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International audience; Biocide disinfectants are used in agro-food industries in order to limit the development of pathogens present in environment or on surfaces in contact with food for human or animal consumption. Biocide residues remaining on food surfaces may constitute a toxicological risk for the consumer. Very little feedback from the field on the rates of biocide residues in the industry exist due to a lack of simple, fast and responsive self-checking methods. The development of biosensors for the detection of biocide disinfectants represents a promising way to explore this, but most of this research remains limited.

International audience; 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.

Veterinary drugs could contaminate animal-derived food products for human consumption. Some antibiotic residues (e.g., chloramphenicol (CAP), nitrofuran metabolites) are banned in foodstuffs of animal origin (e.g., milk, honey, etc.) in the European Union because of toxicological risks for the consumer. Screening methods applied for food safety monitoring should be sensitive, specific, cheap, quick, and portable for field testing (e.g., self-control). Electrochemical biosensors make it possible to develop a promising and economically interesting approach. An innovative and cheap electrochemical method based on disposable screen-printed carbon electrodes (SPCE), coupled to magnetic beads (MB), that allows the simultaneous detection of three families of antibiotics in milk was published by a Spanish academic team. When the biosensor method was applied to detect CAP residues in honey, two major issues were identified: firstly, the very low levels of residues to reach (i.e., regulatory limits below 1 µg/kg), and secondly, the complexity of the honey matrix; there is not a single honey matrix. Honey composition and color vary considerably depending on the botanical origin. Moreover, some honey ingredients can interfere with the electrochemical detection, especially substances with antioxidant activities (e.g., polyphenols). Therefore, in parallel with the optimization of the electrochemical method, the reduction of matrix effects was a big challenge.

International audience; 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.

International audience; The Infiniplex for milk(R) (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(R) 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 CCbeta 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 CCbeta 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 CCbeta of thiamphenicol, cloxacillin, danofloxacin, sulphathiazol, ceftiofur and sulphamonomethoxine were lower than or at the MRL. However, it was difficult to approach an accurate CCbeta 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.

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.

International audience; Different types of contaminants (e.g., pesticides, veterinary drugs) can be found in food products intended for human consumption (e.g., water, food from animal or plant origin). The risks for the consumers' health are multiple (e.g., endocrine disruptor's effect, carcinogenic effect, allergic risks). The detection of contaminants in food products is the first critical step of the control. Conventional screening methods could be bioassays, immunological methods, or physicochemical methods. Biosensors are identified as innovative screening methods. Electrochemical biosensors make it possible to develop a promising and economically interesting approach. Technological advances (e.g., nanomaterials, microfluidics) improved the methods' sensitivity.

