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101.
Metabolic control analysis, co-invented by Reinhart Heinrich, is a formalism for the analysis of biochemical networks, and is a highly important intellectual forerunner of modern systems biology. Exchanging ideas and exchanging models are part of the international activities of science and scientists, and the Systems Biology Markup Language (SBML) allows one to perform the latter with great facility. Encoding such models in SBML allows their distributed analysis using loosely coupled workflows, and with the advent of the Internet the various software modules that one might use to analyze biochemical models can reside on entirely different computers and even on different continents. Optimization is at the core of many scientific and biotechnological activities, and Reinhart made many major contributions in this area, stimulating our own activities in the use of the methods of evolutionary computing for optimization. 相似文献
102.
Didier Pont Alice Valentini Mathieu Rocle Anthony Maire Olivier Delaigue Pauline Jean Tony Dejean 《Journal of fish biology》2021,98(2):354-366
Most of the present EU Water Framework Directive (WFD) compliant fish-based assessment methods of European rivers are multi-metric indices computed from traditional electrofishing (TEF) samples, but this method has known shortcomings, especially in large rivers. The probability of detecting rare species remains limited, which can alter the sensitivity of the indices. In recent years, environmental (e)DNA metabarcoding techniques have progressed sufficiently to allow applications in various ecological domains as well as eDNA-based ecological assessment methods. A review of the 25 current WFD-compliant methods for river fish shows that 81% of the metrics used in these methods are expressed in richness or relative abundance and thus compatible with eDNA samples. However, more than half of the member states' methods include at least one metric related to age or size structure and would have to adapt their current fish index if reliant solely on eDNA-derived information. Most trait-based metrics expressed in richness are higher when computed from eDNA than when computed from TEF samples. Comparable values are obtained only when the TEF sampling effort increases. Depending on the species trait considered, most trait-based metrics expressed in relative abundance are significantly higher for eDNA than for TEF samples or vice versa due to over-estimation of sub-surface species or under-estimation of benthic and rare species by TEF sampling, respectively. An existing predictive fish index, adapted to make it compatible with eDNA data, delivers an ecological assessment comparable with the current approved method for 22 of the 25 sites tested. Its associated uncertainty is lower than that of current fish indices. Recommendations for the development of future fish eDNA-based indices and the associated eDNA water sampling strategy are discussed. 相似文献
103.
Under the Water Framework Directive (WFD) benthic Ecological Quality Ratios (EQRs) are important tools for assessing Ecological Status (ES) of coastal and transitional waters. Calculation of the Multivariate-AZTI Marine Biotic Index (M-AMBI) EQR is based on the proportions of sensitive and stress tolerant benthic invertebrate species, number of species and Shannon–Wiener diversity. The sensitivity of many tropical/sub-tropical taxa has not yet been determined, presenting a barrier to the direct transfer of WFD EQRs, and the ideas underpinning them, to the management of coastal waters beyond Europe. To overcome this we examine using higher taxonomic level data with M-AMBI.Before applying such approaches to assessing ES in new geographical regions it is essential to determine the effects of using higher taxonomic level data on M-AMBI in areas where the tool was developed. To this end, we use macrofaunal data from three well studied sites in north-western Europe to examine the effects of using taxonomic level data higher than species on M-AMBI. Using the European datasets M-AMBI ES classification was shown to be robust to changes in taxonomic level data. We test the suitability of family-level M-AMBI for assessing ES in subtropical Hong Kong waters. Family level M-AMBI was useful in detecting stress in Hong Kong, where it successfully detected temporal and spatial shifts in ES in response to seasonal hypoxia and salinity variability, and anthropogenic organic enrichment. 相似文献
104.
Ralph T. Clarke John Davy-Bowker Leonard Sandin Nikolai Friberg Richard K. Johnson Barbara Bis 《Hydrobiologia》2006,566(1):477-503
The Water Framework Directive (WFD) of the European Union requires all member countries to provide information on the level
of confidence and precision of results in their river monitoring programmes to assess the ecological status class of river
sites. As part of the European Union project STAR, the overall effects of sampling variation for a wide range of commonly
used metrics and sampling methods were assessed. Replicate samples were taken in each of two seasons at 2–6 sites of varying
ecological status class within each of 18 stream types spread over 12 countries, using both the STAR-AQEM method and a national
sampling method or, where unavailable, the RIVPACS sampling protocol. The sampling precision of a combination of sampling
method and metric was estimated by expressing the replicate sampling variance as a percentage Psamp of the total variance in metric values with a stream type; low values of Psamp indicate high precision. Most metrics had percentage sampling variances less than 20% for all or most stream types and methods.
