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1. Analysing the architecture of Corylus avellana and parametrizing L-HAZELNUT FSPM

Author: Grisafi, Francesca, Tombesi, Sergio, Farinelli, Daniela, Boudon, Frédéric, Durand, Jean-Baptiste, Costes, Evelyne, Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt), Università degli Studi di Perugia = University of Perugia (UNIPG), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), Modèles statistiques bayésiens et des valeurs extrêmes pour données structurées et de grande dimension (STATIFY), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Jean Kuntzmann (LJK), Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Dr. Susann Müller, Tsu-Wei Chen, Andreas Fricke, Katrin Kahlen, and Susann Müller and Hartmut Stützel
Subjects: modelling, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], hazelnut, Lpy, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology
Abstract: International audience; Introduction - Tree architecture is a fundamental part of a functional structural plant model. This is particularly evident in perennial tree crops where the structure of the plant influences the position of source and sink organs, as well as light interception inside the canopy, and serves as storage pool for exceeding carbohydrates. Therefore, a precise description of tree 3D structure is essential to realistically allocate carbohydrates in a FSPM (Costes et al., 2006). Hazelnut tree architecture has different characteristics compared to other fruit tree crops that have been modelled (i.e., peach, mango, apple, and kiwi). It is a monoecious species. Female flowers are grouped into inflorescences located into mixed buds, while male flowers are arranged into inflorescences in the apical position of sylleptic shoots. Each node could bear more than one bud and, the following year, the new shoots are much shorter than the shoots from which they were born. The present study aimed to analyse hazelnut one-year-old shoots 'architecture in order to build the structural part of L-HAZELNUT: a functional structural plant model of hazelnut (Corylus avellana). Material and Methods - Own-rooted tree clones of C.avellana, cultivar “Tonda di Giffoni”, were chosen, during winter, in 2020 and 2021 in Deruta (Italy). Plants were normally irrigated and fertilized. No pruning occurred during the two years. 104 one-year-old proleptic shoots were sampled according to four length categories: short (Sh) when shorter than 5 cm, medium (Me) when they were between 5 and 20 cm, long (Lo) when they were between 20 and 40 cm, and very long (VLo) when longer than 40 cm. For each shoot, diameter, length, and number of nodes were recorded. From the base of the shoot to its tip, the fate of each node was noted. Four fates are distinguished in C.avellana: blind nodes, vegetative buds, sylleptic shoots and mixed buds. In the year subsequent to sampling, the same measurements were repeated on the lateral shoots that were born from the buds. Statistical analyses were done in 2022, using packages from RStudio. First, exploratory analyses were performed to investigate the distribution of the bud types or sylleptic shoots depending on the rank node along the one-year-old proleptic shoots and thus, to address if there were some homogeneous zone (i.e., zones characterized by a stable distribution of the possible bud fates (Guédon et al., 2001)). This led us to draw a flux diagram (Figure 1). Each part of the diagram corresponds to specific logical connections, between FSPM components, which were addressed using specific probabilistic models, inferred from the collected data set. Results and Discussion - During this study new knowledge regarding the architecture of C.avellana was acquired. Even though male flowers were stated to be located on proleptic shoots 'nodes (Botta & Valentini, 2018), we instead highlighted the presence of male flowers in the apical position of sylleptic shoots. It was also observed that hazelnut has a sympodial growth. Each statistical model, associated with the FSPM components, was used to define functions to answer each of the questions addressed in the flow diagram. All the functions were coded in L-py (Boudon et al., 2012) to build a L-system program able to generate the architecture of hazelnut (Figure 1). Conclusion - This led to a first coarse FSPM named L-HAZELNUT, in reference to some previous FSPM for fruit tree crops (Lopez et al., 2010). It simulates the growth of a hazelnut tree over two successive years. The conception of an FSPM is a long and meticulous process that requires having in mind a clear scheme that describes the growing and branching processes. Such a scheme can be acquired by appropriate observations and analyses of how the plant grows and develops. However, as many aspects of the plant have to be considered, the accuracy of the presented 3D structure has still to be evaluated and further studies will be necessary to validate them. Moreover, L-HAZELNUT model should be complemented in the next future with a functional part describing carbon acquisition and partitioning within the tree.
Published: 2023

2. Nutritional values of forage-legume-based silages and protein concentrates for growing pigs

Author: David Renaudeau, Søren Krogh Jensen, Morten Ambye-Jensen, Steffen Adler, Paolo Bani, Eric Juncker, Lene Stødkilde, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Aarhus University [Aarhus], Norsk institutt for bioøkonomi=Norwegian Institute of Bioeconomy Research (NIBIO), Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt), Trust'Ing, ProRefine project (AAP) 18ACO 041, and European Project
Subjects: Red clover, Medicago sativa/chemistry, Swine, RED-CLOVER, CLOVER TRIFOLIUM-PRATENSE, GRADED-LEVELS, Proteinconcentrate, ILEAL DIGESTIBILITY, Animals, Lactation, AMINO-ACIDS, NUTRIENT APPARENT DIGESTIBILITIES, Diet/veterinary, Trifolium/chemistry, Swine Diseases, Lucerne, Silage, Protein concentrate, Lactation/metabolism, Silage/analysis, Milk/metabolism, NITROGEN LOSSES, Diet, Milk, [SDV.SA.SPA]Life Sciences [q-bio]/Agricultural sciences/Animal production studies, NEUTRAL DETERGENT FIBER, BARLEY-BASED DIETS, POLYPHENOL OXIDASES, Animal Science and Zoology, Animal Nutritional Physiological Phenomena, Digestion, Female, Trifolium, Nutritive Value, Redclover, Medicago sativa
Abstract: International audience; In organic pig production systems, one of the main challenges is to meet the demand for resources rich in protein. Among the resources available, temperate green plants, such as forage legumes, are potential sources of energy and protein. The aim of the study was to determine the nutritional value of silages (S) from the whole plant of lucerne (L) and red clover (R) and protein pastes (PPs) obtained from L and R leaves. In a first trial, 30 pigs were used in a factorial design to determine the total tract digestibility (TTD) of dietary nutrients and energy in five dietary treatments. The control group was fed a control diet (C1). The lucerne silage (LS) and red clover silage (RS) groups were fed a 78%:22% mixture (on a DM basis) of the C1 diet and LS or RS. The lucerne protein paste (LPP) and the red clover protein paste (RPP) groups were fed an 81%:19% mixture (on a DM basis) of the C1 diet and LPP or RPP. In the second trial, five pigs were used in a 5 x 5 Latin square design to evaluate the standardised ileal digestibility (SID) of amino acids (AAs) in the four legume products. The control diet (C2) was formulated with casein as the sole protein source. The LS and RS groups were fed an 85%:15% mixture (on a DM basis) of the C2 diet and LS or RS. The LPP and RPP groups were fed an 80%:20% mixture (on a DM basis) of the C2 diet and LPP or RPP. Regardless of the plant species, silages obtained from L and R leaves contained less AA and more fibre than protein pastes. While the fresh forages contained the same percentage of protein N in total N (63.6%), lucerne lost more protein N during ensiling than red clover (-75.5 vs -33.8%). The calculated TTD coefficient of energy was higher in silages than in protein pastes and lower in R than in L products (72.8, 71.5, 67.7, and 61.3 for LS, RS, LPP and RPP, respectively). The SID of total essential AA was higher in LPP than in RPP (87.2 vs 79.2%) whereas it was lower in LS than in RS (33.2 vs 56.8%). The lower SID values in silages were explained by the protein degradation during the ensiling process and a high proportion of AA linked to the NDF fraction. The results of the present study show that protein pastes obtained from lucerne and red clover are valuable protein sources for pig. In contrast, legume silages have to be considered as an energy source rather than a protein source.
Published: 2022

3. Has breed any effect on beef sensory quality?

Author: Ian Richardson, S. Failla, John L. Williams, María del Mar Campo, Per Ertbjerg, A. Conanec, M-P. Ellies-Oury, Begoña Panea, Marie Chavent, Jérôme Saracco, J. F. Hocquette, Institut de Mathématiques de Bordeaux (IMB), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Quality control and dynamic reliability (CQFD), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS)-Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS)-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), University of Zaragoza - Universidad de Zaragoza [Zaragoza], Bristol Veterinary School, University of Helsinki, Consiglio per la Ricerca in Agricoltura e l’analisi dell’economia agraria (CREA), Agrifood Research and Technology Centre of Aragon, Av. Monta˜nana, 930, Zaragoza, Spain, Méthodes avancées d’apprentissage statistique et de contrôle (ASTRAL), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Naval Group, Davies Research Centre, University of Adelaide, Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti (DiANA), Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt), Bordeaux Sciences Agro [Gradignan], Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1 (UB)-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1 (UB)-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS)-Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1 (UB)-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS)-Inria Bordeaux - Sud-Ouest, Helsingin yliopisto = Helsingfors universitet = University of Helsinki, and Consiglio per la Ricerca in Agricoltura e l’analisi dell’economia agraria = Council for Agricultural Research and Economics (CREA)
Subjects: Marchigiana, [SDV]Life Sciences [q-bio], Sensory system, Sensory analysis, 0404 agricultural biotechnology, Animal science, medicine, Flavor, Mixed effect models, 2. Zero hunger, General Veterinary, biology, 0402 animal and dairy science, food and beverages, Fixed effect models, 04 agricultural and veterinary sciences, biology.organism_classification, 040401 food science, 040201 dairy & animal science, Breed, Tenderness, Lipid content, Animal Science and Zoology, Analysis of variance, medicine.symptom, Beef
Abstract: International audience; A total of 436 young cattle from 15 cattle breeds were reared in as similar conditions as possible to evaluate the impact of breed on sensory quality of beef from longissimus muscle determined by sensory analysis. Two statistical methods for processing the sensory data were compared. The analysis of variance with or without the panelist effect gave similar conclusions indicating that the robustness of the results was not dependent on the method chosen. The 4 meat descriptors (tenderness, juiciness, beef flavor and off-flavor) placed breeds into 5 groups using an unsupervised classification (hierarchical ascending classification). Aberdeen Angus, Highland and Jersey, that have a high lipid content in the muscle studied, differed from the other breeds in that they had a higher beef flavour. The dual-purpose and rustic breeds, Simmental, Casina and Marchigiana, produced significantly less juicy and less tender meat than that from breeds selected for meat production. Overall, despite significant differences previously identified for animal, carcass, muscle and beef traits for the same animals, differences in sensory scores between most of the breeds were small, with only significant differences between the few breeds that had extreme sensory profiles (such as Simmental and Pirenaica).
Published: 2021

4. Approaches for reducing wastes in the agricultural sector. An analysis of Millennials’ willingness to buy food with upcycled ingredients

Author: Silvia Coderoni, Maria Angela Perito, Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt), Facoltà di Bioscienze e tecnologie agro-alimentari e ambientali - Faculty of Bioscience and Agro-Food and Environmental Technology [Teramo], Universita degli studi di Teramo - University of Teramo [Italie] (UNITE), Alimentation et sciences sociales (ALISS), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and AGER 2 Project, grant no. 2016-0105
Subjects: Food industry, Settore AGR/01 - ECONOMIA ED ESTIMO RURALE, Circular economy, 020209 energy, Food technology, Novel food, 02 engineering and technology, Certification, 010501 environmental sciences, Millennial consumer, 01 natural sciences, 12. Responsible consumption, Millennial consumers, Food neophobia, Surveys and Questionnaires, Food waste, Sustainable consumption, Upcycled food, 0202 electrical engineering, electronic engineering, information engineering, Food Industry, Marketing, Waste Management and Disposal, 0105 earth and related environmental sciences, 2. Zero hunger, business.industry, Consumer Behavior, [SHS.ECO]Humanities and Social Sciences/Economics and Finance, Italy, Agriculture, Food Technology, business, Upcycled food Food neophobia
Abstract: International audience; Upcycled ingredients are one of the most significant current trends in the food industry aimed to tackle the challenge of solid food loss reduction. This study investigates the potential market among Millennial consumers for products enriched with upcycled ingredients in Italy. We surveyed a sample of 317 Italian Millennial consumers, using a web-based survey. 62% of respondents declared to be informed about the existence of food made from upcycled ingredients and 53% declared to be willing to buy this novel food. Also, 69% of respondents think that food enriched with upcycled ingredients can bring environmental benefits, while only 40% believe that it can bring health benefits.Using a logit model to analyse consumer preferences, we found that food neophobia and food technology neophobia negatively impact on the likelihood of being willing to buy food produced with upcycled ingredients. Also, consumers who give high importance to food certification are less likely to be willing to buy upcycled foods. Contrariwise, reading labels and believing that upcycled foods are healthier or more environmentally friendly positively impacts on the willingness of Millennial consumers to buy these foods.Results for the sample analysed eventually suggest that giving right information to consumers about the environmental and health characteristics of the products, through clear labelling, could increase their market uptake thus helping to reduce food loss and contributing to reaching circular economy objectives in the agricultural sector.
Published: 2021

5. Hyperspectral Imaging to Characterize Table Grapes

Author: Vanessa Lançon-Verdier, Mario Gabrielli, Pierre Picouet, Chantal Maury, Groupe de Recherche en Agroalimentaire sur les Produits et les Procédés (GRAPPE), Ecole supérieure d'Agricultures d'Angers (ESA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), SFR UA 4207 QUAlité et SAnté du Végétal (QUASAV), Université d'Angers (UA)-Université de Nantes (UN)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Ecole supérieure d'Agricultures d'Angers (ESA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt)
Subjects: hyperspectral imaging, phenolics, Derivative, PLS, 01 natural sciences, anthocyanin, MLR, Analytical Chemistry, lcsh:Biochemistry, 0404 agricultural biotechnology, Linear regression, total soluble solids, [CHIM]Chemical Sciences, lcsh:QD415-436, Physical and Theoretical Chemistry, Sugar, Projection (set theory), acoustics, Mathematics, model, 010401 analytical chemistry, Table grape, Hyperspectral imaging, table grapes, 04 agricultural and veterinary sciences, prediction, 040401 food science, 0104 chemical sciences, Settore AGR/15 - SCIENZE E TECNOLOGIE ALIMENTARI, Table (database), Biological system, Predictive modelling
Abstract: Table grape quality is of importance for consumers and thus for producers. The objective quality determination is usually destructive and very simple with the assessment of only a couple of parameters. This study proposed to evaluate the possibility of hyperspectral imaging to characterize table grapes quality through its sugar, total flavonoid and total anthocyanin contents. Different pre-treatments (WB, SNV, 1st and 2nd derivative) and different methods were tested: PLS with full spectra, then Multiple Linear Regression (MLR) were realized after selecting the optimal wavelengths thanks to the regression coefficients (-coefficients) and the Variable Importance in Projection (VIP) scores from the full spectra. All models were good showing that hyperspectral imaging is a relevant method to assess sugar content and global phenolic content. The best model was dependent on the variable. The best models were from the full spectra and with the 2nd derivative pre-treatment for TSS; from VIPs optimal wavelengths using SNV pre-treatment for Total Flavonoid and total Anthocyanin content. Thus, relevant models were proposed using the full spectra, as well as specific windows and wavelengths in order to reduce the data sets and limit the data storage to enable an industrial use.
Published: 2021

6. Trade Shocks, Fertility, and Marital Behavior

Author: Giuntella, Osea, Rotunno, Lorenzo, Stella, Luca, University of Pittsburgh, Department of Economics, Aix-Marseille Sciences Economiques (AMSE), École des hautes études en sciences sociales (EHESS)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt), This project has received funding from the European Research Council (ERC) under the European Union’s Horizon2020 research and innovation programme (grant agreement n. 694262), project DisCont - Discontinuities in Household and Family Formation. Lorenzo Rotunno acknowledges funding received from the French National Research Agency Grants ANR-17-EURE-0020., ANR-17-EURE-0020,AMSE (EUR),Aix-Marseille School of Economics(2017), Lhuillier, Elisabeth, Aix-Marseille School of Economics - - AMSE (EUR)2017 - ANR-17-EURE-0020 - EURE - VALID, and École des hautes études en sciences sociales (EHESS)-Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: History, labor market outcomes, Polymers and Plastics, Industrial and Manufacturing Engineering, JEL: F - International Economics/F.F1 - Trade/F.F1.F16 - Trade and Labor Market Interactions, JEL: J - Labor and Demographic Economics/J.J1 - Demographic Economics/J.J1.J13 - Fertility • Family Planning • Child Care • Children • Youth, 0502 economics and business, ddc:330, 050207 economics, Business and International Management, Marriage, [SHS.ECO] Humanities and Social Sciences/Economics and Finance, marriage, fertility, F14, JEL: F - International Economics/F.F1 - Trade/F.F1.F14 - Empirical Studies of Trade, 05 social sciences, F16, international trade, J13, International Trade, [SHS.ECO]Humanities and Social Sciences/Economics and Finance, Labor Market Outcomes, Fertility, 050902 family studies, 8. Economic growth, 0509 other social sciences
Abstract: Using longitudinal data from the German Socio-Economic Panel, we analyze the effects of exposure to trade on the fertility and marital behavior of German workers. We find that individuals working in sectors that were more affected by import competition from Eastern Europe and suffered worse labor market outcomes were less likely to have children. In contrast, workers in sectors that benefited from increased exports had better employment prospects and higher fertility. These effects are driven by low-educated and married men, and reflect changes in the likelihood of having any child (extensive margin). While among workers exposed to import competition there is evidence of some fertility postponement, we find a significant reduction of completed fertility. There is instead little evidence of any significant effect on marital behavior.
Published: 2021

7. The research output on interventions for the behavioural risk factors alcohol and drug use and dietary risk is not related to their respective burden of ill health in countries at differing World Bank income levels

Author: Meisser Madera, Karen Megranahan, David L. Roberts, Emma Plugge, Maximilian Siebert, Carlo Frassetto, Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt), University of Cartagena, Centre d'Investigation Clinique [Rennes] (CIC), Université de Rennes (UR)-Hôpital Pontchaillou-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Pontchaillou [Rennes], Goldsmiths, University of London (Goldsmiths College), University of London [London], University of Oxford, HAL UR1, Admin, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Hôpital Pontchaillou-Institut National de la Santé et de la Recherche Médicale (INSERM), and University of Oxford [Oxford]
Subjects: Inequality, Alcohol Drinking, Substance-Related Disorders, media_common.quotation_subject, 030231 tropical medicine, Psychological intervention, MEDLINE, Health Promotion, Health Risk Behaviors, 03 medical and health sciences, 0302 clinical medicine, Cost of Illness, Risk Factors, Environmental health, Medicine, Humans, 030212 general & internal medicine, Risk factor, media_common, Research ethics, business.industry, Dietary risk, Health Policy, 1. No poverty, Public Health, Environmental and Occupational Health, Articles, 3. Good health, Diet, [SDV.AEN] Life Sciences [q-bio]/Food and Nutrition, Systematic review, Cross-Sectional Studies, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Income level, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Quality-Adjusted Life Years, business, Alcohol-Related Disorders, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition
Abstract: International audience; BACKGROUND: Alcohol and drug use (AandD) and dietary risks are two increasingly important risk factors. This study examines whether there is a relationship between the burden of these risk factors in countries of specific income bands as defined by the World Bank, and the number of primary studies included in Cochrane Systematic Reviews (CSRs) conducted in those countries.METHODS: Data was extracted from primary studies included in CSRs assessing two risk factors as outcomes. For each risk factor, data was obtained on its overall burden in disability-adjusted life years (DALYs) by World Bank Income Levels and examined for a link between DALYs, the number of primary studies and participants.RESULTS: A total of 1601 studies from 95 CSRs were included. Only 18.3% of the global burden for AandD is in high income-countries (HICs) but they produced 90.5% of primary studies and include 99.5% of participants. Only 14.2% of the dietary risk burden is in HICs but they produced 80.5% of primary studies and included 98.1% of participants.CONCLUSIONS: This study demonstrates the unequal output of research heavily weighted towards HICs. More initiatives with informed contextual understanding are required to address this inequality and promote health research in low and middle-income countries.
Published: 2020

