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Maatschappelijke betrokkenheid bij natuur in beleid en praktijk : verkennende studie onder burgers en bedrijven
No full textStructural variants in the great tit genome and their effect on seasonal timing
No full textThe great tit (Parus major) is a songbird that has been extensively explored in ecological and evolutionary studies, shedding light on the effects of the global warming on nature. Genomic structural variability was never explored in detail in these species. The aim of this thesis was to detect, map, characterize and associate, with seasonal timing, structural variants that are present in the great tit genome such as copy number variations (CNVs) and inversions. First, this thesis presents a genome-wide map of CNV regions in the great tit genome, showing how these variants are associated with genomic architecture underlying their molecular formation. Second, CNVs were associated with breeding timing. Finally, this thesis investigate the genomic complexity of a large inversion in the Chromosome 1A. The inversion is recessive lethal and is inherited twice more than expected from male carriers but are normally inherited from female carriers, suggesting a selfish gene
Accuracy of estimates of milk production per lactation from limited test-day and recall data collected at smallholder dairy farms
No full textMilk production per lactation (MPL) is a key metric of dairy farms. Accurate estimation of MPL requires regular recording, which is laborious and costly. In smallholder systems in the tropics, therefore, generally very few records are available to estimate MPL. Cross-sectional studies collect only one single record per lactation, and even longitudinal studies usually yield only a limited number of records per lactation. Such data recording methods, therefore, are sometimes extended with records recalled by farmers. The accuracy of MPL-estimates based on such limited and imperfect data, however, is unknown. The aim of the present study was to assess the accuracy of MPL-estimates from a single record and a limited number of records per lactation, obtained from smallholder dairy farms in Nakuru County, Kenya. Test-day records from a milk recording scheme for 114 smallholders were used to prepare three datasets with: i) a complete number of test-days (CTD, 5803 records), ii) a limited number of test-days (LTD, 1583 records), and iii) a single test-day (STD, 471 records). In addition, farmers’ recall data (i.e. farmers retrieve information from the past, through memory) from a survey of 29 farms with 56 lactations were used to prepare two datasets with: i) a limited number of recall moments per lactation (LRM, 200 records), and ii) a single recall moment per lactation (SRM, 56 records). These five datasets were used to derive MPL-estimates, at individual cow level or at herd level. The latter was done to mimic a situation without individual cow data, but only herd data (i.e. yield and size). MPL-estimates for CTD were set as a benchmark to quantify the accuracies, based on the relative mean absolute error (RMAE) and root mean square error (RMSE), of MPL-estimates for LTD and STD. As a benchmark dataset was absent for recall data, we computed a virtual benchmark to quantify the accuracies of MPL-estimates for LRM and SRM. At cow level, accuracy of MPL-estimates was highest for LTD (RMAE 15%), and lowest for SRM (RMAE 28%), while accuracies for STD and LRM were intermediate (RMAEs ~ 20%). At herd level, accuracy was higher for STD (RMAE 13%) than for SRM (RMAE 25%). We also showed that to detect a difference of, for example, 100 kg in MPL we need 3002 cows for CTD, and between 3620 and 5003 cows when using alternative data collection methods. Hence, depending on the study objective, alternative data recording methods provide labor-saving and cost-effective ways to estimate MPL in data-scarce smallholder dairy systems.</p
Piper anisum as a promising new source of bioactive metabolites
