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Santos AP, Gaudin V, Mozgová I, Pontvianne F, Schubert D, Tek AL, Dvořáčková M, Liu C, Fransz P, Rosa S, Farrona S. Corrigendum to: Tidying-up the plant nuclear space: domains, functions, and dynamics. J Exp Bot 2021; 72:5782. [PMID: 34196709 PMCID: PMC8318252 DOI: 10.1093/jxb/erab134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Ana Paula Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Valérie Gaudin
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Iva Mozgová
- Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Frédéric Pontvianne
- CNRS, Laboratoire Génome et Développement des Plantes (LGDP), Université de Perpignan Via Domitia, Perpignan, France
| | - Daniel Schubert
- Institute for Biology, Freie Universität Berlin, Berlin, Germany
| | - Ahmet L Tek
- Agricultural Genetic Engineering Department, Niğde Ömer Halisdemir University, Niğde, Turkey
| | | | - Chang Liu
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
- Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Paul Fransz
- University of Amsterdam, Amsterdam, The Netherlands
| | - Stefanie Rosa
- Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sara Farrona
- Plant and AgriBiosciences Centre, Ryan Institute, NUI Galway, Galway, Ireland
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Arpòn J, Sakai K, Gaudin V, Andrey P. Publisher Correction: Spatial modeling of biological patterns shows multiscale organization of Arabidopsis thaliana heterochromatin. Sci Rep 2021; 11:10425. [PMID: 33976277 PMCID: PMC8113264 DOI: 10.1038/s41598-021-87458-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Javier Arpòn
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Kaori Sakai
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Valérie Gaudin
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France.
| | - Philippe Andrey
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France.
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Gaudin V, Hédou C, Rault A, Verdon E, Soumet C. Evaluation of ELISA kits for the screening of four nitrofuran metabolites in aquaculture products according to the European guideline for the validation of screening methods. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2020; 38:237-254. [PMID: 33301356 DOI: 10.1080/19440049.2020.1849821] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The administration of nitrofurans to livestock to treat or prevent animal diseases has been banned in the EU for the production of food of animal origin. The corresponding marker residues are tissue-related metabolites AMOZ, AHD, SEM, and AOZ. The MRPL (minimum required performance limit)/RPA (Reference point for action) was set at 1 µg kg-1 in the EU. Thus, all the laboratories involved in the control of nitrofuran metabolites must detect at least at this analytical limit of performance. The objectives of the work reported here were to evaluate the performance of ELISA kits from two different manufacturers (R-Biopharm, Germany; Europroxima, the Netherlands) for the individual screening of the four nitrofuran metabolites (AOZ, AMOZ; AHD; and SEM) in aquaculture products (fish, shrimps), and then to validate the kits according to the European Decision EC/2002/657 and to the European guideline for the validation of screening methods. The false positive rates were below 9 % for the kits from both manufacturers. The detection capabilities CCβ determined were all below the current RPA (1 µg/kg). However, regarding the updated RPA at 0.5 µg/kg that shall apply in 2022, the AMOZ and SEM kits from R-Biopharm and the SEM kit from Europroxima will not be able to reach it.
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Affiliation(s)
- Valérie Gaudin
- Anses, Laboratory of Fougeres, European Union Reference Laboratory (EU-RL) for Antimicrobial and Dye Residue Control in Food-Producing Animals , Fougères, France
| | - Céline Hédou
- Anses, Laboratory of Fougeres, European Union Reference Laboratory (EU-RL) for Antimicrobial and Dye Residue Control in Food-Producing Animals , Fougères, France
| | - Annie Rault
- Anses, Laboratory of Fougeres, European Union Reference Laboratory (EU-RL) for Antimicrobial and Dye Residue Control in Food-Producing Animals , Fougères, France
| | - Eric Verdon
- Anses, Laboratory of Fougeres, European Union Reference Laboratory (EU-RL) for Antimicrobial and Dye Residue Control in Food-Producing Animals , Fougères, France
| | - Christophe Soumet
- Anses, Laboratory of Fougeres, European Union Reference Laboratory (EU-RL) for Antimicrobial and Dye Residue Control in Food-Producing Animals , Fougères, France
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Gaudin V, Hédou C, Rault A, Verdon E, Soumet C. Evaluation of three ELISA kits for the screening of colistin residue in porcine and poultry muscle according to the European guideline for the validation of screening methods. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2020; 37:1651-1666. [PMID: 32870104 DOI: 10.1080/19440049.2020.1778191] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Colistin is a polypeptide antibiotic mainly used in porcine and poultry to treat gastrointestinal infections. It has been included by the World Health Organisation (WHO) in the list of critically important human antibiotics of high priority for antimicrobial resistance since 2017. Therefore, it is necessary to develop specific and sensitive screening methods for this molecule. Screening for colistin with immunoassays is an interesting alternative to LC-MS/MS screening methods. The performance of three commercially available ELISA kits was evaluated in poultry and porcine muscles for the detection of colistin in regards to its European maximum residue limit (MRL) (150 µg/kg). The applicability of the three ELISA kits to the detection of colistin at or below the MRL in porcine and poultry muscles was demonstrated. The detection capabilities (CCβ) of two kits were or lower than or equal to the MRL (150 µg/kg). The lowest detection capability (30 µg/kg) was achieved with the third ELISA kit. The specificity of the three kits was very satisfactory (false positive rates 0%). The three kits are very specific for the detection of colistin (colistin A and B) and polymyxin B.
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Affiliation(s)
- Valérie Gaudin
- Anses, Laboratory of Fougeres, European Union Reference Laboratory (EU-RL) for Antimicrobial and Dye Residue Control in Food-Producing Animals, Bâtiment Bioagropolis , Fougères, France
| | - Céline Hédou
- Anses, Laboratory of Fougeres, European Union Reference Laboratory (EU-RL) for Antimicrobial and Dye Residue Control in Food-Producing Animals, Bâtiment Bioagropolis , Fougères, France
| | - Annie Rault
- Anses, Laboratory of Fougeres, European Union Reference Laboratory (EU-RL) for Antimicrobial and Dye Residue Control in Food-Producing Animals, Bâtiment Bioagropolis , Fougères, France
| | - Eric Verdon
- Anses, Laboratory of Fougeres, European Union Reference Laboratory (EU-RL) for Antimicrobial and Dye Residue Control in Food-Producing Animals, Bâtiment Bioagropolis , Fougères, France
| | - Christophe Soumet
- Anses, Laboratory of Fougeres, European Union Reference Laboratory (EU-RL) for Antimicrobial and Dye Residue Control in Food-Producing Animals, Bâtiment Bioagropolis , Fougères, France
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Santos AP, Gaudin V, Mozgová I, Pontvianne F, Schubert D, Tek AL, Dvořáčková M, Liu C, Fransz P, Rosa S, Farrona S. Tidying-up the plant nuclear space: domains, functions, and dynamics. J Exp Bot 2020; 71:5160-5178. [PMID: 32556244 PMCID: PMC8604271 DOI: 10.1093/jxb/eraa282] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 06/12/2020] [Indexed: 05/07/2023]
Abstract
Understanding how the packaging of chromatin in the nucleus is regulated and organized to guide complex cellular and developmental programmes, as well as responses to environmental cues is a major question in biology. Technological advances have allowed remarkable progress within this field over the last years. However, we still know very little about how the 3D genome organization within the cell nucleus contributes to the regulation of gene expression. The nuclear space is compartmentalized in several domains such as the nucleolus, chromocentres, telomeres, protein bodies, and the nuclear periphery without the presence of a membrane around these domains. The role of these domains and their possible impact on nuclear activities is currently under intense investigation. In this review, we discuss new data from research in plants that clarify functional links between the organization of different nuclear domains and plant genome function with an emphasis on the potential of this organization for gene regulation.
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Affiliation(s)
- Ana Paula Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova
de Lisboa, Oeiras, Portugal
| | - Valérie Gaudin
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université
Paris-Saclay, Versailles, France
| | - Iva Mozgová
- Biology Centre of the Czech Academy of Sciences, České
Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České
Budějovice, Czech Republic
| | - Frédéric Pontvianne
- CNRS, Laboratoire Génome et Développement des Plantes (LGDP), Université de
Perpignan Via Domitia, Perpignan, France
| | - Daniel Schubert
- Institute for Biology, Freie Universität Berlin, Berlin, Germany
| | - Ahmet L Tek
- Agricultural Genetic Engineering Department, Niğde Ömer Halisdemir
University, Niğde, Turkey
| | | | - Chang Liu
- Center for Plant Molecular Biology (ZMBP), University of
Tübingen, Tübingen, Germany
- Institute of Biology, University of Hohenheim, Stuttgart,
Germany
| | - Paul Fransz
- University of Amsterdam, Amsterdam, The
Netherlands
| | - Stefanie Rosa
- Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sara Farrona
- Plant and AgriBiosciences Centre, Ryan Institute, NUI Galway,
Galway, Ireland
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Leung J, Gaudin V. Who Rules the Cell? An Epi-Tale of Histone, DNA, RNA, and the Metabolic Deep State. Front Plant Sci 2020; 11:181. [PMID: 32194593 PMCID: PMC7066317 DOI: 10.3389/fpls.2020.00181] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/06/2020] [Indexed: 05/23/2023]
Abstract
Epigenetics refers to the mode of inheritance independent of mutational changes in the DNA. Early evidence has revealed methylation, acetylation, and phosphorylation of histones, as well as methylation of DNA as part of the underlying mechanisms. The recent awareness that many human diseases have in fact an epigenetic basis, due to unbalanced diets, has led to a resurgence of interest in how epigenetics might be connected with, or even controlled by, metabolism. The Next-Generation genomic technologies have now unleashed torrents of results exposing a wondrous array of metabolites that are covalently attached to selective sites on histones, DNA and RNA. Metabolites are often cofactors or targets of chromatin-modifying enzymes. Many metabolites themselves can be acetylated or methylated. This indicates that the acetylome and methylome can actually be deep and pervasive networks to ensure the nuclear activities are coordinated with the metabolic status of the cell. The discovery of novel histone marks also raises the question on the types of pathways by which their corresponding metabolites are replenished, how they are corralled to the specific histone residues and how they are recognized. Further, atypical cytosines and uracil have also been found in eukaryotic genomes. Although these new and extensive connections between metabolism and epigenetics have been established mostly in animal models, parallels must exist in plants, inasmuch as many of the basic components of chromatin and its modifying enzymes are conserved. Plants are chemical factories constantly responding to stress. Plants, therefore, should lend themselves readily for identifying new endogenous metabolites that are also modulators of nuclear activities in adapting to stress.
