25 results on '"Trontin C"'
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2. Guidelines for the reliable use of high throughput sequencing technologies to detect plant pathogens and pests
- Author
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Massart, Sébastien, Adams, Ian, Al Rwahnih, M., Baeyen, Steve, Bilodeau, Guillaume J., Blouin, Arnaud G., Boonham, Neil, Candresse, Thierry, Chandelier, Anne, de Jonghe, Kris, Fox, Adrian, Gaafar, Yahya Z.A., Gentit, Pascal, Haegeman, Annelies, Ho, Wellcome, Hurtado-Gonzales, Oscar, Jonkers, Wilfried, Kreuze, Jan, Kutnjak, D., Landa, Blanca, Liu, M., Maclot, François, Malapi-Wight, Martha, Maree, Hano J., Martoni, Francesco, Mehle, Nataša, Minafra, Angelantonio, Mollov, Dimitre, Moreira, Adriana, Nakhla, Mark, Petter, F., Piper, Alexander M., Ponchart, Julien, Rae, Robbie, Remenant, Benoit, Rivera, Yazmin, Rodoni, Brendan, Boterans, M., Roenhorst, J.W., Rollin, Johan, Saldarelli, Pasquale, Santala, Johanna, Souza-Richards, Rose, Spadaro, Davide, Studholme, David J., Sultmanis, Stefanie, van der Vlugt, R.A.A., Tamisier, Lucie, Trontin, C., Vazquez-Iglesias, Ines, Vicente, Claudia S.L., Vossenberg, Bart T.L.H., Westenberg, Marcel, Wetzel, Thierry, Ziebell, Heiko, Lebas, Benedicte, Massart, Sébastien, Adams, Ian, Al Rwahnih, M., Baeyen, Steve, Bilodeau, Guillaume J., Blouin, Arnaud G., Boonham, Neil, Candresse, Thierry, Chandelier, Anne, de Jonghe, Kris, Fox, Adrian, Gaafar, Yahya Z.A., Gentit, Pascal, Haegeman, Annelies, Ho, Wellcome, Hurtado-Gonzales, Oscar, Jonkers, Wilfried, Kreuze, Jan, Kutnjak, D., Landa, Blanca, Liu, M., Maclot, François, Malapi-Wight, Martha, Maree, Hano J., Martoni, Francesco, Mehle, Nataša, Minafra, Angelantonio, Mollov, Dimitre, Moreira, Adriana, Nakhla, Mark, Petter, F., Piper, Alexander M., Ponchart, Julien, Rae, Robbie, Remenant, Benoit, Rivera, Yazmin, Rodoni, Brendan, Boterans, M., Roenhorst, J.W., Rollin, Johan, Saldarelli, Pasquale, Santala, Johanna, Souza-Richards, Rose, Spadaro, Davide, Studholme, David J., Sultmanis, Stefanie, van der Vlugt, R.A.A., Tamisier, Lucie, Trontin, C., Vazquez-Iglesias, Ines, Vicente, Claudia S.L., Vossenberg, Bart T.L.H., Westenberg, Marcel, Wetzel, Thierry, Ziebell, Heiko, and Lebas, Benedicte
- Abstract
High-throughput sequencing (HTS) technologies have the potential to become one of the most significant advances in molecular diagnostics. Their use by researchers to detect and characterize plant pathogens and pests has been growing steadily for more than a decade and they are now envisioned as a routine diagnostic test to be deployed by plant pest diagnostics laboratories. Nevertheless, HTS technologies and downstream bioinformatics analysis of the generated datasets represent a complex process including many steps whose reliability must be ensured. The aim of the present guidelines is to provide recommendations for researchers and diagnosticians aiming to reliably use HTS technologies to detect plant pathogens and pests. These guidelines are generic and do not depend on the sequencing technology or platform. They cover all the adoption processes of HTS technologies from test selection to test validation as well as their routine implementation. A special emphasis is given to key elements to be considered: undertaking a risk analysis, designing sample panels for validation, using proper controls, evaluating performance criteria, confirming and interpreting results. These guidelines cover any HTS test used for the detection and identification of any plant pest (viroid, virus, bacteria, phytoplasma, mycetes, nematodes, arthropods, plants) from any type of matrix. Overall, their adoption by diagnosticians and researchers should greatly improve the reliability of pathogens and pest diagnostics and foster the use of HTS technologies in plant health.