8. Affective, Social, and Informative Gestures Reproduction in Human Interaction: Hyperscanning and Brain Connectivity

Author: Michela Balconi, Angela Bartolo, Giulia Fronda, Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt), Sciences Cognitives et Sciences Affectives (SCALab) - UMR 9193 (SCALab), Université de Lille-Centre National de la Recherche Scientifique (CNRS), and Laboratoire Sciences Cognitives et Sciences Affectives - UMR 9193 (SCALab)
Subjects: Settore M-PSI/02 - PSICOBIOLOGIA E PSICOLOGIA FISIOLOGICA, Cognitive Neuroscience, Biophysics, Experimental and Cognitive Psychology, fNIRS, 050105 experimental psychology, 03 medical and health sciences, [SCCO]Cognitive science, 0302 clinical medicine, Social neuroscience, Human interaction, medicine, Humans, 0501 psychology and cognitive sciences, Orthopedics and Sports Medicine, Valence (psychology), hyperscanning, informative, Brain Mapping, Spectroscopy, Near-Infrared, Gestures, Reproduction, 05 social sciences, Brain, social, Frontal eye fields, Joint action, Dorsolateral prefrontal cortex, medicine.anatomical_structure, Superior frontal gyrus, Psychology, Keywords: affective, 030217 neurology & neurosurgery, Cognitive psychology, Gesture
Abstract: Gestural communication characterizes daily individuals' interactions in order to share information and to modify others' behavior. Social neuroscience has investigated the neural bases which support recognizing of different gestures. The present research, through the use of the hyperscanning approach, that allows the simultaneously recording of the activity of two or more individuals involved in a joint action, aims to investigate the neural bases of gestural communication. Moreover, by using hyperscanning paradigm we explore the inter-brain connectivity between two inter-agents, the one who performed the gesture (encoder) and the one who received it (decoder), with functional Near-infrared Spectroscopy (fNIRS) during the reproduction of affective, social and informative gestures with positive and negative valence. Result showed an increase in oxygenated hemoglobin concentration (O2Hb) and inter-brain connectivity in the dorsolateral prefrontal cortex (DLPFC) for affective gestures, in the superior frontal gyrus (SFG) for social gestures and the frontal eye fields (FEF) for informative gestures, for both encoder and decoder. Furthermore, it emerged that positive gestures activate more the left DLPFC, with an increase in inter-brain connectivity in DLPFC and SFG. The present study revealed the relevant function of the type and valence of gestures in affecting intra- and inter-brain connectivity.
Published: 2020

9. Adherence to Treat-to-target Management in Rheumatoid Arthritis and Associated Factors: Data from the International RA BIODAM Cohort

Author: Marina Backhaus, Ori Elkayam, J. Carter Thorne, Gianfranco Ferraccioli, Paul P. Tak, Mikkel Østergaard, M. Govoni, Joanne Homik, Clifton O. Bingham, Walter P. Maksymowych, Hilde Berner Hammer, Dirkjan van Schaardenburg, Alexandre Sepriano, Maxime Dougados, Joel Paschke, Désirée van der Heijde, Sofia Ramiro, Robert Landewé, Alain Cantagrel, Alain Saraux, Cheryl Barnabe, Oliver FitzGerald, Maggie Larché, Luigi Sinigaglia, E. Hutchings, Maurizio Rossini, Thierry Schaeverbeke, Gerd R Burmester, Bernard Combe, Gilles Boire, R. Dadashova, Leiden University Medical Center (LUMC), Zuyderland Hospital [Heerlen, The Netherlands], St Vincent's University Hospital, Rigshospitalet [Copenhagen], Copenhagen University Hospital, University of Alberta, Tel Aviv Sourasky Medical Center [Te Aviv], The Arthritis Program Research Group, McMaster University [Hamilton, Ontario], Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt), Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], Université de Sherbrooke (UdeS), Département de Rhumatologie[Montpellier], Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Hôpital Lapeyronie, CHU de Bordeaux Pellegrin [Bordeaux], Centre National de Référence CERAINO, Service de Rhumatologie (Hôpital de la Cavale Blanche), Centre Hospitalier Régional Universitaire de Brest (CHRU Brest), Lymphocytes B, Autoimmunité et Immunothérapies (LBAI), Université de Brest (UBO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-LabEX IGO Immunothérapie Grand Ouest, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Institut Brestois Santé Agro Matière (IBSAM), Université de Brest (UBO), Service de rhumatologie [CHU Cochin], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Cochin [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Equipe 4 : ECaMO - Épidémiologie clinique appliquée aux maladies rhumatismales et musculo-squelettiques (CRESS - U1153), Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS (U1153 / UMR_A_1125 / UMR_S_1153)), Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Università degli studi di Verona = University of Verona (UNIVR), Università degli Studi di Ferrara = University of Ferrara (UniFE), Clinica Ortopedica, ASST Centro Specialistico Ortopedico Traumatologico Gaetano Pini-CTO, parent, Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), University of Calgary, Johns Hopkins University School of Medicine [Baltimore], VU University Medical Center [Amsterdam], Diakonhjemmet Hospital, CaRE Arthritis Ltd, Academic Medical Center - Academisch Medisch Centrum [Amsterdam] (AMC), University of Amsterdam [Amsterdam] (UvA), Salvy-Córdoba, Nathalie, Lymphocyte B et Auto-immunité (LBAI), Université de Brest (UBO)-Institut Brestois Santé Agro Matière (IBSAM), Université de Brest (UBO)-Institut National de la Santé et de la Recherche Médicale (INSERM), Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Verona (UNIVR), Università degli Studi di Ferrara (UniFE), Hôpital Pierre-Paul Riquet [Toulouse], CHU Toulouse [Toulouse], Clinical Immunology and Rheumatology, and AII - Inflammatory diseases
Subjects: 0301 basic medicine, medicine.medical_specialty, MESH: Antirheumatic Agents, MESH: Remission Induction, MESH: Rheumatoid Factor, Immunology, Best Treatment Practices, Rheumatoid Arthritis, Severity of Illness Index, Longitudinal model, Gee, NO, Arthritis, Rheumatoid, 03 medical and health sciences, 0302 clinical medicine, Rheumatology, Rheumatoid Factor, Internal medicine, MESH: Severity of Illness Index, medicine, Humans, Immunology and Allergy, Generalized estimating equation, MESH: Treatment Outcome, 030203 arthritis & rheumatology, MESH: Arthritis, Rheumatoid, [SDV.MHEP.RSOA] Life Sciences [q-bio]/Human health and pathology/Rhumatology and musculoskeletal system, MESH: Humans, business.industry, Remission Induction, Protocol Requirement, Baseline model, Treat to target, rheumatoid arthritis, T2T. rheumatology, medicine.disease, T2T. rheumatology, Treatment Outcome, 030104 developmental biology, Rheumatoid Arthritis, Best Treatment Practices, Treat-to-target, [SDV.MHEP.RSOA]Life Sciences [q-bio]/Human health and pathology/Rhumatology and musculoskeletal system, Antirheumatic Agents, Rheumatoid arthritis, Cohort, Tumor Necrosis Factor Inhibitors, Treat-to-Target, MESH: Tumor Necrosis Factor Inhibitors, business
Abstract: Objective.Compelling evidence supports a treat-to-target (T2T) strategy for optimal outcomes in rheumatoid arthritis (RA). There is limited knowledge regarding the factors that impede implementation of T2T, particularly in a setting where adherence to T2T is protocol-specified. We aimed to assess clinical factors that associate with failure to adhere to T2T.Methods.Patients with RA from 10 countries who were starting or changing conventional synthetic disease-modifying antirheumatic drugs and/or starting tumor necrosis factor inhibitors were followed for 2 years. Participating physicians were required per protocol to adhere to the T2T strategy. Factors influencing adherence to T2T low disease activity (T2T-LDA; 44-joint count Disease Activity Score ≤ 2.4) were analyzed in 2 types of binomial generalized estimating equations models: (1) including only baseline features (baseline model); and (2) modeling variables that inherently vary over time as such (longitudinal model).Results.A total of 571 patients were recruited and 439 (76.9%) completed 2-year followup. Failure of adherence to T2T-LDA was noted in 1765 visits (40.5%). In the baseline multivariable model, a high number of comorbidities (OR 1.10, 95% CI 1.02–1.19), smoking (OR 1.32, 95% CI 1.08–1.63) and high number of tender joints (OR 1.03, 95% CI 1.02–1.04) were independently associated with failure to implement T2T, while anticitrullinated protein antibody/rheumatoid factor positivity (OR 0.63, 95% CI 0.50–0.80) was a significant facilitator of T2T. Results were similar in the longitudinal model.Conclusion.Lack of adherence to T2T in the RA BIODAM cohort was evident in a substantial proportion despite being a protocol requirement, and this could be predicted by clinical features. [Rheumatoid Arthritis (RA) BIODAM cohort; ClinicalTrials.gov: NCT01476956].
Published: 2020

10. An in silico structural approach to characterize human and rainbow trout estrogenicity of mycotoxins: Proof of concept study using zearalenone and alternariol

Author: Dellafiora, Luca, Oswald, Isabelle P., Dorne, Jean-Lou, Galaverna, Gianni, Battilani, Paola, Dall'Asta, Chiara, University of Parma = Università degli studi di Parma [Parme, Italie], Biosynthèse & Toxicité des Mycotoxines (ToxAlim-BioToMyc), ToxAlim (ToxAlim), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), European Food Safety Authority (EFSA), and Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt)
Subjects: [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, mycotoxins, [SDV.TOX]Life Sciences [q-bio]/Toxicology, zearalenone, toxicodynamic, [SDV.TOX.TVM]Life Sciences [q-bio]/Toxicology/Vegetal toxicology and mycotoxicology, estrogen receptors, [SDV.TOX.TCA]Life Sciences [q-bio]/Toxicology/Toxicology and food chain, in silico toxicology, alternariol
Abstract: International audience; The mycotoxins zearalenone and alternariol may contaminate food and feed raising toxicological concerns due to their estrogenicity. Inter-species differences in their toxicokinetics and toxicodynamics may occur depending on evolution of taxa-specific traits. As a proof of principle, this manuscript investigates the comparative toxicodynamics of zearalenone, its metabolites (alpha-zearalenol and beta-zearalenol), and alternariol with regards to estrogenicity in humans and rainbow trout. An in silico structural approach based on docking simulation, pharmacophore modeling and molecular dynamics was applied and computational results were analyzed in comparison with available experimental data. The differences of estrogenicity among species of zearalenone and its metabolites have been structurally explained. Also, the low estrogenicity of alternariol in trout has been characterized here for the first time. This approach can provide a powerful tool for the characterization of interspecies differences in mycotoxin toxicity for a range of protein targets and relevant compounds for the food-and feed-safety area.
Published: 2020

11. Soybean aphid biotype 1 genome: Insights into the invasive biology and adaptive evolution of a major agricultural pest

Author: Nick Miller, Richard Hall, Jose A.P. Marcelino, Chiun-Cheng Ko, Deirdre Prischmann-Voldseth, Michela Panini, Ravi Kiran Donthu, Giulia Melchiori, Christina D. DiFonzo, Minh Nguyen, Everett Weber, Curt B. Hill, Brian W. Diers, Anthony Bretaudeau, Alejandra Flores, George E. Heimpel, Toni Gabaldon, John F. Tooker, Jonathan H. Badger, Andrew Aschwanden, Ana Micijevic, Anitha Chirumamilla, Tugrul Giray, Peter Desborough, Rosanna Giordano, Massimo Pessino, Brad S. Coates, Fabrice Legeai, Janet Knodel, David J. Voegtlin, Matthew E. O'Neal, Manuella van Munster, Bruce D Potter, Glen L. Hartman, Christopher J. Fields, Doris Lagos-Kutz, Brian A. Nault, Joon-Ho Lee, Hojun Song, Giuseppe E. Massimino Cocuzza, Aleksey V. Zimin, Felipe N. Soto-Adames, Olga Chiesa, Hugh M. Robertson, Genevieve Labrie, Sijun Liu, Arian Avalos, Eileen Cullen, Bryony C. Bonning, Seunghwan Lee, Mauro Mandrioli, Emanuele Mazzoni, Mark Band, Yongping Huanga, Irene Consuelo Julca Chavez, Kelley J. Tilmon, Kongming Wu, Theresa K. Herman, Lawrence Hon, Andi Nasuddin, Tatsiana Akraiko, Gian Carlo Manicardi, Shuai Zhan, Puerto Rico Science, Know Your Bee Inc, Johns Hopkins University (JHU), Barcelona Institute of Science and Technology (BIST), Barcelona Supercomputing Center - Centro Nacional de Supercomputacion (BSC - CNS), Center for Genomic Regulation (CRG-UPF), CIBER de Epidemiología y Salud Pública (CIBERESP), Institute for Research in Biomedicine [Barcelona, Spain] (IRB), University of Barcelona-Barcelona Institute of Science and Technology (BIST), Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Color Genomics, Pacific Biosciences [Menlo Park], Pacific Biosciences of California, National Cancer Institute [Bethesda] (NCI-NIH), National Institutes of Health [Bethesda] (NIH), Columbia University Irving Medical Center (CUIMC), University of Illinois at Urbana-Champaign [Urbana], University of Illinois System, Southwest Research and Outreach Center [Lamberton], University of Minnesota [Twin Cities] (UMN), University of Minnesota System-University of Minnesota System, University of Puerto Rico (UPR), University of Florida [Gainesville] (UF), Agricen Sciences, USDA-ARS : Agricultural Research Service, Pennsylvania State University (Penn State), Penn State System, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt), North Dakota State University (NDSU), Iowa State University (ISU), University of Catania [Italy], University of Wisconsin - Milwaukee, New South Wales Department of Primary Industries (NSW DPI), Michigan State University [East Lansing], Michigan State University System, University of Minnesota [Morris], University of Minnesota System, Chinese Academy of Sciences [Beijing] (CAS), National Taiwan University [Taiwan] (NTU), Centre de Recherche sur les Grains [Québec] (CEROM), United States Department of Agriculture (USDA), Seoul National University [Seoul] (SNU), University of Haifa [Haifa], Università degli Studi di Modena e Reggio Emilia = University of Modena and Reggio Emilia (UNIMORE), Università cattolica del Sacro Cuore [Milano] (Unicatt), South Dakota State University (SDSTATE), Illinois Institute of Technology (IIT), Hasanuddin University (Unhas), Cornell AgriTech, College of Agriculture and Life Sciences [Cornell University] (CALS), Cornell University [New York]-Cornell University [New York], Department of Entomology [CALS], Texas A&M University [College Station], Ohio State University [Columbus] (OSU), Chinese Academy of Agricultural Sciences (CAAS), United Soybean Board, Agricultural Research Service, 432114, Integrated Management of Soybean Pathogens and Pests, 2018-67015-28199, USDA NIFA, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Innovation et Développement dans l'Agriculture et l'Alimentation (UMR Innovation), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Scalable, Optimized and Parallel Algorithms for Genomics (GenScale), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Università degli Studi di Modena e Reggio Emilia, and Cornell University [New York]
Subjects: 0106 biological sciences, Pesticide resistance, Population genetics, [SDV]Life Sciences [q-bio], Genome, Insect, Adaptation, Biological, Zoology, SNP, Phylome, Polymorphism, Single Nucleotide, 01 natural sciences, Biochemistry, 03 medical and health sciences, Animals, Polymorphism, Adaptation, Soybean aphid, Biotype 1, Molecular Biology, Rhamnus cathartica, Aphid, Alleles, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Ecotype, 0303 health sciences, Genome, biology, food and beverages, Aphididae, Single Nucleotide, Biological, biology.organism_classification, Biological Evolution, Hemiptera, United States, 010602 entomology, Settore AGR/11 - ENTOMOLOGIA GENERALE E APPLICATA, Aphids, Insect Science, PEST analysis, Aphis glycines, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Introduced Species, Insect
Abstract: International audience; The soybean aphid, Aphis glycines Matsumura (Hemiptera: Aphididae) is a serious pest of the soybean plant, Glycine max, a major world-wide agricultural crop. We assembled a de novo genome sequence of Ap. glycines Biotype 1, from a culture established shortly after this species invaded North America. 20.4% of the Ap. glycines proteome is duplicated. These in-paralogs are enriched with Gene Ontology (GO) categories mostly related to apoptosis, a possible adaptation to plant chemistry and other environmental stressors. Approximately one-third of these genes show parallel duplication in other aphids. But Ap. gossypii, its closest related species, has the lowest number of these duplicated genes. An Illumina GoldenGate assay of 2380 SNPs was used to determine the world-wide population structure of Ap. Glycines. China and South Korean aphids are the closest to those in North America. China is the likely origin of other Asian aphid populations. The most distantly related aphids to those in North America are from Australia. The diversity of Ap. glycines in North America has decreased over time since its arrival. The genetic diversity of Ap. glycines North American population sampled shortly after its first detection in 2001 up to 2012 does not appear to correlate with geography. However, aphids collected on soybean Rag experimental varieties in Minnesota (MN), Iowa (IA), and Wisconsin (WI), closer to high density Rhamnus cathartica stands, appear to have higher capacity to colonize resistant soybean plants than aphids sampled in Ohio (OH), North Dakota (ND), and South Dakota (SD). Samples from the former states have SNP alleles with high FST values and frequencies, that overlap with genes involved in iron metabolism, a crucial metabolic pathway that may be affected by the Rag-associated soybean plant response. The Ap. glycines Biotype 1 genome will provide needed information for future analyses of mechanisms of aphid virulence and pesticide resistance as well as facilitate comparative analyses between aphids with differing natural history and host plant range.
Published: 2020

12. An in silico structural approach to characterize human and rainbow trout estrogenicity of mycotoxins: Proof of concept study using zearalenone and alternariol

Author: Gianni Galaverna, Isabelle P. Oswald, Paola Battilani, Jean-Lou Dorne, Chiara Dall'Asta, Luca Dellafiora, University of Parma = Università degli studi di Parma [Parme, Italie], ToxAlim (ToxAlim), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), European Food Safety Authority (EFSA), and Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt)
Subjects: Toxicodynamics, Estrone, In silico, Alternariol, toxicodynamic, Estrogen receptors, In silico toxicology, Mycotoxins, Toxicodynamic, Zearalenone, Computational biology, in silico toxicology, Proof of Concept Study, 01 natural sciences, alternariol, Analytical Chemistry, Lactones, chemistry.chemical_compound, 0404 agricultural biotechnology, mycotoxins, Animals, Humans, Computer Simulation, Mycotoxin, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Molecular Structure, biology, 010401 analytical chemistry, zearalenone, estrogen receptors, 04 agricultural and veterinary sciences, General Medicine, biology.organism_classification, 040401 food science, 0104 chemical sciences, Trout, chemistry, Oncorhynchus mykiss, [SDV.TOX]Life Sciences [q-bio]/Toxicology, Rainbow trout, Pharmacophore, Settore AGR/12 - PATOLOGIA VEGETALE, Food Science
Abstract: International audience; The mycotoxins zearalenone and alternariol may contaminate food and feed raising toxicological concerns due to their estrogenicity. Inter-species differences in their toxicokinetics and toxicodynamics may occur depending on evolution of taxa-specific traits. As a proof of principle, this manuscript investigates the comparative toxicodynamics of zearalenone, its metabolites (alpha-zearalenol and beta-zearalenol), and alternariol with regards to estrogenicity in humans and rainbow trout. An in silico structural approach based on docking simulations, pharmacophore modeling and molecular dynamics was applied and computational results were analyzed in comparison with available experimental data. The differences of estrogenicity among species of zearalenone and its metabolites have been structurally explained. Also, the low estrogenicity of alternariol in trout has been characterized here for the first time. This approach can provide a powerful tool for the characterization of interspecies differences in mycotoxin toxicity for a range of protein targets and relevant compounds for the food- and feed-safety area.
Published: 2020

13. Les couverts végétaux. Un atout majeur pour réduire les intrants de synthèse et augmenter les services écosystémiques au vignoble

