Publications by authors named "J Carlier"

323 Publications

A landscape classification map of Ireland and its potential use in national land use monitoring.

J Environ Manage 2021 Jul 17;289:112498. Epub 2021 Apr 17.

Agroecology and Rural Development Group, Marine and Freshwater Research Centre, Galway-Mayo Institute of Technology, Galway Campus, Dublin Road, Galway, Ireland.

This study presents a novel landscape classification map of the Republic of Ireland and is the first to identify broad landscape classes by incorporating physiographic and land cover data. The landscape classification responds to commitments to identify and classify the Irish landscape as a signatory to the European Landscape Convention. The methodology applied a series of clustering iterations to determine an objective multivariate classification of physiographic landscape units and land cover datasets. The classification results determined nine statistically significant landscape classes and the development of a landscape classification map at a national scale. A statistical breakdown of land cover area and diversity of each class was interpreted, and a comparison was extended using independent descriptive variables including farmland use intensity, elevation, and dominant soil type. Each class depicts unique spatial and composition characteristics, from coastal, lowland and elevated, to distinct and dominating land cover types, further explained by the descriptive variables. The significance of individual classes and success of the classification is discussed with particular reference to the wider applicability of the map. The transferability of the methodology to other existing physiographic maps and environmental datasets to generate new landscape classifications is also considered. This novel work facilitates the development of a strategic framework to efficiently monitor, compare and analyse ecological and other land use data that is spatially representative of the distribution and extent of land cover in the Irish countryside.
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http://dx.doi.org/10.1016/j.jenvman.2021.112498DOI Listing
July 2021

A world-wide analysis of reduced sensitivity to DMI fungicides in the banana pathogen Pseudocercospora fijiensis.

Pest Manag Sci 2021 Mar 25. Epub 2021 Mar 25.

Wageningen Research, Wageningen University and Research, Wageningen, The Netherlands.

Background: Pseudocercospora fijiensis is the causal agent of the black leaf streak disease (BLSD) of banana. Bananas are important global export commodities and a major staple food. Their susceptibility to BLSD pushes disease management towards excessive fungicide use, largely relying on multisite inhibitors and sterol demethylation inhibitors (DMIs). These fungicides are ubiquitous in plant disease control, targeting the CYP51 enzyme. We examined sensitivity to DMIs in P. fijiensis field isolates collected from various major banana production zones in Colombia, Costa Rica, Dominican Republic, Ecuador, the Philippines, Guadalupe, Martinique and Cameroon and determined the underlying genetic reasons for the observed phenotypes.

Results: We observed a continuous range of sensitivity towards the DMI fungicides difenoconazole, epoxiconazole and propiconazole with clear cross-sensitivity. Sequence analyses of PfCYP51 in 266 isolates showed 28 independent amino acid substitutions, nine of which correlated with reduced sensitivity to DMIs. In addition to the mutations, we observed up to six insertions in the Pfcyp51 promoter. Such promoter insertions contain repeated elements with a palindromic core and correlate with the enhanced expression of Pfcyp51 and hence with reduced DMI sensitivity. Wild-type isolates from unsprayed bananas fields did not contain any promoter insertions.

Conclusion: The presented data significantly contribute to understanding of the evolution and global distribution of DMI resistance mechanisms in P. fijiensis field populations and facilitate the prediction of different DMI efficacy. The overall reduced DMI sensitivity calls for the deployment of a wider range of solutions for sustainable control of this major banana disease.
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http://dx.doi.org/10.1002/ps.6372DOI Listing
March 2021

Convergent Adaptation to Quantitative Host Resistance in a Major Plant Pathogen.

mBio 2021 02 23;12(1). Epub 2021 Feb 23.

University of Toronto, Toronto, Ontario, Canada.