- Published
- 2022
3. VALITEST - D6.9 Final Plan for the Dissemination and Exploitation of project Results (PDER)
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Petter, F., Trontin, C., and Gianinazzi, C.
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communication ,exploitable results ,plant health - Abstract
This document describes the final strategy developed to ensure the appropriate dissemination and exploitation of the outputs of the VALITEST project (Validation of diagnostic tests to support plant health). It presents the objectives of the dissemination and exploitation strategy, the tools used to ensure the dissemination of VALITEST outputs and the training activities organized in the framework of VALITEST. It also details VALITEST exploitation potential and how project partners, end-users and stakeholders can benefit from the final results of the project.
- Published
- 2021
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4. VALITEST - D6.8 Report on the organisation of training activities (webinars, video tutorial, practical training sessions)
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Petter F. and Trontin C.
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education ,test performance study ,concept of validation ,HTS ,plant health - Abstract
This deliverable presents the training activities organized in the framework of the VALITEST project. Due to the Covid-19 pandemic, the physical workshops planned for diagnostic laboratories could not be organised. All the training activities were held online in the format of webinars, practical training sessions and videos. Three series of activities covering different topics were organised: one on the concept of test validation in plant health, one on TPS organisation and one on the use and validation of High Throughput sequencing (HTS) tests for diagnostics of plant pests. The participation to those series and satisfaction of the participants are also described in this deliverable.
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- 2021
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5. VALITEST : Validation of diagnostic tests to support plant health
- Author
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Trontin, C., Agstner, B., Altenbach, D., Anthoine, G., Bagińska, H., Brittain, I., Chabirand, A., Chappé, A.M., Dahlin, P., Dreo, T., Freye-Minks, C., Gianinazzi, C., Harrison, C., Jones, G., Luigi, M., Massart, S., Mehle, N., Mezzalama, M., Mouaziz, H., Petter, F., Ravnikar, M., Raaymakers, T.M., Renvoisé, J.P., Rolland, M., Santos Paiva, M., Seddas, S., van der Vlugt, R., Vučurović, A., Trontin, C., Agstner, B., Altenbach, D., Anthoine, G., Bagińska, H., Brittain, I., Chabirand, A., Chappé, A.M., Dahlin, P., Dreo, T., Freye-Minks, C., Gianinazzi, C., Harrison, C., Jones, G., Luigi, M., Massart, S., Mehle, N., Mezzalama, M., Mouaziz, H., Petter, F., Ravnikar, M., Raaymakers, T.M., Renvoisé, J.P., Rolland, M., Santos Paiva, M., Seddas, S., van der Vlugt, R., and Vučurović, A.
- Abstract
VALITEST is an EU-funded project built to improve the reliability of diagnostic tests performed in plant health laboratories across the European and Mediterranean region. The project is undertaken by a consortium of 16 partners composed of research institutions, private companies (such as diagnostic kit providers), national plant protection organizations and one intergovernmental organization (EPPO). Current harmonized procedures for the validation and organization of test performance studies will be improved based on the experience gained from the project and by including appropriate statistical approaches, by adapting the process for new promising technologies (e.g. high-throughput sequencing) and by providing new guidelines for the production of reference materials for validation studies. The project will provide a more complete and precise description of the performance of 82 diagnostic tests targeting 11 pests of interest for stakeholders of the region. It will also tackle the need for proficient users by developing a horizontal approach for the evaluation of laboratories’ proficiency and by organizing training activities on the concept of validation. The outcomes of the project will stimulate, optimize and strengthen the interactions between stakeholders in plant health for better diagnostics and lay the foundations for structuring the quality and the commercial offers for plant health diagnostics tools thanks to the creation of a dedicated association and a quality charter.
- Published
- 2021
6. VALITEST - D6.4 Dissemination and Training plan
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Boutron N., Trontin C., and Petter F.
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education ,genetic structures ,communication ,guidelines ,plant health - Abstract
The training and dissemination plan presents the objectives of training and disseminations and the tools provided to ensure that the objectives will be met.