Author: Pierre Antoine Noceto, Hériché, Mathilde, Jérôme Fromentin, Vittorio Rossi, Sasa Sirca, Aurora Ranca, Patrik Kehrli, Josep Armengol, Sophie TROUVELOT, Diederik van Tuinen, Pierre-Emmanuel Courty, Daniel Wipf, EL Mjiyad, Noureddine, Agroécologie [Dijon], Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt), Plant Protection Department, Agricultural Institute of Slovenia – Ljubljana – Slovénie, SCDVV Murfatlar – Murfatlar – Constanta – Roumanie, Agroscope, Instituto Agroforestal Mediterráneo (IAM) – Universitat Politècnica de València (UPV) – Valencia – Espagne, Plant Protection Department, Agricultural Institute of Slovenia – Ljubljana – Slovénie., and Instituto Agroforestal Mediterráneo (IAM) – Universitat Politècnica de València (UPV) – Valencia – Espagne.
Subjects: [SDE] Environmental Sciences, enherbement, plantes de couvert, couvert vegetaux, écosysteme, legumineuses, [SDE]Environmental Sciences, graminees, defenses mycorhyzes, brassicacees, biovine, champignons mycorhiziens a arbuscules, controle des pathogenes
Abstract: International audience; De manière générale, un couvert végétal se définit par une espèce ou une communauté d’espèces végétales recouvrant le sol de manière permanente ou temporaire. L’agriculteur a la possibilité de semer ces couverts, selon un choix raisonné, ou bien de laisser la végétation spontanée se développer. Il existe 3 types de couverts semés avec des objectifs différents pour l’exploitant : le couvert hivernal, installé pour faire face au phénomène d’érosion du sol important pendant cette période de repos végétatif ; les engrais verts, installés avec l’objectif d’amender naturellement la parcelle, en détruisant et en enfouissant les résidus du couvert qui libèrent ainsi de la matière organique plus ou moins rapidement, qui servira à alimenter la plante au cycle suivant, après des étapes de minéralisation ; les cultures intermédiaires pièges à nitrate (CIPAN), installées au tout début de l’automne pour capter dans le sol les nitrates en excès et des quantités d’eau importantes dans le but de limiter la lixiviation et la contamination des eaux souterraines et de surfaces par les nitrates.Les couverts et leurs intérêts en production végétaleLes espèces végétales les plus couramment utilisées dans ces couverts font essentiellement partie de trois familles présentant chacune différents avantages quant à leur utilisation. Nous retrouvons : les graminées (avoine, seigle, ray grass, brome, fétuque, orge…), avantageuses avec un rapport C/N élevé, produisent une biomasse (figure 1) importante bénéfique lors de la destruction ; les brassicacées (anciennement « crucifères ») (moutarde, navette fourragère, radis chinois, colza fourrager…) servent couramment de « pompe à azote » mais aussi de biofumigateur (figure 1), ce qui peut avoir un impact négatif sur certains champignons bénéfiques du sol (champignons mycorhiziens) si la proportion est trop importante. Elles présentent l’avantage de s’implanter rapidement, empêchant le développement important des adventices (appelées également fréquemment mauvaises herbes) ; les légumineuses (vesce, féverole, trèfle, luzerne…) sont de plus en plus utilisées, seules ou en mélange, pour leur capacité à réaliser une symbiose avec des bactéries du sol, leur permettant ainsi de fixer le diazote atmosphérique. Avec un rapport C/N alors très faible, le relargage de l’azote assimilé et des nutriments se fait très rapidement, et ceux-ci deviennent donc disponibles pour la culture.Les plantes de couvert sont fortement plébiscitées en polyculture pour couvrir les parcelles lorsqu’elles ne sont pas utilisées par une culture d’intérêt. L’utilisation de ces couverts d’interculture s’est développée notamment pour contrer des phénomènes de battance et d’érosion des sols, qualifiés d’anthropogènes car liés à l’exploitation, parfois intensive, des milieux agricoles et à la destruction de la couverture végétale naturelle.
Published: 2020

14. Sam68 binds Alu-rich introns in SMN and promotes pre-mRNA circularization

Author: Claudio Sette, Pierre de la Grange, Vittoria Pagliarini, Valentina Di Rosa, Pamela Bielli, Ariane Jolly, Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt), Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), Centre d'investigation clinique Biothérapie [CHU Pitié-Salpêtrière] (CIC-BTi), Centre d'investigation clinique pluridisciplinaire [CHU Pitié Salpêtrière] (CIC-P 1421), Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Fondazione Santa Lucia [IRCCS], Clinical and Behavioral Neurology [IRCCS Santa Lucia], Gestionnaire, Hal Sorbonne Université, Fondazione 'Policlinico Universitario A. Gemelli' [Rome], CIC Pitié BT, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)
Subjects: animal diseases, SAM68, SMN1, Biology, Muscular Atrophy, Spinal, Mice, 03 medical and health sciences, 0302 clinical medicine, Alu Elements, Circular RNA, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], RNA Precursors, Genetics, Animals, Humans, Gene, Adaptor Proteins, Signal Transducing, 030304 developmental biology, Settore BIO/16 - ANATOMIA UMANA, 0303 health sciences, Settore BIO/16, Binding Sites, Gene regulation, Chromatin and Epigenetics, Intron, RNA-Binding Proteins, RNA, SMN Complex Proteins, Exons, RNA, Circular, Survival of Motor Neuron 1 Protein, Introns, Cell biology, nervous system diseases, DNA-Binding Proteins, Survival of Motor Neuron 2 Protein, Alternative Splicing, nervous system, 030220 oncology & carcinogenesis, RNA splicing, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Human genome, Precursor mRNA
Abstract: The Spinal Muscular Atrophy (SMA) gene SMN wasrecently duplicated (SMN1 and SMN2) in higher primates.Furthermore, invasion of the locus by repetitiveelements almost doubled its size with respectto mouse Smn, in spite of an almost identicalprotein-coding sequence. Herein, we found that SMNranks among the human genes with highest densityof Alus, which are evolutionary conserved inprimates and often occur in inverted orientation. Invertedrepeat Alus (IRAlus) negatively regulate splicingof long introns within SMN, while promotingwidespread alternative circular RNA (circRNA) biogenesis.Bioinformatics analyses revealed the presenceof ultra-conserved Sam68 binding sites in SMNIRAlus. Cross-link-immunoprecipitation (CLIP), mutagenesisand silencing experiments showed thatSam68 binds in proximity of intronic Alus in theSMN pre-mRNA, thus favouring circRNA biogenesisin vitro and in vivo. These findings highlight a novellayer of regulation in SMN expression, uncover thecrucial impact exerted by IRAlus and reveal a role forSam68 in SMN circRNA biogenesis.
Published: 2020

15. β-Lactam Exposure Triggers Reactive Oxygen Species Formation in Enterococcus faecalis via the Respiratory Chain Component DMK

Author: Loïc Léger, Aurélie Budin-Verneuil, Margherita Cacaci, Abdellah Benachour, Axel Hartke, Nicolas Verneuil, Unité de Recherche Risques Microbiens (U2RM), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Istituto di Microbiologia - Institute of Microbiology [Rome], Università Cattolica del S. Cuore - Catholic University of the Sacred Hearth, Laboratoire de Microbiologie de l’Environnement (LME), Institut National de la Recherche Agronomique (INRA)-Université de Caen Normandie (UNICAEN), Normandie Université (NU), and Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt)
Subjects: Oxidative Stress, lcsh:Biology (General), [SDV]Life Sciences [q-bio], Enterococcus faecalis, Escherichia coli, Amoxicillin, Vitamin K 2, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Reactive Oxygen Species, beta-Lactams, lcsh:QH301-705.5, ComputingMilieux_MISCELLANEOUS
Abstract: Summary: Whereas the primary actions of β-lactams are well characterized, their downstream effects are less well understood. Although their targets are extracellular, β-lactams stimulate respiration in Escherichia coli leading to increased intracellular accumulation of reactive oxygen species (ROS). Here, we show that β-lactams over a large concentration range trigger a strong increase in ROS production in Enterococcus faecalis under aerobic, but not anaerobic, conditions. Both amoxicillin, to which the bacterium is susceptible, and cefotaxime, to which E. faecalis is resistant, triggers this response. This stimulation of ROS formation depends mainly on demethylmenaquinone (DMK), a component of the E. faecalis respiratory chain, but in contrast to E. coli is observed only in the absence of respiration. Our results suggest that in E. faecalis, β-lactams increase electron flux through the respiratory chain, thereby stimulating the auto-oxidation of reduced DMK in the absence of respiration, which triggers increased extracellular ROS production. : Léger et al. show that β-lactams treatment enhances superoxide and hydrogen peroxide production in Enterococcus faecalis in a mainly demethylmenaquinone (DMK)-dependent process. In the absence of respiration, the antibiotics trigger the accumulation of the reduced form of DMK, a respiratory chain component, which increases the adventitious reactivity with oxygen. Keywords: Enterococcus, β-lactams, oxidative stress, ROS, respiratory chain
Published: 2019

16. VarGoats international initiative, a 1000 goat genomes project

Author: Colli, Licia, Crepaldi, Paola, Ajmone-Marsan, Paolo, Stella, Alessandra, Tosser-Klopp, Gwenola, Consortium Vargoats, ., Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti (DiANA), Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt), Research Center on Biodiversity and Ancient DNA [Piacenza] (BioDNA), Dipartimento di Medicina Veterinaria (DIMEVET), Università degli Studi di Milano [Milano] (UNIMI), Consiglio Nazionale delle Ricerche [Milano] (CNR), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, and TOSSER-KLOPP, GWENOLA
Subjects: [SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio]
Abstract: International audience; Goats were domesticated ~10,000 years ago from their bezoar wild ancestor Capra aegagrus. These founder animals spread out from domestication centres in Europe, Asia, and Africa during the next few thousand years, which resulted in many populations becoming locally adapted to diverse environmental constraints such as heat, altitude, disease resistance, etc. After a very long period of soft selection for production traits, the situation changed dramatically with the emergence of the breed concept about 200 years ago. Selection pressure was strongly increased, and gene flow between populations (or newly formed breeds) was seriously reduced, leading to the fragmentation of the initial gene pool. Currently, there are more than 1000 goat breeds worldwide, 18% of which are either threatened or already extinct. Through the generation of domestic breeds sequence data and their analysis together with existing data of domestic and wild animals, VarGoats collaborative project aims at becoming the first step of a 1000 goat genomes project. VarGoats Consortium is coordinated by the Institut National de la Recherche Agronomique INRA (France), and includes an international team of partners
Published: 2019

17. Modeling from functioning of a grape berry to the whole plant

Author: Dai, Zhanwu, CHEN, Jinliang, Zhu, Junqi, GENARD, Michel, Beauvoit, Bertrand, PONI, Stefano, GAMBETTA, Gregory, Vivin, Philippe, Ollat, Nathalie, Delrot, Serge, GOMES, Eric, Gibon, Yves, Admin, Oskar, Ecophysiologie et Génomique Fonctionnelle de la Vigne (UMR EGFV), Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Unité de recherche Plantes et Systèmes de Culture Horticoles (PSH), Institut National de la Recherche Agronomique (INRA), Biologie du fruit et pathologie (BFP), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt), and GiESCO
Subjects: berry quality, Vitis vinifera, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, modeling, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, ComputingMilieux_MISCELLANEOUS, Environmental adaptation
Abstract: International audience
Published: 2019

18. Convergent genomic signatures of domestication in sheep and goats

Author: Alberto, Florian J., Boyer, Frédéric, Orozco-terWengel, Pablo, Streeter, Ian, Servin, Bertrand, de Villemereuil, Pierre, Benjelloun, Badr, Librado, Pablo, Biscarini, Filippo, Colli, Licia, Barbato, Mario, Zamani, Wahid, Alberti, Adriana, Engelen, Stefan, Stella, Alessandra, Joost, Stéphane, Ajmone-Marsan, Paolo, Negrini, Riccardo, Orlando, Ludovic, Rezaei, Hamid Reza, Naderi, Saeid, Clarke, Laura, Flicek, Paul, Wincker, Patrick, Coissac, Eric, Kijas, James, Tosser-Klopp, Gwenola, Chikhi, Abdelkader, Bruford, Michael W., Taberlet, Pierre, Pompanon, François, Laboratoire d'Ecologie Alpine (LECA), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA), School of Biosciences [Cardiff], Cardiff University, European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), PTP Science Park, Institute of Zootechnics [Piacenza], Università Cattolica del S. Cuore - Catholic University of the Sacred Hearth, Department of Environmental Sciences [Tarbiat], Faculty of Natural Resources and Marine Sciences [Tarbiat], Tarbiat Modaras University-Tarbiat Modaras University, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratory of Geographical Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Research Center on Biodiversity and Ancient DNA [Piacenza] (BioDNA), Environmental Sciences Department [Gorgan], Gorgan University of Agricultural Sciences and Natural Resources, Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), CSIRO Agriculture Flagship, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Institut national de la recherche agronomique [Maroc] (INRA Maroc), ANR-14-JFAC-0002,ClimGen,Climate Genomics for farm animal adaptation(2014), ANR10 LABX56,ANR10 LABX56, European Project: 244356,EC:FP7:KBBE,FP7-KBBE-2009-3,NEXTGEN(2010), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt), Tarbiat Modares University [Tehran]-Tarbiat Modares University [Tehran], Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), FACCE ERA-NET Plus project CLIMGEN ANR-14-JFAC-0002-01 / LabEx OSUG (Investissements d'avenir) ANR10LABX56 / Wellcome Trust WT108749/Z/15/Z, ANR-10-LABX-0056,OSUG@2020,Innovative strategies for observing and modelling natural systems(2010), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)
Subjects: sheep, Science, [SDV]Life Sciences [q-bio], selection signature, selection, Article, domestication, evolution, genomics, Animals, dna-sequencing data, animal domestication, population history, analysis toolkit, gene, discovery, reveals, association, Selection, Genetic, lcsh:Science, Phylogeny, Sheep, Domestic, Genome, Settore AGR/17 - ZOOTECNICA GENERALE E MIGLIORAMENTO GENETICO, Whole Genome Sequencing, Goats, goat, evolutionary basis of domestication, Genetic Variation, Biological Evolution, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Phenotype, Haplotypes, Animals, Domestic, lcsh:Q
Abstract: The evolutionary basis of domestication has been a longstanding question and its genetic architecture is becoming more tractable as more domestic species become genome-enabled. Before becoming established worldwide, sheep and goats were domesticated in the fertile crescent 10,500 years before present (YBP) where their wild relatives remain. Here we sequence the genomes of wild Asiatic mouflon and Bezoar ibex in the sheep and goat domestication center and compare their genomes with that of domestics from local, traditional, and improved breeds. Among the genomic regions carrying selective sweeps differentiating domestic breeds from wild populations, which are associated among others to genes involved in nervous system, immunity and productivity traits, 20 are common to Capra and Ovis. The patterns of selection vary between species, suggesting that while common targets of selection related to domestication and improvement exist, different solutions have arisen to achieve similar phenotypic end-points within these closely related livestock species., The sheep and goat were domesticated ~10,500 years ago in the same region of the Middle-East. Here, Alberto et al compare the genomes of wild Asiatic mouflon and Bezoar ibex with that of domestics from local, traditional and improved breeds and find common targets of selection related to domestication and improvement in sheep and goats.
Published: 2018

19. From Privacy to Algorithms’ Fairness

Author: Mariachiara Tallacchini, Chiara Sabelli, Chercheur indépendant, Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt), Marit Hansen, Eleni Kosta, Igor Nai-Fovino, Simone Fischer-Hübner, TC 9, TC 11, WG 9.2, WG 9.5, WG 9.6, WG 11.7, and WG 11.6
Subjects: Fairness, Equal opportunities, Cover (telecommunications), Big data, Space (commercial competition), 01 natural sciences, Economic Justice, 010104 statistics & probability, 03 medical and health sciences, 0302 clinical medicine, Political science, media_common.cataloged_instance, [INFO]Computer Science [cs], Settore IUS/20 - FILOSOFIA DEL DIRITTO, 0101 mathematics, European union, media_common, Ethics, business.industry, 16. Peace & justice, Models of justice, Equal opportunity, Privacy, Normative, Construct (philosophy), business, Algorithm, Law, Algorithms, 030217 neurology & neurosurgery
Abstract: Part 3: Privacy in the Era of the Smart Revolution; International audience; This article aims to show how the legal and ethical debate – as far as ethics has become an indispensable complementary normative tool within legal frameworks – on the digital world in the United States (US) and the European Union (EU) has significantly opened up to include new dimensions other than privacy, particularly in connection with machine learning algorithms and Big Data. If privacy still remains the main interpretive construct to normatively forge the digital space, increasingly issues of discrimination, equal opportunity, fairness and, more broadly, models of justice, are entering the picture. While offering some examples of the inadequacy of privacy to cover new normative concerns related to Big Data and machine learning, the article also argues that attempts to grant algorithmic fairness represent just the first step in addressing the wider question about what models of digital justice we are willing to apply.
Published: 2018