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Affiliation(s)
- Jeffrey Leung
- Institut Jean-Pierre Bourgin, ERL3559 CNRS, INRAE, Versailles, France
| | - Valérie Gaudin
- Institut Jean-Pierre Bourgin, UMR1318 INRAE-AgroParisTech, Université Paris-Saclay, Versailles, France
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Abstract
Abstract
A biosensor based on surface plasmon resonance (SPR) measurement was developed for use in an immunoassay for detection of sulfamethazine (SMZ) in milk. The biospecific surface was a carboxymethyl dextran¯modified gold-surface sensor chip to which SMZ was covalently bound. The assay was based on inhibition of the binding of polyclonal antibodies to immobilized SMZ by SMZ in the sample. The SPR response changed inversely in relation to the antibiotic concentration in the sample. Calibration curves were constructed for SMZ in buffer and in milk at a concentration which included the maximum residue limit (0 to 200 μg/kg). The analysis time per sample varied from 8 to 30 min. Different flow rates and antibodies were modified alternatively during the study to assess their influence on the performance of the assay. The active antibody concentration was calculated at approximately 1880 and 180 nM for the antibody anti-SMZ 1 and the antibody anti-SMZ 2, respectively. No cross-reactivity of antibodies with other antibiotics was found. Under optimal conditions, the detection limits in milk for SMZ were 8 and 1.7 μg/kg, respectively, for antibody 1 and antibody 2, at a flow rate of 20 μL/min.
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Affiliation(s)
- Valérie Gaudin
- Community Reference Laboratory for Veterinary Drug Residues, CNEVA, BP 203, 35302 Fougeres, France
| | - Marie-Laure Pavy
- Community Reference Laboratory for Veterinary Drug Residues, CNEVA, BP 203, 35302 Fougeres, France
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Gaudin V, Hédou C, Sanders P. Validation of a Biacore Method for Screening Eight Sulfonamides in Milk and Porcine Muscle Tissues According to European Decision 2002/657/EC. J AOAC Int 2019. [DOI: 10.1093/jaoac/90.6.1706] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Sulfonamides are commonly used for prophylactic or therapeutic purposes in veterinary medicine. A maximum residue limit (MRL) for sulfonamides has been set at 100 g/kg in milk and muscle. A multisulfonamide antibody was used for the development of 2 different Biacore<sup/> protocols, one for the screening of milk samples, the other for muscle samples. Two different Biacore systems were used: Biacore X system (milk protocol), which is considered a research and development apparatus, and Biacore 3000 system (muscle protocol), which is a completely automated system used for high-throughput screening. This report describes the validation of semiquantitative immunological methods according to the European Decision 2002/657/EC concerning the performance of analytical methods. The different performance characteristics (detection capability CC, specificity/selectivity, precision, stability, and applicability) were determined in relation to the European Union MRL of 100 g/kg for sulfonamides. The applicability of the method to porcine, bovine, and poultry muscle was studied. The detection capabilities CC were calculated to be 40 g/L in milk and 60 g/kg in porcine, bovine, and poultry muscles. Eight different sulfonamides, of which 3 (sulfamethazine, sulfamerazine, and sulfadiazine) are authorized in France, were detected simultaneously, at or below the MRL level, with both Biacore systems.
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Affiliation(s)
- Valérie Gaudin
- Community Reference Laboratory for Antimicrobial Residues in Food, Agence Française de Sécurité Sanitaire des Aliments, Laboratoire d’Etude et de Recherche sur les Médicaments Vétérinaires et Désinfectants, BP 90203, 35302 Fougères, France
| | - Céline Hédou
- Community Reference Laboratory for Antimicrobial Residues in Food, Agence Française de Sécurité Sanitaire des Aliments, Laboratoire d’Etude et de Recherche sur les Médicaments Vétérinaires et Désinfectants, BP 90203, 35302 Fougères, France
| | - Pascal Sanders
- Community Reference Laboratory for Antimicrobial Residues in Food, Agence Française de Sécurité Sanitaire des Aliments, Laboratoire d’Etude et de Recherche sur les Médicaments Vétérinaires et Désinfectants, BP 90203, 35302 Fougères, France
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Del Prete S, Molitor A, Charif D, Bessoltane N, Soubigou-Taconnat L, Guichard C, Brunaud V, Granier F, Fransz P, Gaudin V. Extensive nuclear reprogramming and endoreduplication in mature leaf during floral induction. BMC Plant Biol 2019; 19:135. [PMID: 30971226 PMCID: PMC6458719 DOI: 10.1186/s12870-019-1738-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 03/24/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND The floral transition is a complex developmental event, fine-tuned by various environmental and endogenous cues to ensure the success of offspring production. Leaves are key organs in sensing floral inductive signals, such as a change in light regime, and in the production of the mobile florigen. CONSTANS and FLOWERING LOCUS T are major players in leaves in response to photoperiod. Morphological and molecular events during the floral transition have been intensively studied in the shoot apical meristem. To better understand the concomitant processes in leaves, which are less described, we investigated the nuclear changes in fully developed leaves during the time course of the floral transition. RESULTS We highlighted new putative regulatory candidates of flowering in leaves. We observed differential expression profiles of genes related to cellular, hormonal and metabolic actions, but also of genes encoding long non-coding RNAs and new natural antisense transcripts. In addition, we detected a significant increase in ploidy level during the floral transition, indicating endoreduplication. CONCLUSIONS Our data indicate that differentiated mature leaves, possess physiological plasticity and undergo extensive nuclear reprogramming during the floral transition. The dynamic events point at functionally related networks of transcription factors and novel regulatory motifs, but also complex hormonal and metabolic changes.
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Affiliation(s)
- Stefania Del Prete
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, INRA Centre de Versailles-Grignon, Bât. 2, RD10 Route de Saint-Cyr, 78000 Versailles, France
| | - Anne Molitor
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, INRA Centre de Versailles-Grignon, Bât. 2, RD10 Route de Saint-Cyr, 78000 Versailles, France
| | - Delphine Charif
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, INRA Centre de Versailles-Grignon, Bât. 2, RD10 Route de Saint-Cyr, 78000 Versailles, France
| | - Nadia Bessoltane
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, INRA Centre de Versailles-Grignon, Bât. 2, RD10 Route de Saint-Cyr, 78000 Versailles, France
| | - Ludivine Soubigou-Taconnat
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, Plateau du Moulon, 91192 Gif-sur-Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, Plateau du Moulon, 91192 Gif-sur-Yvette, 91405 Orsay, France
| | - Cécile Guichard
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, Plateau du Moulon, 91192 Gif-sur-Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, Plateau du Moulon, 91192 Gif-sur-Yvette, 91405 Orsay, France
| | - Véronique Brunaud
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, Plateau du Moulon, 91192 Gif-sur-Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, Plateau du Moulon, 91192 Gif-sur-Yvette, 91405 Orsay, France
| | - Fabienne Granier
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, INRA Centre de Versailles-Grignon, Bât. 2, RD10 Route de Saint-Cyr, 78000 Versailles, France
| | - Paul Fransz
- Swammerdam Institute for Life Sciences, University of Amsterdam, 1098XH Amsterdam, The Netherlands
| | - Valérie Gaudin
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, INRA Centre de Versailles-Grignon, Bât. 2, RD10 Route de Saint-Cyr, 78000 Versailles, France
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Gaudin V, Hedou C, Soumet C, Verdon E. Multiplex immunoassay based on biochip technology for the screening of antibiotic residues in milk: validation according to the European guideline. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2018; 35:2348-2365. [PMID: 30513250 DOI: 10.1080/19440049.2018.1538572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The Infiniplex for milk® (IPM) kit is a quick method for the simultaneous and qualitative detection of more than 100 molecules including antibiotic residues, mycotoxins, anti-inflammatories and antiparasitic drugs into a single test that does not require milk treatment. The IPM® kit was validated according to the European decision EC/2002/657 and according to the European guideline for the validation of screening methods (2010). Our validation was focused only on antibiotic residues. The washing step was identified as the most critical step of the assay. Insufficient washes could cause a significant background noise that prevents imaging. Positive controls have to be freshly prepared each day (insufficient stability). The method was specific with a low false-positive rate of 1.7% on 5 discrete test regions (DTR) ((beta-lactams, lincomycin, virginiamycin, quinolones and sulphonamides)) and a false-positive rate of 0% on the 26 other DTR. During our validation, the 42 determined detection capabilities CCβ for 12 antibiotic families (aminoglycosides, cephalosporins, lincosamides, macrolides, miscellaneous antibiotics, penicillins, phenolated polymixins, polypeptide antibiotics, quinolones, sulphonamides, tetracyclines) were at between once and twice the decision levels stated by the manufacturer. Forty CCβ determined were lower than the respective regulatory limits (i.e. MRL, RC, MRPL) in milk, except for tilmicosin (1.5 times the MRL) and neospiramycin (>1.25 times the MRL). The estimated CCβ of thiamphenicol, cloxacillin, danofloxacin, sulphathiazol, ceftiofur and sulphamonomethoxine were lower than or at the MRL. However, it was difficult to approach an accurate CCβ with only qualitative results. It is impossible to know whether or not we were close to the cut-off value. The software could be improved by differentiating between low-positive and high-positive results. The results of our participation in three qualitative proficiency tests in 2016 and 2017 for the detection of quinolones, tetracyclines and sulphonamides in cows' milk were very satisfactory.