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- 2020
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7. VALITEST: Validation of diagnostic tests to support plant health
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Trontin, C., primary, Agstner, B., additional, Altenbach, D., additional, Anthoine, G., additional, Bagińska, H., additional, Brittain, I., additional, Chabirand, A., additional, Chappé, A. M., additional, Dahlin, P., additional, Dreo, T., additional, Freye‐Minks, C., additional, Gianinazzi, C., additional, Harrison, C., additional, Jones, G., additional, Luigi, M., additional, Massart, S., additional, Mehle, N., additional, Mezzalama, M., additional, Mouaziz, H., additional, Petter, F., additional, Ravnikar, M., additional, Raaymakers, T. M., additional, Renvoisé, J. P., additional, Rolland, M., additional, Santos Paiva, M., additional, Seddas, S., additional, Vlugt, R., additional, and Vučurović, A., additional
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- 2021
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8. VALITEST - D8.2 Technical periodic report M1-M18
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Anthoine G., Rolland M., Mouaziz H., Ravnikar M., Westenberg M., Massart S., van der Vlugt R., Agstner B., Jones G., Petter F., Trontin C., and Gianinazzi C.
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progress overview ,performed work ,plant health - Abstract
TheVALITEST technical periodic report M1-M18 details the work carried out by the partners and overviews the progress of the tasks as described in the Description of Actions (DoA) during the first reporting period M1-M18 (May 2018-October 2019).
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- 2020
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9. VALITEST - D6.6 Report on improved version of the validation section of the EPPO Database on diagnostic expertise, including new data provided by laboratories
- Author
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Boutron N., Petter F., and Trontin C.
- Subjects
validation section ,searching capacity improvement ,plant health - Abstract
The EPPO Database on Diagnostic expertise (http://dc.eppo.int/index.php) includes a specific section on validation data for diagnostic tests (http://dc.eppo.int/validationlist.php). Laboratories can deposit online validation data that they have generated on specific tests and these can be made visible to all users of the database. The validation data can then be retrieved from the database in the form of a PDF file including the description of the test evaluated (pest x matrix x method) and the performance data related to the test (the information is presented in a harmonized format). There is currently no possibility to sort the data except by pest and method. One of the objectives of VALITEST is to improve the searching capacity of the database to ensure optimal use. This report presents the new features of the validation section that have been identified from the survey and from discussions with users and with VALITEST partners. IT developments are ongoing. The new version of the EPPO Database on diagnostic expertise will be launched in April 2020.
- Published
- 2019
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10. VALITEST - D3.3 Guidelines and Standard Operating Procedures (SOP) finalised for the production of the reference materials
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Chappé AM., Chabirand A., Dahlin P., de Krom C., Dreo T., Gentit P., Laurenson L., Petter F., Spadaro D., Trontin C., van Diepeningen AD., van der Vlugt R., van Veen E., and Westenberg M.
- Subjects
RM ,plant health ,validation studies - Abstract
A general standard operating procedure (SOP) for the production of reference material (RM) for use in plant health diagnostics was developed within the VALITEST project. The general SOP was designed based on information on existing SOPs and guidelines available with the consortium partners (Deliverable 3.2) and partly incorporates the quality criteria for reference material (Deliverable 3.1). The general SOP describes the different steps required in the production process, ranging from the different possible sources of the reference material, tests to confirm its identity, possibly required multiplication steps to the actual production process. For each step in the process, criteria and critical points can be identified, but they will depend on the nature of the RM and on the target test in which the RM will be used. The original Deliverable 3.2 (February 2019) was evaluated by all partners (Milestone 3.4 Evaluation report) and updated towards this new version. The updated general standard operating procedure (SOP) for the production of reference material (RM) includes a stand-alone version of a template for the production of RM (Annex I) and an example of a full SOP for the production of RM of Fusarium circinatum to be used in (Real-Time) PCR assays (Annex II).
