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Anticipating the impact of pitfalls in kinetic biodegradation parameter estimation from substrate depletion curves of organic pollutants
2019
[EN] Accurate and reliable estimation of kinetic parameters of pollutant biodegradation processes is essential for environmental and health risk assessment. Common biodegradation models proposed in the literature, such as the nonlinear Monod equation and its simplified versions (e.g. Michaelis-Menten-like and first-order equations), are problematic in terms of accuracy of kinetic parameters due to the parameter correlation. However, a comparison between these models in terms of accuracy and reliability, related to data imprecision, has not been performed in the literature. This task is necessary, mainly because the model selection cannot be straightforward, as shown in this work. To facilit…
Geomeasure: GIS and Scripting for Measuring Morphometric Variability
2019
This paper presents Geomeasure, a methodological tool developed to recover typometric information with a twofold objective. First, to speed up the process of gathering data by automatizing the way in which it is recovered. Second, it adds higher accuracy and the possibility of re-measuring archeological items without further directly interacting with the piece. Based on a combination of R scripting with GIS features, Geomeasure is at the time able to automatically gather 125–130 typometric variables per archaeological item, with the only input of vectorized photographs. It can be used as a reliable methodological aid to extract detailed information on patterns and trends of shape variabilit…
Open data and digital morphology
2017
International audience; Over the past two decades, the development of methods for visualizing and analysing specimens digitally, in three and even four dimensions, has transformed the study of living and fossil organisms. However, the initial promise that the widespread application of such methods would facilitate access to the underlying digital data has not been fully achieved. The underlying datasets for many published studies are not readily or freely available, introducing a barrier to verification and reproducibility, and the reuse of data. There is no current agreement or policy on the amount and type of data that should be made available alongside studies that use, and in some cases…
Do mosses really exhibit so large distribution ranges? Insights from the integrative taxonomic study of the Lewinskya affinis complex (Orthotrichacea…
2019
The strikingly lower number of bryophyte species, and in particular of endemic species, and their larger distribution ranges in comparison with angiosperms, have traditionally been interpreted in terms of their low diversification rates associated with a high long-distance dispersal capacity. This hypothesis is tested here with Lewinskya affinis (≡ Orthotrichum affine), a moss species widely spread across Europe, North and East Africa, southwestern Asia, and western North America. We tested competing taxonomic hypotheses derived from separate and combined analyses of multilocus sequence data, morphological characters, and geographical distributions. The best hypothesis, selected by a Bayes …
Cost-efficiency assessments of marine monitoring methods lack rigor—a systematic mapping of literature and an end-user view on optimal cost-efficienc…
2021
Global deterioration of marine ecosystems, together with increasing pressure to use them, has created a demand for new, more efficient and cost-efficient monitoring tools that enable assessing changes in the status of marine ecosystems. However, demonstrating the cost-efficiency of a monitoring method is not straightforward as there are no generally applicable guidelines. Our study provides a systematic literature mapping of methods and criteria that have been proposed or used since the year 2000 to evaluate the cost-efficiency of marine monitoring methods. We aimed to investigate these methods but discovered that examples of actual cost-efficiency assessments in literature were rare, contr…
Why ruminating ungulates chew sloppily: Biomechanics discern a phylogenetic pattern.
2019
Altres ajuts: "Beatriu de Pinos" 2014 - BP-A 00048 There is considerable debate regarding whether mandibular morphology in ungulates primarily reflects phylogenetic affinities or adaptation to specific diet. In an effort to help resolve this debate, we use three-dimensional finite element analysis (FEA) to assess the biomechanical performance of mandibles in eleven ungulate taxa with well-established but distinct dietary preferences. We found notable differences in the magnitude and the distribution of von Mises stress between Artiodactyla and Perissodactyla, with the latter displaying lower overall stress values. Additionally, within the order Artiodactyla the suborders Ruminantia and Tylo…
Drosophila cuticular hydrocarbons revisited : Mating status alters cuticular profiles
2010
Editor: Frederic Marion-Poll, INRA - Paris 6 - AgroParisTech, France.; International audience; Most living organisms use pheromones for inter-individual communication. In Drosophila melanogaster flies, several pheromones perceived either by contact/at a short distance (cuticular hydrocarbons, CHs), or at a longer distance (cis-vaccenyl acetate, cVA), affect courtship and mating behaviours. However, it has not previously been possible to precisely identify all potential pheromonal compounds and simultaneously monitor their variation on a time scale. To overcome this limitation, we combined Solid Phase Micro-Extraction with gas-chromatography coupled with mass-spectrometry. This allowed us (i…
Image analysis methods for assessment of H2O2 production and Plasmopara viticola development in grapevine leaves: application to the evaluation of re…
2013
article i nfo The grapevine downy mildew (Plasmopara viticola) provokes severe damages and destroys the harvest in the absence of an effective protection. Numerous fungicide treatments are thus generally necessary. To promote a sustainable production, alternative strategies of protection including new antifungal molecules, resistant geno- types or elicitor-induced resistance are under trial. To evaluate the relevance of these strategies, resistance tests are required. In this context, three image analysis methods were developed to read the results of tests performed to assessP.viticolasporulation and mycelial development, and H 2 O 2 production in leaves. They have been validated using elic…
Engineering CRISPR guide RNA riboswitches for in vivo applications
2019
CRISPR-based genome editing provides a simple and scalable toolbox for a variety of therapeutic and biotechnology applications. Whilst the fundamental properties of CRISPR proved easily transferable from the native prokaryotic hosts to eukaryotic and multicellular organisms, the tight control of the CRISPR-editing activity remains a major challenge. Here we summarise recent developments of CRISPR and riboswitch technologies and recommend novel functionalised synthetic-gRNA (sgRNA) designs to achieve inducible and spatiotemporal regulation of CRISPR-based genetic editors in response to cellular or extracellular stimuli. We believe that future advances of these tools will have major implicati…
Construction and validation of cDNA-based Mt6k-RIT macro- and microarrays to explore root endosymbioses in the model legume Medicago truncatula
2004
To construct macro- and microarray tools suitable for expression profiling in root endosymbioses of the model legume Medicago truncatula, we PCR-amplified a total of 6048 cDNA probes representing genes expressed in uninfected roots, mycorrhizal roots and young root nodules [Nucleic Acids Res. 30 (2002) 5579]. Including additional probes for either tissue-specific or constitutively expressed control genes, 5651 successfully amplified gene-specific probes were used to grid macro- and to spot microarrays designated Mt6k-RIT (M. truncatula 6k root interaction transcriptome). Subsequent to a technical validation of microarray printing, we performed two pilot expression profiling experiments usin…