Introduction Chemical (eg pesticides, veterinary drugs, etc.) and bacteriological contaminants (eg. foodborne pathogens) could contaminate animal and plant derived food products for human consumption. Some antibiotic residues (eg. chloramphenicol, nitrofuran metabolites, dyes) are banned in foodstuffs of animal origin (eg. milk, meat, eggs, etc.) in European Union because of toxicological risks for the consumer. The European Regulation has set Minimum Required Performance Limits (MRPL) [1] or Reference Point for Action (RPA) for banned substances [2]. Food containing residues of substances at or above the MRPL or RPA are declared non-compliant and consignments are rejected from the consumer's market. Screening methods are the first stage of food control and so are essential for food safety monitoring. Conventional screening methods are microbiological methods (eg. plate tests, tube tests), immunological methods (eg. ELISA, radioimmunoassays) or physico-chemical methods (Thin Layer Chromatography, High Performance Liquid Chromatography (HPLC), liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS)). These methods sometimes lack of sensitivity or specificity; they also could be time and money consuming. There is thus a need to develop novel screening methods for antibiotic residues detection, preferably with the potential for the field-testing (eg. farm control, self-control). Electrochemical biosensors make it possible to develop a promising and economically interesting approach. Electrochemical immunosensor An innovative electrochemical method based on disposable Screen Printed Carbon Electrodes (SPCE), coupled to magnetic beads (MB), allowing the simultaneous detection of 3 families of antibiotics in milk, was published by a Spanish academic team [3]. This technique presents major advantages: low cost (eg. disposable electrodes, potentiostat), promising detection limits, portability, and possible automatisation. Our laboratory has evaluated the transferability of the method. An electrochemical immunosensor has been developed for the detection of chloramphenicol residues in honey as a proof of concept. Honey composition and colour varies considerably depending on the botanical origin. Moreover some honey ingredients can interfere with the electrochemical detection, especially substances with antioxidant activities (eg. polyphenols). Therefore a lot of work had to be done to improve sample extraction to reduce matrix effects. The objective is to develop an electrochemical bead-based immunosensor for the multiplex detection of banned antibiotics (eg. chloramphenicol, nitrofuran metabolites, dyes) in bovine milk. Method Antibodies (Abs) against antibiotics are grafted on the surface of magnetic beads (MBs). Milk samples and antibiotic conjugated with Horseradish peroxidase (HRP) are mixed with MBs-Abs. A competition occurs between the HRP conjugates and the antibiotic residues if present in the sample, for the binding to the antibody. The MBs are washed to remove free antibiotics and conjugates. Then, a Screen Printed Carbon Electrode (SPCE) with MBs on its surface (maintained by a magnet) is soaked into a buffer solution containing hydroquinone; when adding hydrogen peroxide (H2O2) to the solution, an electrochemical signal is produced, due to the enzymatic activity of HRP and measured. The electrochemical signal is inversely proportional to the antibiotic concentration in the sample. Results and Conclusions Screening methods for the detection of veterinary drugs in food products have to be validated according to the European regulation [1] and to the European guideline for the validation of screening methods [4]. After the development and the optimization of the analytical parameters (eg. sample preparation, HRP concentration, incubation time, applied potential, etc), the methods developed for single compounds will be evaluated and validated according to the European regulations. Then the single compound methods will be merged into one multiplex method if possible. The results will be presented to the conference, discussing the advantages and drawbacks of electrochemical biosensors for the screening of antibiotic residues in food products. References 1. Commission Decision (EC) N° 2002/657 of 12 August 2002 implementing Council Directive 96/23/EC concerning the performance of analytical methods and interpretation of results. 2002: Official Journal of European Communities. p. 8-36. 2. Commission Regulation (EC) N° 470/2009 laying down Community procedures for the establishment of residue limits of pharmacologically active substances in foodstuffs of animal origin 2009, The European parliement and the Council: Official Journal of the European Union p. 11-22. 3. Conzuelo F, Ruiz-Valdepeñas Montiel V, Campuzano S, Gamella M, Torrente-Rodríguez RM, Reviejo AJ, Pingarrón JM. 2014. Rapid screening of multiple antibiotic residues in milk using disposable amperometric magnetosensors. Anal. Chim. Acta. 820:32-38. 4. CRL, Guideline for the validation of screening methods for residues of veterinary medicines (initial validation and transfer). 2010: Available from:: Guideline_Validation_Screening_en.pdf. p. 1-18.