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- 2019
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11. Innovation technologique, changements organisationnels : quels enjeux pour la prévention ? Conférence scientifique de l'INRS. Nancy, 29-31 mars 2017
- Author
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Aublet-Cuvelier, A., Boini, S., Claudon, L., DELECROIX, B., GOVAERE, V., Guyot, S., Savescu, A., TRONTIN, C., LEICHLE, J., Département Homme au Travail (HT), Institut national de recherche et de sécurité (Vandoeuvre lès Nancy) (INRS ( Vandoeuvre lès Nancy)), Département Expertise et Conseil Technique (ECT), and Institut national de recherche et de sécurité (Paris) (INRS (Paris))
- Subjects
INFORMATION ,HYGIENE DU TRAVAIL ,FABRICATION ,ROBOT ,SECURITE DU TRAVAIL ,COMPTE RENDU ,[SHS.GESTION]Humanities and Social Sciences/Business administration ,ORGANISATION DU TRAVAIL ,TECHNOLOGIE AVANCEE ,INFORMATISATION ,TECHNOLOGIE DE L'INFORMATION ET DE LA COMMUNICATION ,CONGRES ,[SDV.MHEP]Life Sciences [q-bio]/Human health and pathology - Abstract
International audience; Les nouveaux outils d'aide à la production, les dispositifs informatiques de gestion de la production et des flux d'information obligent à repenser les méthodes de prévention. Dans un contexte d'intensification du travail, d’allongement de la vie active, de vieillissement de la population et de concurrence mondialisée, innovation technologique et changements organisationnels associés peuvent être des facteurs de risque pour la santé, notamment mentale, et la sécurité des travailleurs. Ces journées ont abordé la prévention des risques professionnels en lien avec trois principales familles émergentes d’innovations technologiques : celles de l’information, les nouveaux outils d’aide à la production et enfin les dispositifs informatiques de gestion de la production et des flux d’information. L’ensemble des présentations et le recueil de résumés sont disponibles sur le site : www.inrs-innovorg2017.fr/presentations-powerpoint/.
- Published
- 2017
12. Erratum: A pair of receptor-like kinases is responsible for natural variation in shoot growth response to mannitol treatment in Arabidopsis thaliana (Plant Journal (2014) 78 (121-133))
- Author
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Trontin, C, Kiani, S, Corwin, JA, Hématy, K, Yansouni, J, Kliebenstein, DJ, and Loudet, O
- Published
- 2014
13. Beyond the Barrier: Communication in the Root through the Endodermis
- Author
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Robbins, N. E., primary, Trontin, C., additional, Duan, L., additional, and Dinneny, J. R., additional
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- 2014
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14. Évaluation coût-bénéfice de la prevention du risque de manutention des maladies dans un hôpital public de soins, de réadaptation et de longue durée
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Trontin, C., primary, Glomot, L., additional, Saurel, D., additional, and Tresse, J., additional
- Published
- 2006
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15. VALITEST - D3.3 Guidelines and Standard Operating Procedures (SOP) finalised for the production of the reference materials
- Author
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Chappé AM., Chabirand, A., Dahlin, P., De Krom, C., Dreo, T., Gentit, P., Laurenson, L., Petter, F., Spadaro, D., Trontin, C., Van Diepeningen AD., Van Der Vlugt, R., Van Veen, E., and Westenberg, M.
- Subjects
RM ,8. Economic growth ,plant health ,validation studies - Abstract
A general standard operating procedure (SOP) for the production of reference material (RM) for use in plant health diagnostics was developed within the VALITEST project. The general SOP was designed based on information on existing SOPs and guidelines available with the consortium partners (Deliverable 3.2) and partly incorporates the quality criteria for reference material (Deliverable 3.1). The general SOP describes the different steps required in the production process, ranging from the different possible sources of the reference material, tests to confirm its identity, possibly required multiplication steps to the actual production process. For each step in the process, criteria and critical points can be identified, but they will depend on the nature of the RM and on the target test in which the RM will be used. The original Deliverable 3.2 (February 2019) was evaluated by all partners (Milestone 3.4 Evaluation report) and updated towards this new version. The updated general standard operating procedure (SOP) for the production of reference material (RM) includes a stand-alone version of a template for the production of RM (Annex I) and an example of a full SOP for the production of RM of Fusarium circinatum to be used in (Real-Time) PCR assays (Annex II).
16. Managing the deluge of newly discovered plant viruses and viroids: an optimized scientific and regulatory framework for their characterization and risk analysis.