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Affiliation(s)
- Valérie Gaudin
- a Antibiotic Biocide Residue Resistance Unit , ANSES, Laboratoire de Fougères , FOUGERES Cedex , France
| | - Celine Hedou
- a Antibiotic Biocide Residue Resistance Unit , ANSES, Laboratoire de Fougères , FOUGERES Cedex , France
| | - Christophe Soumet
- a Antibiotic Biocide Residue Resistance Unit , ANSES, Laboratoire de Fougères , FOUGERES Cedex , France
| | - Eric Verdon
- a Antibiotic Biocide Residue Resistance Unit , ANSES, Laboratoire de Fougères , FOUGERES Cedex , France
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Abstract
The cell nucleus is a structurally complex and dynamic organelle ensuring key biological functions. Complex relationships between nuclear structure and functions require a better understanding of the three-dimensional organization of the genome and of the subnuclear compartments. Quantitative image analysis coupled with spatial statistics and modeling is a relevant approach to address these questions. In this chapter, we describe a step-by-step procedure to process images and to test a spatial random model for the distribution of nuclear objects using chromocenters as an example. More elaborate models can be designed on the basis of the random model by introducing additional and more complex constraints to better fit observations and to question determinants of these spatial organizations.
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Affiliation(s)
- Javier Arpòn
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, F-78000, Versailles, France
| | - Valérie Gaudin
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, F-78000, Versailles, France
| | - Philippe Andrey
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, F-78000, Versailles, France.
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Gaudin V. State of the art in the validation of screening methods for the control of antibiotic residues: is there a need for further development? Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2017; 34:1528-1552. [PMID: 28675343 DOI: 10.1080/19440049.2017.1350288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Screening methods are used as a first-line approach to detect the presence of antibiotic residues in food of animal origin. The validation process guarantees that the method is fit-for-purpose, suited to regulatory requirements, and provides evidence of its performance. This article is focused on intra-laboratory validation. The first step in validation is characterisation of performance, and the second step is the validation itself with regard to pre-established criteria. The validation approaches can be absolute (a single method) or relative (comparison of methods), overall (combination of several characteristics in one) or criterion-by-criterion. Various approaches to validation, in the form of regulations, guidelines or standards, are presented and discussed to draw conclusions on their potential application for different residue screening methods, and to determine whether or not they reach the same conclusions. The approach by comparison of methods is not suitable for screening methods for antibiotic residues. The overall approaches, such as probability of detection (POD) and accuracy profile, are increasingly used in other fields of application. They may be of interest for screening methods for antibiotic residues. Finally, the criterion-by-criterion approach (Decision 2002/657/EC and of European guideline for the validation of screening methods), usually applied to the screening methods for antibiotic residues, introduced a major characteristic and an improvement in the validation, i.e. the detection capability (CCβ). In conclusion, screening methods are constantly evolving, thanks to the development of new biosensors or liquid chromatography coupled to tandem-mass spectrometry (LC-MS/MS) methods. There have been clear changes in validation approaches these last 20 years. Continued progress is required and perspectives for future development of guidelines, regulations and standards for validation are presented here.
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Affiliation(s)
- Valérie Gaudin
- a European Union Reference Laboratory (EU-RL) for Antimicrobial and Dye Residue Control in Food-Producing Animal , Anses , Fougères , France
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Gaudin V, Rault A, Hedou C, Soumet C, Verdon E. Strategies for the screening of antibiotic residues in eggs: comparison of the validation of the classical microbiological method with an immunobiosensor method. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2017; 34:1510-1527. [PMID: 28585900 DOI: 10.1080/19440049.2017.1339331] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Efficient screening methods are needed to control antibiotic residues in eggs. A microbiological kit (Explorer® 2.0 test (Zeu Inmunotech, Spain)) and an immunobiosensor kit (Microarray II (AM® II) on Evidence Investigator™ system (Randox, UK)) have been evaluated and validated for screening of antibiotic residues in eggs, according to the European decision EC/2002/657 and to the European guideline for the validation of screening methods. The e-reader™ system, a new automatic incubator/reading system, was coupled to the Explorer 2.0 test. The AM II kit can detect residues of six different families of antibiotics in different matrices including eggs. For both tests, a different liquid/liquid extraction of eggs had to be developed. Specificities of the Explorer 2.0 and AM II kit were equal to 8% and 0% respectively. The detection capabilities were determined for 19 antibiotics, with representatives from different families, for Explorer 2.0 and 12 antibiotics for the AM II kit. For the nine antibiotics having a maximum residue limit (MRL) in eggs, the detection capabilities CCβ of Explorer 2.0 were below the MRL for four antibiotics, equal to the MRL for two antibiotics and between 1 and 1.5 MRLs for the three remaining antibiotics (tetracyclines). For the antibiotics from other families, the detection capabilities were low for beta-lactams and sulfonamides and satisfactory for dihydrostreptomycin (DHS) and fluoroquinolones, which are usually difficult to detect with microbiological tests. The CCβ values of the AM II kit were much lower than the respective MRLs for three detected antibiotics (tetracycline, oxytetracycline, tylosin). Concerning the nine other antibiotics, the detection capabilities determined were low. The highest CCβ was obtained for streptomycin (100 µg kg-1).
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Affiliation(s)
| | - Annie Rault
- a European Union Reference Laboratory , Cedex , France
| | - Celine Hedou
- a European Union Reference Laboratory , Cedex , France
| | | | - Eric Verdon
- a European Union Reference Laboratory , Cedex , France
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Molitor AM, Latrasse D, Zytnicki M, Andrey P, Houba-Hérin N, Hachet M, Battail C, Del Prete S, Alberti A, Quesneville H, Gaudin V. The Arabidopsis hnRNP-Q Protein LIF2 and the PRC1 Subunit LHP1 Function in Concert to Regulate the Transcription of Stress-Responsive Genes. Plant Cell 2016; 28:2197-2211. [PMID: 27495811 PMCID: PMC5059796 DOI: 10.1105/tpc.16.00244] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 07/28/2016] [Accepted: 08/05/2016] [Indexed: 05/03/2023]
Abstract
LHP1-INTERACTING FACTOR2 (LIF2), a heterogeneous nuclear ribonucleoprotein involved in Arabidopsis thaliana cell fate and stress responses, interacts with LIKE HETEROCHROMATIN PROTEIN1 (LHP1), a Polycomb Repressive Complex1 subunit. To investigate LIF2-LHP1 functional interplay, we mapped their genome-wide distributions in wild-type, lif2, and lhp1 backgrounds, under standard and stress conditions. Interestingly, LHP1-targeted regions form local clusters, suggesting an underlying functional organization of the plant genome. Regions targeted by both LIF2 and LHP1 were enriched in stress-responsive genes, the H2A.Z histone variant, and antagonistic histone marks. We identified specific motifs within the targeted regions, including a G-box-like motif, a GAGA motif, and a telo-box. LIF2 and LHP1 can operate both antagonistically and synergistically. In response to methyl jasmonate treatment, LIF2 was rapidly recruited to chromatin, where it mediated transcriptional gene activation. Thus, LIF2 and LHP1 participate in transcriptional switches in stress-response pathways.
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Affiliation(s)
- Anne M Molitor
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, F-78000 Versailles, France
| | - David Latrasse
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, F-78000 Versailles, France
| | | | - Philippe Andrey
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, F-78000 Versailles, France
- Sorbonne Universités, UPMC Université Paris 06, UFR927, F-75005 Paris, France
| | - Nicole Houba-Hérin
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, F-78000 Versailles, France
| | - Mélanie Hachet
- URGI, INRA, Université Paris-Saclay, F-78000 Versailles, France
| | - Christophe Battail
- CEA-Institut de Génomique, Centre National de Séquençage, F-91057 Evry, France
| | - Stefania Del Prete
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, F-78000 Versailles, France
| | - Adriana Alberti
- CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, F-91057 Evry, France
| | | | - Valérie Gaudin
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, F-78000 Versailles, France
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Gaudin V, Hedou C, Soumet C, Verdon E. Evaluation and validation of a multi-residue method based on biochip technology for the simultaneous screening of six families of antibiotics in muscle and aquaculture products. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2016; 33:403-19. [DOI: 10.1080/19440049.2015.1125529] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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16
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Mozgová I, Köhler C, Gaudin V, Hennig L. The many faces of plant chromatin: Meeting summary of the 4th European workshop on plant chromatin 2015, Uppsala, Sweden. Epigenetics 2015; 10:1084-90. [PMID: 26646904 DOI: 10.1080/15592294.2015.1106674] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
In June 2015, the fourth European Workshop on Plant Chromatin took place in Uppsala, Sweden, bringing together 80 researchers studying various aspects of plant chromatin and epigenetics. The intricate relationships between plant chromatin dynamics and gene expression change, chromatin organization within the plant cell nucleus, and the impact of chromatin structure on plant development were discussed. Among the main highlights of the meeting were an ever-growing list of newly identified players in chromatin structure establishment and the development of novel tools and approaches to foster our understanding of chromatin-mediated gene regulation, taking into account the context of the plant cell nucleus and its architecture. In this report, we summarize some of the main advances and prospects of plant chromatin research presented at this meeting.
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Affiliation(s)
- Iva Mozgová
- a Department of Plant Biology ; Uppsala BioCenter; Swedish University of Agricultural Sciences and Linnean Center for Plant Biology ; Uppsala , Sweden
| | - Claudia Köhler
- a Department of Plant Biology ; Uppsala BioCenter; Swedish University of Agricultural Sciences and Linnean Center for Plant Biology ; Uppsala , Sweden
| | - Valérie Gaudin
- b INRA-AgroParisTech; Institut Jean-Pierre Bourgin ; Versailles , France
| | - Lars Hennig
- a Department of Plant Biology ; Uppsala BioCenter; Swedish University of Agricultural Sciences and Linnean Center for Plant Biology ; Uppsala , Sweden
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Hecker A, Brand LH, Peter S, Simoncello N, Kilian J, Harter K, Gaudin V, Wanke D. The Arabidopsis GAGA-Binding Factor BASIC PENTACYSTEINE6 Recruits the POLYCOMB-REPRESSIVE COMPLEX1 Component LIKE HETEROCHROMATIN PROTEIN1 to GAGA DNA Motifs. Plant Physiol 2015; 168:1013-24. [PMID: 26025051 PMCID: PMC4741334 DOI: 10.1104/pp.15.00409] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 05/26/2015] [Indexed: 05/19/2023]
Abstract
Polycomb-repressive complexes (PRCs) play key roles in development by repressing a large number of genes involved in various functions. Much, however, remains to be discovered about PRC-silencing mechanisms as well as their targeting to specific genomic regions. Besides other mechanisms, GAGA-binding factors in animals can guide PRC members in a sequence-specific manner to Polycomb-responsive DNA elements. Here, we show that the Arabidopsis (Arabidopsis thaliana) GAGA-motif binding factor protein basic pentacysteine6 (BPC6) interacts with like heterochromatin protein1 (LHP1), a PRC1 component, and associates with vernalization2 (VRN2), a PRC2 component, in vivo. By using a modified DNA-protein interaction enzyme-linked immunosorbant assay, we could show that BPC6 was required and sufficient to recruit LHP1 to GAGA motif-containing DNA probes in vitro. We also found that LHP1 interacts with VRN2 and, therefore, can function as a possible scaffold between BPC6 and VRN2. The lhp1-4 bpc4 bpc6 triple mutant displayed a pleiotropic phenotype, extreme dwarfism and early flowering, which disclosed synergistic functions of LHP1 and group II plant BPC members. Transcriptome analyses supported this synergy and suggested a possible function in the concerted repression of homeotic genes, probably through histone H3 lysine-27 trimethylation. Hence, our findings suggest striking similarities between animal and plant GAGA-binding factors in the recruitment of PRC1 and PRC2 components to Polycomb-responsive DNA element-like GAGA motifs, which must have evolved through convergent evolution.