Introduction Chemical (eg pesticides, veterinary drugs, etc.) and bacteriological contaminants (eg. foodborne pathogens) could contaminate animal and plant derived food products for human consumption. Some antibiotic residues (eg. chloramphenicol, nitrofuran metabolites, dyes) are banned in foodstuffs of animal origin (eg. milk, meat, eggs, etc.) in European Union because of toxicological risks for the consumer. The European Regulation has set Minimum Required Performance Limits (MRPL) [1] or Reference Point for Action (RPA) for banned substances [2]. Food containing residues of substances at or above the MRPL or RPA are declared non-compliant and consignments are rejected from the consumer’s market. Screening methods are the first stage of food control and so are essential for food safety monitoring. Conventional screening methods are microbiological methods (eg. plate tests, tube tests), immunological methods (eg. ELISA, radioimmunoassays) or physico-chemical methods (Thin Layer Chromatography, High Performance Liquid Chromatography (HPLC), liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS)). These methods sometimes lack of sensitivity or specificity; they also could be time and money consuming. There is thus a need to develop novel screening methods for antibiotic residues detection, preferably with the potential for the field-testing (eg. farm control, self-control). Electrochemical biosensors make it possible to develop a promising and economically interesting approach. Electrochemical immunosensor An innovative electrochemical method based on disposable Screen Printed Carbon Electrodes (SPCE), coupled to magnetic beads (MB), allowing the simultaneous detection of 3 families of antibiotics in milk, was published by a Spanish academic team [3]. This technique presents major advantages: low cost (eg. disposable electrodes, potentiostat), promising detection limits, portability, and possible automatisation. Our laboratory has evaluated the transferability of the method. An electrochemical immunosensor has been developed for the detection of chloramphenicol residues in milk as a proof of concept. The matrix effect (milk samples) was high and so sample preparation has to be improved to reduce matrix effects. The objective is to develop an amperometric bead-based immunosensor for the multiplex detection of banned antibiotics (eg. chloramphenicol, nitrofuran metabolites, dyes) in bovine milk. Method Antibodies (Abs) against antibiotics are grafted on the surface of magnetic beads (MBs). Milk samples and antibiotic conjugated with Horseradish peroxidase (HRP) are mixed with MBs-Abs. A competition occurs between the HRP conjugates and the antibiotic residues if present in the sample, for the binding to the antibody. The MBs are washed to remove free antibiotics and conjugates. Then, a Screen Printed Carbon Electrode (SPCE) with MBs on its surface (maintained by a magnet) is soaked into a buffer solution containing hydroquinone; when adding hydrogene peroxide (H2O2) to the solution, an amperometric signal is produced, due to the enzymatic activity of HRP and measured. The amperometric signal is inversely proportional to the antibiotic concentration in the sample. Results and Conclusions Screening methods for the detection of veterinary drugs in food products have to be validated according to the European regulation [1] and to the European guideline for the validation of screening methods [4]. After the development and the optimization of the analytical parameters (eg. sample preparation, HRP concentration, incubation time, applied potential, etc), the methods developed for single compounds will be evaluated and validated according to the European regulations. Then the single compound methods will be merged into one multiplex method if possible. The results will be presented to the conference, discussing the advantage sand drawbacks of amperometric biosensors for the screening of antibiotic residues in food products. References 1. Commission Decision (EC) N° 2002/657 of 12 August 2002 implementing Council Directive 96/23/EC concerning the performance of analytical methods and interpretation of results. 2002: Official Journal of European Communities. p. 8-36. 2. Commission Regulation (EC) N° 470/2009 laying down Community procedures for the establishment of residue limits of pharmacologically active substances in foodstuffs of animal origin 2009, The European parliement and the Council: Official Journal of the European Union p. 11-22. 3. Conzuelo F, Ruiz-Valdepeñas Montiel V, Campuzano S, Gamella M, Torrente-Rodríguez RM, Reviejo AJ, Pingarrón JM. 2014. Rapid screening of multiple antibiotic residues in milk using disposable amperometric magnetosensors. Anal. Chim. Acta. 820:32-38. 4. CRL, Guideline for the validation of screening methods for residues of veterinary medicines (initial validation and transfer). 2010: Available from:: Guideline_Validation_Screening_en.pdf. p. 1-18.

Chapitre 29; International audience; 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.

International audience; Polycomb group (PcG) proteins contribute to the formation and maintenance of a specific repressive chromatin state that prevents the expression of genes in a particular space and time. Polycomb repressive complexes (PRCs) consist of several PcG proteins with specific regulatory or catalytic properties. PRCs are recruited to thousands of target genes, and various recruitment factors, including DNA-binding proteins and non-coding RNAs, are involved in the targeting. PcG proteins contribute to a multitude of biological processes by altering chromatin features at different scales. PcG proteins mediate both biochemical modifications of histone tails and biophysical modifications (e.g., chromatin fiber compaction and three-dimensional (3D) chromatin conformation). Here, we review the role of PcG proteins in nuclear architecture, describing their impact on the structure of the chromatin fiber, on chromatin interactions, and on the spatial organization of the genome in nuclei. Although little is known about the role of plant PcG proteins in nuclear organization, much is known in the animal field, and we highlight similarities and differences in the roles of PcG proteins in 3D gene regulation in plants and animals.

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.

International audience; 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 (CCbeta). 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.

International audience; 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).