- Author
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Fontdevila Pareta N, Khalili M, Maachi A, Rivarez MPS, Rollin J, Salavert F, Temple C, Aranda MA, Boonham N, Botermans M, Candresse T, Fox A, Hernando Y, Kutnjak D, Marais A, Petter F, Ravnikar M, Selmi I, Tahzima R, Trontin C, Wetzel T, and Massart S
- Abstract
The advances in high-throughput sequencing (HTS) technologies and bioinformatic tools have provided new opportunities for virus and viroid discovery and diagnostics. Hence, new sequences of viral origin are being discovered and published at a previously unseen rate. Therefore, a collective effort was undertaken to write and propose a framework for prioritizing the biological characterization steps needed after discovering a new plant virus to evaluate its impact at different levels. Even though the proposed approach was widely used, a revision of these guidelines was prepared to consider virus discovery and characterization trends and integrate novel approaches and tools recently published or under development. This updated framework is more adapted to the current rate of virus discovery and provides an improved prioritization for filling knowledge and data gaps. It consists of four distinct steps adapted to include a multi-stakeholder feedback loop. Key improvements include better prioritization and organization of the various steps, earlier data sharing among researchers and involved stakeholders, public database screening, and exploitation of genomic information to predict biological properties., Competing Interests: AF was employed by Fera Science Ltd. AyM and YH were employed by Abiopep S.L. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Fontdevila, Khalili, Maachi, Rivarez, Rollin, Salavert, Temple, Aranda, Boonham, Botermans, Candresse, Fox, Hernando, Kutnjak, Marais, Petter, Ravnikar, Selmi, Tahzima, Trontin, Wetzel and Massart.)
- Published
- 2023
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17. New Strategies and Tools in Quantitative Genetics: How to Go from the Phenotype to the Genotype.
- Author
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Bazakos C, Hanemian M, Trontin C, Jiménez-Gómez JM, and Loudet O
- Subjects
- Genotype, Phenotype, Quantitative Trait Loci, Chromosome Mapping methods, Genome-Wide Association Study methods, Plants genetics
- Abstract
Quantitative genetics has a long history in plants: It has been used to study specific biological processes, identify the factors important for trait evolution, and breed new crop varieties. These classical approaches to quantitative trait locus mapping have naturally improved with technology. In this review, we show how quantitative genetics has evolved recently in plants and how new developments in phenotyping, population generation, sequencing, gene manipulation, and statistics are rejuvenating both the classical linkage mapping approaches (for example, through nested association mapping) as well as the more recently developed genome-wide association studies. These strategies are complementary in most instances, and indeed, one is often used to confirm the results of the other. Despite significant advances, an emerging trend is that the outcome and efficiency of the different approaches depend greatly on the genetic architecture of the trait in the genetic material under study.
- Published
- 2017
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18. Assessment of work-related asthma prevalence, control and severity: protocol of a field study.
- Author
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Mével H, Demange V, Penven E, Trontin C, Wild P, and Paris C
- Subjects
- Adult, Asthma economics, Asthma etiology, Asthma, Occupational economics, Clinical Protocols, Disease Progression, Female, France epidemiology, Humans, Male, Prevalence, Quality of Life, Surveys and Questionnaires, Young Adult, Asthma epidemiology, Asthma, Occupational epidemiology, Cost of Illness, Health Care Costs statistics & numerical data
- Abstract
Background: There are still uncertainties regarding the respective prevalence, diagnosis and management of occupational asthma (OA) and work-exacerbated asthma (WEA). There is as yet no standardized methodology to differentiate their diagnosis. A proper management of both OA and WEA requires tools for a good phenotyping in terms of control, severity and quality of life in order to propose case-specific therapeutical and preventive measures. Moreover, there is a lack of knowledge concerning their actual costs., Methods: This project aims at comparing 3 groups of asthmatic subjects at work: subjects with OA, with WEA, and with non-work-related asthma (NWRA) in terms of control, severity and quality of life on the one hand, and estimating the prevalence of OA, WEA and NWRA in active workers and the economic costs of OA and WEA, on the other hand. Control will be assessed using the Asthma Control Test questionnaire and the daily Peak Exploratory Flow variability, severity from the treatment level, and quality of life using the Asthma Quality of Life Questionnaire. A first step will be to apply a standardized diagnosis procedure of WEA and OA. This study includes an epidemiological part in occupational health services by volunteering occupational physicians, and a clinical case-study based on potentially asthmatic subjects referred to ten participating University Hospital Occupational Diseases Departments (UHODD) because of a suspected WRA. The subjects' characterization with respect to OA and WEA is organized in three steps. In Step 1 (epidemiological part), occupational physicians screen for potentially actively asthmatics through a questionnaire given to workers seen in mandatory medical visit. In step 2 (both parts), the subjects with a suspicion of work-related respiratory symptoms answer a detailed questionnaire and perform a two-week OASYS protocol enabling us, using a specifically developed algorithm, to classify them into probably NWRA, suspected OA, suspected WEA. The two latter groups are referred to UHODD for a final harmonized diagnosis (step 3). Finally, direct and indirect disease-related costs during the year preceding the diagnosis will be explored among WRA cases, as well as these costs and the intangible costs, during the year following the diagnosis., Discussion: This project is an attempt to obtain a global picture of occupational asthma in France thanks to a multidisciplinary approach.