20. Rare coding variants in PLCG2, ABI3, and TREM2 implicate microglial-mediated innate immunity in Alzheimer's disease

Author: John Hardy, Nick C. Fox, Lena Lilius, Christine Van Broeckhoven, Mindy J. Katz, Carlos Cruchaga, Joshua W. Miller, Carol Brayne, Letizia Concari, Christopher Shaw, Minerva M. Carrasquillo, Richard Mayeux, Anne Boland, Charles DeCarli, Helena C. Chui, Laura B. Cantwell, Yoland Aladro Benito, Chuang Kuo Wu, Elaine R. Peskind, Andrew McDavid, M. Ilyas Kamboh, Amanda Smith, Pascual Sánchez-Juan, Jean-François Deleuze, Jayanadra J. Himali, Thomas H. Mosley, Thomas J. Montine, Chuanhai Cao, Andreas J. Forstner, Thomas G. Beach, Robert Barber, Miquel Aguilar, Liming Qu, Jerome I. Rotter, Matthew J. Huentelman, Christiane Reitz, Christopher J. O'Donnell, Steven G. Younkin, Bradley T. Hyman, Bruce L. Miller, Rachelle S. Doody, Eric B. Larson, Ronald L. Hamilton, Todd E. Golde, Steven E. Arnold, Melissa E. Garcia, Rachel Raybould, Lena Kilander, Mark A. Sager, Kevin Morgan, Kathryn L. Lunetta, William Perry, Joseph D. Buxbaum, Craig S. Atwood, Thomas D. Bird, Michael Conlon O'Donovan, Robert Olaso, Juan Fortea, Susanne Moebus, Lisa L. Barnes, Rachel Marshall, Huntington Potter, Mercè Boada, Shahzad Ahmad, Paolo Caffarra, Daniel C. Marson, Jonathan L. Haines, Perrie M. Adams, John M Olichney, Lars Lannfelt, Stefanie Heilmann-Heimbach, Markus M. Nöthen, Shubhabrata Mukherjee, John Malamon, Xue Wang, Christopher S. Carlson, Karen Ritchie, Roger N. Rosenberg, Paul K. Crane, Alexa S. Beiser, Céline Bellenguez, Robert C. Green, Maria Urbano, Petra Proitsi, John Powell, Elisa Majounie, Ammar Al-Chalabi, Hakon Hakonarson, Yogen Patel, Martin Scherer, Julie Williams, Richard B. Lipton, Vincent Dermecourt, Adam L. Boxer, Gerard D. Schellenberg, David G. Clark, Anita L. DeStefano, Joel H. Kramer, Victoria Alvarez, Nandini Badarinarayan, Oscar L. Lopez, Chris Corcoran, Ubaldo Bonuccelli, Donald R. Royall, James Bowen, Monica Diez Fairen, Tricia A. Thornton-Wells, Nilufer Ertekin-Taner, Florence Pasquier, Martin Ingelsson, Yi Zhao, John R. Gilbert, Valentina Escott-Price, Amanda B. Kuzma, Fabienne Garzia, Reinhard Heun, Otto Valladares, Andrew J. Saykin, Sara Ortega-Cubero, Liana G. Apostolova, Henry L. Paulson, John K Kauwe, Imelda Barber, Carolina Ceballos Diaz, Douglas Galasko, M. Arfan Ikram, Lluís Tárraga, Carlo Caltagirone, Joan S. Reisch, Wolfgang Maier, Bruno Vellas, Rebecca Sims, Angela Hodges, Matthew P. Frosch, Isabel Henández, Annakaisa Haapasalo, Thor Aspelund, Håkan Thonberg, Aimee Pierce, Roger L. Albin, Wayne W. Poon, Rebecca Sussams, Amy Braddel, Ranjan Duara, Albert V. Smith, Kirk C. Wilhelmsen, Gianfranco Spalletta, Simon Lovestone, Peter Passmore, Ana Frank-García, Cynthia M. Carlsson, Jade Chapman, Nathan D. Price, Philip L. De Jager, John M. Ringman, Seung Hoan Choi, Nicola Denning, Michael John Owen, Clinton T. Baldwin, Amalia C. Bruni, Denis A. Evans, Rudolph E. Tanzi, Dominique Campion, Laura Fratiglioni, Alberto Lleó, Per Hoffmann, Carole Dufouil, Charlotte Forsell, Alun Meggy, Charlene Thomas, Robert S. Stern, James B. Leverenz, Tatiana Foroud, William W. Seeley, James J. Lah, Brian A. Lawlor, Kenneth B. Fallon, Matthias Riemenschneider, Ryan M. Huebinger, Regina M. Carney, Clinton B. Wright, Didier Hannequin, Deborah Blacker, Anne Kinhult-Ståhlbom, Ekaterina Rogaeva, Andrew P. Lieberman, Bernardino Ghetti, Linda J. Van Eldik, Bernadette McGuinness, Thomas Fairchild, Margaret A. Pericak-Vance, Ashok Raj, Reinhold Schmidt, Ronald C. Petersen, Harald Hampel, María J. Bullido, Steven L. Carroll, Maria Candida Deniz Naranjo, Kathleen A. Welsh-Bohmer, Myriam Fornage, Joseph F. Quinn, Caroline Graff, Claudia L. Satizabal, Patrice L. Whitehead, David Wallon, Christopher Medway, Lindsay A. Farrer, Vilmundur Gudnason, Peter St George-Hyslop, Pau Pastor, Frank Jessen, Erin L. Abner, Johanna Jakobsdottir, Hieab H.H. Adams, Roberta Cecchetti, Walter A. Kukull, Thomas S. Wingo, Michelle K. Lupton, Valur Emilsson, Susan M. McCurry, Simon Mead, Hilkka Soininen, Sandra Weintraub, Amy Gerrish, Lindy E. Harrell, Lina Keller, Jean-Charles Lambert, Denise Harold, Stephen Todd, Wei Gu, Maura Gallo, Najaf Amin, Lenore J. Launer, Eleonora Sacchinelli, Mikko Hiltunen, Cécile Dulary, Eliecer Coto, Xueqiu Jian, Nathalie Fievet, Patrizia Mecocci, Sarah Taylor, Eric Boerwinkle, Maria Serpente, Ronald G. Munger, Ina Giegling, Carlo Masullo, Aoibhinn Lynch, Eliezer Masliah, Anne M. Koivisto, Chang En Yu, Qiong Yang, Benedetta Nacmias, Wayne C. McCormick, Kristelle Brown, Alessio Squassina, Deborah C. Mash, Brian W. Kunkle, Makrina Daniilidou, Alison Goate, David Carrell, Kara L. Hamilton-Nelson, Sandra Barral, Vincent Chouraki, Kristel Sleegers, Frank J. Wolters, Joseph E. Parisi, Iwona Kłoszewska, Ronald C. Kim, Sonia Moreno-Grau, Marina Arcaro, Carmen Muñoz Fernadez, Vernon S. Pankratz, Duane Beekly, Sabrina Pichler, Gislain Septier, Delphine Bacq, Amanda J. Myers, Adam C. Naj, Frank Martiniuk, Sudha Seshadri, Badri N. Vardarajan, Joshua A. Sonnen, M.-Marsel Mesulam, Howard J. Rosen, James T. Becker, Chiara Fenoglio, Ge Li, Alberto Pilotto, Mary Sano, Olivier Hanon, Honghuang Lin, Jean Paul G. Vonsattel, W. T. Longstreth, Daniela Galimberti, David C. Rubinsztein, RoseMarie Brundin, Vilmantas Giedraitis, Christine M. Hulette, Peter Holmans, Martin Dichgans, Maria Vronskaya, Céline Derbois, Michelangelo Mancuso, Constantine G. Lyketsos, Christophe Tzourio, Jacques Epelbaum, Raffaele Maletta, Mariet Allen, Hong-Dong Li, James R. Burke, Rik Vandenberghe, David G. Mann, Bruce M. Psaty, Lawrence S. Honig, Beth A. Dombroski, Erik D. Roberson, Cornelia M. van Duijn, Benjamin Grenier-Boley, Seppo Helisalmi, Jean-François Dartigues, Russell H. Swerdlow, Paola Bossù, Ashley R. Winslow, Elio Scarpini, Lesley Jones, Sebastien Engelborghs, John Q. Trojanowski, Jeffrey Kaye, Jenny Lord, Chiara Cupidi, Janet A. Johnston, Dan Rujescu, Feroze Golamaully, Anne Braae, Rafael Blesa, L. Adrienne Cupples, Dennis W. Dickson, Gail P. Jarvik, David W. Fardo, David H. Cribbs, Michael Gill, Jose Bras, Allan I. Levey, Jennifer Williamson, Rhodri Thomas, John C. Morris, Lei Yu, Debby W. Tsuang, Annette M. Hartmann, John H. Growdon, John Collinge, Claudine Berr, Fernando Rivadeneira, Oliver Peters, Albert Hofman, Frank M. LaFerla, Vivianna M. Van Deerlin, James Uphill, David A. Bennett, Onofre Combarros, Gudny Eiriksdottir, Jeremy D. Burgess, Melanie L. Dunstan, Elizabeth Crocco, Keeley J. Brookes, Robert R. Graham, Lon S. Schneider, Eden R. Martin, Matt Hill, Neill R. Graff-Radford, Joseph T. Hughes, Vincenzo Solfrizzi, Taniesha Morgan, Antonio Ciaramella, Bruno Dubois, Juan C. Troncoso, Paolo Bosco, Jordi Clarimón, Daniel H. Geschwind, Virginia Boccardi, Barry Reisberg, Timothy W. Behrens, Annette L. Fitzpatrick, Salvatore Spina, Alexis Brice, Eileen H. Bigio, Marla Gearing, Jeffrey M. Burns, Carol A. Miller, Marilyn S. Albert, Sven J. van der Lee, Sandro Sorbi, C. Dirk Keene, Daniel Levy, Antonio Daniele, Eric M. Reiman, Paramita Chakrabarty, Oscar Sotolongo-Grau, Helena Schmidt, Francesco Panza, Murray A. Raskind, Rita Guerreiro, Gyungah Jun, Anna Karydas, Markus Leber, Harry V. Vinters, Cory C. Funk, Charles C. White, Jill R. Murrell, Sid E. O'Bryant, Nigel J. Cairns, Josée Dupuis, Ann C. McKee, Julie A. Schneider, Megan L. Grove, Malcolm B. Dick, Bradley F. Boeve, Jennifer A. Brody, Sanjay Asthana, Agustín Ruiz, Stefan Herms, Yuning Chen, David Craig, Neil W. Kowall, Maria Donata Orfei, JoAnn T. Tschanz, Florentino Sanchez Garcia, Manuel Mayhaus, Alfredo Ramirez, James Turton, André G. Uitterlinden, Davide Seripa, Lee-Way Jin, Kelley Faber, Maria C. Norton, Shuo Li, Steven H. Ferris, Steffi G. Riedel-Heller, Joshua C. Bis, Li-San Wang, Johannes Kornhuber, Peter Paul De Deyn, Martin R. Farlow, Randall L. Woltjer, Gary W. Beecham, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Erasmus University Medical Center [Rotterdam] (Erasmus MC), Hospital of the University of Pennsylvania (HUP), Perelman School of Medicine, University of Pennsylvania [Philadelphia]-University of Pennsylvania [Philadelphia], Facteurs de Risque et Déterminants Moléculaires des Maladies liées au Vieillissement - U 1167 (RID-AGE), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Icelandic Heart Association [Kopavogur, Iceland] (IHA), John P. Hussman Institute for Human Genomics [Miami, FL, USA], University of Miami [Coral Gables], Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Department of Medicine, University of Washington [Seattle], Dr. John T. Macdonald Foundation [Miami, FL, USA] (Department of Human Genetics), Epidémiologie des maladies chroniques : impact des interactions gène environnement sur la santé des populations, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille, Droit et Santé, Department of Genomics [Bonn, Germany] (Institute of Human Genetics), University of Bonn-Institute of Human Genetics [Bonn, Germany], Department of Molecular Genetics, Institut Català de Neurociències Aplicades [Barcelona, Spain], Well Advanced Solutions, Centre National de Génotypage (CNG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Translational Centre for Regenerative Medicine (TRM), Department of Cell Therapy, Universität Leipzig [Leipzig]-Universität Leipzig [Leipzig], The University of Texas Health Science Center at Houston (UTHealth), Columbia University [New York], University of Eastern Finland, Life & Brain Center - Department of Genomics, Rheinische Friedrich-Wilhelms-Universität Bonn, Génétique, Reproduction et Développement (GReD), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Santé et de la Recherche Médicale (INSERM), John P. Hussman Institute for Human Genomics, Neurobiologie de la Croissance et de la Senescence, Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Emmy Noether Project (SFB 833), Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Boston University [Boston] (BU), Department of Genomics, Institute for Systems Biology [Seattle, WA, USA], Universitätsklinikum Bonn (UKB), Centre of Excellence for Robotic Vision [Canberra], Australian Research Council [Canberra] (ARC), Neuroscience and Mental Health Research Institute [Cardiff, UK] (School of Medicine), Boston University School of Medicine (BUSM), Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, University of Pennsylvania [Philadelphia], Section of Neuroscience and Clinical Pharmacology, University of Cagliari, Department of Epidemiology and Biostatistics, ERASMUS, Hospital Universitario Doctor Negrín [Las Palmas de Gran Canaria, Spain], Department of Neurodegenerative Diseases, University of Mississippi Medical Center (UMMC), Pathology and Laboratory Medicine [Philadelphia, PA, USA] (Penn Neurodegeneration Genomics Center), UNIROUEN - UFR Santé (UNIROUEN UFR Santé), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Génétique du cancer et des maladies neuropsychiatriques (GMFC), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Bioinformatics, GlaxoSmithKline, Aging Research Center [Karolinska Institutet] (ARC ), Stockholm University-Karolinska Institutet [Stockholm], University of Nottingham, UK (UON), University of Texas Health Science Center, Department of Neurobiology, Caring Sciences and Society (NVS), University of Bari Aldo Moro (UNIBA), Ageing Group, Centre for Public Health, Queen's University [Belfast] (QUB), Mayo Clinic [Jacksonville], Maurice Wohl Clinical Neuroscience Institut, King‘s College London, Istituto di Ricovero e Cura a Carattere Scientifico, Ospedale Casa Sollievo della Sofferenza [San Giovanni Rotondo] (IRCCS), Università degli Studi di Perugia (UNIPG), Framingham Heart Study, Boston University [Boston] (BU)-National Heart, Lung, and Blood Institute [Bethesda] (NHLBI), CHU Rouen, Normandie Université (NU), Universidad Autonoma de Madrid (UAM), Centro de Investigacion Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III [Madrid] (ISC), National Heart, Lung, and Blood Institute [Bethesda] (NHLBI), University of Florida [Gainesville] (UF), University of Parma = Università degli studi di Parma [Parme, Italie], Center for Cognitive Disorders AUSL [Parma, Italy], School of Public Health [Boston], Uppsala University, Institut de la Mémoire et de la Maladie d'Alzheimer [Paris] (IM2A), Université Pierre et Marie Curie - Paris 6 (UPMC), National Institute on Aging [Bethesda, USA] (NIA), National Institutes of Health [Bethesda] (NIH), Xi'an Jiaotong University (Xjtu), Department of Public health and Caring Sciences, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden, Institute of Gerontology and Geriatrics, Troubles cognitifs dégénératifs et vasculaires - U 1171 (TCDV), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Geriatric Medicine and Metabolic Diseases, Departments of Nuclear Medicine, University Medical Centre Hamburg-Eppendorf [Hamburg, Germany], University of Texas Southwestern Medical Center [Dallas], University of Cologne, Laboratoire d'Etudes et de Recherche en Informatique d'Angers (LERIA), Université d'Angers (UA), Johns Hopkins University (JHU), Universität Leipzig [Leipzig], University of Iceland [Reykjavik], Metacohorts Consortium, Harvard School of Public Health, Catholic University of Rome, Medical University Graz, Baylor College of Medicine (BCM), Baylor University, University of North Texas Health Science Center [Fort Worth], Santa Lucia Foundation (IRCCS), Nextel S.A. [Bilbao], Massachusetts General Hospital [Boston], Department of Pathology and Laboratory Medicine and Indiana Alzheimer disease Center, Indiana University School of Medicine, Indiana University System-Indiana University System, Joint Institute for the Study of the Atmosphere and Ocean (JISAO), Beijing University of Technology, University of Pittsburgh (PITT), Pennsylvania Commonwealth System of Higher Education (PCSHE), Saul B. Korey Department of Neurology, Albert Einstein College of Medicine [New York]-Yeshiva University, Utah State University (USU), Fundació per la Recerca Biomèdica i Social Mútua Terrassa [Barcelona, Spain], Hospital Universitario Mutua de Terrassa, Département de neurologie [Montpellier], Université Montpellier 1 (UM1)-Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Hôpital Gui de Chauliac [Montpellier]-Université de Montpellier (UM), Department of neurology, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland, Department of neurology, University of Eastern Finland-University Hospital of Kuopio-University of Eastern Finland-University Hospital of Kuopio, Medical University of Łódź (MUL), University of Leicester, MRC Prion Unit, Fondazione IRCCS Ca' Granda - Ospedale Maggiore Policlinico, University of Milan, Fondazione Istituto di Ricerca e Cura Carattere Scientifico [Rome], Università degli Studi di Roma Tor Vergata [Roma], Saarland University Hospital, Universitat Autònoma de Barcelona (UAB), Regional Neurogenetic Centre [Lamezia Terme, Italy] (CRN - ASP Catanzaro), Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Institute for Medical Informatics, Biometry and Epidemiology, University Hospital of Essen, Universidade do Porto, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Experimental and Clinical Pharmacology, St. James Hospital and Trinity College [Dublin, Ireland], School of Medicine [Dublin], Trinity College Dublin, University of Sheffield [Sheffield], Lancaster University, University of Michigan [Ann Arbor], University of Michigan System, David Geffen School of Medicine [Los Angeles], University of California [Los Angeles] (UCLA), University of California-University of California, University of Wisconsin-Madison, Rush Alzheimer Disease Center [Chicago, IL, États-Unis], Rush University Medical Center [Chicago], Institute for Advanced Biosciences / Institut pour l'Avancée des Biosciences (Grenoble) (IAB), Centre Hospitalier Universitaire [Grenoble] (CHU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Etablissement français du sang - Auvergne-Rhône-Alpes (EFS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), School of Engineering [Cardiff], Department of Psychiatry [Pittsburgh], University of Pittsburgh School of Medicine, Pennsylvania Commonwealth System of Higher Education (PCSHE)-Pennsylvania Commonwealth System of Higher Education (PCSHE), Northwestern University Feinberg School of Medicine, Mayo Clinic [Rochester], Swedish Medical Center [Seattle, WA, USA], University of California [San Francisco] (UCSF), University of California, Duke University [Durham], University of Kansas Medical Center [Lawrence], Laboratory of Molecular Neuropsychiatry, Icahn School of Medicine at Mount Sinai [New York] (MSSM), Washington University in Saint Louis (WUSTL), University of South Florida [Tampa] (USF), Fred Hutchinson Cancer Research Center [Seattle] (FHCRC), Medical University of South Carolina [Charleston] (MUSC), University of Southern California (USC), Los Alamos National Laboratory (LANL), Centre de biologie du développement (CBD), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Neurology Department, University of California, Davis (UCDavis-Neuro), University of California [Davis] (UC Davis), University of California [Irvine] (UCI), Mount Sinai Medical Center, Indiana State University, University of Alabama at Birmingham [ Birmingham] (UAB), University of Kentucky, New York University [New York] (NYU), NYU System (NYU), Department of Medical and Molecular Genetics, Department of Epidemiology and biostatistics, VU University Medical Center [Amsterdam], Emory University [Atlanta, GA], Department of Neurology, University of California-University of California-David Geffen School of Medicine [Los Angeles], Brigham & Women’s Hospital [Boston] (BWH), Harvard Medical School [Boston] (HMS), Department of Medical Genetics, HMNC Brain Health, Alzheimer Disease Research Laboratory, Harvard Medical School [Boston] (HMS)-Massachusetts General Hospital [Boston], Oregon Health and Science University [Portland] (OHSU), Cleveland Clinic, Laboratoire d'Informatique, Systèmes, Traitement de l'Information et de la Connaissance (LISTIC), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Department of Psychiatry, School of Medicine-Johns Hopkins University and Johns Hopkins Bayview Medical Center, Douglas Mental Health University Institute [Montréal], McGill University = Université McGill [Montréal, Canada], Department of neurosciences, University of California [San Diego] (UC San Diego), Department of Physics and Astronomy [Fort Worth], Texas Christian University (TCU), Department of Computer Science [University of California, Davis], Indiana University System, Institute for Aging and Alzheimer’s Disease Research [Fort Worth] (IAADR), Department of Laboratory Medicine and Pathology, Mayo Clinic, Institute for Memory Impairments and Neurological Disorders [Irvine], University of Colorado Anschutz [Aurora], Tanz Center Research in Neurodegenerative Diseases [Toronto], University of Toronto, Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], Keck School of Medicine [Los Angeles], Indiana University [South Bend], Massachusetts General Hospital, Novartis Institutes for Biomedical Research [Cambridge, MA, USA], Departments of Pathology and Laboratory Medicine (Neuropathology) and Neurology, UCLA Medical Center-David Geffen School of Medicine [Los Angeles], University of California-University of California-University of California [Los Angeles] (UCLA), University of North Carolina [Chapel Hill] (UNC), University of North Carolina System (UNC), Institut de Génomique d'Evry (IG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, University of Antwerp (UA), Institute Born-Bunge, Karolinska Institutet [Stockholm], Karolinska University Hospital [Stockholm], University of Kuopio, Centre Mémoire de Ressources et de Recherche [Lille-Bailleul] (CMRR), Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Hôpital Roger Salengro [Lille], Laboratoire d'Analyse Génomique, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Inserm-U1167, Dpt Gériatrie [CHU Broca], AP-HP - Hôpital Cochin Broca Hôtel Dieu [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Neuroépidémiologie, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut du Cerveau et de la Moëlle Epinière = Brain and Spine Institute (ICM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Neuropsychiatrie : recherche épidémiologique et clinique (PSNREC), Université Montpellier 1 (UM1)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Alzheimer Precision Medicine [CHU Pitié-Salpétriêre] (GRC 21 AMP), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Department of Epidemiology, University of Washington, School of Medicine [Los Angeles], Albert Einstein College of Medicine [New York], IdiPAZ - Instituto de Investigación La Paz [Madrid, Spain], Instituto de Física Teórica UAM/CSIC (IFT), Universidad Autonoma de Madrid (UAM)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Department of Internal Medicine, University of Central Asturias [Oviedo, Spain], Human Genome Sequencing Center, Baylor College of Medicine, Baylor University-Baylor University, Department of Epidemiology, Erasmus Medical Centre, Translational Genomics Research Institute [Phoenix, AZ, USA], University of Arizona, Banner Alzheimer's Institute [Phoenix, AZ, États-Unis], University of Texas Health Science Center at San Antonio [San Antonio], Mount Sinai School of Medicine, Department of Psychiatry-Icahn School of Medicine at Mount Sinai [New York] (MSSM), Department. of Neurological Sciences, University of Milan, IRCCS Ospedale Maggiore Policlinico, Centre for Research in Neurodegenerative Diseases, VA Puget Sound Health Care System/GRECC [Seattle, WA, USA], University of Pisa - Università di Pisa, Pfizer Worldwide Research and Development [Cambridge, MA, USA], Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt), Texas Tech University Health Sciences Center, Texas Tech University [Lubbock] (TTU), Saarland University [Saarbrücken], University of Bonn, Department of Public Health and Primary Care, University of Cambridge [UK] (CAM), Cambridge Institute for Medical Research (CIMR), Department of Molecular Neurosciences, Institute of Neurology, UCL, Institute of Psychiatry, Institute of psychiatry, University of British Columbia (UBC), the Clinical Neuroscience Research Group, University of Manchester [Manchester]-Greater Manchester Neurosciences Centre, Aristotle University of Thessaloniki, Memory and Dementia Centre, 3rd Department of Neurology, G. Pa, University of Barcelona, University of Southampton, Department of Psychiatry [Oxford] (POWIC), University of Oxford [Oxford]-The Warneford Hospital, School of Psychology [Cardiff University], Department of Medical Sciences, UCL, Institute of Neurology [London], Washington University School of Medicine, Netherlands Genomics Initiative, Netherlands Consortium for Healthy Aging [Leiden, Netherlands] (NCHA), School of Medecine, Center for Translational and Computational Neuroimmunology [New York, NY, États-Unis] (CTCN), Department of Neurology [New York, NY, États-Unis], Columbia University Medical Center (CUMC), Columbia University [New York]-Columbia University [New York]-Columbia University Medical Center (CUMC), Columbia University [New York]-Columbia University [New York], School of Life Sciences, Department of Neuroscience, Mayo Clinic Jacksonville, Icelandic Heart Association, Heart Preventive Clinic and Research Institute, Klinik für Psychiatrie, Martin-Luther-University Halle-Wittenberg, Epidémiologie et Biostatistique [Bordeaux], Université Bordeaux Segalen - Bordeaux 2-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM), The Center for Applied Genomics, Children’s Hospital of Philadelphia (CHOP ), Clínica Universidad de Navarra [Pamplona], Neurodegenerative Brain Diseases Group, VIB, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University-Medical Research Council, Brigham Young University (BYU), Institut de Santé Publique, d'Epidémiologie et de Développement (ISPED), Université Bordeaux Segalen - Bordeaux 2, The Gertrude H Sergivesky Center, Columbia University College of Physicians and Surgeons, Genetic Epidemiology Unit, Section of Clinical and Molecular Neurogenetics, Universität zu Lübeck [Lübeck], University of Pennsylvania - Department of Pathology & Laboratory Medecine, Framingham Heart Study [Framingham, MA, USA], ANR-10-IAHU-0006,IHU-A-ICM,Institut de Neurosciences Translationnelles de Paris(2010), European Project: 29845,LSH-ACC-MENTOR, University of Pennsylvania-University of Pennsylvania, Universität Bonn = University of Bonn-Institute of Human Genetics [Bonn, Germany], Universität Leipzig-Universität Leipzig, Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), University of Pennsylvania, Università degli studi di Bari Aldo Moro = University of Bari Aldo Moro (UNIBA), Università degli Studi di Perugia = University of Perugia (UNIPG), Universidad Autónoma de Madrid (UAM), Università degli studi di Parma = University of Parma (UNIPR), Institut de la Mémoire et de la Maladie d'Alzheimer [CHU Pitié-Salpétriêre] (IM2A), Université Pierre et Marie Curie - Paris 6 (UPMC)-CHU Pitié-Salpêtrière [AP-HP], Troubles cognitifs dégénératifs et vasculaires - U 1171 - EA 1046 (TCDV), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille, Droit et Santé-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Universität Leipzig, Università cattolica del Sacro Cuore = Catholic University of the Sacred Heart [Roma] (Unicatt), Yeshiva University- Albert Einstein College of Medicine [New York], Université Montpellier 1 (UM1)-Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Hôpital Gui de Chauliac [CHU Montpellier], Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Université de Montpellier (UM), Università degli Studi di Milano = University of Milan (UNIMI), Saarland University Hospital (UKS), Università degli Studi di Firenze = University of Florence (UniFI), Universidade do Porto = University of Porto, University of California (UC)-University of California (UC), University of California [San Francisco] (UC San Francisco), University of California (UC), University of Kansas Medical Center [Kansas City, KS, USA], Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), University of California [Irvine] (UC Irvine), University of Kentucky (UK), University of California (UC)-University of California (UC)-David Geffen School of Medicine [Los Angeles], Department of Computer Science [Univ California Davis] (CS - UC Davis), University of California (UC)-University of California (UC)-University of California [Los Angeles] (UCLA), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Groupe de recherche clinique Alzheimer Precision Medicine (GRC 21 - APM), Sorbonne Université (SU), Universidad Autónoma de Madrid (UAM)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), University of Texas Health Science Center at San Antonio [San Antonio, Tx, USA], Universität Bonn = University of Bonn, University of Oxford-The Warneford Hospital, Medical Research Council-Cardiff University, Universität zu Lübeck = University of Lübeck [Lübeck], Epidemiology, Neurology, Gastroenterology & Hepatology, Internal Medicine, Facteurs de Risque et Déterminants Moléculaires des Maladies liées au Vieillissement (Inserm U1167 - RID-AGE - Institut Pasteur), Génétique, Reproduction et Développement - Clermont Auvergne (GReD), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne (UCA)-Centre National de la Recherche Scientifique (CNRS), Eberhard Karls Universität Tübingen, IRCCS 'Casa Sollievo della Sofferenza', Centro de Investigación Biomédica en Red para Enfermedades Neurodegenerativas (Ciberned), University of Florida [Gainesville], University of Parma, Troubles cognitifs dégénératifs et vasculaires (U1171), Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-INSERM, Yeshiva University- Albert Einstein College of Medicine, Institut d’Électronique, de Microélectronique et de Nanotechnologie (IEMN) - UMR 8520 (IEMN), Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Université Polytechnique Hauts-de-France (UPHF)-Ecole Centrale de Lille-Université Polytechnique Hauts-de-France (UPHF)-Institut supérieur de l'électronique et du numérique (ISEN), Autonomous University of Barcelona (UAB), Università degli Studi di Firenze [Firenze], Universidade do Porto [Porto], Centre Hospitalier Universitaire [Grenoble] (CHU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Etablissement français du sang - Auvergne-Rhône-Alpes (EFS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Washington University in St Louis, University of South Florida (USF), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, McGill University, Charité - Universitätsmedizin Berlin / Charite - University Medicine Berlin, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [APHP]-Centre National de la Recherche Scientifique (CNRS), Neuropsychiatrie : recherche épidémiologique et clinique, Alzheimer Precision Medicine GRC n°21 (APM), CHU Pitié-Salpêtrière [APHP], Albert Einstein College of Medicine, Universidad Autonoma de Madrid (UAM)-Consejo Superior de Investigaciones Científicas [Spain] (CSIC), Università Cattolica del S. Cuore - Catholic University of the Sacred Hearth, University of Florence (UNIFI), CIBER de Enfermedades Neurodegenerativas (CIBERNED), Universität zu Lübeck [Lübeck] - University of Lübeck [Lübeck], [ANR-10-IAIHU-06],« Investissements d'avenir » ,Agence nationale de la recherche (ANR), Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Centre Hospitalier Universitaire [Grenoble] (CHU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Etablissement français du sang - Auvergne-Rhône-Alpes (EFS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-CHU Pitié-Salpêtrière [AP-HP], Icahn School of Medicine at Mount Sinai [New York] (MSSM)-Department of Psychiatry, van der Lee, Sven J [0000-0003-1606-8643], Naj, Adam C [0000-0002-9621-2942], Badarinarayan, Nandini [0000-0002-6944-748X], Chouraki, Vincent [0000-0002-4698-1794], Graham, Robert R [0000-0001-7151-4277], Hoffmann, Per [0000-0002-6573-983X], Smith, Albert V [0000-0003-1942-5845], Satizabal, Claudia L [0000-0002-1115-4430], Brody, Jennifer A [0000-0001-8509-148X], Wolters, Frank J [0000-0003-2226-4050], Lupton, Michelle K [0000-0002-7274-7299], Lin, Honghuang [0000-0003-3043-3942], Adams, Hieab H [0000-0003-3687-2508], Giedraitis, Vilmantas [0000-0003-3423-2021], Pasquier, Florence [0000-0001-9880-9788], Chen, Yuning [0000-0002-7358-7055], Bossù, Paola [0000-0002-1432-0078], Ghetti, Bernardino [0000-0002-1842-8019], Yang, Qiong [0000-0002-3658-1375], Aspelund, Thor [0000-0002-7998-5433], Bullido, María J [0000-0002-6477-1117], Rivadeneira, Fernando [0000-0001-9435-9441], Rubinsztein, David C [0000-0001-5002-5263], Al-Chalabi, Ammar [0000-0002-4924-7712], Tsolaki, Magda [0000-0002-2072-8010], De Jager, Philip L [0000-0002-8057-2505], Dickson, Dennis W [0000-0001-7189-7917], Van Broeckhoven, Christine [0000-0003-0183-7665], Ikram, M Arfan [0000-0003-0372-8585], Amouyel, Philippe [0000-0001-9088-234X], Lambert, Jean-Charles [0000-0003-0829-7817], Apollo - University of Cambridge Repository, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Alzheimer Precision Medicine [CHU Pitié-Salpétriêre] (GRC 21 APM), Berr, Claudine, Institut de Neurosciences Translationnelles de Paris - - IHU-A-ICM2010 - ANR-10-IAHU-0006 - IAHU - VALID, and Mentoring of LifeSciHealth-Multipliers in the Accession Candidate Countries - LSH-ACC-MENTOR - 29845 - OLD
Subjects: 0301 basic medicine, Linkage disequilibrium, [SDV]Life Sciences [q-bio], Medizin, Sequence Homology, Genome-wide association study, genetics [Alzheimer Disease], metabolism [Microglia], Linkage Disequilibrium, 0302 clinical medicine, genetics [Protein Interaction Maps], genetics [Membrane Glycoproteins], Gene Frequency, Immunologic, genetics [Adaptor Proteins, Signal Transducing], Receptors, genetics [Exome], Odds Ratio, Innate, genetics [Receptors, Immunologic], Exome, Protein Interaction Maps, genetics [Genetic Predisposition to Disease], Receptors, Immunologic, ABI3 protein, human, Genetics, Adaptor Proteins, Signal Transducing, Alzheimer Disease, Amino Acid Sequence, Case-Control Studies, Gene Expression Profiling, Genetic Predisposition to Disease, Genotype, Humans, Immunity, Innate, Membrane Glycoproteins, Microglia, Phospholipase C gamma, Sequence Homology, Amino Acid, Polymorphism, Single Nucleotide, Adaptor Proteins, Single Nucleotide, 3. Good health, [SDV] Life Sciences [q-bio], Amino Acid, Settore MED/26 - NEUROLOGIA, genetics [Phospholipase C gamma], [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], Alzheimer's disease, Common disease-common variant, Biology, Article, 03 medical and health sciences, ddc:570, medicine, Journal Article, [SDV.NEU] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], Polymorphism, Allele frequency, TREM2 protein, human, TREM2, Case-control study, Signal Transducing, Immunity, medicine.disease, R1, Minor allele frequency, genetics [Immunity, Innate], 030104 developmental biology, Human medicine, 030217 neurology & neurosurgery
Abstract: International audience; We identified rare coding variants associated with Alzheimer's disease in a three-stage case-control study of 85,133 subjects. In stage 1, we genotyped 34,174 samples using a whole-exome microarray. In stage 2, we tested associated variants (P < 1 × 10-4) in 35,962 independent samples using de novo genotyping and imputed genotypes. In stage 3, we used an additional 14,997 samples to test the most significant stage 2 associations (P < 5 × 10-8) using imputed genotypes. We observed three new genome-wide significant nonsynonymous variants associated with Alzheimer's disease: a protective variant in PLCG2 (rs72824905: p.Pro522Arg, P = 5.38 × 10-10, odds ratio (OR) = 0.68, minor allele frequency (MAF)cases = 0.0059, MAFcontrols = 0.0093), a risk variant in ABI3 (rs616338: p.Ser209Phe, P = 4.56 × 10-10, OR = 1.43, MAFcases = 0.011, MAFcontrols = 0.008), and a new genome-wide significant variant in TREM2 (rs143332484: p.Arg62His, P = 1.55 × 10-14, OR = 1.67, MAFcases = 0.0143, MAFcontrols = 0.0089), a known susceptibility gene for Alzheimer's disease. These protein-altering changes are in genes highly expressed in microglia and highlight an immune-related protein-protein interaction network enriched for previously identified risk genes in Alzheimer's disease. These genetic findings provide additional evidence that the microglia-mediated innate immune response contributes directly to the development of Alzheimer's disease.
Published: 2017