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Affiliation(s)
- Andreas Hecker
- Center for Plant Molecular Biology, Plant Physiology, and Biophysical Chemistry, University of Tübingen, 72076 Tuebingen, Germany (A.H., L.H.B., S.P., J.K., K.H., D.W.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1318 AgroParisTech, Institut J.-P. Bourgin, Institut National de la Recherche Agronomique Centre de Versailles-Grignon, F-78026 Versailles, France (N.S., V.G.); andUniversität des Saarlandes, Molekulare Pflanzenbiologie, 66123 Saarbruecken, Germany (D.W.)
| | - Luise H Brand
- Center for Plant Molecular Biology, Plant Physiology, and Biophysical Chemistry, University of Tübingen, 72076 Tuebingen, Germany (A.H., L.H.B., S.P., J.K., K.H., D.W.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1318 AgroParisTech, Institut J.-P. Bourgin, Institut National de la Recherche Agronomique Centre de Versailles-Grignon, F-78026 Versailles, France (N.S., V.G.); andUniversität des Saarlandes, Molekulare Pflanzenbiologie, 66123 Saarbruecken, Germany (D.W.)
| | - Sébastien Peter
- Center for Plant Molecular Biology, Plant Physiology, and Biophysical Chemistry, University of Tübingen, 72076 Tuebingen, Germany (A.H., L.H.B., S.P., J.K., K.H., D.W.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1318 AgroParisTech, Institut J.-P. Bourgin, Institut National de la Recherche Agronomique Centre de Versailles-Grignon, F-78026 Versailles, France (N.S., V.G.); andUniversität des Saarlandes, Molekulare Pflanzenbiologie, 66123 Saarbruecken, Germany (D.W.)
| | - Nathalie Simoncello
- Center for Plant Molecular Biology, Plant Physiology, and Biophysical Chemistry, University of Tübingen, 72076 Tuebingen, Germany (A.H., L.H.B., S.P., J.K., K.H., D.W.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1318 AgroParisTech, Institut J.-P. Bourgin, Institut National de la Recherche Agronomique Centre de Versailles-Grignon, F-78026 Versailles, France (N.S., V.G.); andUniversität des Saarlandes, Molekulare Pflanzenbiologie, 66123 Saarbruecken, Germany (D.W.)
| | - Joachim Kilian
- Center for Plant Molecular Biology, Plant Physiology, and Biophysical Chemistry, University of Tübingen, 72076 Tuebingen, Germany (A.H., L.H.B., S.P., J.K., K.H., D.W.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1318 AgroParisTech, Institut J.-P. Bourgin, Institut National de la Recherche Agronomique Centre de Versailles-Grignon, F-78026 Versailles, France (N.S., V.G.); andUniversität des Saarlandes, Molekulare Pflanzenbiologie, 66123 Saarbruecken, Germany (D.W.)
| | - Klaus Harter
- Center for Plant Molecular Biology, Plant Physiology, and Biophysical Chemistry, University of Tübingen, 72076 Tuebingen, Germany (A.H., L.H.B., S.P., J.K., K.H., D.W.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1318 AgroParisTech, Institut J.-P. Bourgin, Institut National de la Recherche Agronomique Centre de Versailles-Grignon, F-78026 Versailles, France (N.S., V.G.); andUniversität des Saarlandes, Molekulare Pflanzenbiologie, 66123 Saarbruecken, Germany (D.W.)
| | - Valérie Gaudin
- Center for Plant Molecular Biology, Plant Physiology, and Biophysical Chemistry, University of Tübingen, 72076 Tuebingen, Germany (A.H., L.H.B., S.P., J.K., K.H., D.W.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1318 AgroParisTech, Institut J.-P. Bourgin, Institut National de la Recherche Agronomique Centre de Versailles-Grignon, F-78026 Versailles, France (N.S., V.G.); andUniversität des Saarlandes, Molekulare Pflanzenbiologie, 66123 Saarbruecken, Germany (D.W.)
| | - Dierk Wanke
- Center for Plant Molecular Biology, Plant Physiology, and Biophysical Chemistry, University of Tübingen, 72076 Tuebingen, Germany (A.H., L.H.B., S.P., J.K., K.H., D.W.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1318 AgroParisTech, Institut J.-P. Bourgin, Institut National de la Recherche Agronomique Centre de Versailles-Grignon, F-78026 Versailles, France (N.S., V.G.); andUniversität des Saarlandes, Molekulare Pflanzenbiologie, 66123 Saarbruecken, Germany (D.W.)
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Gaudin V, Hedou C, Soumet C, Verdon E. Evaluation and validation of a biochip multi-array technology for the screening of 14 sulphonamide and trimethoprim residues in honey according to the European guideline for the validation of screening methods for veterinary medicines. FOOD AGR IMMUNOL 2014. [DOI: 10.1080/09540105.2014.968767] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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Gaudin V, Hedou C, Soumet C, Verdon E. Evaluation and validation of biochip multi-array technology for the screening of six families of antibiotics in honey according to the European guideline for the validation of screening methods for residues of veterinary medicines. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2014; 31:1699-711. [DOI: 10.1080/19440049.2014.952784] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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20
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Del Prete S, Arpón J, Sakai K, Andrey P, Gaudin V. Nuclear architecture and chromatin dynamics in interphase nuclei of Arabidopsis thaliana. Cytogenet Genome Res 2014; 143:28-50. [PMID: 24992956 DOI: 10.1159/000363724] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The interphase cell nucleus is extraordinarily complex, ordered, and dynamic. In the last decade, remarkable progress has been made in deciphering the functional organisation of the cell nucleus, and intricate relationships between genome functions (transcription, DNA repair, or replication) and various nuclear compartments have been revealed. In this review, we describe the architecture of the Arabidopsis thaliana interphase cell nucleus and discuss the dynamic nature of its organisation. We underline the need for further developments in quantitative and modelling approaches to nuclear organization.
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Affiliation(s)
- Stefania Del Prete
- INRA, UMR1318-AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), INRA-Centre de Versailles-Grignon, Versailles, France
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21
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Le Roux C, Del Prete S, Boutet-Mercey S, Perreau F, Balagué C, Roby D, Fagard M, Gaudin V. The hnRNP-Q protein LIF2 participates in the plant immune response. PLoS One 2014; 9:e99343. [PMID: 24914891 DOI: 10.1371/journal.pone.0099343.s007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 05/02/2014] [Indexed: 05/25/2023] Open
Abstract
Eukaryotes have evolved complex defense pathways to combat invading pathogens. Here, we investigated the role of the Arabidopsis thaliana heterogeneous nuclear ribonucleoprotein (hnRNP-Q) LIF2 in the plant innate immune response. We show that LIF2 loss-of-function in A. thaliana leads to changes in the basal expression of the salicylic acid (SA)- and jasmonic acid (JA)- dependent defense marker genes PR1 and PDF1.2, respectively. Whereas the expression of genes involved in SA and JA biosynthesis and signaling was also affected in the lif2-1 mutant, no change in SA and JA hormonal contents was detected. In addition, the composition of glucosinolates, a class of defense-related secondary metabolites, was altered in the lif2-1 mutant in the absence of pathogen challenge. The lif2-1 mutant exhibited reduced susceptibility to the hemi-biotrophic pathogen Pseudomonas syringae and the necrotrophic ascomycete Botrytis cinerea. Furthermore, the lif2-1 sid2-2 double mutant was less susceptible than the wild type to P. syringae infection, suggesting that the lif2 response to pathogens was independent of SA accumulation. Together, our data suggest that lif2-1 exhibits a basal primed defense state, resulting from complex deregulation of gene expression, which leads to increased resistance to pathogens with various infection strategies. Therefore, LIF2 may function as a suppressor of cell-autonomous immunity. Similar to its human homolog, NSAP1/SYNCRIP, a trans-acting factor involved in both cellular processes and the viral life cycle, LIF2 may regulate the conflicting aspects of development and defense programs, suggesting that a conserved evolutionary trade-off between growth and defense pathways exists in eukaryotes.