In plants the adult organs are not determined during embryogenesis. Throughout their life cycle, plants undergo different developmental changes, which require deep alterations in the overall gene expression patterns. The timing at which these phase changes occur can have a strong impact on plant viability and fitness and therefore needs to be tightly regulated to assure they take place under optimal conditions. On the other hand, in Arabidopsis thaliana, once a transition is initiated, it is usually stable, independently of the surrounding environment, suggesting it should be memorized. Over the last years, several studies have shown that epigenetics plays an important role in the regulation of phase transitions in plants. For instance, Arabidopsis mutants where the repressive trimethylation of lysine 27 of histone 3 (H3K27me3) is absent were shown to germinate and further revert into calli-like structures bearing somatic embryos. Moreover, this histone mark has recently been shown to also regulate the transition from vegetative to reproductive development, as some mutants with reduced H3K27me3 levels are incapable of memorizing floral inducible stimuli, when transferred to suboptimal conditions. On the other hand, the epigenetic modifications need to be reset at the end of each generation, to ensure the normal development of the progeny. In fact, plants have developed an entire reprogramming machinery that culminates at gametogenesis, where a genome-wide resetting of gene programs takes place.

International audience; Honey could be contaminated by antibiotic residues. There is still a great need for a cheap and single multi-residue method. The Evidence Investigator™ system is a biochip and semi-automated system. The microarray kit I (AM I) for the detection of sulphonamide and trimethoprim (TMP) residues in honey was evaluated, and then validated according to the European decision EC/2002/657 and to the European guideline for the validation of screening methods for veterinary medicines (2010). The method was found to be rapid and able to screen simultaneously 14 sulphonamides and TMP in honey with a very easy sample preparation procedure. The false–positive rate of 4% maximum is very satisfactory. All detection capabilities (CCβ) were well below the recommended concentration (RC) of 50 µg kg−1. The applicability of AM I kit with different types of honey (monofloral or multifloral, liquid or solid, different floral origins, etc.) has been proved.

International audience; The main chemicals used against varoa are acaricides, and the antibiotics used for the control of bee bacterial diseases are mainly tetracyclines, streptomycins, sulfonamides and chloramphenicol. No maximum residue limits (MRLs) have been set for any antibiotics in honey. Therefore, in the European Union, minimum recommended concentrations (RC) for the analytical performance of methods to control a certain set of these non-authorised chemicals in honey were published by the European Union Reference Laboratory (EU-RL) in 2007. Concerning the strategy for the control for antibiotic residues in honey, there is still a great need for a cheap and single multi-residue method. Biochip array technology is an innovative assay technology for the multi-analyte screening of biological samples in a rapid and easy-to-use format. A multi-array system, called Evidence Investigator™ (Randox, Crumlin, Co., Antrim, UK), was evaluated in our laboratory. It is a semi-automated biochip system designed for research, clinical applications and veterinary use. A competitive chemiluminescent immunoassay is employed for the detection of antimicrobials. The MicroArray II kit (AM II) dedicated to the screening of six different families of antibiotic residues was validated according to the European guideline for the validation of screening methods for residues of veterinary medicines. The specificity was proven to be very satisfactory, and applicability to different kinds of honey was demonstrated. The detection capabilities (CCβ) of six antibiotic residues were determined and were below the RCs when exist. The AM II kit could detect at least six quinolones, four tetracyclines and three epimers, three aminoglycosides, three macrolides, thiamphenicol, florfenicol and ceftiofur along with one of its stabilised metabolites, the desfuroylceftiofurcysteine disulfide (DCCD).

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.

Advance Publication; International audience; 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 (PRC1) 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.