21. Commentary on the 6th International Symposium of Animal Functional Genomics

Author: Alessandra Stella, Paolo Ajmone-Marsan, and Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt)
Subjects: 0301 basic medicine, Emerging technologies, [SDV]Life Sciences [q-bio], education, Library science, Developing country, Biology, 03 medical and health sciences, Genetics, Animalia, Genetics(clinical), health care economics and organizations, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Settore AGR/17 - ZOOTECNICA GENERALE E MIGLIORAMENTO GENETICO, business.industry, 0402 animal and dairy science, 04 agricultural and veterinary sciences, General Medicine, 040201 dairy & animal science, humanities, Biotechnology, 030104 developmental biology, Sustainability, Animal Science and Zoology, business, Functional genomics, Genome architecture
Abstract: On the year of Expo 2015, “Feeding the Planet”, prominent scientists from different countries and with a wide range of expertise convened at the Universita Cattolica del Sacro Cuore in Piacenza to attend the 6th International Symposium on Animal Functional Genomics (http://www.isafg2015.it) and discuss the role of functional genomics and post-genomic perspectives in animal breeding. Topics included genome architecture and regulation, the role of microbes in health and production, and the best use of new technologies for improving livestock sustainability in developed and developing countries. One major achievement of the symposium was full integration of the separate sessions through a very interactive exchange among representatives of academia, biotech industries and breeding organizations.
Published: 2016

22. Whole mitochondrial genomes unveil the impact of domestication on goat matrilineal variability

Author: Francesca Gandini, Alessandro Achilli, Licia Colli, Frédéric Boyer, Baldassare Portolano, Saif Agha, Irene Cardinali, Petros Lymberakis, Marcin Rzepus, S.M.F. Vahidi, Wahid Zamani, Marco Pellecchia, Hamid Reza Rezaei, Paolo Ajmone Marsan, Anna Olivieri, Hovirag Lancioni, Marco Rosario Capodiferro, Ettore Randi, François Pompanon, Maria Teresa Sardina, Vincenza Battaglia, Saeid Naderi, Pierre Taberlet, Eric Coissac, Institute of Zootechnics [Piacenza], Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt), Research Center on Biodiversity and Ancient DNA – BioDNA, Dipartimento di Chimica [Perugia], Università degli Studi di Perugia (UNIPG), Dipartimento di Biologia e Biotecnologie 'L. Spallanzani', Institute of Food Science and Nutrition [Piacenza] (ISAN), Department of Environmental Sciences [Tarbiat], Faculty of Natural Resources and Marine Sciences [Tarbiat], Tarbiat Modaras University-Tarbiat Modaras University, Laboratoire d'Ecologie Alpine (LECA), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Natural Ressource Faculty [Guilan], University of Guilan, School of Applied Sciences [Huddersfield], University of Huddersfield, Agricultural Biotechnology Research Institute of Iran, Department of Animal Production, Université Ain Shams, Laboratorio di Genetica [Bologna], Italian National Institute of Environmental Protection and Research (ISPRA), Dipartimento Scienze Agrarie e Forestali [Palermo], Università degli studi di Palermo - University of Palermo, Environmental Sciences Department [Gorgan], Gorgan University of Agricultural Sciences and Natural Resources, Natural History Museum of Crete, Colli, L., Lancioni, H., Cardinali, I., Olivieri, A., Capodiferro, M., Pellecchia, M., Rzepus, M., Zamani, W., Naderi, S., Gandini, F., Vahidi, S., Agha, S., Randi, E., Battaglia, V., Sardina, M., Portolano, B., Rezaei, H., Lymberakis, P., Boyer, F., Coissac, E., Pompanon, F., Taberlet, P., Ajmone Marsan, P., and Achilli, A.
Subjects: Most recent common ancestor, [SDV]Life Sciences [q-bio], Population, Molecular Sequence Data, MtDNA haplogroups, Capra aegagrus, Biology, DNA, Mitochondrial, Haplogroup, Domestication, QH301, Settore AGR/17 - Zootecnica Generale E Miglioramento Genetico, Capra hircus, Genetics, Animals, Capra aegagru, education, QH426, Phylogeny, 2. Zero hunger, education.field_of_study, Origin of Capra hircus, Genome, MtDNA haplogroup, Phylogenetic tree, Goats, Haplotype, Genetic Variation, DNA, Origin of Capra hircu, Mitochondrial, Goat mitochondrial genome, Biotechnology, Haplotypes, Evolutionary biology, Genome, Mitochondrial, Female, mtDNA haplogroups, Research Article, Human mitochondrial DNA haplogroup
Abstract: Background The current extensive use of the domestic goat (Capra hircus) is the result of its medium size and high adaptability as multiple breeds. The extent to which its genetic variability was influenced by early domestication practices is largely unknown. A common standard by which to analyze maternally-inherited variability of livestock species is through complete sequencing of the entire mitogenome (mitochondrial DNA, mtDNA). Results We present the first extensive survey of goat mitogenomic variability based on 84 complete sequences selected from an initial collection of 758 samples that represent 60 different breeds of C. hircus, as well as its wild sister species, bezoar (Capra aegagrus) from Iran. Our phylogenetic analyses dated the most recent common ancestor of C. hircus to ~460,000 years (ka) ago and identified five distinctive domestic haplogroups (A, B1, C1a, D1 and G). More than 90 % of goats examined were in haplogroup A. These domestic lineages are predominantly nested within C. aegagrus branches, diverged concomitantly at the interface between the Epipaleolithic and early Neolithic periods, and underwent a dramatic expansion starting from ~12–10 ka ago. Conclusions Domestic goat mitogenomes descended from a small number of founding haplotypes that underwent domestication after surviving the last glacial maximum in the Near Eastern refuges. All modern haplotypes A probably descended from a single (or at most a few closely related) female C. aegagrus. Zooarchaelogical data indicate that domestication first occurred in Southeastern Anatolia. Goats accompanying the first Neolithic migration waves into the Mediterranean were already characterized by two ancestral A and C variants. The ancient separation of the C branch (~130 ka ago) suggests a genetically distinct population that could have been involved in a second event of domestication. The novel diagnostic mutational motifs defined here, which distinguish wild and domestic haplogroups, could be used to understand phylogenetic relationships among modern breeds and ancient remains and to evaluate whether selection differentially affected mitochondrial genome variants during the development of economically important breeds. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2342-2) contains supplementary material, which is available to authorized users.
Published: 2015

23. Transitive and intransitive gesture execution and observation compared to resting state: the hemodynamic measures (fNIRS)