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Affiliation(s)
- Clémentine Le Roux
- INRA-AgroParisTech, UMR1318, Institut J.-P. Bourgin, Centre de Versailles-Grignon, Versailles, France
| | - Stefania Del Prete
- INRA-AgroParisTech, UMR1318, Institut J.-P. Bourgin, Centre de Versailles-Grignon, Versailles, France
| | - Stéphanie Boutet-Mercey
- INRA-AgroParisTech, UMR1318, Institut J.-P. Bourgin, Centre de Versailles-Grignon, Versailles, France
| | - François Perreau
- INRA-AgroParisTech, UMR1318, Institut J.-P. Bourgin, Centre de Versailles-Grignon, Versailles, France
| | - Claudine Balagué
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France; CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France
| | - Dominique Roby
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France; CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France
| | - Mathilde Fagard
- INRA-AgroParisTech, UMR1318, Institut J.-P. Bourgin, Centre de Versailles-Grignon, Versailles, France
| | - Valérie Gaudin
- INRA-AgroParisTech, UMR1318, Institut J.-P. Bourgin, Centre de Versailles-Grignon, Versailles, France
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22
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Le Roux C, Del Prete S, Boutet-Mercey S, Perreau F, Balagué C, Roby D, Fagard M, Gaudin V. The hnRNP-Q protein LIF2 participates in the plant immune response. PLoS One 2014; 9:e99343. [PMID: 24914891 PMCID: PMC4051675 DOI: 10.1371/journal.pone.0099343] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 05/02/2014] [Indexed: 12/21/2022] Open
Abstract
Eukaryotes have evolved complex defense pathways to combat invading pathogens. Here, we investigated the role of the Arabidopsis thaliana heterogeneous nuclear ribonucleoprotein (hnRNP-Q) LIF2 in the plant innate immune response. We show that LIF2 loss-of-function in A. thaliana leads to changes in the basal expression of the salicylic acid (SA)- and jasmonic acid (JA)- dependent defense marker genes PR1 and PDF1.2, respectively. Whereas the expression of genes involved in SA and JA biosynthesis and signaling was also affected in the lif2-1 mutant, no change in SA and JA hormonal contents was detected. In addition, the composition of glucosinolates, a class of defense-related secondary metabolites, was altered in the lif2-1 mutant in the absence of pathogen challenge. The lif2-1 mutant exhibited reduced susceptibility to the hemi-biotrophic pathogen Pseudomonas syringae and the necrotrophic ascomycete Botrytis cinerea. Furthermore, the lif2-1 sid2-2 double mutant was less susceptible than the wild type to P. syringae infection, suggesting that the lif2 response to pathogens was independent of SA accumulation. Together, our data suggest that lif2-1 exhibits a basal primed defense state, resulting from complex deregulation of gene expression, which leads to increased resistance to pathogens with various infection strategies. Therefore, LIF2 may function as a suppressor of cell-autonomous immunity. Similar to its human homolog, NSAP1/SYNCRIP, a trans-acting factor involved in both cellular processes and the viral life cycle, LIF2 may regulate the conflicting aspects of development and defense programs, suggesting that a conserved evolutionary trade-off between growth and defense pathways exists in eukaryotes.
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Affiliation(s)
- Clémentine Le Roux
- INRA-AgroParisTech, UMR1318, Institut J.-P. Bourgin, Centre de Versailles-Grignon, Versailles, France
| | - Stefania Del Prete
- INRA-AgroParisTech, UMR1318, Institut J.-P. Bourgin, Centre de Versailles-Grignon, Versailles, France
| | - Stéphanie Boutet-Mercey
- INRA-AgroParisTech, UMR1318, Institut J.-P. Bourgin, Centre de Versailles-Grignon, Versailles, France
| | - François Perreau
- INRA-AgroParisTech, UMR1318, Institut J.-P. Bourgin, Centre de Versailles-Grignon, Versailles, France
| | - Claudine Balagué
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France
| | - Dominique Roby
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France
| | - Mathilde Fagard
- INRA-AgroParisTech, UMR1318, Institut J.-P. Bourgin, Centre de Versailles-Grignon, Versailles, France
| | - Valérie Gaudin
- INRA-AgroParisTech, UMR1318, Institut J.-P. Bourgin, Centre de Versailles-Grignon, Versailles, France
- * E-mail:
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Jarillo JA, Gaudin V, Hennig L, Köhler C, Piñeiro M. Plant chromatin warms up in Madrid: meeting summary of the 3rd European Workshop on Plant Chromatin 2013, Madrid, Spain. Epigenetics 2014; 9:644-52. [PMID: 24504145 DOI: 10.4161/epi.28094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The 3rd European Workshop on Plant Chromatin (EWPC) was held on August 2013 in Madrid, Spain. A number of different topics on plant chromatin were presented during the meeting, including new factors mediating Polycomb Group protein function in plants, chromatin-mediated reprogramming in plant developmental transitions, the role of histone variants, and newly identified chromatin remodeling factors. The function of interactions between chromatin and transcription factors in the modulation of gene expression, the role of chromatin dynamics in the control of nuclear processes and the influence of environmental factors on chromatin organization were also reported. In this report, we highlight some of the new insights emerging in this growing area of research, presented at the 3rd EWPC.
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Affiliation(s)
- José A Jarillo
- Centro de Biotecnología y Genómica de Plantas (CBGP), INIA-UPM; INIA, Campus de Montegancedo; Madrid, Spain
| | - Valérie Gaudin
- NRA; AgroParis Tech; UMR1318; Insitut Jean Pierre Bourgin; Versailles, France
| | - Lars Hennig
- Swedish University of Agricultural Sciences; Uppsala BioCenter; Uppsala, Sweden
| | - Claudia Köhler
- Swedish University of Agricultural Sciences; Uppsala BioCenter; Uppsala, Sweden
| | - Manuel Piñeiro
- Centro de Biotecnología y Genómica de Plantas (CBGP), INIA-UPM; INIA, Campus de Montegancedo; Madrid, Spain
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Chupeau MC, Granier F, Pichon O, Renou JP, Gaudin V, Chupeau Y. Characterization of the early events leading to totipotency in an Arabidopsis protoplast liquid culture by temporal transcript profiling. Plant Cell 2013; 25:2444-63. [PMID: 23903317 PMCID: PMC3753376 DOI: 10.1105/tpc.113.109538] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 05/31/2013] [Accepted: 07/03/2013] [Indexed: 05/19/2023]
Abstract
The molecular mechanisms underlying plant cell totipotency are largely unknown. Here, we present a protocol for the efficient regeneration of plants from Arabidopsis thaliana protoplasts. The specific liquid medium used in our study leads to a high rate of reentry into the cell cycle of most cell types, providing a powerful system to study dedifferentiation/regeneration processes in independent somatic cells. To identify the early events in the establishment of totipotency, we monitored the genome-wide transcript profiles of plantlets and protoplast-derived cells (PdCs) during the first week of culture. Plant cells rapidly dedifferentiated. Then, we observed the reinitiation and reorientation of protein synthesis, accompanied by the reinitiation of cell division and de novo cell wall synthesis. Marked changes in the expression of chromatin-associated genes, especially of those in the histone variant family, were observed during protoplast culture. Surprisingly, the epigenetic status of PdCs and well-established cell cultures differed, with PdCs exhibiting rare reactivated transposons and epigenetic changes. The differentially expressed genes identified in this study are interesting candidates for investigating the molecular mechanisms underlying plant cell plasticity and totipotency. One of these genes, the plant-specific transcription factor ABERRANT LATERAL ROOT FORMATION4, is required for the initiation of protoplast division.
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Affiliation(s)
- Marie-Christine Chupeau
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1318–AgroParisTech, Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique–Centre de Versailles-Grignon, F-78026 Versailles cedex, France
| | - Fabienne Granier
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1318–AgroParisTech, Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique–Centre de Versailles-Grignon, F-78026 Versailles cedex, France
| | - Olivier Pichon
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1165, Unité Mixte de Recherche en Génomique Végétale, F-91057 Évry cedex 2, France
| | - Jean-Pierre Renou
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1165, Unité Mixte de Recherche en Génomique Végétale, F-91057 Évry cedex 2, France
| | - Valérie Gaudin
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1318–AgroParisTech, Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique–Centre de Versailles-Grignon, F-78026 Versailles cedex, France
| | - Yves Chupeau
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1318–AgroParisTech, Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique–Centre de Versailles-Grignon, F-78026 Versailles cedex, France
- Address correspondence to
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Gaudin V, Rault A, Verdon E. Validation of a commercial receptor kit for tetracycline residues in honey according to the European guideline for screening methods. FOOD AGR IMMUNOL 2013. [DOI: 10.1080/09540105.2011.651446] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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Gaudin V, De Courville A, Hedou C, Rault A, Diomandé S, Creff-Froger C, Verdon E. Evaluation and validation of two microbiological tests for screening antibiotic residues in honey according to the European guideline for the validation of screening methods. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2013; 30:234-43. [DOI: 10.1080/19440049.2012.738367] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Gaudin V, Hedou C, Verdon E. Validation of two ELISA kits for the screening of tylosin and streptomycin in honey according to the European decision 2002/657/EC. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2013; 30:93-109. [DOI: 10.1080/19440049.2012.722696] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Gaudin V, Rault A, Verdon E. Validation of a commercial receptor kit Sulfasensor® Honey for the screening of sulfonamides in honey according to Commission Decision 2002/657/EC. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2012; 29:942-50. [DOI: 10.1080/19440049.2012.668718] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- V. Gaudin
- a European Union Reference Laboratory , Anses Fougères, La Haute Marche – BP 0203, F-35302 Fougeres Cedex , France
| | - A. Rault
- a European Union Reference Laboratory , Anses Fougères, La Haute Marche – BP 0203, F-35302 Fougeres Cedex , France
| | - E. Verdon
- a European Union Reference Laboratory , Anses Fougères, La Haute Marche – BP 0203, F-35302 Fougeres Cedex , France
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Houba-Hérin N, Hennig L, Köhler C, Gaudin V. A fruitful chromatin harvest: meeting summary of the Second European Workshop on Plant Chromatin 2011 in Versailles, France. Epigenetics 2012; 7:307-11. [PMID: 22430807 DOI: 10.4161/epi.7.3.19104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In September 2011, the Second European Workshop on Plant Chromatin took place in Versailles, France. The workshop covered a range of topics related to plant chromatin biology, including regulation of gene expression by Polycomb group proteins, chromatin dynamics, reconfiguration of epigenetic marks in response to various cues and chromatin assembly. Here, we summarize some of the highlights discussed during the meeting.