International audience; The Evidence Investigator™ system (Randox, UK) is a biochip and semi-automated system. The microarray kit II (AM II) is capable of detecting several compounds belonging to different families of antibiotics: quinolones, ceftiofur, thiamphenicol, streptomycin, tylosin and tetracyclines. The performance of this innovative system was evaluated for the detection of antibiotic residues in new matrices, in muscle of different animal species and in aquaculture products. The method was validated according to the European Decision No. EC/2002/657 and the European guideline for the validation of screening methods, which represents a complete initial validation. The false-positive rate was equal to 0% in muscle and in aquaculture products. The detection capabilities CCβ for 12 validated antibiotics (enrofloxacin, difloxacin, ceftiofur, desfuroyl ceftiofur cysteine disulfide, thiamphenicol, florfenicol, tylosin, tilmicosin, streptomycin, dihydrostreptomycin, tetracycline, doxycycline) were all lower than the respective maximum residue limits (MRLs) in muscle from different animal origins (bovine, ovine, porcine, poultry). No cross-reactions were observed with other antibiotics, neither with the six detected families nor with other families of antibiotics. The AM II kit could be applied to aquaculture products but with higher detection capabilities from those in muscle. The detection capabilities CCβ in aquaculture products were respectively at 0.25, 0.10 and 0.5 of the respective MRL in aquaculture products for enrofloxacin, tylosin and oxytetracycline. The performance of the AM II kit has been compared with other screening methods and with the performance characteristics previously determined in honey.

International audience; Antibiotic residues may be found in food of animal origin, since veterinary drugs are used for preventive and curative purposes to treat animals. The control of veterinary drug residues in food is necessary to ensure consumer safety. Screening methods are the first step in the control of antibiotic residues in food of animal origin. Conventional screening methods are based on different technologies, microbiological methods, immunological methods or physico-chemical methods (e.g. thin-layer chromatography, HPLC, LC-MS/MS). Screening methods should be simple, quick, inexpensive and specific, with low detection limits and high sample throughput. Biosensors can meet some of these requirements. Therefore, the development of biosensors for the screening of antibiotic residues has been increasing since the 1980s. The present review provides extensive and up-to-date findings on biosensors for the screening of antibiotic residues in food products of animal origin. Biosensors are constituted of a bioreceptor and a transducer. In the detection of antibiotic residues, even though antibodies were the first bioreceptors to be used, new kinds of bioreceptors are being developed more and more (enzymes, aptamers, MIPs); their advantages and drawbacks are discussed in this review. The different categories of transducers (electrochemical, mass-based biosensors, optical and thermal) and their potential applications for the screening of antibiotic residues in food are presented. Moreover, the advantages and drawbacks of the different types of transducers are discussed. Lastly, outlook and the future development of biosensors for the control of antibiotic residues in food are highlighted.

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.

International audience; 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.; Modéliser l'architecture tri-dimensionnelle du noyau dans des cellules animales et végétales. L'organisation en comparti-ments est un des principes fondamentaux qui gouverne le fonctionnement du noyau. De nombreuses études montrent des relations complexes et parfois contradictoires entre la position d'un gène dans le noyau et son état transcriptionnel. Deux questions se posent : existe-t-il des principes généraux gouvernant l'organisation nucléaire, et, si oui, ces principes sont-ils analogues dans les règnes animal et végétal ? Dans le cadre d'un programme agroBI-INRA sur l'architecture nucléaire, nous avons développé une ap-proche multidisciplinaire combinant expériences biologiques, statistiques spatiales et modélisation en 3 dimensions pour analyser l'organisation spatiale d'un compartiment nucléaire dans des cellules animales et végétales, dans leur environnement physiolo-gique. Dans cet article, nous faisons une revue autour des questions posées dans ce programme et présentons la méthodologie de ce travail

International audience; The screening of antimicrobial residues in eggs is an especially important subject. Three different commercial kits for the screening of sulphonamides and other antimicrobials in eggs were validated in accordance with Decision 2002/657/EC: one enzyme-linked immunoabsorbant assay (ELISA) kit multi-sulphonamides (from RAISIO Diagnostics) and two microbiological tests (a Premi® test from DSM and an Explorer® kit from Zeu-Inmunotec). The false-positive rates were lower than 2% for all kits. The detection capabilities (CCβ) have to be as low as possible for banned substances and lower than the maximum residue limit (MRL) when MRLs have been set. The sensitivity of the Premi® test was better than that of the Explorer® test, probably because of the dilution of the eggs before the Explorer® test was used. The CCβ values towards most of the tested sulphonamides were satisfactory with the Premi® test (≤100 μg kg-1). Performance in a proficiency test for the detection of sulphonamides in eggs with the Premi® test confirmed these results. The detection capabilities of tetracycline and doxycycline were at the level of the MRL or twice the MRL maximum. The detection capabilities for chlortetracycline and oxytetracycline were higher (four to six times the MRL). The detection capabilities for amoxicillin, neomycin, tylosin and erythromycin were lower than their respective MRLs. Detection capabilities for sulphonamides were much lower for the ELISA kit than for microbiological tests. The ELISA kit could be recommended for the targeted screening of sulphonamides in eggs. On the other hand, the Explorer® and Premi® tests could be used as wide screening tests allowing the detection of most of the antimicrobial families.

