Evaluating the performance of benthic multi-metric indices across broad-scale environmental gradients

The usefulness of benthic multi-metric indices when assessing seafloor integrity across broad environmental gradients should be deliberated, as their lack of transparency might hide important sources of variation and fail to identify environmental change. This study compares the performance of two multi-metric indices; the Benthic Quality Index (BQI) and the Brackish water Benthic Index (BBI) between three sub-basins in the Baltic Sea. Both indices reflect the salinity-driven gradient in macroinvertebrate diversity and composition as well as changes in bottom water oxygen concentrations. The relative contribution of predictor variables for explaining index variation does, however, differ between sub-basins, resulting in the indices representing different aspects of the benthic community along the environmental gradient. This context-dependency is caused by inherent differences in benthic community characteristics between the sub-basins of the Baltic Sea, and how the communities are portrayed by the indices. An increased transparency of the importance of the different predictors for directing index values is needed for coherent classifications over broad environmental gradients, such as those occurring in large estuarine water bodies. Use of a weight of evidence table to combine multiple indicators would preserve transparency and be more likely to provide a robust assessment method that would detect seafloor degradation at an early stage.     

DPHL:A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery

To address the increasing need for detecting and validating protein biomarkers in clinical specimens, mass spectrometry (MS)-based targeted proteomic techniques, including the selected reaction monitoring (SRM), parallel reaction monitoring (PRM), and massively parallel data-independent acquisition (DIA), have been developed. For optimal performance, they require the fragment ion spectra of targeted peptides as prior knowledge. In this report, we describe a MS pipeline and spectral resource to support targeted proteomics studies for human tissue samples. To build the spectral resource, we integrated common open-source MS computational tools to assemble a freely accessible computational workflow based on Docker. We then applied the workflow to generate DPHL, a comprehensive DIA pan-human library, from 1096 data-dependent acquisition (DDA) MS raw files for 16 types of cancer samples. This extensive spectral resource was then applied to a proteomic study of 17 prostate cancer (PCa) patients. Thereafter, PRM validation was applied to a larger study of 57 PCa patients and the differential expression of three proteins in prostate tumor was validated. As a second application, the DPHL spectral resource was applied to a study consisting of plasma samples from 19 diffuse large B cell lymphoma (DLBCL) patients and 18 healthy control subjects. Differentially expressed proteins between DLBCL patients and healthy control subjects were detected by DIA-MS and confirmed by PRM. These data demonstrate that the DPHL supports DIA and PRM MS pipelines for robust protein biomarker discovery. DPHL is freely accessible at https://www.iprox.org/page/project.html?id=IPX0001400000.     

Responses of aquatic macrophyte assemblages to nutrient enrichment in a lowland river basin of western Greece

Abstract

In Greece, as in many other Mediterranean countries, there is a lack of information enabling the use of aquatic macrophytes as biological indicators of the water trophic status. This research aimed to investigate the trophic preferences of the aquatic macrophyte assemblages encountered in selected standing water bodies of a lowland river basin of western Greece. It also aimed to assess the response of the macrophyte species that occur in the studied water bodies to different nutrient concentrations. A total of 56 macrophyte species were identified. TWINSPAN analysis distinguished four main vegetation groups potentially related to three trophic types. The Trophic Ranking Score developed in the UK was applied in order to investigate the trend in aquatic macrophytes in response to the different trophic conditions. The results indicated that TRS_UK was not in accordance to the water trophic indices. After the addition of 14 new species and the re-scoring of the plants from the UK list, the re-calculation of TRS enabled a better classification of the trophic status convergent with the information from the water trophic indices. The current study constitutes a reference document providing basic information, and must be improved by updating the plant list with new data from other sites.     

The Biochemical Significance of Parallel DNA Duplexes

Abstract

Structural and synthetic model are given for (modified) parallel DNAs with non-Watson and Crick duplex formation.     

The method matters: A guide for indicator aggregation in ecological assessments

Ecological assessment requires the integration of many physical, chemical, and/or biological quality elements. The choice of the aggregation method of such partial assessments into an overall assessment can considerably affect the assessment outcome – an issue that has been controversially discussed within the scientific community for the last decade. Current practice often considers only two different aggregation methods, the weighted arithmetic mean (additive aggregation) and the one-out, all-out method (minimum aggregation). However, both have important drawbacks. Additive aggregation compensates a bad status of one quality element by a number of elements featuring good status. Minimum aggregation can lead to overly pessimistic assessment results, since only the quality element in the worst status is considered. Here, we introduce a toolbox containing current and new aggregation methods, demonstrate and discuss their properties with simple, didactical examples, and suggest in which situations best to use them. Then, we illustrate the consequences of selected aggregation schemes for ecological river assessment with the case study of the Swiss Modular Concept of stream assessment (SMC), which we apply to ten river reaches in the Mönchaltdorfer Aa catchment in Switzerland. To be able to do so, we used multi-criteria decision analysis, i.e., multi-attribute value theory, to arrange the SMC quality elements into an objectives hierarchy, and to translate their individual assessments into value functions. Our case study revealed that choosing the most appropriate aggregation method particularly matters, if objectives with significantly different qualities are aggregated. We argue that redundant objectives (i.e., quality elements), often found at the lower levels of the objectives hierarchy, should best be aggregated additively allowing for compensation to increase the statistical significance of the results. Further, we suggest that complementary sub-objectives that often occur at higher levels may be optimally aggregated with a mixture of additive and minimum aggregation. Such a mixed method will allow some compensation, but nevertheless penalize for very bad states. Since here we compare commonly used aggregation methods with some which we believe have never been discussed in an assessment context before, our study concurrently informs ecological assessment in theory and in practice.     