Author: Angela Bartolo, Livia Cortesi, Maria Elide Vanutelli, Michela Balconi, Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt), Laboratoire Sciences Cognitives et Sciences Affectives - UMR 9193 (SCALab), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Sciences Cognitives et Sciences Affectives (SCALab) - UMR 9193 (SCALab), Balconi, M, Vanutelli, M, Bartolo, A, and Cortesi, L
Subjects: Male, Time Factors, Brain activity and meditation, Settore M-PSI/02 - PSICOBIOLOGIA E PSICOLOGIA FISIOLOGICA, Observation, Functional Laterality, [SCCO]Cognitive science, 0302 clinical medicine, Computer vision, Transitive/intransitive, Resting state, Cerebral Cortex, Brain Mapping, Spectroscopy, Near-Infrared, Gestures, 05 social sciences, General Medicine, medicine.anatomical_structure, Gesture execution, observation, Female, M-PSI/01 - PSICOLOGIA GENERALE, Psychology, PPC, Cognitive psychology, Gesture, Motor cortex, Adult, Rest, Cognitive Neuroscience, Posterior parietal cortex, Experimental and Cognitive Psychology, Context (language use), fNIRS, M-PSI/02 - PSICOBIOLOGIA E PSICOLOGIA FISIOLOGICA, 050105 experimental psychology, Premotor cortex, Young Adult, 03 medical and health sciences, Artificial Intelligence, medicine, Humans, 0501 psychology and cognitive sciences, Gesture execution and observation, Analysis of Variance, Transitive relation, Resting state fMRI, business.industry, Hemodynamics, Oxyhemoglobins, Artificial intelligence, business, Photic Stimulation, Psychomotor Performance, 030217 neurology & neurosurgery
Abstract: The present study explored cortical correlates of gesture execution and observation in peripersonal space, using functional near-infrared spectroscopy (fNIRS). Moreover, a direct comparison was realized between resting state condition and execution/observation. Meaningful gestures produced in the presence (transitive action) or in the absence (intransitive action) of the object were considered in a real context (situated representation of gestures). Subjects were required to execute or observe transitive versus intransitive gestures during fNIRS registration. Gesture execution was related to higher brain activity (increased oxygenated hemoglobin levels) with respect to observation in motor areas (premotor cortex, PMC; supplementary motor cortex, SM1). In contrast, the posterior parietal cortex was similarly activated in case of both execution and observation task. Moreover, both tasks showed increased brain activity within these areas compared to resting state. Finally, it was shown that action execution and observation of transitive gestures was supported by similar parietal posterior areas. These findings support the hypothesis of a partial common network for observation and execution of gestures within peripersonal space, mainly in transitive condition.
Published: 2015

24. The Intraperitoneal Transcriptome of the Opportunistic Pathogen Enterococcus faecalis in Mice

Author: Muller, Cécile, Cacaci, Margherita, Sauvageot, Nicolas, Sanguinetti, Maurizio, Rattei, Thomas, Eder, Thomas, Giard, Jean-Christophe, Kalinowski, Jörn, Hain, Torsten, Hartke, Axel, Unité de Recherche Risques Microbiens (U2RM), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Università cattolica del Sacro Cuore [Milano] (Unicatt), Istituto di Microbiologia - Institute of Microbiology [Rome], Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt), University of Vienna [Vienna], Universität Bielefeld, Institut für Medizinische Mikrobiologie - Institute of Medical Microbiology, and Justus-Liebig-Universität Gießen (JLU)
Subjects: Glycerol, Mice, Inbred BALB C, Virulence factors, Reverse Transcriptase Polymerase Chain Reaction, [SDV]Life Sciences [q-bio], Enterococcus infections, lcsh:R, lcsh:Medicine, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Gene Expression Regulation, Bacterial, Peritonitis, Mice, RNA, Bacterial, Genes, Bacterial, Enterococcus faecalis, Animals, lcsh:Q, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Gene expression, Peritoneum, Operons, Transcriptome, lcsh:Science, Gram-Positive Bacterial Infections, Research Article
Abstract: International audience; Enterococcus faecalis is a Gram-positive lactic acid intestinal opportunistic bacterium with virulence potential. For a better understanding of the adapation of this bacterium to the host conditions, we performed a transcriptome analysis of bacteria isolated from an infection site (mouse peritonitis) by RNA-sequencing. We identified a total of 211 genes with significantly higher transcript levels and 157 repressed genes. Our in vivo gene expression database reflects well the infection process since genes encoding important virulence factors like cytolysin, gelatinase or aggregation substance as well as stress response proteins, are significantly induced. Genes encoding metabolic activities are the second most abundant in vivo induced genes demonstrating that the bacteria are metabolically active and adapt to the special nutrient conditions of the host. α- and β- glucosides seem to be important substrates for E. faecalis inside the host. Compared to laboratory conditions, the flux through the upper part of glycolysis seems to be reduced and more carbon may enter the pentose phosphate pathway. This may reflect the need of the bacteria under infection conditions to produce more reducing power for biosynthesis. Another important substrate is certainly glycerol since both pathways of glycerol catabolism are strongly induced. Strongly in vivo induced genes should be important for the infection process. This assumption has been verified in a virulence test using well characterized mutants affected in glycerol metabolism. This showed indeed that mutants unable to metabolize this sugar alcohol are affected in organ colonisation in a mouse model.
Published: 2015

25. Redox Balance via Lactate Dehydrogenase Is Important for Multiple Stress Resistance and Virulence in Enterococcus faecalis

Author: Alain Rincé, Yinyin Bao, Nosheen Fatima Rana, Maurizio Sanguinetti, Jean-Marie Laplace, Nicolas Sauvageot, Brunella Posteraro, Ingolf F. Nes, Axel Hartke, Unité de Recherche Risques Microbiens (U2RM), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Aliments Bioprocédés Toxicologie Environnements (ABTE), Normandie Université (NU)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU), Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Istituto di Microbiologia - Institute of Microbiology [Rome], and Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt)
Subjects: [SDV]Life Sciences [q-bio], Immunology, Mutant, Virulence, medicine.disease_cause, Microbiology, Settore MED/07 - MICROBIOLOGIA E MICROBIOLOGIA CLINICA, Enterococcus faecalis, 03 medical and health sciences, chemistry.chemical_compound, Mice, Bacterial Proteins, Stress, Physiological, Lactate dehydrogenase, medicine, Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, 030304 developmental biology, 0303 health sciences, biology, L-Lactate Dehydrogenase, 030306 microbiology, Wild type, biology.organism_classification, Molecular Pathogenesis, Glycopeptide, 3. Good health, Infectious Diseases, Biochemistry, chemistry, Staphylococcus aureus, Parasitology, Oxidation-Reduction, Bacteria
Abstract: Enterococcus faecalis is a highly stress resistant opportunistic pathogen. The intrinsic ruggedness of this bacterium is supposed to be the basis of its capacity to colonize the hostile environments of hospitals and to cause several kinds of infections. We show in this work that general resistance to very different environmental stresses depends on the ability of E. faecalis to maintain redox balance via lactate dehydrogenase (LDH). Furthermore, LDH-deficient mutants are less successful than the wild type at colonizing host organs in a murine model of systemic infection. Taken together, our results, as well as those previously published for Staphylococcus aureus (A. R. Richardson, S. J. Libby, and F. C. Fang, Science 319:1672–1676, 2008), identify LDH as an attractive drug target. These drugs may have additional applications, as in the fight against glycopeptide antibiotic-resistant bacteria and even cancer.
Published: 2013

26. AsrR Is an Oxidative Stress Sensing Regulator Modulating Enterococcus faecium Opportunistic Traits, Antimicrobial Resistance, and Pathogenicity

Author: Willem van Schaik, Nicolas Verneuil, Xinglin Zhang, Vincent Cattoir, Jean-Christophe Giard, Anne Dhalluin, Maurizio Sanguinetti, Florian Le Bras, Brunella Posteraro, Riccardo Torelli, Rob J. L. Willems, Roland Leclercq, Francois Lebreton, Unité de Recherche Risques Microbiens (U2RM), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), University Medical Center [Utrecht], Istituto di Microbiologia - Institute of Microbiology [Rome], Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt), Laboratoire de Microbiologie de l’Environnement (LME), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Recherche Agronomique (INRA), Interactions hôte et microorganismes des épithéliums, ARN régulateurs bactériens et médecine (BRM), Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), and dhalluin, anne
Subjects: Bacterial Diseases, Male, [SDE] Environmental Sciences, Enterococcus faecium, Pathogenesis, medicine.disease_cause, Transcriptome, Mice, Enterococcus Infection, lcsh:QH301-705.5, ComputingMilieux_MISCELLANEOUS, Mice, Inbred BALB C, 0303 health sciences, Oxidants, Bacterial Pathogens, Anti-Bacterial Agents, Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Medical Microbiology, [SDE]Environmental Sciences, Medicine, [SDV.IMM]Life Sciences [q-bio]/Immunology, Oxidation-Reduction, Research Article, lcsh:Immunologic diseases. Allergy, [SDV.IMM] Life Sciences [q-bio]/Immunology, Immunology, Biology, beta-Lactams, Microbiology, beta-Lactam Resistance, Enterococcus faecalis, Settore MED/07 - MICROBIOLOGIA E MICROBIOLOGIA CLINICA, 03 medical and health sciences, Quantitative Trait, Heritable, Bacterial Proteins, Virology, Genetics, medicine, Animals, Humans, Microbial Pathogens, Molecular Biology, Gene, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Gram-Positive Bacterial Infections, 030304 developmental biology, Gram Positive, 030306 microbiology, Biofilm, Hydrogen Peroxide, biology.organism_classification, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, Response regulator, Regulon, lcsh:Biology (General), Macrophages, Peritoneal, Parasitology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, lcsh:RC581-607, Oxidative stress, Transcription Factors
Abstract: Oxidative stress serves as an important host/environmental signal that triggers a wide range of responses in microorganisms. Here, we identified an oxidative stress sensor and response regulator in the important multidrug-resistant nosocomial pathogen Enterococcus faecium belonging to the MarR family and called AsrR (antibiotic and stress response regulator). The AsrR regulator used cysteine oxidation to sense the hydrogen peroxide which results in its dissociation to promoter DNA. Transcriptome analysis showed that the AsrR regulon was composed of 181 genes, including representing functionally diverse groups involved in pathogenesis, antibiotic and antimicrobial peptide resistance, oxidative stress, and adaptive responses. Consistent with the upregulated expression of the pbp5 gene, encoding a low-affinity penicillin-binding protein, the asrR null mutant was found to be more resistant to β-lactam antibiotics. Deletion of asrR markedly decreased the bactericidal activity of ampicillin and vancomycin, which are both commonly used to treat infections due to enterococci, and also led to over-expression of two major adhesins, acm and ecbA, which resulted in enhanced in vitro adhesion to human intestinal cells. Additional pathogenic traits were also reinforced in the asrR null mutant including greater capacity than the parental strain to form biofilm in vitro and greater persistance in Galleria mellonella colonization and mouse systemic infection models. Despite overexpression of oxidative stress-response genes, deletion of asrR was associated with a decreased oxidative stress resistance in vitro, which correlated with a reduced resistance to phagocytic killing by murine macrophages. Interestingly, both strains showed similar amounts of intracellular reactive oxygen species. Finally, we observed a mutator phenotype and enhanced DNA transfer frequencies in the asrR deleted strain. These data indicate that AsrR plays a major role in antimicrobial resistance and adaptation for survival within the host, thereby contributes importantly to the opportunistic traits of E. faecium., Author Summary Multiple antibiotic-resistant isolates of the opportunistic pathogen Enterococcus faecium have emerged and spread worldwide. However, studies aimed at identifying mechanisms that underlie the transformation of E. faecium from its commensal nature into a nosocomial pathogen are scarce. We report pleiotropic roles for a novel oxidative-sensing regulator, called AsrR (antibiotic and stress response regulator), in E. faecium. Based on transcriptomic analysis, phenotypic studies, and animal models, we demonstrate that asrR deletion is responsible for i) diminished susceptibility to penicillins, vancomycin, and cationic antimicrobial peptides, ii) increased adhesion to human cells and biofilm formation, iii) a mutator phenotype and enhanced DNA transfer frequencies, iv) decreased resistance to oxidative stress both in vitro and in murine macrophages, and v) increased host-persistence in both insect and mouse models. AsrR is a stress-sensor and is promptly inactivated in the presence of hydrogen peroxide. Therefore, oxidative stress, which is a main challenge during infection, may be a significant signal used by E. faecium to promote opportunistic traits. This provides a significant resource combining, for the first time in E. faecium, a global transcriptomic approach and a thorough phenotypic study, which places AsrR as a key regulator modulating pathogenicity, antimicrobial resistance, and environmental adaptation.
Published: 2012

27. Involvement of Peptidylprolyl cis / trans Isomerases in Enterococcus faecalis Virulence

Author: Reffuveille, Fany, Connil, Nathalie, Sanguinetti, Maurizio, Posteraro, Brunella, Chevalier, Sylvie, Auffray, Yanick, Rince, Alain, Camilli, A., Laboratoire de Microbiologie de l’Environnement (LME), Institut National de la Recherche Agronomique (INRA)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM), Université de Rouen Normandie (UNIROUEN), Istituto di Microbiologia - Institute of Microbiology [Rome], Università Cattolica del S. Cuore - Catholic University of the Sacred Hearth, Inst Hyg, Università Cattolica del Sacro Cuore, Laboratoire de Microbiologie du Froid – Signaux et Micro-Environnement (LMDF-SME), Unité de Recherche Risques Microbiens (U2RM), Université de Caen Normandie (UNICAEN), Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt), Università cattolica del Sacro Cuore [Milano] (Unicatt), and Inst Microbiol
Subjects: Enzymologic, Parvulin, STREPTOCOCCUS-PNEUMONIAE, COLONIZATION, Mice, [SDV.BC.IC]Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB], Enterococcus faecalis, OXIDATIVE STRESS, Peptide sequence, Inbred BALB C, Cyclophilin, ComputingMilieux_MISCELLANEOUS, Mice, Inbred BALB C, 0303 health sciences, Virulence, SURFACE PROTEIN, Bacterial, Bacterial Infections, Peptidylprolyl Isomerase, 3. Good health, Infectious Diseases, Biochemistry, Female, EXPRESSION, Molecular Sequence Data, Immunology, Biology, Microbiology, Gene Expression Regulation, Enzymologic, Settore MED/07 - MICROBIOLOGIA E MICROBIOLOGIA CLINICA, 03 medical and health sciences, Bacterial Proteins, ENDOCARDITIS, Animals, Amino Acid Sequence, Gene, Gram-Positive Bacterial Infections, 030304 developmental biology, Peptidylprolyl isomerase, IDENTIFICATION, 030306 microbiology, Genetic Complementation Test, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Gene Expression Regulation, Bacterial, AGGREGATION, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, LIPOPROTEIN, Gene Expression Regulation, Cis-trans-Isomerases, Mutation, Parasitology, GENERATION
Abstract: Peptidylprolyl cis / trans isomerases (PPIases) are enzymes involved in protein folding. Analysis of the genome sequence of Enterococcus faecalis V583 allowed for identification of 3 PPIases carrying genes. ef2898 encodes an intracellular PPIase which was not shown to be important for the E. faecalis stress response or virulence. The other two PPIases, the parvulin family rotamase EF0685 and the cyclophilin family member EF1534, are expected to be surface-exposed proteins. They were shown to be important for virulence and resistance to NaCl. A Δ ef0685 Δ ef1534 mutant was also more resistant to oxidative stress, was able to grow under a high manganese concentration, and showed altered resistance to ampicillin and quinolone antibiotics.
Published: 2012

28. SlyA Is a Transcriptional Regulator Involved in the Virulence of Enterococcus faecalis

Author: Michaux, Charlotte, Sanguinetti, Maurizio, Reffuveille, Fanny, Auffray, Yanick, Posteraro, Brunella, Gilmore, Michael, Hartke, Axel, Giard, Jean-Christophe, Camilli, A., Laboratoire de Microbiologie de l’Environnement (LME), Institut National de la Recherche Agronomique (INRA)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Istituto di Microbiologia - Institute of Microbiology [Rome], Università Cattolica del S. Cuore - Catholic University of the Sacred Hearth, Harvard Medical School [Boston] (HMS), Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt), Inst Microbiol, Università cattolica del Sacro Cuore [Milano] (Unicatt), Inst Hyg, Unité de Recherche Risques Microbiens (U2RM), Université de Caen Normandie (UNICAEN), Università Cattolica del Sacro Cuore, and Normandie Université (NU)-Normandie Université (NU)-Institut National de la Recherche Agronomique (INRA)
Subjects: family, Transcription, Genetic, [SDV]Life Sciences [q-bio], Mutant, Regulator, oxidative stress response, Moths, Polymerase Chain Reaction, Enterococcus faecalis, Transcriptional regulation, ComputingMilieux_MISCELLANEOUS, Phylogeny, Genetics, 0303 health sciences, biology, pathogenesis, gelatinase, Bacterial, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Infectious Diseases, Larva, Transcription, Sequence Analysis, Immunology, Virulence, Microbiology, Settore MED/07 - MICROBIOLOGIA E MICROBIOLOGIA CLINICA, resistance, 03 medical and health sciences, Genetic, Bacterial Proteins, expression, typhimurium, Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, gene, Transcription factor, Gene, 030304 developmental biology, intracellular macrophage survival, Base Sequence, 030306 microbiology, Gene Expression Profiling, DNA, Gene Expression Regulation, Bacterial, Sequence Analysis, DNA, Microarray Analysis, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Molecular Pathogenesis, Regulon, Gene Expression Regulation, Parasitology, urinary tract infection, Transcription Factors
Abstract: Phylogenetic analysis of the crystal structure of the Enterococcus faecalis SlyA (EF_3002) transcriptional factor places it between the SlyA and MarR regulator subfamilies. Proteins of these families are often involved in the regulation of genes important for bacterial virulence and stress response. To gather evidence for the role of this putative regulator in E. faecalis biology, we dissected the genetic organization of the slyA -EF_3001 locus and constructed a slyA deletion mutant as well as complemented strains. Interestingly, compared to the wild-type parent, the Δ slyA mutant is more virulent in an insect infection model ( Galleria mellonella ), exhibits increased persistence in mouse kidneys and liver, and survives better inside peritoneal macrophages. In order to identify a possible SlyA regulon, global microarray transcriptional analysis was performed. This study revealed that the slyA -EF_3001 locus appears to be autoregulated and that 117 genes were differentially regulated in the Δ slyA mutant. In the mutant strain, 111 were underexpressed and 6 overexpressed, indicating that SlyA functions mainly as an activator of transcription.
Published: 2011

29. Role of the (Mn)superoxide dismutase of Enterococcus faecalis in the in vitro interaction with microglia

Author: Samuele Peppoloni, Lidia Manca, Jean-Christophe Giard, Elisabetta Blasi, Giovanni Fadda, Maurizio Sanguinetti, Axel Hartke, Brunella Posteraro, Bruna Colombari, Università degli Studi di Modena e Reggio Emilia, Istituto di Microbiologia - Institute of Microbiology [Rome], Università Cattolica del S. Cuore - Catholic University of the Sacred Hearth, Laboratoire de Microbiologie de l’Environnement (LME), Institut National de la Recherche Agronomique (INRA)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Azienda Ospedaleria Universitaria di Modena, and Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt)
Subjects: PROTEINS, Phagocytosis, [SDV]Life Sciences [q-bio], Superoxide dismutase, RESISTANT, IMMUNITY, medicine.disease_cause, Microbiology, Enterococcus faecalis, Settore MED/07 - MICROBIOLOGIA E MICROBIOLOGIA CLINICA, Cell Line, 03 medical and health sciences, Mice, Bacterial Proteins, In vivo, medicine, Animals, Humans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, MACROPHAGES, 030304 developmental biology, 0303 health sciences, biology, Microglia, 030306 microbiology, Superoxide Dismutase, Intracellular killing, In vitro assay, biology.organism_classification, VANCOMYCIN, In vitro, 3. Good health, medicine.anatomical_structure, INFECTIONS, CELLS, Host-Pathogen Interactions, biology.protein, Neuroglia, PHAGOSOMAL MATURATION, Oxidative stress, Gene Deletion
Abstract: Enterococcus faecalis is a significant human pathogen worldwide and is responsible for severe nosocomial and community-acquired infections. Although enterococcal meningitis is rare, mortality is considerable, reaching 21 %. Nevertheless, the pathogenetic mechanisms of this infection remain poorly understood, even though the ability of E. faecalis to avoid or survive phagocytic attack in vivo may be very important during the infection process. We previously showed that the manganese-cofactored superoxide dismutase (MnSOD) SodA of E. faecalis was implicated in oxidative stress responses and, interestingly, in the survival within mouse peritoneal macrophages using an in vivo–in vitro infection model. In the present study, we investigated the role of MnSOD in the interaction of E. faecalis with microglia, the brain-resident macrophages. By using an in vitro infection model, murine microglial cells were challenged in parallel with the wild-type strain JH2-2 and its isogenic sodA deletion mutant. While both strains were phagocytosed by microglia efficiently and to a similar extent, the ΔsodA mutant was found to be significantly more susceptible to microglial killing than JH2-2, as assessed by the antimicrobial protection assay. In addition, a significantly higher percentage of acidic ΔsodA-containing phagosomes was found and these also underwent enhanced maturation as determined by the expression of endolysosomal markers. In conclusion, these results show that the MnSOD of E. faecalis contributes to survival of the bacterium in microglial cells by influencing their antimicrobial activity, and this could even be important for intracellular killing in neutrophils and thus for E. faecalis pathogenesis.
Published: 2011

