, and recession-phases of the plant growth cycle. We show that the relative importance of biotic and abiotic factors varied between plant community properties and between different phases of the plant growth cycle. Herbivory became more important during the later phases of peak abundance and recession due to an influx of swans from adjacent pasture fields. Shading by riparian vegetation also had a greater depressing effect on biomass in later seasons, probably due to increased leaf abundance reducing light intensity reaching the aquatic plants. The effect of temperature on community diversity varied between upstream and downstream sites by altering the relative competitiveness of species at these sites. These results highlight the importance of seasonal patterns in the regulation of plant community structure and function by multiple factors.