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.

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 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.

International audience; 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.

International audience; 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.

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.

An interlaboratory study was proposed to the European Community and Third Countries National Reference Laboratories (NRL) for the analysis of aminoglycoside residues in bovine milk by ELISA. This test was intended to allow the participants to control their aminoglycoside ELISA methods and also to compare the performance of various ELISA kits (neomycin, gentamicin, streptomycin and DHS) in bovine milk. Twelve random coded frozen samples were sent in dried ice (including 2 blank samples and 10 spiked milk samples). Each sample had to be analysed in triplicate (that means three different extractions for each sample) with the ELISA kits of their choice (commercial or in-house), if possible looking for streptomycin/DHS, gentamicin and neomycin. If not, it was recommended to test only streptomycin/DHS twice, with two different batches of the same kit. The 14 participants performed the analyses with ELISA kits (or biosensor methods) for the detection of streptomycin/DHS. Seven participants tested the samples for the detection of neomycin and six for the detection of gentamicin with ELISA kits. Then qualitative and quantitative analyses of the results were performed. Four parameters were calculated according to a reference publication for the validation of screening qualitative methods: false non-compliant and false compliant rates, sensitivity and specificity. A quantitative exploitation was also performed by calculating the assigned value for each material. Then the evaluation of laboratory’s performance was carried out by calculating the accuracy and repeatability Z-scores.

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.

The use of chloramphenicol in veterinary medicine was banned in the EU in 1994. As the Community Reference Laboratory for antibiotic residues in food of animal origin, one of our functions is to organize inter-laboratory studies. A first inter-laboratory study for the analysis of chloramphenicol (CAP) in milk by ELISA kits was organized in 2001 and a second one for the detection of CAP in pig muscle by ELISA kits in 2002. These studies were intended to allow participants to control their CAP ELISA methods when used routinely and also to compare the performances of various ELISA kits for the detection of chloramphenicol in milk (commercial or in-house kits). In 2001, 15 participants received ten randomly coded frozen milk samples (four blank samples and six spiked milk samples from 0.5 to 5.0 μg/l). In 2002, 20 participants received eight randomly coded frozen muscle samples (two blank samples and six incurred muscle samples from 2.1 to 6.5 μg/kg). They were asked to analyse each sample in triplicate with ...

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.

Antibiotic residue survey. Contribution of mass analytical methods to identification of contaminants. Antibiotic residue surveys are defined by a European legislation where analytical methods for screening and confirmatory residue analyses are codified. For screening antibiotic residues, mainly biological methods such as microbiological (fourth plate method) or immunological (Biosensor method) methods are used. In terms of confirmation of residue samples, positive samples are confirmed by a method based on liquid chromatography with MS Mass spectrometry detection. These methods offer many advantages. One advantage is that extraction of residues from biological samples is simplified, reducing the cost of analysis and increasing the reliability of the results. Another advantage is the identification of the antibiotic compound which leads to residues. The European community has defined clear-cut criteria that allow identification of authorised and banned compounds. The methods can be used in any biological tissue or matrix (fat, muscle, liver, honey). Residues of many different compounds can be detected and identified by these methods such as in the case of antiparasitic drugs, hormones, beta-agonists, NSAIDs or pesticides. In conclusion, we make the case that especially MS is a main tool in performing drug residue surveys. It can identify the presence of residue in positive samples and quantify if the level present is above the autorised MRL (maximum residue limit)., La surveillance des résidus de médicaments vétérinaires est réglementée par une directive européenne dans laquelle sont définies les méthodes utilisables pour la détection et la confirmation des résidus. Les méthodes biologiques (microbiologiques ou immunologiques) sont largement utilisées en routine pour effectuer un dépistage des antibiotiques dans les échantillons prélevés. La confirmation des échantillons positifs est effectuée au moyen de méthodes analytiques basées sur la chromatographie liquide haute performance associée à des détecteurs de masse (SM). Les avantages proposés par cette technologie sont nombreux. La préparation des échantillons est simplifiée, ce qui se traduit par des gains de temps d'analyse, mais également par une augmentation de la fiabilité des résultats. Un autre point majeur est l’identification sans discussion de la molécule trouvée. La réglementation européenne a défini pour cette technologie des critères simples et précis permettant une identification des molécules autorisées ou interdites. Cette technologie est applicable à tout type de matrice, quelles soient complexes (graisse, muscle, foie, miel, etc.) ou non. De même, cette technique peut être utilisée pour rechercher des résidus d’antiparasitaires, des hormones et bêta-agonistes, d’anti-inflammatoire non stéroïdien et de pesticides. En conclusion, la spectrométrie de masse est un outil majeur dans la surveillance des résidus. Elle permet de confirmer sans discussion la présence de résidus et de déterminer si leur concentration est supérieure à la LMR., Laurentie Michel, Creff-Froger Catherine, Gaudin Valérie. Surveillance des résidus d'antibiotiques. Apport des méthodes de spectrométrie de masse à l'identification des contaminants. In: Bulletin de l'Académie Vétérinaire de France tome 155 n°3-4, 2002. pp. 283-294.