30. Increasing complexity in electricity regulation: to whose benefit?

Author: Solimene, Laura and Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt)
Subjects: Electricity, Incentives, Settore SECS-P/06 - ECONOMIA APPLICATA, [SHS.ECO]Humanities and Social Sciences/Economics and Finance, ComputingMilieux_MISCELLANEOUS, Regulation
Abstract: International audience; After a short description of the evolution of incentive regulation, this paper explores some of the issues that have arisen with its implementation in the electricity sector both in the UK and Italy. It illustrates the challenge facing a regulator in implementing an incentive mechanism under imperfect information, and focuses on some distortions emerging as a result of the design of the incentive scheme itself.
Published: 2011

31. Physiological effects of temperature and a herbicide mixture on the soft-shell clam Mya arenaria (Mollusca, Bivalvia)

Author: Dominique Lapointe, Michel Fournier, Patrice Couture, Luna Greco, Ettore Capri, Jocelyne Pellerin, Marco Fusi, Angela Sacchi, Séverine Louis, Florent Garnerot, Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt), Institut des Sciences de la MER de Rimouski (ISMER), Université du Québec à Rimouski (UQAR), Institut Armand Frappier (INRS-IAF), Institut National de la Recherche Scientifique [Québec] (INRS)-Réseau International des Instituts Pasteur (RIIP), Centre Eau Terre Environnement [Québec] (INRS - ETE), and Institut National de la Recherche Scientifique [Québec] (INRS)
Subjects: Mecoprop, Male, Health, Toxicology and Mutagenesis, Mya, Fresh Water, 010501 environmental sciences, 01 natural sciences, MESH: Dose-Response Relationship, Drug, Toxicology, chemistry.chemical_compound, Malondialdehyde, Climate change, MESH: Animals, Food science, MESH: Superoxide Dismutase, 0303 health sciences, MESH: Oxidative Stress, biology, Dicamba, Temperature, Catalase, MESH: Temperature, Gonadosomatic Index, Drug Combinations, MESH: Water Pollutants, Chemical, MESH: 2-Methyl-4-chlorophenoxyacetic Acid, [SDV.TOX]Life Sciences [q-bio]/Toxicology, MESH: Fresh Water, Acetylcholinesterase, Female, 2,4-Dichlorophenoxyacetic Acid, Soft-shell clam, MESH: Mya, MESH: Malondialdehyde, 2-Methyl-4-chlorophenoxyacetic Acid, Superoxide dismutase, Electron Transport Complex IV, 03 medical and health sciences, MESH: Electron Transport Complex IV, Settore AGR/13 - CHIMICA AGRARIA, MESH: Catalase, MESH: 2,4-Dichlorophenoxyacetic Acid, Environmental Chemistry, Animals, Seawater, 030304 developmental biology, 0105 earth and related environmental sciences, MESH: Dicamba, MESH: Drug Combinations, Dose-Response Relationship, Drug, Superoxide Dismutase, MESH: Biological Markers, MESH: Seawater, Pesticide, MESH: Acetylcholinesterase, Bivalvia, biology.organism_classification, MESH: Male, Sexual development, Chlorophenoxy herbicides, chemistry, Oxidative stress, biology.protein, MESH: Female, Biomarkers, Water Pollutants, Chemical
Abstract: The aim of the current study was to investigate effects of temperature and a mixture of herbicides on the physiological status of the bivalve Mya arenaria. Bivalves acclimated to two temperatures (7 and 18°C) were exposed for 28 d to 0.01 mg/L of a pesticide formulation containing dichlorophenoxyacetic acid (2,4-D), 2-(2-methyl-4-chlorophenoxy) propionic acid (mecoprop), and 3,6-dichloro-2-methoxybenzoic acid (dicamba). At days 7, 14, and 28, mortality, immune parameters (hemocyte number, phagocytic activity, and efficiency), biomarkers of oxidative stress (catalase [CAT] and superoxide dismutase [SOD] activities and malondialdehyde [MDA] content), the metabolic enzyme cytochrome C oxidase (CCO), a biomarker of pesticide exposure (acetylcholinesterase [AChE]), and the activity of an enzyme related to gametogenesis (aspartate transcarbamylase [ATCase]) were monitored in clam tissues. Gonadosomatic index (GSI), condition factor (CF), and sex were also assessed. In clams acclimated to 7°C, exposure to pesticide enhanced CCO activity and CF and decreased MDA content, hemocyte number, CAT, and SOD activities. In clams kept at 18°C, pesticide effects appeared minor compared with samples kept at 7°C. In bivalves acclimated to 18°C, CCO, SOD, and ATCase activity and MDA content were enhanced, and hemocyte number, CAT, and AchE activities and phagocytosis were suppressed. In samples exposed to pesticides, increased temperature enhanced MDA content and CCO and SOD activity and suppressed hemocyte number and CAT and AchE activity. A gradual sexual maturation was observed in both sexes through experimental time, but females had a higher sensitivity to temperature and pesticides compared to males. Increased temperature altered the ability of the sentinel species Mya arenaria to respond to pesticide exposures. Further work is needed to understand the impacts of increasing temperature on the whole St. Lawrence estuary ecosystem. Environ. Toxicol. Chem. 2011;30:132–141. © 2010 SETAC
Published: 2011

32. Role of Methionine Sulfoxide Reductases A and B of Enterococcus faecalis in Oxidative Stress and Virulence

Author: Marilena La Sorda, Brunella Posteraro, Yanick Auffray, Jean-Marie Laplace, Maurizio Sanguinetti, Chen Zhao, Axel Hartke, Laboratoire de Microbiologie de l’Environnement (LME), Institut National de la Recherche Agronomique (INRA)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Istituto di Microbiologia - Institute of Microbiology [Rome], Università Cattolica del S. Cuore - Catholic University of the Sacred Hearth, and Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt)
Subjects: [SDV]Life Sciences [q-bio], Immunology, Mutant, Virulence, Microbiology, Enterococcus faecalis, Settore MED/07 - MICROBIOLOGIA E MICROBIOLOGIA CLINICA, Mice, 03 medical and health sciences, chemistry.chemical_compound, Operon, Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Promoter Regions, Genetic, Gene, 030304 developmental biology, chemistry.chemical_classification, Mice, Inbred BALB C, 0303 health sciences, Methionine, biology, 030306 microbiology, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, biology.organism_classification, Molecular Pathogenesis, 3. Good health, Oxidative Stress, Infectious Diseases, Enzyme, chemistry, Methionine Sulfoxide Reductases, Methionine sulfoxide reductase, Female, Parasitology, MSRA
Abstract: Methionine sulfoxide reductases A and B are antioxidant repair enzymes that reduce the S - and R -diastereomers of methionine sulfoxides back to methionine, respectively. Enterococcus faecalis , an important nosocomial pathogen, has one msrA gene and one msrB gene situated in different parts of the chromosome. Promoters have been mapped and mutants have been constructed in two E. faecalis strains (strains JH2-2 and V583) and characterized. For both backgrounds, the mutants are more sensitive than the wild-type parents to exposure to H 2 O 2 , and in combination the mutations seem to be additive. The virulence of the mutants has been analyzed in four different models. Survival of the mutants inside mouse peritoneal macrophages stimulated with recombinant gamma interferon plus lipopolysaccharide but not in naïve phagocytes is significantly affected. The msrA mutant is attenuated in the Galleria mellonella insect model. Deficiency in either Msr enzyme reduced the level of virulence in a systemic and urinary tract infection model. Virulence was reconstituted in the complemented strains. The combined results show that Msr repair enzymes are important for the oxidative stress response, macrophage survival, and persistent infection with E. faecalis.
Published: 2010

33. The Extracytoplasmic Function Sigma Factor SigV Plays a Key Role in the Original Model of Lysozyme Resistance and Virulence of Enterococcus faecalis

Author: Yanick Auffray, Axel Hartke, Jean-Christophe Giard, Maurizio Sanguinetti, Riccardo Torelli, Abdellah Benachour, André Le Jeune, Laboratoire de Microbiologie de l’Environnement (LME), Institut National de la Recherche Agronomique (INRA)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Istituto di Microbiologia - Institute of Microbiology [Rome], Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt), and Università Cattolica del S. Cuore - Catholic University of the Sacred Hearth
Subjects: [SDV]Life Sciences [q-bio], Mutant, lcsh:Medicine, medicine.disease_cause, Infectious Diseases/Bacterial Infections, Mice, chemistry.chemical_compound, Sigma factor, Enterococcus faecalis, lcsh:Science, 0303 health sciences, Multidisciplinary, Virulence, Infectious Diseases/Nosocomial and Healthcare-Associated Infections, Microbiology/Immunity to Infections, 3. Good health, Staphylococcus aureus, Lysozyme, Research Article, Sigma Factor, Biology, Settore MED/07 - MICROBIOLOGIA E MICROBIOLOGIA CLINICA, Microbiology, 03 medical and health sciences, Bacterial Proteins, Acetyltransferases, medicine, Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, Carbon-Oxygen Ligases, DNA Primers, 030304 developmental biology, Innate immune system, Infectious Diseases/Antimicrobials and Drug Resistance, Models, Genetic, 030306 microbiology, lcsh:R, Enterococcu faecalis, biology.organism_classification, Immunity, Innate, chemistry, Mutagenesis, Mutation, Muramidase, lcsh:Q, Bacteria, Antimicrobial Cationic Peptides
Abstract: International audience; Background: Enterococcus faecalis is one of the leading agents of nosocomial infections. To cause diseases, pathogens or opportunistic bacteria have to adapt and survive to the defense systems encountered in the host. One of the most important compounds of the host innate defense response against invading microorganisms is lysozyme. It is found in a wide variety of body fluids, as well as in cells of the innate immune system. Lysozyme could act either as a muramidase and/or as a cationic antimicrobial peptide. Like Staphylococcus aureus, E. faecalis is one of the few bacteria that are completely lysozyme resistant.Results: This study revealed that oatA (O-acetyl transferase) and dlt (D-Alanylation of lipoteicoic acids) genes contribute only partly to the lysozyme resistance of E. faecalis and that a specific transcriptional regulator, the extracytoplasmic function SigV sigma factor plays a key role in this event. Indeed, the sigV single mutant is as sensitive as the oatA/dltA double mutant, and the sigV/oatA/dltA triple mutant displays the highest level of lysozyme sensitivity suggesting synergistic effects of these genes. In S. aureus, mutation of both oatA and dlt genes abolishes completely the lysozyme resistance, whereas this is not the case in E. faecalis. Interestingly SigV does not control neither oatA nor dlt genes. Moreover, the sigV mutants clearly showed a reduced capacity to colonize host tissues, as they are significantly less recovered than the parental JH2-2 strain from organs of mice subjected to intravenous or urinary tract infections.Conclusions: This work led to the discovery of an original model of lysozyme resistance mechanism which is obviously more complex than those described for other Gram positive pathogens. Moreover, our data provide evidences for a direct link between lysozyme resistance and virulence of E. faecalis.
Published: 2010

34. ace, Which Encodes an Adhesin in Enterococcus faecalis, Is Regulated by Ers and Is Involved in Virulence

Author: Yanick Auffray, Maurizio Sanguinetti, Brunella Posteraro, Pascale Serror, Axel Hartke, Jean-Christophe Giard, Francois Lebreton, Eliette Riboulet-Bisson, Riccardo Torelli, Laboratoire de Microbiologie de l’Environnement (LME), Institut National de la Recherche Agronomique (INRA)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Bactéries Lactiques et Pathogènes Opportunistes (UBLO), Institut National de la Recherche Agronomique (INRA), Istituto di Microbiologia - Institute of Microbiology [Rome], Università Cattolica del S. Cuore - Catholic University of the Sacred Hearth, Lebreton, François, Riboulet-Bisson, Eliette, and Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt)
Subjects: enterococcus, [SDV]Life Sciences [q-bio], Immunology, Colony Count, Microbial, Repressor, Virulence, Kidney, Microbiology, Settore MED/07 - MICROBIOLOGIA E MICROBIOLOGIA CLINICA, Virulence factor, Enterococcus faecalis, Bile Acids and Salts, Mice, 03 medical and health sciences, Bacterial Proteins, Transcriptional regulation, Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Transcription factor, Cells, Cultured, 030304 developmental biology, Mice, Inbred BALB C, 0303 health sciences, biology, 030306 microbiology, Gene Expression Profiling, Macrophages, Genetic Complementation Test, Promoter, Gene Expression Regulation, Bacterial, biology.organism_classification, Molecular Pathogenesis, 3. Good health, Lepidoptera, Repressor Proteins, Bacterial adhesin, Infectious Diseases, Female, Parasitology, Carrier Proteins, Gene Deletion, Transcription Factors
Abstract: Enterococcus faecalis is an opportunistic pathogen that causes numerous infectious diseases in humans and is a major agent of nosocomial infections. In this work, we showed that the recently identified transcriptional regulator Ers (PrfA like), known to be involved in the cellular metabolism and the virulence of E. faecalis , acts as a repressor of ace , which encodes a collagen-binding protein. We characterized the promoter region of ace , and transcriptional analysis by reverse transcription-quantitative PCR and mobility shift protein-DNA binding assays revealed that Ers directly regulates the expression of ace . Transcription of ace appeared to be induced by the presence of bile salts, probably via the deregulation of ers . Moreover, with an ace deletion mutant and the complemented strain and by using an insect ( Galleria mellonella ) virulence model, as well as in vivo-in vitro murine macrophage models, we demonstrated for the first time that Ace can be considered a virulence factor for E. faecalis . Furthermore, animal experiments revealed that Ace is also involved in urinary tract infection by E. faecalis .
Published: 2009

35. Effects of species traits on the genetic diversity of high-mountain plants: a multi-species study across the Alps and the Carpathians

Author: Delphine Rioux, Grażyna Korbecka, Licia Colli, Sabine Brodbeck, Michał Ronikier, Pierre Taberlet, Nadir Alvarez, Myriam Gaudeul, Ovidiu Paun, Andreas Tribsch, Felix Gugerli, T. Englisch, Marco Pellecchia, Elżbieta Cieślak, Fanny Schüpfer, Ludovic Gielly, Manuela Winkler, Rolf Holderegger, Riccardo Negrini, Marcela van Loo, Peter Schönswetter, Conny Thiel-Egenter, WSL Swiss Federal Research Institute, SWISS FEDERAL RESEARCH INSTITUTE WSL, Laboratoire de Botanique Evolutive, Universite de Neuchdtel, Institute of Botany, Polska Akademia Nauk = Polish Academy of Sciences (PAN), Istituto di Zootecnica, Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt), Department of Biogeography, University of Vienna [Vienna], Département Systématique et Évolution, Muséum national d'Histoire naturelle (MNHN), Laboratoire d'Ecologie Alpine (LECA), Université Joseph Fourier - Grenoble 1 (UJF)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS), Department of Systematic and Evolutionary Botany, Department of Organismic Biology/Ecology and Diversity of Plants, and Universität Salzburg
Subjects: 0106 biological sciences, Range (biology), elevation, Biogeography, Seed dispersal, consequences, [SDE.MCG]Environmental Sciences/Global Changes, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, 010603 evolutionary biology, 01 natural sciences, Saxifraga oppositifolia, ice ages, Quaternary, 03 medical and health sciences, Life-history traits, phylogeographical history, glacial refugia, population-size, Nei's gene diversity, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, Global and Planetary Change, Genetic diversity, AFLPs, Ecology, alpine plants, Alps, saxifraga-oppositifolia, alpine, conservation, genetic diversity, differentiation, 15. Life on land, respiratory system, biology.organism_classification, campanulaceae, range-wide sampling grid, Anemophily, Carpathians, glaciations, Biological dispersal, Alpha diversity, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, human activities
Abstract: International audience; To test the influence of various species traits, elevation and phylogeographical history on the genetic diversity of high-mountain plants in the Alps and Carpathians. The regular sampling grid comprised the whole range of the European Alps and the Carpathians. Twenty-two high-mountain plant species were exhaustively sampled and their genetic diversity was assessed with amplified fragment length polymorphisms (AFLPs). ANOVAs were used to check for relationships between species traits and species genetic diversity, and to test whether genetic diversity was influenced by altitude and phylogeographical history (i.e. Alps versus Carpathians). In both mountain systems, species dispersed and pollinated by wind showed higher genetic diversity than species with self or insect pollination, and with animal- or gravity-dispersed seeds. Only in the Alps did altitudinal range size affect species genetic diversity significantly: species with narrow altitudinal ranges in the highest vegetation belts had significantly higher genetic diversity than those expanding over wide altitudinal ranges. Genetic diversity was species specific and significantly higher in the Alps than in the Carpathians, but it was not influenced by elevation. Wind pollination and wind dispersal seem to foster high genetic diversity. However, species traits are often associated and their effects on genetic diversity cannot be clearly disentangled. As genetic diversity is species specific, comparisons across species need to be interpreted with care. Genetic diversity was generally lower in the Carpathians than in the Alps, due to higher topographical isolation of alpine habitats in the Carpathians and this mountain massif's divergent phylogeographical history. Elevation did not influence genetic diversity, challenging the long-held view of decreasing genetic diversity with increasing elevation in mountain plants.
Published: 2009

36. The goat domestication process inferred from large-scale mitochondrial DNA analysis of wild and domestic individuals

Author: François Pompanon, Marjan Mashkour, Riccardo Negrini, Hamid Reza Rezaei, Özge Balkız, Hamid-Reza Naghash, Jean-Denis Vigne, Oscar E. Gaggiotti, Pierre Taberlet, Saeid Naderi, Paolo Ajmone-Marsan, Michael G. B. Blum, Aykut Kence, Laboratoire d'Ecologie Alpine (LECA), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA), TIMB, Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble - UMR 5525 (TIMC-IMAG), Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-IMAG-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-IMAG-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Station Biologique de la Tour du Valat, Archéologies et Sciences de l'Antiquité (ArScAn), Université Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Institut national de recherches archéologiques préventives (Inrap)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Archéozoologie et histoire des sociétés (AHS), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Natural Resources Faculty, University of Guilan, Environmental Sciences Department, Gorgan University of Agriculture and Natural Resources, Ulstituto di Zootecnica, Università Cattolica del S. Cuore - Catholic University of the Sacred Hearth, Biology Department, Middle East Technical University [Ankara] (METU), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Archéozoologie, histoire des sociétés et des peuplements animaux (AHS), Université Joseph Fourier - Grenoble 1 (UJF)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS), and Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt)
Subjects: MESH: Sequence Analysis, DNA, Turkey, MESH: Geography, Range (biology), Population Dynamics, Social Sciences, Iran, phylogeography, Haplogroup, Capra hircus, MESH: Turkey, genetics, MESH: Animals, MESH: Genetic Variation, MESH: Phylogeny, Phylogeny, 2. Zero hunger, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, education.field_of_study, Multidisciplinary, Geography, Ecology, Goats, Agriculture, 04 agricultural and veterinary sciences, humanities, Animals, Domestic, initial domestication, Neolithic expansion, Livestock, MESH: Agriculture, [SDE.MCG]Environmental Sciences/Global Changes, MESH: Bayes Theorem, Molecular Sequence Data, Population, Animals, Wild, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, DNA, Mitochondrial, MESH: Goats, 03 medical and health sciences, Middle East, Animals, MESH: Animals, Domestic, MESH: Animals, Wild, education, Domestication, 030304 developmental biology, livestock origins, inference, MESH: Molecular Sequence Data, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], business.industry, Maximum-likelihood, 0402 animal and dairy science, MESH: DNA, Mitochondrial, Genetic Variation, Bayes Theorem, Sequence Analysis, DNA, MESH: Haplotypes, MESH: Population Dynamics, 040201 dairy & animal science, phylogenetic trees, Phylogeography, Haplotypes, MESH: Iran, sequences, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, Human mitochondrial DNA haplogroup
Abstract: The emergence of farming during the Neolithic transition, including the domestication of livestock, was a critical point in the evolution of human kind. The goat ( Capra hircus ) was one of the first domesticated ungulates. In this study, we compared the genetic diversity of domestic goats to that of the modern representatives of their wild ancestor, the bezoar, by analyzing 473 samples collected over the whole distribution range of the latter species. This partly confirms and significantly clarifies the goat domestication scenario already proposed by archaeological evidence. All of the mitochondrial DNA haplogroups found in current domestic goats have also been found in the bezoar. The geographic distribution of these haplogroups in the wild ancestor allowed the localization of the main domestication centers. We found no haplotype that could have been domesticated in the eastern half of the Iranian Plateau, nor further to the east. A signature of population expansion in bezoars of the C haplogroup suggests an early domestication center on the Central Iranian Plateau (Yazd and Kerman Provinces) and in the Southern Zagros (Fars Province), possibly corresponding to the management of wild flocks. However, the contribution of this center to the current domestic goat population is rather low (1.4%). We also found a second domestication center covering a large area in Eastern Anatolia, and possibly in Northern and Central Zagros. This last domestication center is the likely origin of almost all domestic goats today. This finding is consistent with archaeological data identifying Eastern Anatolia as an important domestication center.
Published: 2008