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Affiliation(s)
- Nicole Houba-Hérin
- INRA, AgroParisTech, UMR1318, Institut Jean-Pierre Bourgin, Versailles, France
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Latrasse D, Germann S, Houba-Hérin N, Dubois E, Bui-Prodhomme D, Hourcade D, Juul-Jensen T, Le Roux C, Majira A, Simoncello N, Granier F, Taconnat L, Renou JP, Gaudin V. Control of flowering and cell fate by LIF2, an RNA binding partner of the polycomb complex component LHP1. PLoS One 2011; 6:e16592. [PMID: 21304947 PMCID: PMC3031606 DOI: 10.1371/journal.pone.0016592] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2010] [Accepted: 12/29/2010] [Indexed: 01/31/2023] Open
Abstract
Polycomb Repressive Complexes (PRC) modulate the epigenetic status of key cell fate and developmental regulators in eukaryotes. The chromo domain protein LIKE HETEROCHROMATIN PROTEIN1 (LHP1) is a subunit of a plant PRC1-like complex in Arabidopsis thaliana and recognizes histone H3 lysine 27 trimethylation, a silencing epigenetic mark deposited by the PRC2 complex. We have identified and studied an LHP1-Interacting Factor2 (LIF2). LIF2 protein has RNA recognition motifs and belongs to the large hnRNP protein family, which is involved in RNA processing. LIF2 interacts in vivo, in the cell nucleus, with the LHP1 chromo shadow domain. Expression of LIF2 was detected predominantly in vascular and meristematic tissues. Loss-of-function of LIF2 modifies flowering time, floral developmental homeostasis and gynoecium growth determination. lif2 ovaries have indeterminate growth and produce ectopic inflorescences with severely affected flowers showing proliferation of ectopic stigmatic papillae and ovules in short-day conditions. To look at how LIF2 acts relative to LHP1, we conducted transcriptome analyses in lif2 and lhp1 and identified a common set of deregulated genes, which showed significant enrichment in stress-response genes. By comparing expression of LHP1 targets in lif2, lhp1 and lif2 lhp1 mutants we showed that LIF2 can either antagonize or act with LHP1. Interestingly, repression of the FLC floral transcriptional regulator in lif2 mutant is accompanied by an increase in H3K27 trimethylation at the locus, without any change in LHP1 binding, suggesting that LHP1 is targeted independently from LIF2 and that LHP1 binding does not strictly correlate with gene expression. LIF2, involved in cell identity and cell fate decision, may modulate the activity of LHP1 at specific loci, during specific developmental windows or in response to environmental cues that control cell fate determination. These results highlight a novel link between plant RNA processing and Polycomb regulation.
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Affiliation(s)
- David Latrasse
- Institut J.-P. Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Versailles, France
| | - Sophie Germann
- Institut J.-P. Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Versailles, France
- Centre Léon Bérard, Inserm U590, Oncogenèse et progression tumorale, Lyon, France
| | - Nicole Houba-Hérin
- Institut J.-P. Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Versailles, France
| | - Emeline Dubois
- Institut J.-P. Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Versailles, France
- Centre de Génétique Moléculaire, CNRS FRE3144, Gif-sur-Yvette, France
| | - Duyen Bui-Prodhomme
- Institut J.-P. Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Versailles, France
- Biologie du Fruit, UMR 619 INRA Centre de Bordeaux, Villenave-d'Ornon, France
| | - Delphine Hourcade
- Institut J.-P. Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Versailles, France
| | - Trine Juul-Jensen
- Institut J.-P. Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Versailles, France
| | - Clémentine Le Roux
- Institut J.-P. Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Versailles, France
| | - Amel Majira
- Institut J.-P. Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Versailles, France
| | - Nathalie Simoncello
- Institut J.-P. Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Versailles, France
| | - Fabienne Granier
- Institut J.-P. Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Versailles, France
| | | | | | - Valérie Gaudin
- Institut J.-P. Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Versailles, France
- * E-mail:
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Abstract
DamID (DNA adenine methylation identification) is an adenine methylation-based tagging method designed to map protein-DNA interactions in vivo. DamID, an alternative method to chromatin immunoprecipitation (ChIP), is based on the covalent linking of a "fingerprint" in the vicinity of the DNA-binding sites of the protein of interest. The fingerprints can be further mapped by simple molecular approaches. First developed by van Steensel's group in Drosophila melanogaster, DamID was successfully adapted to Arabidopsis thaliana, and its feasibility demonstrated by using the well-known yeast GAL4 transcription factor. The method was further used to establish a genome-wide map of the target sites of LHP1, a regulatory chromatin protein in A. thaliana.
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Affiliation(s)
- Sophie Germann
- Institut National de la Santé et de la Recherche Médicale (Inserm), Centre Léon Bérard, Lyon Cedex, France.
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Gaudin V, Hedou C, Rault A, Verdon E. Validation of a Five Plate Test, the STAR protocol, for the screening of antibiotic residues in muscle from different animal species according to European Decision 2002/657/EC. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2010; 27:935-52. [PMID: 20432095 DOI: 10.1080/19440041003677483] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The STAR protocol is a Five Plate Test (FPT) developed several years ago at the Community Reference Laboratory (CRL) for the screening of antimicrobial residues in milk and muscle. This paper presents the validation of this method according to European Decision 2002/657/EC and to an internal guideline for validation. A validation protocol based on 'simulated tissues' and on a list of 16 representative antimicrobials to be validated was implemented in our laboratory during several months for the STAR protocol. The performance characteristics of the method were determined (specificity, detection capabilities CCbeta, applicability, ruggedness). In conclusion, the STAR protocol is applicable to the broad-spectrum detection of antibiotic residues in muscles of different animal species (pig, cattle, sheep, poultry). The method has good specificity (false-positive rate = 4%). The detection capabilities were determined for 16 antibiotics from different families in relation to their respective maximum residue limit (MRL): beta-lactams (penicillins and cephalosporins < or = MRL), tetracyclines (< or = MRL and < or = 2.5 MRL), macrolides (2 MRL), quinolones (< or = 2 MRL), some sulphonamides (< or = 3 MRL), and trimethoprim (2 MRL). However, the sensitivity of the STAR protocol towards aminoglycosides (> 8 MRL) and florfenicol (< or = 10 MRL) was unsatisfactory (>>MRL). The two objectives of this study were met: firstly, to validate the STAR protocol according to European Decision 2002/657/EC, then to demonstrate that the validation guideline developed to implement this decision is applicable to microbiological plate tests even for muscle. The use of simulated tissue appeared a good compromise between spiked discs with antibiotic solutions and incurred tissues. In addition, the choice of a list of representative antibiotics allowed the reduction of the scope of the validation, which was already costly in time and effort.
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Affiliation(s)
- V Gaudin
- Community Reference Laboratory, AFSSA Fougères-LERMVD, La Haute Marche-BP 90203, F-35302 Fougere Cedex, France.
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Gaudin V, Cadieu N, Maris P. Inter-laboratory studies for the evaluation of ELISA kits for the detection of chloramphenicol residues in milk and muscle. FOOD AGR IMMUNOL 2010. [DOI: 10.1080/09540100400003519] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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Andrey P, Kiêu K, Kress C, Lehmann G, Tirichine L, Liu Z, Biot E, Adenot PG, Hue-Beauvais C, Houba-Hérin N, Duranthon V, Devinoy E, Beaujean N, Gaudin V, Maurin Y, Debey P. Statistical analysis of 3D images detects regular spatial distributions of centromeres and chromocenters in animal and plant nuclei. PLoS Comput Biol 2010; 6:e1000853. [PMID: 20628576 PMCID: PMC2900307 DOI: 10.1371/journal.pcbi.1000853] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2009] [Accepted: 06/03/2010] [Indexed: 12/16/2022] Open
Abstract
In eukaryotes, the interphase nucleus is organized in morphologically and/or functionally distinct nuclear “compartments”. Numerous studies highlight functional relationships between the spatial organization of the nucleus and gene regulation. This raises the question of whether nuclear organization principles exist and, if so, whether they are identical in the animal and plant kingdoms. We addressed this issue through the investigation of the three-dimensional distribution of the centromeres and chromocenters. We investigated five very diverse populations of interphase nuclei at different differentiation stages in their physiological environment, belonging to rabbit embryos at the 8-cell and blastocyst stages, differentiated rabbit mammary epithelial cells during lactation, and differentiated cells of Arabidopsis thaliana plantlets. We developed new tools based on the processing of confocal images and a new statistical approach based on G- and F- distance functions used in spatial statistics. Our original computational scheme takes into account both size and shape variability by comparing, for each nucleus, the observed distribution against a reference distribution estimated by Monte-Carlo sampling over the same nucleus. This implicit normalization allowed similar data processing and extraction of rules in the five differentiated nuclei populations of the three studied biological systems, despite differences in chromosome number, genome organization and heterochromatin content. We showed that centromeres/chromocenters form significantly more regularly spaced patterns than expected under a completely random situation, suggesting that repulsive constraints or spatial inhomogeneities underlay the spatial organization of heterochromatic compartments. The proposed technique should be useful for identifying further spatial features in a wide range of cell types. Several reports suggest functional relationships within the spatial organization of the nucleus, gene regulation and cell differentiation. However, it still remains difficult to extract common rules, mostly because i) most data have been gathered on limited sets of nuclear elements and in nuclei outside their normal physiological environment, and ii) few three-dimensional (3D) quantitative measures have been performed. Thus, we questioned whether common nuclear organization principles exist in the animal and plant kingdoms. For that purpose, we investigated the 3D distribution of centromeres/chromocenters in five populations of animal and plant nuclei: rabbit embryos at 8-cell and blastocyst stages, rabbit mammary gland epithelial cells and Arabidopsis thaliana plantlets. We set up adapted procedures to segment confocal images and developed a new analytical methodology based on distances between positions within the nucleus and centromeres/chromocenters. We showed that in all systems, despite large differences in chromosome number (44 in rabbit; 10 in A. thaliana) and genome size (rabbit estimated size 2.77 Gbp; A. thaliana 125 Mbp), centromeres/chromocenters form significantly more regularly spaced patterns than expected under a completely random situation. This suggests that, whatever their specific features, conserved rules govern the spatial distribution of genomes in nuclei of differentiated cells.