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. © 2014 Landes Bioscience.

In plants, recent studies have demonstrated links between the regulation of developmental processes and chromatin dynamics and organisation. Analysis of new mutations affecting overall plant architecture, leaf development and flowering time in Arabidopsis has allowed us to clone and characterise LHP1, the Drosophila heterochromatin protein 1 (HP1) homologue. LHP1 has the chromo and chromo shadow domains central to the function of animal proteins. Yeast two hybrid studies and in planta deletion experiments suggest similar modes of action in plants and animals via homodimer formation. In vivo localisation experiments revealed a specific subnuclear protein distribution in foci throughout the nucleus. Our data suggest that LHP1 may act as a main regulator of gene expression in plants, through formation of heterochromatin-like repressive complexes, to control developmental pathways involved in organ and cell size, and the vegetative to reproductive phase transition.

A biosensor-based immunoassay for the screening of penicillin residues in milk was developed. The BIAcore biosensor which was employed was based on surface plasmon resonance detection. One commercial antibody against ampicillin which had much higher affinity for open beta-lactam ring than for closed ring was chosen. Two different pre-treatments were tested prior to the biosensor assay to open the ring in order to increase the assay sensitivity. These two ways were enzymatic (penicillinase) and chemical pre-treatment of the samples. Limits of detection for ampicillin in milk were 33 and 12.5 μg l −1 after enzymatic and chemical pre-treatment, respectively. There were no cross-reactions with cephalosporins and other families of antibiotics or proteins in the buffer and in milk after both the pre-treatments. Percentages of cross-reactivity with nine tested penicillins were often clearly higher in milk than in buffer. Moreover, a lack of sensitivity after penicillinase pre-treatment was observed. Conversely, penicillins G and penicillins M could be detected at or below their respective MRLs (4 and 30 μg l −1 in milk) and ampicillin and amoxicillin could be detected only at about three MRLs after chemical pre-treatment. However, the enzymatic pre-treatment was much easier to perform and led to more stable results.

Biosensor immunoassays were developed recently for antibiotics with an established maximum residue limit (MRL). In this study, according to the regulatory banning of chloramphenicol (CAP) use for food producing animals, the main objectives were: the specificity of the biosensor assay and the lowest detection limit possible. The assay was based on the inhibition of the binding of polyclonal antibodies against CAP to immobilized CAP on a sensor chip by CAP in solution. The response varied inversely with the antibiotic concentration in the sample. Two different antibodies and two immobilization protocols were tested. As in ELISA tests the antibody influenced the assay performances. Moreover, we showed that particular care should be concentrated on the immobilization step because it is a critical point in the assay development. Three different protocols were developed in milk. The best assay was obtained with antibody 1 in milk on the CAP base surface because of its very low detection limit (0.1 w g l−1) and ...

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.