37. Comparative study of the physiological roles of three peroxidases (NADH peroxidase, Alkyl hydroperoxide reductase and Thiol peroxidase) in oxidative stress response, survival inside macrophages and virulence of Enterococcus faecalis

Author: Brunella Posteraro, Abdellah Benachour, Axel Hartke, Jean-Christophe Giard, Stéphanie La Carbona, Maurizio Sanguinetti, Nicolas Sauvageot, Yanick Auffray, Laboratoire de Microbiologie de l’Environnement (LME), Institut National de la Recherche Agronomique (INRA)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Istituto di Microbiologia - Institute of Microbiology [Rome], Università Cattolica del S. Cuore - Catholic University of the Sacred Hearth, and Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt)
Subjects: Cells, [SDV]Life Sciences [q-bio], Colony Count, Mutant, Colony Count, Microbial, Virulence, Biology, Reductase, Peritonitis, Microbiology, Settore MED/07 - MICROBIOLOGIA E MICROBIOLOGIA CLINICA, Enterococcus faecalis, 03 medical and health sciences, Mice, Microbial, Peritoneal, Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, ENTEROCOCCUS FAECALIS, NADH peroxidase, HYDROGEN PEROXIDE, Molecular Biology, Cells, Cultured, REGULON, 030304 developmental biology, 0303 health sciences, Cultured, Microbial Viability, 030306 microbiology, Macrophages, PEROXIDASE, Peroxiredoxins, biology.organism_classification, Oxidants, Survival Analysis, Aerobiosis, Anti-Bacterial Agents, OXYDATIVE STRESS, Oxidative Stress, Regulon, Biochemistry, Peroxidases, Catalase, biology.protein, Macrophages, Peritoneal, VIRULENCE, Gene Deletion, Peroxidase
Abstract: International audience; The opportunistic pathogen Enterococcus faecalis is well equipped with peroxidatic activities. It harbours three loci encoding a NADH peroxidase, an alkyl hydroperoxide reductase and a protein (EF2932) belonging to the AhpC/TSA family. We present results demonstrating that ef2932 does encode a thiol peroxidase (Tpx) and show that it is part of the regulon of the hydrogen peroxide regulator HypR. Characterization of unmarked deletion mutants showed that all three peroxidases are important for the defence against externally provided H2O2. Exposure to internal generated H2O2 by aerobic growth on glycerol, lactose, galactose or ribose showed that Npr was absolutely required for aerobic growth on glycerol and optimal growth on the other substrates. Growth on glycerol was also dependent on Ahp. Addition of catalase restored growth of the mutants, and therefore, extracellular H2O2 concentrations have been determined. This showed that the time point of growth arrest of the Δnpr mutant correlated with the highest H2O2 concentration measured. Analysis of the survival of the different strains inside peritoneal macrophages revealed that Tpx was the most important antioxidant activity for protecting the cells against the hostile phagocyte environment. Finally, the Δtpx and the triple mutant showed attenuated virulence in a mouse peritonitis model.
Published: 2007

38. Implication of (Mn)superoxide dismutase of Enterococcus faecalis in oxidative stress responses and survival inside macrophages

Author: Maurizio Sanguinetti, Nicolas Verneuil, Yanick Auffray, Axel Hartke, Jean-Christophe Giard, Jean-Marie Laplace, Alain Mazé, Abdellah Benachour, Laboratoire de Microbiologie de l’Environnement (LME), Institut National de la Recherche Agronomique (INRA)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Istituto di Microbiologia - Institute of Microbiology [Rome], Università Cattolica del S. Cuore - Catholic University of the Sacred Hearth, and Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt)
Subjects: Male, MnSOD, Manganese-containing superoxide dismutase, Diaminopimelate epimerase, [SDV]Life Sciences [q-bio], Mutant, DAPE, medicine.disease_cause, Virulence factor, chemistry.chemical_compound, Mice, Rapid amplification of cDNA ends PCR, Menadione, Cm, Enterococcus faecalis, 0303 health sciences, Mice, Inbred BALB C, Strain (chemistry), biology, ROS, Erythromycin, Deferoxamine, RACE-PCR, medicine.drug, tBOOH, Superoxide dismutase, Microbiology, 03 medical and health sciences, Em, medicine, Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Tert-butylhydroperoxide, SOD, 030304 developmental biology, 030306 microbiology, Genetic Complementation Test, biology.organism_classification, Molecular biology, Kinetics, Oxidative Stress, Chloramphenicol, chemistry, Mutation, biology.protein, Macrophages, Peritoneal, Reactive oxygen species, Oxidative stress
Abstract: The gene encoding the manganese-containing superoxide dismutase (MnSOD) ofEnterococcus faecaliswas characterized. It is transcribed monocistronically from an upstream promoter identified by rapid amplification of cDNA ends (RACE)-PCR. AsodAmutant was constructed and characterized. Growth of the mutant strain was not significantly different from that of its wild-type counterpart in standing and aerated cultures. However, the mutant was more sensitive towards menadione and hydroperoxide stresses. The response to H2O2stress was analysed in more detail, and the mode of killing of this oxidant was different under anaerobic and aerobic conditions. Cultures grown and challenged under anaerobic conditions were highly sensitive to treatment with 35 mM H2O2. They were largely protected by the iron chelator deferoxamine, which suggested that killing was mainly due to an enhanced Fenton reaction. In contrast, neither strain was protected by the iron chelators deferoxamine and diethylenetriaminepentaacteic acid when grown and challenged under aerobic conditions, which suggested that inactivation of the cells by H2O2was due to another killing mode. ThesodAmutant was more sensitive under these conditions, showing that MnSOD is also important for protecting the cells from damage under aerobic conditions. Finally, the MnSOD ofEnt. faecalismay be considered to be a virulence factor, since survival of the corresponding mutant strain was highly affected inside mouse peritoneal macrophages.
Published: 2006

39. Characterization of Ers, a PrfA-like regulator of Enterococcus faecalis

Author: Nicolas Verneuil, Eliette Riboulet, Axel Hartke, Maurizio Sanguinetti, Jean-Christophe Giard, Yanick Auffray, Laboratoire de Microbiologie de l’Environnement (LME), Institut National de la Recherche Agronomique (INRA)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Istituto di Microbiologia - Institute of Microbiology [Rome], Università Cattolica del S. Cuore - Catholic University of the Sacred Hearth, and Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt)
Subjects: Microbiology (medical), [SDV]Life Sciences [q-bio], Immunology, Mutant, Molecular Sequence Data, Regulator, Virulence, Biology, medicine.disease_cause, Microbiology, Enterococcus faecalis, 03 medical and health sciences, Mice, PrfA-like, Listeria monocytogenes, Genes, Regulator, medicine, Transcriptional regulation, Immunology and Allergy, Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acid Sequence, Gene, Gram-Positive Bacterial Infections, 030304 developmental biology, 0303 health sciences, Base Sequence, 030306 microbiology, Reverse Transcriptase Polymerase Chain Reaction, Genetic Complementation Test, General Medicine, biology.organism_classification, 3. Good health, Mutagenesis, Insertional, Oxidative Stress, RNA, Bacterial, Infectious Diseases, Transcriptional regulator, Streptococcus pyogenes, Macrophages, Peritoneal, Sequence Alignment, Peptide Termination Factors
Abstract: International audience; We have identified a transcriptional regulator, named Ers (for enterococcal regulator of survival), of Enterococcus faecalis, an important opportunistic bacterium commonly recovered from hospitalized patients. Ers is a member of the Crp/Fnr family and is 69% similar to Srv, a PrfA-like regulator of Streptococcus pyogenes implicated in virulence, and is the E. faecalis protein most closely related to PrfA, a positive regulator of virulence genes in Listeria monocytogenes. In an in vivo–in vitro macrophage infection model, the survival of an ers mutant was highly significantly decreased compared with that of the parental strain JH2-2. This mutant was more than 10-fold more sensitive to oxidative challenge by hydrogen peroxide. In order to identify genes whose expression was under Ers control, the RNA levels of 31 likely candidates were measured by real-time quantitative PCR. The results indicate that ers may be autoregulated and that the locus ef0082 appears to be positively regulated by Ers. Nevertheless, mutation of ef0082 did not result in any detectable changes in the survival of the bacterium within murine macrophages.
Published: 2006

40. Contribution of a PerR-like regulator to the oxidative-stress response and virulence of Enterococcus faecalis

Author: Brunella Posteraro, Alain Rincé, Yanick Auffray, Axel Hartke, Jean-Christophe Giard, Nicolas Verneuil, Maurizio Sanguinetti, Giovanni Fadda, Laboratoire de Microbiologie de l’Environnement (LME), Institut National de la Recherche Agronomique (INRA)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Istituto di Microbiologia - Institute of Microbiology [Rome], Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt), and Università Cattolica del S. Cuore - Catholic University of the Sacred Hearth
Subjects: Transcription, Genetic, [SDV]Life Sciences [q-bio], Mutant, Molecular Sequence Data, Virulence, Locus (genetics), bacillus subtillis, Bacillus subtilis, Microbiology, Enterococcus faecalis, 03 medical and health sciences, Bacterial Proteins, régulation, Transcriptional regulation, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Gene, 030304 developmental biology, bactérie, 0303 health sciences, biology, 030306 microbiology, Microbiology and Parasitology, ROS, Gene Expression Regulation, Bacterial, stress oxydant, biology.organism_classification, Phenotype, Microbiologie et Parasitologie, VIRULENCE, OXIDATIVE STRESS, GENE EXPRESSION REGULATION, TRANSCRIPTIONAL ACTIVITY, PERR GENE, Repressor Proteins, Oxidative Stress, Reactive oxygen species, facteur de transcription, Transcription Factors
Abstract: PerR is one of the most important transcriptional regulators involved in the oxidative-stress response in Bacillus subtilis. Here, the homologous gene in Enterococcus faecalis, ranked among the leading causes of nosocomial infection, was characterized and analysed. Phenotype analysis showed that the perR mutant was significantly more resistant to H2O2 challenge (PperR-mutant strains by real-time quantitative PCR. Surprisingly, low quantitative differences in the transcriptional activity of these genes in the mutant versus wild-type were observed. Likewise, this locus was not involved in survival within murine macrophages, but in the mouse peritonitis model, the perR mutant appeared less lethal than the JH2-2 wild-type strain. The combined results show that PerR affects E. faecalis virulence and that its implication in the transcriptional regulation in this bacterium deviates from the B. subtilis model.
Published: 2005

41. Implication of hypR in the virulence and oxidative stress response of Enterococcus faecalis

Author: Nicolas Verneuil, Maurizio Sanguinetti, Yanick Auffray, Jean-Christophe Giard, Alain Rincé, Axel Hartke, Laboratoire de Microbiologie de l’Environnement (LME), Institut National de la Recherche Agronomique (INRA)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Istituto di Microbiologia - Institute of Microbiology [Rome], Università Cattolica del S. Cuore - Catholic University of the Sacred Hearth, and Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt)
Subjects: Transcription, Genetic, [SDV]Life Sciences [q-bio], Glutathione reductase, Virulence, Peritonitis, Reductase, medicine.disease_cause, Microbiology, Virulence factor, Enterococcus faecalis, Mice, 03 medical and health sciences, Bacterial Proteins, Animals, Outbred Strains, Genetics, Transcriptional regulation, medicine, Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, Gram-Positive Bacterial Infections, 030304 developmental biology, Mice, Inbred ICR, 0303 health sciences, biology, 030306 microbiology, HypR, Gene Expression Regulation, Bacterial, biology.organism_classification, Molecular biology, Regulon, Oxidative stress, Female, Heat-Shock Response
Abstract: International audience; HypR has recently been described as the first transcriptional regulator involved in the oxidative stress response and in the intracellular survival of Enterococcus faecalis within macrophages. In order to characterize the HypR regulon, real-time quantitative RT-PCR experiments were performed. The expression of four genes involved in the oxidative stress response encoding catalase, glutathione reductase, and the two subunits of alkyl hydroperoxide reductase were down regulated in the hypR background under H2O2 condition. These findings show that HypR acts as a transcriptional activator, especially during oxidative stress. In addition, DNAse I footprinting assays allowed us to identify the HypR-protected DNA regions corresponding to the “HypR box” in the hypR promoter. Moreover, the effect of the hypR mutation on the virulence of E. faecalis was evaluated in comparison with the wild-type JH2–2 strain using a mouse peritonitis model. Our results revealed that HypR appears to be an important virulence factor in E. faecalis.
Published: 2005

42. Effects of the Enterococcus faecalis hypR Gene Encoding a New Transcriptional Regulator on Oxidative Stress Response and Intracellular Survival within Macrophages

Author: Jean-Christophe Giard, Yanick Auffray, Yoann Le Breton, Maurizio Sanguinetti, Nicolas Verneuil, Brunella Posteraro, Giovanni Fadda, Axel Hartke, Laboratoire de Microbiologie de l’Environnement (LME), Institut National de la Recherche Agronomique (INRA)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Istituto di Microbiologia - Institute of Microbiology [Rome], Università Cattolica del S. Cuore - Catholic University of the Sacred Hearth, and Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt)
Subjects: Male, Transcription, Genetic, Operon, [SDV]Life Sciences [q-bio], Immunology, Mutant, Molecular Sequence Data, Microbiology, Enterococcus faecalis, Insertional mutagenesis, 03 medical and health sciences, Mice, Bacterial Proteins, Animals, Humans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Northern blot, Gene, 030304 developmental biology, Regulator gene, Regulation of gene expression, 0303 health sciences, Mice, Inbred BALB C, biology, Base Sequence, 030306 microbiology, Gene Expression Regulation, Bacterial, Hydrogen Peroxide, biology.organism_classification, Oxidants, Molecular biology, Molecular Pathogenesis, Oxidative Stress, Infectious Diseases, Macrophages, Peritoneal, Parasitology, Heat-Shock Response
Abstract: In order to identify regulators of the oxidative stress response in Enterococcus faecalis , an important human pathogen, several genes annotated as coding for transcriptional regulators were inactivated by insertional mutagenesis. One mutant, affected in the ef2958 locus (designated hypR [hydrogen peroxide regulator]), appeared to be highly sensitive to oxidative challenge caused by hydrogen peroxide. Moreover, testing of the hypR mutant by using an in vivo-in vitro macrophage infection model resulted in a highly significant reduction in survival compared to the survival of parent strain JH2-2. Northern blot analyses were carried out with probes specific for genes encoding known antioxidant enzymes, and they showed that the ahpCF (alkyl hydro p eroxide reductase) transcript was expressed less in mutant cells. Mobility shift protein-DNA binding assays revealed that HypR regulated directly the expression of hypR itself and the ahpCF operon. Our combined results showed that HypR appeared to be directly involved in the expression of ahpCF genes under oxidative stress conditions and suggested that this regulator could contribute to the virulence of E. faecalis .
Published: 2004

43. Geographic structure in goat diversity as revealed by AFLP molecular markers

Author: Marsan, P. A., Negrini, R., Milanesi, E., Paola Crepaldi, Cicogna, M., Zagdsuren, Y., Ertugrul, O., Luikart, G., Taberlet, P., Istituto di Zootecnica, Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt), Istituto di Zootecnia Generale, Università degli Studi di Milano [Milano] (UNIMI), Research Institute of Animal Husbandry, Mongolian State University of Agriculture, Department of Biostatistique, Ankara University, Laboratoire d'Ecologie Alpine (LECA), and Université Joseph Fourier - Grenoble 1 (UJF)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV.EE]Life Sciences [q-bio]/Ecology, environment, genetic distance, genetic diversity, mitochondrial DNA, [SDV.BID]Life Sciences [q-bio]/Biodiversity, microsatellites, polymorphism, genetic variation, loci, genetic markers, geographical distribution, genetics, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, genes, genomes
Abstract: International audience; We investigated the genetic variation in domestic goats (Capra hircus) and compared the geographic and genetic diversity in this species on a large scale (world-wide) and on a local scale (Italian Alps). A total of 392 domestic goats belonging to 16 populations from Turkey, Mongolia, Malaysia, Nigeria, Italy and Switzerland were analysed with 118 AFLP markers. A high correlation between genetic and geographic distance (r=0.75; Pless than or equal to 0.01) was observed on a worldwide scale. AFLP data were in contrast with mitochondrial DNA data that showed weak geographic structure in goats. We hypothesized that in the process of breed formation, local wild and domesticated males significantly contributed their genomes to the geographic partition and present characteristics of the local breeds.
Published: 2002

44. A European test of pesticide-leaching models: methodology and major recommendations

Author: Marco Trevisan, B. Gottesbüren, V. Gouy, Colin D. Brown, O. M. Eklo, A.M.A. van der Linden, Ettore Capri, Marnik Vanclooster, J.J.T.I. Boesten, Université Catholique de Louvain = Catholic University of Louvain (UCL), ALTERRA WAGENINGEN NLD, Partenaires IRSTEA, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt), Cranfield University, THE NORWEGIAN CROP RESEARCH INSTITUTE AS NOR, BASF AG LIMBURGERHOF DEU, Qualité des eaux et prévention des pollutions (UR QELY), Centre national du machinisme agricole, du génie rural, des eaux et forêts (CEMAGREF), and RIVM NLD
Subjects: Engineering, Operations research, CEMAGREF, ROYAUME UNI, Soil Science, Pesticide-leaching modelling, Pesticide leaching, 010501 environmental sciences, 01 natural sciences, Civil engineering, Model validation, media_common.cataloged_instance, Wageningen Environmental Research, European union, ITALIE, QELY, 0105 earth and related environmental sciences, Earth-Surface Processes, Water Science and Technology, media_common, Risk assessment, POL, Water transport, business.industry, 04 agricultural and veterinary sciences, PAYS BAS, [SDE]Environmental Sciences, 040103 agronomy & agriculture, Process description, 0401 agriculture, forestry, and fisheries, business, Agronomy and Crop Science, ALLEMAGNE
Abstract: Testing of pesticide-leaching models is important in view of their increasing use in pesticide registration procedures in the European Union. This paper presents the methodology and major conclusions of a test of pesticide-leaching models. Twelve models simulating the vertical one-dimensional movement of water, solute, heat, and, in particular, pesticides, through the soil profile were used by 36 different modellers. The adopted modelling codes differ in terms of modelling concepts and modelling hypothesis. Modellers were affiliated to industry and to the scientific community as well. Four quality datasets were identified to perform the analysis. The dataset included field and lysimeter data, collected in the Netherlands, Germany, Italy and the UK. As well, non-structured as structured soils were available in the dataset. To elucidate the ability to model correctly water transport, solute transport, heat transport and pesticide transport in soils, a stepwise evaluation approach was followed. Splitting up the experimental dataset enabled us to quantify the calibration capability and the prediction capability of the models. The simulations were performed by different model users enabling us also to characterise output variability in terms of user dependent interpretation of the model input and parameters. Recommendations are formulated for improving the quality of modelling datasets, and the process description of water, solute, and heat transport in a pesticide-leaching model, plus the process description of pesticide fate. Application of the principles of good modelling practice (GMP) is briefly described. (C) 2000 Elsevier Science B.V. All rights reserved.
Published: 2000

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