Most national methods including RIVPACS had sampling precisions at least as good as those for the STAR-AQEM method as used
in their country at the same sites; the main exceptions were the national methods used in Latvia and Sweden. The national
methods used in the Czech Republic, Denmark, France, Poland and the RIVPACS method used in the UK and Austria all had percentage
sampling variances of less than 10% for the majority of metrics assessed. In contrast, none of the metrics had percentage
sampling variances less than 10% when based on either the Italian (IBE) method, which used bank-side sorting, or the Latvian
national method which identifies only a limited set of taxa. Psamp was lowest on average for the two stream types sampled in the Czech Republic using either the PERLA national method or the
STAR-AQEM method. Averaged over all stream types and methods, the three Saprobic-based metrics had the lowest average percentage
sampling variances (3–6%) amongst the 26 metrics assessed. These estimates of sampling standard deviation can be used to help
assess the uncertainty in single or multi-metric systems for estimating site ecological status using the general STAR Bioassessment
Guidance Software (STARBUGS) developed within the STAR project. 相似文献
105.
Environmental data produced throughout monitoring activities in the framework of the implementation of Water Framework Directive 2000/60/EC (WFD) in Eastern Mediterranean (Greece) were used to assess the sensitivity and response of ecological indices against trace metals, eutrophication and multiple stress factors. The applied ecological indices include multi-metric eutrophication indices, a physicochemical status index applied for the first time in the Greek marine area, benthic indices, phytoplankton biomass index, and integrated status indices assessed through the application of the decision tree integration scheme. To investigate the exceedances in the eco-stoichiometric relationship between nutrients, considered a stressing factor, all physicochemical elements influenced directly or indirectly by eutrophication, such as nutrient concentrations, water transparency, oxygen saturation, particulates concentration, and sediment organic content, were related to ecological indices. Also, chemical contaminant stress factors represented by heavy metal concentrations in the water, as well as multiple stress factors represented by a pressure index, were related to ecological indices. A graphical visualization multivariate tool and statistical correlations were used to evaluate the sensitivity or explanatory power of the tested ecological indices against single and multiple stress factors. Results showed a strong response of all ecological indices to stress factors, although a diversification of sensitivity was evident. Primary production-related indices, i.e., macroalgae and chlorophyll-a indices, are more sensitive to particulates and nitrogen, while secondary production-related indices, i.e., benthic macroinvertebrates indices and eutrophication indices, including nutrients, are more sensitive to phosphates in the water column. The macroalgae index shows the strongest sensitivity to multiple stress factors. Among metals, mostly cadmium seems to match all indices performance. Nutrient relationships were shown as critical to eutrophication and ecological status. 相似文献
106.
107.
The management of biodiversity in aquatic ecosystems requires knowing the state of water quality linked to regime shifts in various taxonomic groups. We examine this question by studying the fish ponds in the Dombes region, France. These waterbodies are characterized by a high diversity of species. High levels of nutrients due to certain fish farming practices may cause significant eutrophication leading to loss in biodiversity and a shift from high coverage of aquatic vegetation to phytoplankton dominance may also be observed. The aim of this study is to assess tipping points, thresholds for effect, along a gradient of chlorophyll α in different taxonomic groups: aquatic vascular plants, phytoplankton, dragonflies and aquatic macro-invertebrates. Tipping points are analyzed with three different statistical methods: a method which evaluates tipping points with a difference in the mean (TMEAN), a second method which evaluates tipping point by comparing the mean and linear regressions before and after the tipping point (FSTAT) and third a method which evaluates linear regressions with a pivotal tipping point (SEGMENTED). We also compare tipping points for the different taxonomic groups using five different diversity indices: Observed richness, Jackknife first order, Fisher's alpha, Simpson index and Evenness.Our results show that there is an important variation in tipping points following the three statistical methods, but the SEGMENTED is the best method for evaluating tipping points. We observe a high difference of tipping point values for the different taxonomic groups depending on the diversity indices used. Jackknife first order has a better performance to evaluate a eutrophic change according to the diversity than the other indices.In all taxonomic groups, aquatic vascular plants are the most impacted by the chlorophyll α and almost all their tipping points are observed around 60 μg/L chlorophyll α concentrations. No significant relationship is found between chlorophyll α and phytoplankton diversity, while the two other groups, dragonflies and macro-invertebrates, are both impacted by the chlorophyll α but their relevant tipping points are situated in higher values than aquatic vascular plants. 相似文献
108.