No full textPiper species are commonly used by indigenous communities to treat several gastrointestinal diseases. In China, they are also used as an active ingredient in formulae to treat cancer. The objective of the study was to perform a large-scale metabolite profiling analysis to identify bioactive compounds in Piper anisum. Antioxidant capacity was assessed by the DPPH assay and total phenolics were assessed by Folin–Ciocalteu’s method. Antimicrobial activity was assessed against several Gram-positive and Gram-negative bacteria, whereas cytotoxicity was assessed against tumor cell lines MCF-7, HCT116, HepG2 and HL-60, and non-tumor cell line MRC-5. The multiplatform metabolite profiling approach encompassed NMR, GC–MS and LC–MS analyses. P. anisum root extract showed the greatest antioxidant capacity and total phenolic content, followed by the stem and leaf extracts. P. anisum extracts showed a highly selective antimicrobial profile, being specifically active against C. albicans (MIC of 500 μg mL−1). Additionally, the root extract (50 μg mL−1) showed the highest cell inhibition percentages against tumor cell lines MCF-7 (59.5%), HCT116 (49.2%), and HepG2 (61.0%). Forty-eight metabolites were annotated by GC–MS and 27 by LC–MS. These included alkaloids, carbohydrates, fatty acids, hydrocarbons, organic acids, phenolic compounds, and terpenes. Taken together, these results showed that P. anisum root extract is a promising source of bioactive compounds.</p
Responses of macroinvertebrate communities to land use specific sediment food and habitat characteristics in lowland streams
No full textThe input of land use specific organic matter into lowland streams may impact sediment characteristics in terms of food resources and habitat structure, resulting in differences in macroinvertebrate community composition. Therefore, we investigated to what extent land use specific sediment food and habitat characteristics structure macroinvertebrate communities. To this purpose linear multiple regression models were constructed, in which macroinvertebrate biotic indices were considered as response variables and sediment characteristics as predictor variables, analysed in 20 stream stretches running through five different land use types. Sediment characteristics and macroinvertebrate community composition were land use specific. The carbon/nitrogen (C/N) ratio, woody debris substrate cover and the origin of fatty acids influenced macroinvertebrate community composition. Shannon-Wiener diversity was better explained by fatty acids origin, such as in grassland streams, where a higher relative content of plant derived fatty acids related to a higher macroinvertebrate diversity. In cropland and wastewater treatment plant (WWTP) streams with a low C/N ratio and dominated by microbial derived fatty acids, higher abundances of Oligochaeta and Chironomus sp. were observed. Ephemeroptera, Plecoptera, and Trichoptera (EPT) richness was positively related to woody debris substrate cover, which only occurred in forest streams. Hence, macroinvertebrate community composition was influenced by the origin of the organic material, being either allochthonous or autochthonous and when autochthonous being either autotrophic or heterotrophic. It is therefore concluded that sediment food and habitat characteristics are key ecological filters.</p
The role of metabolism in the developmental toxicity of polycyclic aromatic hydrocarbon-containing extracts of petroleum substances
No full textIn vitro assays presently used for prenatal developmental toxicity (PDT) testing only assess the embryotoxic potential of parent substances and not that of potentially embryotoxic metabolites. Here we combined a biotransformation system, using hamster liver microsomes, with the ES-D3 cell differentiation assay of the embryonic stem cell test (EST) to compare the in vitro PDT potency of two 5-ring polycyclic aromatic hydrocarbons (PAHs), benzo[a]pyrene (BaP) and dibenz[a,h]anthracene (DBA), and dimethyl sulfoxide extracts from five PAH-containing petroleum substances (PS) and a gas-to-liquid base oil (GTLb), with and without bioactivation. In the absence of bioactivation, DBA, but not BaP, inhibited the differentiation of ES-D3 cells into beating cardiomyocytes in a concentration-dependent manner. Upon bioactivation, BaP induced in vitro PDT, while its major metabolite 3-hydroxybenzo[a]pyrene was shown to be active in the EST as well. This means BaP needs biotransformation to exert its embryotoxic effects. GTLb extracts tested negative in the EST, with and without bioactivation. The PS-induced PDT in the EST was not substantially changed following bioactivation, implying that metabolism may not play a crucial role for the PS extracts under study to exert the in vitro PDT effects. Altogether, these results indicate that although some PAH require bioactivation to induce PDT, some do not and this latter appears to hold for the (majority of) the PS constituents responsible for the in vitro PDT of these complex substances.</p
Large‐scale genomic sequence data resolve the deepest divergences in the legume phylogeny and support a near‐simultaneous evolutionary origin of all six subfamilies