- Published
- 2016
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19. Grasses suppress shoot-borne roots to conserve water during drought.
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Sebastian J, Yee MC, Goudinho Viana W, Rellán-Álvarez R, Feldman M, Priest HD, Trontin C, Lee T, Jiang H, Baxter I, Mockler TC, Hochholdinger F, Brutnell TP, and Dinneny JR
- Subjects
- Mutation, Plant Roots genetics, Plant Roots metabolism, Plant Shoots genetics, Plant Shoots metabolism, Poaceae genetics, Poaceae metabolism, Setaria Plant genetics, Setaria Plant growth & development, Setaria Plant metabolism, Soil, Zea mays genetics, Zea mays growth & development, Zea mays metabolism, Droughts, Plant Roots growth & development, Plant Shoots growth & development, Poaceae growth & development, Water metabolism
- Abstract
Many important crops are members of the Poaceae family, which develop root systems characterized by a high degree of root initiation from the belowground basal nodes of the shoot, termed the crown. Although this postembryonic shoot-borne root system represents the major conduit for water uptake, little is known about the effect of water availability on its development. Here we demonstrate that in the model C4 grass Setaria viridis, the crown locally senses water availability and suppresses postemergence crown root growth under a water deficit. This response was observed in field and growth room environments and in all grass species tested. Luminescence-based imaging of root systems grown in soil-like media revealed a shift in root growth from crown-derived to primary root-derived branches, suggesting that primary root-dominated architecture can be induced in S. viridis under certain stress conditions. Crown roots of Zea mays and Setaria italica, domesticated relatives of teosinte and S. viridis, respectively, show reduced sensitivity to water deficit, suggesting that this response might have been influenced by human selection. Enhanced water status of maize mutants lacking crown roots suggests that under a water deficit, stronger suppression of crown roots actually may benefit crop productivity.
- Published
- 2016
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20. GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown root systems.
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Rellán-Álvarez R, Lobet G, Lindner H, Pradier PL, Sebastian J, Yee MC, Geng Y, Trontin C, LaRue T, Schrager-Lavelle A, Haney CH, Nieu R, Maloof J, Vogel JP, and Dinneny JR
- Subjects
- Genes, Reporter, Luminescence, Image Processing, Computer-Assisted methods, Optical Imaging methods, Plant Roots growth & development, Soil
- Abstract
Root systems develop different root types that individually sense cues from their local environment and integrate this information with systemic signals. This complex multi-dimensional amalgam of inputs enables continuous adjustment of root growth rates, direction, and metabolic activity that define a dynamic physical network. Current methods for analyzing root biology balance physiological relevance with imaging capability. To bridge this divide, we developed an integrated-imaging system called Growth and Luminescence Observatory for Roots (GLO-Roots) that uses luminescence-based reporters to enable studies of root architecture and gene expression patterns in soil-grown, light-shielded roots. We have developed image analysis algorithms that allow the spatial integration of soil properties, gene expression, and root system architecture traits. We propose GLO-Roots as a system that has great utility in presenting environmental stimuli to roots in ways that evoke natural adaptive responses and in providing tools for studying the multi-dimensional nature of such processes.
- Published
- 2015
- Full Text
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21. A pair of receptor-like kinases is responsible for natural variation in shoot growth response to mannitol treatment in Arabidopsis thaliana.