An efficient algorithm for DNA fragment assembly in MapReduce

Fragment assembly is one of the most important problems of sequence assembly. Algorithms for DNA fragment assembly using de Bruijn graph have been widely used. These algorithms require a large amount of memory and running time to build the de Bruijn graph. Another drawback of the conventional de Bruijn approach is the loss of information. To overcome these shortcomings, this paper proposes a parallel strategy to construct de Bruijin graph. Its main characteristic is to avoid the division of de Bruijin graph. A novel fragment assembly algorithm based on our parallel strategy is implemented in the MapReduce framework. The experimental results show that the parallel strategy can effectively improve the computational efficiency and remove the memory limitations of the assembly algorithm based on Euler superpath. This paper provides a useful attempt to the assembly of large-scale genome sequence using Cloud Computing.     

Selection and validation of reference sites in small river basins

Type-specific reference conditions that describe sites with no or only very minor anthropogenic disturbances are a basic requirement of the European Water Framework Directive. The reference condition approach implies a previous determination of criteria acceptable for the definition of near-natural stretches. In this paper, a methodology based on selection and validation procedures is applied to a Portuguese watershed to guide the identification of reference sites. The methodology consisted of three phases: (1) a preliminary site inspection through the use of maps, available data and an extensive screening field campaign that resulted in the selection of 52 potentially undisturbed small- and medium-sized rivers stretches, ranging from 43 to 1069 m in altitude, with catchment areas between 4 and 641 km² and representing siliceous and calcareous riverbeds; (2) a detailed site selection based on ten pre-defined criteria involving physical/social/biological attributes that indicated catchment land use changes and alien vegetal riparian species as major human impacts; (3) a site validation procedure involving detailed investigation of benthic macroinvertebrate communities, riparian vegetation, in-stream habitat quality and chemical parameters that showed riparian wood-related problems as a major restriction to validate a stretch as a near-natural site. Only about 12% of all investigated river sites, accounting for 600 m of all 5200 m studied, could be considered as near-reference stretches or sites retaining essential natural functions. Selection and validation procedures can identify different sites as reference, which reinforces the need for applying both procedures. The results presented can help to accomplish the requirements of the EU – Water Framework Directive by selecting reference sites as the first step to establish biological reference conditions and, simultaneously, to form a basis for nature conservation strategies. Electronic supplementary material Electronic supplementary material is available for this article at and accessible for authorised users.     

Temporal and Spatial Distribution Patterns of Larval Trichoptera in Madeiran Streams

Temporal and spatial distribution patterns of lotic larval trichopteran assemblages in relation to environmental variables were investigated in Madeiran streams using multivariate analyses. TWINSPAN classification detected distinct faunal assemblages related to spatial factors between non-polluted high altitude sites and lower lying enriched sites where tolerant taxa were predominant but showed strong seasonal shifts in species composition and abundance. The 15 TWINSPAN end groups were grouped into five arbitrary clusters based upon the seasonal and spatial changes in the trichopteran assemblages detected by the analysis. Significant differences between environmental variables (distance from source, altitude, temperature, conductivity, alkalinity and nitrate) and the trichopteran assemblages (using trichopteran based metrics) of these clusters were confirmed by the Kruskal-Wallis test (H) and Dunn’s test. Chemical classification of samples within the clusters revealed a strong association between trichopteran assemblages and water quality. Canonical Correspondence Analysis and Monte Carlo global permutation tests also identified significant associations between the larval assemblages and physicochemical variables such as temperature and conductivity along a strong physical gradient (altitude, slope) and nitrate along a weaker seasonal gradient. Analysis of functional feeding group distribution patterns clearly showed that mid to high altitude indigenous woodland sites were trophically diverse whilst the lower reaches of the islands streams are trophically impoverished with strong seasonal shifts between two feeding groups of enrichment tolerant taxa. Trichopteran shredders are exclusive to indigenous woodland sites, indicating a limited distribution associated with land use, allochthonous input and habitat destruction. The results indicate that several ‘environmental filters’ operate at different levels upon the islands trichopteran fauna, producing temporally and spatially distinct ‘subsets’ of species best able to exploit conditions and resources at a given site or time, confounding the direct comparison of these insular systems with the findings of the River Continuum Concept, traditionally associated with unaffected continental lotic systems.     

Generation of initial molecular dynamics configurations in arbitrary geometries and in parallel

A computational pre-processing tool for generating initial configurations of molecules for molecular dynamics simulations in geometries described by a mesh of unstructured arbitrary polyhedra is described. The mesh is divided into separate zones and each can be filled with a single crystal lattice of atoms. Each zone is filled by creating an expanding cube of crystal unit cells, initiated from an anchor point for the lattice. Each unit cell places the appropriate atoms for the user-specified crystal structure and orientation. The cube expands until the entire zone is filled with the lattice; zones with concave and disconnected volumes may be filled. When the mesh is spatially decomposed into portions for distributed parallel processing, each portion may be filled independently, meaning that the entire molecular system never needs to fit onto a single processor, allowing very large systems to be created. The computational time required to fill a zone with molecules scales linearly with the number of cells in the zone for a fixed number of molecules, and better than linearly with the number of molecules for a fixed number of mesh cells. Our tool, molConfig, has been implemented in the open source C++ code OpenFOAM.