No full textPhylogenomics is increasingly used to infer deep‐branching relationships while revealing the complexity of evolutionary processes such as incomplete lineage sorting, hybridization/introgression and polyploidization. We investigate the deep‐branching relationships among subfamilies of the Leguminosae (or Fabaceae), the third largest angiosperm family. Despite their ecological and economic importance, a robust phylogenetic framework for legumes based on genome‐scale sequence data is lacking.We generated alignments of 72 chloroplast genes and 7621 homologous nuclear‐encoded proteins, for 157 and 76 taxa, respectively. We analysed these with maximum likelihood, Bayesian inference, and a multispecies coalescent summary method, and evaluated support for alternative topologies across gene trees.We resolve the deepest divergences in the legume phylogeny despite lack of phylogenetic signal across all chloroplast genes and the majority of nuclear genes. Strongly supported conflict in the remainder of nuclear genes is suggestive of incomplete lineage sorting.All six subfamilies originated nearly simultaneously, suggesting that the prevailing view of some subfamilies as ‘basal’ or ‘early‐diverging’ with respect to others should be abandoned, which has important implications for understanding the evolution of legume diversity and traits. Our study highlights the limits of phylogenetic resolution in relation to rapid successive speciation
Is nitric oxide a critical key factor in ABA-induced stomatal closure?
No full textThe role of nitric oxide (NO) in abscisic acid (ABA)-induced stomatal closure is a matter of debate. We conducted experiments in Vicia faba leaves using NO gas and sodium nitroprusside (SNP), a NO-donor compound, and compared their effects to those of ABA. In epidermal strips, stomatal closure was induced by ABA but not by NO, casting doubt on the role of NO in ABA-mediated stomatal closure. Leaf discs and intact leaves showed a dual dose response to NO: stomatal aperture widened at low dosage and narrowed at high dosage. Overcoming stomatal resistance by means of high CO2 concentration ([CO2]) restored photosynthesis in ABA-treated leaf discs but not in those exposed to NO. NO inhibited photosynthesis immediately, causing an instantaneous increase in intercellular [CO2] (Ci), followed by stomatal closure. However, lowering Ci by using low ambient [CO2] showed that it was not the main factor in NO-induced stomatal closure. In intact leaves, the rate of stomatal closure in response to NO was about one order of magnitude less than after ABA application. Because of the different kinetics of photosynthesis and stomatal closure that were observed, we conclude that NO is not likely to be the key factor in ABA-induced rapid stomatal closure, but that it fine-tunes stomatal aperture via different pathways
Changing fish distributions challenge the effective management of European fisheries
No full textChanges in fish distribution are being observed across the globe. In Europe’s Common Fisheries Policy, the share of the catch of each fish stock is split among management areas using a fixed allocation key known as ‘Relative Stability’: in each management area, member states get the same proportion of the total catch each year. That proportion is largely based on catches made by those member states in the 1970s. Changes in distribution can, therefore, result in a mismatch between quota shares and regional abundances within management areas, with potential repercussions for the status of fish stocks and the fisheries that depend on them. Assessing distribution changes is crucial to ensure adequate management and sustainable exploitation of our fish resources. We analysed scientific survey data using a three-tiered analytical approach to provide, for the first time, an overview of changes in distribution for 19 northeast Atlantic fish species encompassing 73 commercial stocks over 30 yr. All species have experienced changes in distribution, five of which did so across management areas. A cross-species analysis suggested that shifts in areas of suitable thermal habitat, and density-dependent use of these areas, are at least partly responsible for the observed changes. These findings challenge the current use of relative stability to allocate quota
Dynamic modified atmosphere packaging material for fresh horticultural products
No full textThe present invention relates to the use of a sheet for extending shelf-life of biological products, wherein the sheet comprises or consists of a thermoplastic composition with a hydrophobic polymer phase comprising at least one hydrophobic polymer; a hydrophilic polymer phase comprising at least one hydrophilic polymer; and optionally at least one compatibiliser