- Author
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Trontin C, Kiani S, Corwin JA, Hématy K, Yansouni J, Kliebenstein DJ, and Loudet O
- Subjects
- Alleles, Arabidopsis drug effects, Arabidopsis genetics, Arabidopsis growth & development, Arabidopsis Proteins genetics, Chromosome Mapping, Genetic Variation, Host-Pathogen Interactions, Mutation, Phenotype, Plant Shoots drug effects, Plant Shoots enzymology, Plant Shoots genetics, Plant Shoots growth & development, Quantitative Trait Loci, Arabidopsis enzymology, Arabidopsis Proteins metabolism, Mannitol pharmacology, Stress, Physiological
- Abstract
Growth is a complex trait that adapts to the prevailing conditions by integrating many internal and external signals. Understanding the molecular origin of this variation remains a challenging issue. In this study, natural variation of shoot growth under mannitol-induced stress was analyzed by standard quantitative trait locus mapping methods in a recombinant inbred line population derived from a cross between the Col-0 and Cvi-0 Arabidopsis thaliana accessions. Cloning of a major QTL specific to mannitol-induced stress condition led to identification of EGM1 and EGM2, a pair of tandem-duplicated genes encoding receptor-like kinases that are potentially involved in signaling of mannitol-associated stress responses. Using various genetic approaches, we identified two non-synonymous mutations in the EGM2[Cvi] allele that are shared by at least ten accessions from various origins and are probably responsible for a specific tolerance to mannitol. We have shown that the enhanced shoot growth phenotype contributed by the Cvi allele is not linked to generic osmotic properties but instead to a specific chemical property of mannitol itself. This result raises the question of the function of such a gene in A. thaliana, a species that does not synthesize mannitol. Our findings suggest that the receptor-like kinases encoded by EGM genes may be activated by mannitol produced by pathogens such as fungi, and may contribute to plant defense responses whenever mannitol is present., (© 2014 The Authors The Plant Journal © 2014 John Wiley & Sons Ltd.)
- Published
- 2014
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22. Extensive natural epigenetic variation at a de novo originated gene.
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Silveira AB, Trontin C, Cortijo S, Barau J, Del Bem LE, Loudet O, Colot V, and Vincentz M
- Subjects
- 5' Untranslated Regions, Arabidopsis Proteins genetics, Arabidopsis Proteins metabolism, Base Sequence, Genetic Variation, Phenotype, Starch metabolism, Arabidopsis genetics, Arabidopsis metabolism, DNA Methylation genetics, Epigenesis, Genetic, Gene Expression Regulation, Plant
- Abstract
Epigenetic variation, such as heritable changes of DNA methylation, can affect gene expression and thus phenotypes, but examples of natural epimutations are few and little is known about their stability and frequency in nature. Here, we report that the gene Qua-Quine Starch (QQS) of Arabidopsis thaliana, which is involved in starch metabolism and that originated de novo recently, is subject to frequent epigenetic variation in nature. Specifically, we show that expression of this gene varies considerably among natural accessions as well as within populations directly sampled from the wild, and we demonstrate that this variation correlates negatively with the DNA methylation level of repeated sequences located within the 5'end of the gene. Furthermore, we provide extensive evidence that DNA methylation and expression variants can be inherited for several generations and are not linked to DNA sequence changes. Taken together, these observations provide a first indication that de novo originated genes might be particularly prone to epigenetic variation in their initial stages of formation., Competing Interests: The authors have declared that no competing interests exist.
- Published
- 2013
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23. Allelic heterogeneity and trade-off shape natural variation for response to soil micronutrient.
- Author
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Poormohammad Kiani S, Trontin C, Andreatta M, Simon M, Robert T, Salt DE, and Loudet O
- Subjects
- Alleles, Anion Transport Proteins physiology, Arabidopsis Proteins physiology, Genetic Drift, Genetic Heterogeneity, Genetic Variation, Haplotypes, Molybdenum chemistry, Phenotype, Polymorphism, Genetic, Soil chemistry, Anion Transport Proteins genetics, Arabidopsis genetics, Arabidopsis growth & development, Arabidopsis Proteins genetics, Molybdenum metabolism
- Abstract
As sessile organisms, plants have to cope with diverse environmental constraints that may vary through time and space, eventually leading to changes in the phenotype of populations through fixation of adaptive genetic variation. To fully comprehend the mechanisms of evolution and make sense of the extensive genotypic diversity currently revealed by new sequencing technologies, we are challenged with identifying the molecular basis of such adaptive variation. Here, we have identified a new variant of a molybdenum (Mo) transporter, MOT1, which is causal for fitness changes under artificial conditions of both Mo-deficiency and Mo-toxicity and in which allelic variation among West-Asian populations is strictly correlated with the concentration of available Mo in native soils. In addition, this association is accompanied at different scales with patterns of polymorphisms that are not consistent with neutral evolution and show signs of diversifying selection. Resolving such a case of allelic heterogeneity helps explain species-wide phenotypic variation for Mo homeostasis and potentially reveals trade-off effects, a finding still rarely linked to fitness., Competing Interests: The authors have declared that no competing interests exist.