Plant pathogens can adapt to quantitative resistance, eroding its effectiveness. The aim of this work was to reveal the genomic basis of adaptation to such a resistance in populations of the fungus , a major devastating pathogen of banana, by studying convergent adaptation on different cultivars. Samples from populations showing a local adaptation pattern on new banana hybrids with quantitative resistance were compared, based on a genome scan approach, with samples from traditional and more susceptible cultivars in Cuba and the Dominican Republic. Whole-genome sequencing of pools of isolates (pool-seq) sampled from three locations per country was conducted according to a paired population design. The findings of different combined analyses highly supported the existence of convergent adaptation on the study cultivars between locations within but not between countries. Five to six genomic regions involved in this adaptation were detected in each country. An annotation analysis and available biological data supported the hypothesis that some genes within the detected genomic regions may play a role in quantitative pathogenicity, including gene regulation. The results suggested that the genetic basis of fungal adaptation to quantitative plant resistance is at least oligogenic, while highlighting the existence of specific host-pathogen interactions for this kind of resistance. Understanding the genetic basis of pathogen adaptation to quantitative resistance in plants has a key role to play in establishing durable strategies for resistance deployment. In this context, a population genomic approach was developed for a major plant pathogen (the fungus causing black leaf streak disease of banana) whereby samples from new resistant banana hybrids were compared with samples from more susceptible conventional cultivars in two countries. A total of 11 genomic regions for which there was strong evidence of selection by quantitative resistance were detected. An annotation analysis and available biological data supported the hypothesis that some of the genes within these regions may play a role in quantitative pathogenicity. These results suggested a polygenic basis of quantitative pathogenicity in this fungal pathogen and complex molecular plant-pathogen interactions in quantitative disease development involving several genes on both sides.
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http://dx.doi.org/10.1128/mBio.03129-20DOI Listing
February 2021

The role of neuropsychological assessment in adults with attention deficit/hyperactivity disorders.

Rev Neurol (Paris) 2021 Apr 19;177(4):341-348. Epub 2021 Feb 19.

Department of Neurology, Toulouse University Hospital, Toulouse, France; Inserm UMR1214, UPS, Toulouse NeuroImaging Center, Université de Toulouse, Toulouse, France.

Attention-Deficit Hyperactivity Disorder (ADHD) is a neurodevelopmental disorder characterized by inattention, hyperactivity and/or impulsivity. While ADHD was initially recognized as a childhood syndrome, scientific evidence accumulated to indicate that a significant proportion of ADHD children continue to experience symptoms of ADHD in adulthood. Moreover, the question of ADHD diagnosis can arise in adult patients who were not diagnosed in childhood. Currently, the diagnosis of ADHD in adulthood is based on the revised criteria described for children. However, their application for adults may be difficult for many reasons including compensation and comorbid disorders. To date, no clinical, neuropsychological, biological or imaging marker is available for the diagnosis of ADHD. Considering that ADHD is based on a neuropsychological model, in this article we will examine the usefulness of neuropsychological testing in the diagnosis in adults. We will first present diagnostic criteria of ADHD and the limits of their application in adults. We will then detail the neuropsychological data available in adult ADHD and the French and international clinical recommendations for neuropsychological assessment. Finally, we will explore the predictive value of neuropsychological scores in the diagnosis of ADHD and discuss key methodological points and perspectives for clinical research.
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http://dx.doi.org/10.1016/j.neurol.2021.01.006DOI Listing
April 2021

Central American and Caribbean population history of the Pseudocercospora fijiensis fungus responsible for the latest worldwide pandemics on banana.

Fungal Genet Biol 2021 Mar 28;148:103528. Epub 2021 Jan 28.

CIRAD, UMR PHIM, F-97130 Capesterre-Belle-Eau, Guadeloupe, France; PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France.

Among the emerging fungal diseases threatening food security, the Pseudocercospora fijiensis fungus causing black leaf streak disease of banana is one of the most marked examples of a recent worldwide pandemic on a major crop. We assessed how this pathogen spread throughout the latest invaded region, i.e. Central America and the Caribbean. We retraced its population history combining detailed monitoring information on disease outbreaks and population genetic analyses based on large-scale sampling of P. fijiensis isolates from 121 locations throughout the region. The results first suggested that sexual reproduction was not lost during the P. fijiensis expansion, even in the insular Caribbean context, and a high level of genotypic diversity was maintained in all the populations studied. The population genetic structure of P. fijiensis and historical data showed that two disease waves swept northward and southward in all banana-producing countries in the study area from an initial entry point in Honduras, probably mainly through gradual stepwise spore dispersal. Serial founder events accompanying the northern and southern waves led to the establishment of two different genetic groups. A different population structure was detected on the latest invaded islands (Martinique, Dominica and Guadeloupe), revealing multiple introductions and admixture events that may have been partly due to human activities. The results of this study highlight the need to step up surveillance to limit the spread of other known emerging diseases of banana spread mainly by humans, but also to curb gene flow between established pathogen populations which could increase their evolutionary potential.
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http://dx.doi.org/10.1016/j.fgb.2021.103528DOI Listing
March 2021