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Affiliation(s)
- Philippe Andrey
- INRA, UMR1197 Neurobiologie de l'Olfaction et de la Prise Alimentaire, Jouy-en-Josas, France
- Université Paris-Sud 11, UMR 1197, Orsay, France
- IFR144 Neuro-Sud Paris, France
- UPMC, Université Paris 06, France
| | - Kiên Kiêu
- INRA, UR341, Mathématiques et Informatique Appliquées, Jouy-en-Josas, France
| | - Clémence Kress
- INRA, UR1196 Génomique et Physiologie de la Lactation, Jouy-en-Josas, France
| | - Gaëtan Lehmann
- INRA, UMR1198 Biologie du Développement et Reproduction, Jouy-en-Josas, France
- ENVA, Maisons Alfort, France
| | - Leïla Tirichine
- INRA, Institut J.-P. Bourgin, UMR1318 INRA-AgroParisTech, Versailles, France
| | - Zichuan Liu
- INRA, UMR1198 Biologie du Développement et Reproduction, Jouy-en-Josas, France
- ENVA, Maisons Alfort, France
| | - Eric Biot
- INRA, UMR1197 Neurobiologie de l'Olfaction et de la Prise Alimentaire, Jouy-en-Josas, France
- Université Paris-Sud 11, UMR 1197, Orsay, France
- IFR144 Neuro-Sud Paris, France
- INRA, Institut J.-P. Bourgin, UMR1318 INRA-AgroParisTech, Versailles, France
| | - Pierre-Gaël Adenot
- INRA, UMR1198 Biologie du Développement et Reproduction, Jouy-en-Josas, France
- ENVA, Maisons Alfort, France
| | - Cathy Hue-Beauvais
- INRA, UR1196 Génomique et Physiologie de la Lactation, Jouy-en-Josas, France
| | - Nicole Houba-Hérin
- INRA, Institut J.-P. Bourgin, UMR1318 INRA-AgroParisTech, Versailles, France
| | - Véronique Duranthon
- INRA, UMR1198 Biologie du Développement et Reproduction, Jouy-en-Josas, France
- ENVA, Maisons Alfort, France
| | - Eve Devinoy
- INRA, UR1196 Génomique et Physiologie de la Lactation, Jouy-en-Josas, France
| | - Nathalie Beaujean
- INRA, UMR1198 Biologie du Développement et Reproduction, Jouy-en-Josas, France
- ENVA, Maisons Alfort, France
| | - Valérie Gaudin
- INRA, Institut J.-P. Bourgin, UMR1318 INRA-AgroParisTech, Versailles, France
| | - Yves Maurin
- INRA, UMR1197 Neurobiologie de l'Olfaction et de la Prise Alimentaire, Jouy-en-Josas, France
- Université Paris-Sud 11, UMR 1197, Orsay, France
- IFR144 Neuro-Sud Paris, France
| | - Pascale Debey
- INRA, UMR1198 Biologie du Développement et Reproduction, Jouy-en-Josas, France
- ENVA, Maisons Alfort, France
- * E-mail:
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Gaugain-Juhel M, Delépine B, Gautier S, Fourmond M, Gaudin V, Hurtaud-Pessel D, Verdon E, Sanders P. Validation of a liquid chromatography-tandem mass spectrometry screening method to monitor 58 antibiotics in milk: a qualitative approach. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2009; 26:1459-71. [DOI: 10.1080/02652030903150575] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Gaudin V, Andrey P, Devinoy E, Kress C, Kieu K, Beaujean N, Maurin Y, Debey P. Modeling the 3D functional architecture of the nucleus in animal and plant kingdoms. C R Biol 2009; 332:937-46. [PMID: 19909917 DOI: 10.1016/j.crvi.2009.09.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Compartmentalization is one of the fundamental principles which underly nuclear function. Numerous studies describe complex and sometimes conflicting relationships between nuclear gene positioning and transcription regulation. Therefore the question is whether topological landmarks and/or organization principles exist to describe the nuclear architecture and, if existing, whether these principles are identical in the animal and plant kingdoms. In the frame of an agroBI-INRA program on nuclear architecture, we set up a multidisciplinary approach combining biological studies, spatial statistics and 3D modeling to investigate spatial organization of a nuclear compartment in both plant and animal cells in their physiological contexts. In this article, we review the questions addressed in this program and the methodology of our work.
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Affiliation(s)
- Valérie Gaudin
- Laboratoire de biologie cellulaire, UR501, IJPB, route de Saint-Cyr, INRA, 78026 Versailles, France
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Tirichine L, Andrey P, Biot E, Maurin Y, Gaudin V. 3D fluorescent in situ hybridization using Arabidopsis leaf cryosections and isolated nuclei. Plant Methods 2009; 5:11. [PMID: 19650905 PMCID: PMC2731090 DOI: 10.1186/1746-4811-5-11] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2009] [Accepted: 08/03/2009] [Indexed: 05/23/2023]
Abstract
BACKGROUND Fluorescent hybridization techniques are widely used to study the functional organization of different compartments within the mammalian nucleus. However, few examples of such studies are known in the plant kingdom. Indeed, preservation of nuclei 3D structure, which is required for nuclear organization studies, is difficult to fulfill. RESULTS We report a rapid protocol for fluorescent in situ hybridization (FISH) performed on 3D isolated nuclei and thin cryosectioned leaves of Arabidopsis thaliana. The use of direct labeling minimized treatment steps, shortening the overall procedure. Using image analysis, we measured different parameters related to nucleus morphology and overall 3D structure. CONCLUSION Our work describes a 3D-FISH protocol that preserves the 3D structure of Arabidopsis interphase nuclei. Moreover, we report for the first time FISH using cryosections of Arabidopsis leaves. This protocol is a valuable tool to investigate nuclear architecture and chromatin organization.
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Affiliation(s)
- Leïla Tirichine
- Laboratoire de Biologie Cellulaire, INRA UR 501, IJPB, Route de Saint-Cyr, F-78026 Versailles, France
- Institut des Sciences du Végétal, CNRS, avenue de la Terrasse, F-91198 Gif-sur-Yvette, France
| | - Philippe Andrey
- Neurobiologie de l'Olfaction et de la Prise Alimentaire, INRA UMR 1197, Domaine de Vilvert, F-78350 Jouy-en-Josas, France
- Université Paris-Sud 11, UMR 1197, F-91400 Orsay, France
- IFR 144 Neuro-Sud, Paris, France
- Université Pierre et Marie Curie, Paris, France
| | - Eric Biot
- Laboratoire de Biologie Cellulaire, INRA UR 501, IJPB, Route de Saint-Cyr, F-78026 Versailles, France
| | - Yves Maurin
- Neurobiologie de l'Olfaction et de la Prise Alimentaire, INRA UMR 1197, Domaine de Vilvert, F-78350 Jouy-en-Josas, France
- Université Paris-Sud 11, UMR 1197, F-91400 Orsay, France
- IFR 144 Neuro-Sud, Paris, France
| | - Valérie Gaudin
- Laboratoire de Biologie Cellulaire, INRA UR 501, IJPB, Route de Saint-Cyr, F-78026 Versailles, France
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Gaudin V, Laurentie M. Application of total error approach to assess the performance of a biological method (ELISA) to detect nicarbazin residues in eggs. J Chromatogr B Analyt Technol Biomed Life Sci 2009; 877:2358-62. [DOI: 10.1016/j.jchromb.2009.03.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2008] [Revised: 02/20/2009] [Accepted: 03/03/2009] [Indexed: 11/28/2022]
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Gaudin V, Hedou C, Verdon E. Validation of a wide-spectrum microbiological tube test, the EXPLORER® test, for the detection of antimicrobials in muscle from different animal species. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2009. [DOI: 10.1080/02652030902939671] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Gaudin V, Hedou C, Rault A, Sanders P, Verdon E. Comparative study of three screening tests, two microbiological tube tests, and a multi-sulphonamide ELISA kit for the detection of antimicrobial and sulphonamide residues in eggs. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2009; 26:427-40. [DOI: 10.1080/02652030802527626] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Laurentie M, Gaudin V. Use of the total error approach to evaluate the performance of a semi-quantitative immunological method (BIACORE method) for detecting sulfamethazine in bovine milk. J Chromatogr B Analyt Technol Biomed Life Sci 2009; 877:2375-9. [PMID: 19179126 DOI: 10.1016/j.jchromb.2008.12.069] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2008] [Revised: 12/19/2008] [Accepted: 12/23/2008] [Indexed: 11/30/2022]
Abstract
A semi-quantitative immunological method (BIACORE method) for detecting sulfamethazine in bovine milk was developed and validated using the total error approach. The acceptance limits were set at +/-40% and the risk of procedure of (1-beta) proportion measurements falling outside the acceptance limits was chosen at 5%. Different response functions were tested on the basis of the accuracy index (I(A)). The best model was a weighted (1/X(2)) quadratic regression and the simplest one was an unweighted quadratic regression. This approach identified the weak point of the method, which was precision. Finally this BIACORE method was able to detect positive samples containing sulfamethazine in the dosing range between 50 and 150 ng/ml.
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Affiliation(s)
- Michel Laurentie
- Pharmacokinetics-Pharmacodynamics Unit, Laboratory for studies and research on veterinary medicinal products and disinfectants, Afssa Fougères, BP 90203, La Haute Marche, 35302 Fougères, France.
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Pouteau S, Carré I, Gaudin V, Ferret V, Lefebvre D, Wilson M. Diversification of photoperiodic response patterns in a collection of early-flowering mutants of Arabidopsis. Plant Physiol 2008; 148:1465-73. [PMID: 18799658 PMCID: PMC2577249 DOI: 10.1104/pp.108.127639] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2008] [Accepted: 09/09/2008] [Indexed: 05/20/2023]
Abstract
Many plant species exhibit seasonal variation of flowering time in response to daylength. Arabidopsis (Arabidopsis thaliana) flowers earlier under long days (LDs) than under short days (SDs). This quantitative response to photoperiod is characterized by two parameters, the critical photoperiod (Pc), below which there is a delay in flowering, and the ceiling photoperiod (Pce), below which there is no further delay. Thus Pc and Pce define the thresholds beyond which maximum LD and SD responses are observed, respectively. We studied the quantitative response to photoperiod in 49 mutants selected for early flowering in SDs. Nine of these mutants exhibited normal Pce and Pc, showing that their precocious phenotype was not linked to abnormal measurement of daylength. However, we observed broad diversification in the patterns of quantitative responses in the other mutants. To identify factors involved in abnormal measurement of daylength, we analyzed the association of these various patterns with morphogenetic and rhythmic defects. A high proportion of mutants with altered Pce exhibited abnormal hypocotyl elongation in the dark and altered circadian periods of leaf movements. This suggested that the circadian clock and negative regulators of photomorphogenesis may contribute to the specification of SD responses. In contrast, altered Pc correlated with abnormal hypocotyl elongation in the light and reduced photosynthetic light-input requirements for bolting. This indicated that LD responses may be specified by positive elements of light signal transduction pathways and by regulators of resource allocation. Furthermore, the frequency of circadian defects in mutants with normal photoperiodic responses suggested that the circadian clock may regulate the number of leaves independently of its effect on daylength perception.