用离散量预测蛋白质的结构型 总被引:12,自引:2,他引:12
基于蛋白质的结构类型决定了它的二级结构序列的概念,用二级结构序列参数Nα,Nβ,Nβaβ,N(βαβ)构成离散源,并计算离散量D(Xα),D(Xβ),D(Xα+β),利用离散增量预测蛋白质的结构类型,它是由这个蛋白质的离散量D(Xn)与四个标准离散D(Xα),D(Xβ),D(Xα/β),D(Xα+β)之间离散增量的最小值所决定的,预测结果表明,准确率分别达到84.8%(标准集)和83.3%(检验集)。 相似文献
109.
The value of an ecological indicator is no better than the uncertainty associated with its estimate. Nevertheless, indicator uncertainty is seldom estimated, even though legislative frameworks such as the European Water Framework Directive stress that the confidence of an assessment should be quantified. We introduce a general framework for quantifying uncertainties associated with indicators employed to assess ecological status in waterbodies. The framework is illustrated with two examples: eelgrass shoot density and chlorophyll a in coastal ecosystems. Aquatic monitoring data vary over time and space; variations that can only partially be described using fixed parameters, and remaining variations are deemed random. These spatial and temporal variations can be partitioned into uncertainty components operating at different scales. Furthermore, different methods of sampling and analysis as well as people involved in the monitoring introduce additional uncertainty. We have outlined 18 different sources of variation that affect monitoring data to a varying degree and are relevant to consider when quantifying the uncertainty of an indicator calculated from monitoring data. However, in most cases it is not possible to estimate all relevant sources of uncertainty from monitoring data from a single ecosystem, and those uncertainty components that can be quantified will not be well determined due to the lack of replication at different levels of the random variations (e.g. number of stations, number of years, and number of people). For example, spatial variations cannot be determined from datasets with just one station. Therefore, we recommend that random variations are estimated from a larger dataset, by pooling observations from multiple ecosystems with similar characteristics. We also recommend accounting for predictable patterns in time and space using parametric approaches in order to reduce the magnitude of the unpredictable random components and reduce potential bias introduced by heterogeneous monitoring across time. We propose to use robust parameter estimates for both fixed and random variations, determined from a large pooled dataset and assumed common across the range of ecosystems, and estimate a limited subset of parameters from ecosystem-specific data. Partitioning the random variation onto multiple uncertainty components is important to obtain correct estimates of the ecological indicator variance, and the magnitude of the different components provide useful information for improving methods applied and design of monitoring programs. The proposed framework allows comparing different indicators based on their precision relative to the cost of monitoring. 相似文献
110.
Environmental flows and the European Water Framework Directive 总被引:1,自引:0,他引:1
1. Environmental flows is now a widely accepted term that covers the quantity, timing, duration, frequency and quality of water flows required to sustain freshwater, estuarine and near-shore ecosystems and the human livelihoods and well-being that depend on them.
2. The Water Framework Directive (WFD) of the European Union does not use the term environmental flows explicitly, but requires member states to achieve good ecological status (GES) in all waterbodies, which is assessed by reference to aquatic biology. Nevertheless, it is accepted that ecologically appropriate hydrological regimes are necessary to meet this status. Implementing environmental flows will be a key measure for restoring and managing river ecosystems.
3. The WFD explicitly requires stakeholder involvement, but this has been interpreted as largely a dissemination exercise by national government agencies. Stakeholders are no longer involved in negotiation over ecological objectives as these are pre-set in the WFD. However, stakeholders may be more involved in reviewing standards and agreeing to measures to restore river ecosystems to the status required by the WFD.
4. The U.K. has undertaken two major projects to set environmental standards for water resources (i) to define water abstraction limits that maintain a healthy river ecosystem and (ii) to define ecologically appropriate flow releases from reservoirs.
5. Implementation of environmental flows remains a major issue, but new ideas such as time-limited licences and licence trading are being tried. 相似文献
2. The Water Framework Directive (WFD) of the European Union does not use the term environmental flows explicitly, but requires member states to achieve good ecological status (GES) in all waterbodies, which is assessed by reference to aquatic biology. Nevertheless, it is accepted that ecologically appropriate hydrological regimes are necessary to meet this status. Implementing environmental flows will be a key measure for restoring and managing river ecosystems.
3. The WFD explicitly requires stakeholder involvement, but this has been interpreted as largely a dissemination exercise by national government agencies. Stakeholders are no longer involved in negotiation over ecological objectives as these are pre-set in the WFD. However, stakeholders may be more involved in reviewing standards and agreeing to measures to restore river ecosystems to the status required by the WFD.
4. The U.K. has undertaken two major projects to set environmental standards for water resources (i) to define water abstraction limits that maintain a healthy river ecosystem and (ii) to define ecologically appropriate flow releases from reservoirs.
5. Implementation of environmental flows remains a major issue, but new ideas such as time-limited licences and licence trading are being tried. 相似文献