- Published
- 2012
- Full Text
- View/download PDF
24. What does Arabidopsis natural variation teach us (and does not teach us) about adaptation in plants?
- Author
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Trontin C, Tisné S, Bach L, and Loudet O
- Subjects
- Biological Evolution, Environment, Linkage Disequilibrium genetics, Phenotype, Polymorphism, Genetic, Quantitative Trait Loci genetics, Stress, Physiological, Adaptation, Physiological genetics, Arabidopsis genetics, Arabidopsis physiology, Genetic Variation genetics
- Abstract
Sessile organisms such as plants have to develop adaptive responses to face environmental change. In Arabidopsis thaliana populations, natural variation for stress responses have been observed at different levels of integration and the genetic bases of those variations have been analysed using two strategies: classical linkage and association (LD) mapping. The strength of Arabidopsis resides in the huge amount of genomic data and molecular tools available leading to the identification of many polymorphisms responsible for phenotypic variation. Remaining limitations to clearly understand how Arabidopsis adapts to its environment, that is the complexity of the genetic architecture and the lack of ecological data, should be partially solved thanks to the development of new methods and the acquisition of new data., (Copyright © 2011 Elsevier Ltd. All rights reserved.)
- Published
- 2011
- Full Text
- View/download PDF
25. High time for a roll call: gene duplication and phylogenetic relationships of TCP-like genes in monocots.
- Author
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Mondragón-Palomino M and Trontin C
- Subjects
- Amino Acid Sequence, Base Sequence, DNA, Complementary, DNA, Plant chemistry, DNA, Plant genetics, Evolution, Molecular, Genetic Variation, Genome, Plant, Molecular Sequence Data, Phylogeny, Poaceae classification, RNA, Plant genetics, Sequence Alignment, Sequence Analysis, DNA, Gene Duplication genetics, Genes, Plant genetics, Plant Proteins genetics, Poaceae genetics, Transcription Factors genetics
- Abstract
Background and Aims: The TCP family is an ancient group of plant developmental transcription factors that regulate cell division in vegetative and reproductive structures and are essential in the establishment of flower zygomorphy. In-depth research on eudicot TCPs has documented their evolutionary and developmental role. This has not happened to the same extent in monocots, although zygomorphy has been critical for the diversification of Orchidaceae and Poaceae, the largest families of this group. Investigating the evolution and function of TCP-like genes in a wider group of monocots requires a detailed phylogenetic analysis of all available sequence information and a system that facilitates comparing genetic and functional information., Methods: The phylogenetic relationships of TCP-like genes in monocots were investigated by analysing sequences from the genomes of Zea mays, Brachypodium distachyon, Oryza sativa and Sorghum bicolor, as well as EST data from several other monocot species., Key Results: All available monocot TCP-like sequences are associated in 20 major groups with an average identity ≥64 % and most correspond to well-supported clades of the phylogeny. Their sequence motifs and relationships of orthology were documented and it was found that 67 % of the TCP-like genes of Sorghum, Oryza, Zea and Brachypodium are in microsyntenic regions. This analysis suggests that two rounds of whole genome duplication drove the expansion of TCP-like genes in these species., Conclusions: A system of classification is proposed where putative or recognized monocot TCP-like genes are assigned to a specific clade of PCF-, CIN- or CYC/tb1-like genes. Specific biases in sequence data of this family that must be tackled when studying its molecular evolution and phylogeny are documented. Finally, the significant retention of duplicated TCP genes from Zea mays is considered in the context of balanced gene drive.
- Published
- 2011
- Full Text
- View/download PDF
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