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Affiliation(s)
- Sylvie Pouteau
- UR Biologie Cellulaire, INRA, F78026 Versailles, France.
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Gaudin V, Hédou C, Sanders P. Validation of a Biacore method for screening eight sulfonamides in milk and porcine muscle tissues according to European decision 2002/657/EC. J AOAC Int 2007; 90:1706-1715. [PMID: 18196645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Sulfonamides are commonly used for prophylactic or therapeutic purposes in veterinary medicine. A maximum residue limit (MRL) for sulfonamides has been set at 100 microg/kg in milk and muscle. A multisulfonamide antibody was used for the development of 2 different Biacore protocols, one for the screening of milk samples, the other for muscle samples. Two different Biacore systems were used: Biacore X system (milk protocol), which is considered a research and development apparatus, and Biacore 3000 system (muscle protocol), which is a completely automated system used for high-throughput screening. This report describes the validation of semiquantitative immunological methods according to the European Decision 2002/657/EC "concerning the performance of analytical methods." The different performance characteristics (detection capability CCbeta, specificity/selectivity, precision, stability, and applicability) were determined in relation to the European Union MRL of 100 microg/kg for sulfonamides. The applicability of the method to porcine, bovine, and poultry muscle was studied. The detection capabilities CCbeta were calculated to be 40 microg/L in milk and 60 microg/kg in porcine, bovine, and poultry muscles. Eight different sulfonamides, of which 3 (sulfamethazine, sulfamerazine, and sulfadiazine) are authorized in France, were detected simultaneously, at or below the MRL level, with both Biacore systems.
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Tessadori F, Chupeau MC, Chupeau Y, Knip M, Germann S, van Driel R, Fransz P, Gaudin V. Large-scale dissociation and sequential reassembly of pericentric heterochromatin in dedifferentiated Arabidopsis cells. J Cell Sci 2007; 120:1200-8. [PMID: 17376962 DOI: 10.1242/jcs.000026] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Chromocenters in Arabidopsis thaliana are discrete nuclear domains of mainly pericentric heterochromatin. They are characterized by the presence of repetitive sequences, methylated DNA and dimethylated histone H3K9. Here we show that dedifferentiation of specialized mesophyll cells into undifferentiated protoplasts is accompanied by the disruption of chromocenter structures. The dramatic reduction of heterochromatin involves the decondensation of all major repeat regions, also including the centromeric 180 bp tandem repeats. Only the 45S rDNA repeat remained in a partly compact state in most cells. Remarkably, the epigenetic indicators for heterochromatin, DNA methylation and H3K9 dimethylation, did not change upon decondensation. Furthermore, the decondensation of pericentric heterochromatin did not result in transcriptional reactivation of silent genomic elements. The decondensation process was reversible upon prolonged culturing. Strikingly, recondensation of heterochromatin into chromocenters is a stepwise process. Compaction of the tandemly arranged 45S rDNA regions occurs first, followed by the centromeric 180 bp and the 5S rDNA repeats and finally the dispersed repeats, including transposons. The sequence of reassembly seems to be correlated to the size of the repeat domains. Our results indicate that different types of pericentromeric repeats form different types of heterochromatin, which subsequently merge to form a chromocenter.
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Affiliation(s)
- Federico Tessadori
- Nuclear Organization Group, Swammerdam Institute for Life Sciences, University of Amsterdam, BioCentrum Amsterdam, Kruislaan 318, 1098SM Amsterdam, The Netherlands
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Germann S, Juul-Jensen T, Letarnec B, Gaudin V. DamID, a new tool for studying plant chromatin profiling in vivo, and its use to identify putative LHP1 target loci. Plant J 2006; 48:153-63. [PMID: 16972870 DOI: 10.1111/j.1365-313x.2006.02859.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We show here that the in vivo methylation-based tagging technique DamID (DNA adenine methyltransferase identification) can be used for studies of DNA-protein interactions or chromatin profiling in plants. We have demonstrated the feasibility, reproducibility and sensitivity of the method in Arabidopsis thaliana, using the well-known yeast GAL4 transcription factor, for which DNA-binding sites (UAS(G)) were introduced into the plant genome. We monitored the methylation resulting from the activity of DNA adenine methyltransferase fused to the protein of interest, by combining digestion with methylation-sensitive restriction enzymes and quantitative PCR. We then used DamID to identify genomic targets of LHP1, a protein mostly associated with euchromatin. We showed that LHP1 was targeted to the promoter and transcribed regions of four genes: AG, AP3, FT and PI. Our data also demonstrate that LHP1, like its animal homologues, has a high binding affinity for A/T-rich regions, binding particularly strongly to the large regulatory introns of AG and PI. We identified three major characteristics of LHP1 binding, highlighting the similarities between plant LHP1 and animal HP1 proteins.
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Affiliation(s)
- Sophie Germann
- Laboratoire de Biologie Cellulaire, IJPB, INRA, Route de Saint-Cyr, 78026 Versailles Cedex, France
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Libault M, Tessadori F, Germann S, Snijder B, Fransz P, Gaudin V. The Arabidopsis LHP1 protein is a component of euchromatin. Planta 2005; 222:910-25. [PMID: 16244868 DOI: 10.1007/s00425-005-0129-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2005] [Accepted: 08/29/2005] [Indexed: 05/05/2023]
Abstract
The HP1 family proteins are involved in several aspects of chromatin function and regulation in Drosophila, mammals and the fission yeast. Here we investigate the localization of LHP1, the unique Arabidopsis thaliana HP1 homolog known at present time, to approach its function. A functional LHP1-GFP fusion protein, able to restore the wild-type phenotype in the lhp1 mutant, was used to analyze the subnuclear distribution of LHP1 in both A. thaliana and Nicotiana tabacum. In A. thaliana interphase nuclei, LHP1 was predominantly located outside the heterochromatic chromocenters. No major aberrations were observed in heterochromatin content or chromocenter organization in lhp1 plants. These data indicate that LHP1 is mainly involved in euchromatin organization in A. thaliana. In tobacco BY-2 cells, the LHP1 distribution, although in foci, slightly differed suggesting that LHP1 localization is determined by the underlying genome organization of plant species. Truncated LHP1 proteins expressed in vivo allowed us to determine the function of the different segments in the localization. The in foci distribution is dependent on the presence of the two chromo domains, whereas the hinge region has some nucleolus-targeting properties. Furthermore, like the animal HP1beta and HP1gamma subtypes, LHP1 dissociates from chromosomes during mitosis. In transgenic plants expressing the LHP1-GFP fusion protein, two major localization patterns were observed according to cell types suggesting that localization evolves with age or differentiation states. Our results show conversed characteristics of the A. thaliana HP1 homolog with the mammal HP1gamma isoform, besides specific plant properties.
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Affiliation(s)
- Marc Libault
- Laboratoire de Biologie Cellulaire, IJPB, INRA, route de St Cyr, 78026, Versailles Cedex, France
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Gaudin V, Cadieu N, Sanders P. Results of a European proficiency test for the detection of streptomycin/dihydrostreptomycin, gentamicin and neomycin in milk by ELISA and biosensor methods. Anal Chim Acta 2005. [DOI: 10.1016/j.aca.2004.06.058] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Abstract
The plant life cycle involves a series of developmental phase transitions. These transitions require the regulation and highly co-ordinated expression of many genes. Epigenetic controls have now been shown to be a key element of this mechanism of regulation. In the model plant Arabidopsis, recent genetic and molecular studies on chromatin have begun to dissect the molecular basis of these epigenetic controls. Chromatin dynamics represent the emerging and exciting field of gene regulation notably involved in plant developmental transitions. By comparing plant and animal systems, new insights into the molecular complexes and mechanisms governing development can be delineated. We are now beginning to identify the components of chromatin complexes and their functions.
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Affiliation(s)
- Frédéric Berger
- Laboratoire RDP, UMR 5667, ENS-Lyon, 46 allée d'Italie, F-69364 Lyon cedex 07, France
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Pouteau S, Ferret V, Gaudin V, Lefebvre D, Sabar M, Zhao G, Prunus F. Extensive phenotypic variation in early flowering mutants of Arabidopsis. Plant Physiol 2004; 135:201-11. [PMID: 15122022 PMCID: PMC429349 DOI: 10.1104/pp.104.039453] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2004] [Revised: 02/19/2004] [Accepted: 02/25/2004] [Indexed: 05/20/2023]
Abstract
Flowering time, the major regulatory transition of plant sequential development, is modulated by multiple endogenous and environmental factors. By phenotypic profiling of 80 early flowering mutants of Arabidopsis, we examine how mutational reduction of floral repression is associated with changes in phenotypic plasticity and stability. Flowering time measurements in mutants reveal deviations from the linear relationship between the number of leaves and number of days to bolting described for natural accessions and late flowering mutants. The deviations correspond to relative early bolting and relative late bolting phenotypes. Only a minority of mutants presents no detectable phenotypic variation. Mutants are characterized by a broad release of morphological pleiotropy under short days, with leaf characters being most variable. They also exhibit changes in phenotypic plasticity across environments for florigenic-related responses, including the reaction to light and dark, photoperiodic behavior, and Suc sensitivity. Morphological pleiotropy and plasticity modifications are differentially distributed among mutants, resulting in a large diversity of multiple phenotypic changes. The pleiotropic effects observed may indicate that floral repression defects are linked to global developmental perturbations. This first, to our knowledge, extensive characterization of phenotypic variation in early flowering mutants correlates with the reports that most factors recruited in floral repression at the molecular genetic level correspond to ubiquitous regulators. We discuss the importance of functional ubiquity for floral repression with respect to robustness and flexibility of network biological systems.
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Affiliation(s)
- Sylvie Pouteau
- Laboratoire de Biologie Cellulaire, Institut National de la Recherche Agronomique, F78026 Versailles, France.
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