References of "Tocquin, Pierre"
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See detailOn the necessity and biological significance of threshold-free regulon prediction outputs
Rigali, Sébastien ULg; Nivelle, Renaud; Tocquin, Pierre ULg

in Molecular Biosystems (2015)

The in silico prediction of cis-acting elements in a genome is an efficient way to quickly obtain an overview of the biological processes controlled by a trans-acting factor, and connections between ... [more ▼]

The in silico prediction of cis-acting elements in a genome is an efficient way to quickly obtain an overview of the biological processes controlled by a trans-acting factor, and connections between regulatory networks. Several regulon prediction web tools are available, designed to identify DNA motifs predicted to be bound by transcription factors using position weight matrix-based algorithms. In this paper we expose and discuss the conflicting objectives of software creators (bioinformaticians) and software users (biologists), who aim for reliable and exhaustive prediction outputs, respectively. Software makers, concerned with providing tools that minimise the number of false positive hits, often impose a stringent threshold score for a sequence to be included in the list of the putative cis-acting sites. This rigidity eventually results in the identification of strongly reliable but largely straightforward sites, i.e. those associated with genes already anticipated to be targeted by the studied transcription factor. Importantly, this biased identification of strongly bound sequences contrasts with the biological reality where, in many circumstances, a weak DNA-protein interaction is required for the appropriate gene's expression. We show here a series of transcriptionally controlled systems involving weakly bound cis-acting elements that could never have been discovered because of the policy of preventing software users from modifying the screening parameters. Proposing only trustworthy prediction outputs thus prevents biologists from fully utilising their knowledge background and deciding to analyse statistically irrelevant hits that could nonetheless be potentially involved in subtle, unexpected, though essential cis-trans relationships. [less ▲]

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See detailIdentifying root-secreted proteases in Arabidopsis thaliana: an Activity-Based Protein Profiling approach.
Lallemand, Jérôme ULg; Périlleux, Claire ULg; Tocquin, Pierre ULg

Poster (2014, May 15)

Proteases are involved in many physiological processes during the whole life of the plant, such as embryonic development, defense against pathogens, nutrition or mycorrhiza creation. However, the ... [more ▼]

Proteases are involved in many physiological processes during the whole life of the plant, such as embryonic development, defense against pathogens, nutrition or mycorrhiza creation. However, the functions of many of the 800 proteases of Arabidopsis thaliana still remain unknown. Besides discovering new functions, studying proteases can also result in improving plant biotechnology. Indeed, plants can be used as hosts for recombinant protein production. Some proteins of interest require to be secreted in order to fold properly, but production yields are limited due to their degradation by endogenous extracellular proteases. The aim of our study is to identify active root-secreted proteases of Arabidopsis thaliana. Their activity was first analyzed by in vitro incubation with a target protein (BSA) at different values of pH and in the presence of proteases inhibitors. This analysis identified serine proteases as the major protease class involved in BSA degradation. Then, an Activity-Based Protein Profiling approach led to the labeling of two active serine proteases in the root-secreted sample. Finally, a further step towards the identification by mass spectrometry, based on affinity purification, was developed. [less ▲]

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See detailFlowering Goes Underground
Bouché, Frédéric ULg; Lobet, Guillaume ULg; D'Aloia, Maria ULg et al

Conference (2014, May 15)

Flowering is a crucial step in plant life cycle and is therefore tightly controlled by both environmental and endogenous cues. The involvement of the aerial organs of the plant in the molecular mechanisms ... [more ▼]

Flowering is a crucial step in plant life cycle and is therefore tightly controlled by both environmental and endogenous cues. The involvement of the aerial organs of the plant in the molecular mechanisms controlling floral transition has been extensively documented while the participation of the roots remains poorly investigated. However, the induction of flowering by photoperiod involves systemic signals that move in the phloem from leaves to sinks, and hence presumably reach the roots. We therefore performed a transcriptomic analysis of the roots during the induction of flowering in Arabidopsis thaliana and indeed identified a large number of differentially expressed genes. A reverse genetic approach further confirmed the pleiotropic effects of flowering time genes on root architecture. [less ▲]

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See detailStudy of an undershoot in chlorophyll fluorescence signal after a saturating pulse in PAM measurements
Fratamico, Anthony ULg; Cardol, Pierre ULg; Tocquin, Pierre ULg et al

Conference (2014, April 14)

In 1989, Larcher and Neuner have reported the observation of a sudden reversible drop in modulated chlorophyll fluorescence measurements (PAM) immediately after a saturating pulse, and called it “low ... [more ▼]

In 1989, Larcher and Neuner have reported the observation of a sudden reversible drop in modulated chlorophyll fluorescence measurements (PAM) immediately after a saturating pulse, and called it “low-wave”. 25 years later, whereas some papers reported this phenomenon as a trivial detail, scarcely two works have investigated the origin of this particular signal, in which a link with a low CO2 availability seems clear. Our work on Haematococcus pluvialis, a freshwater green microalga, provides a new point of view on this fluorescence undershoot, caused by a rapidly established non-photochemical quenching. We have demonstrated that in the light-adapted state, a low-wave after a saturating flash can be considered as a consequence of an induction process engaged in response to the brief light increase under low CO2 conditions. The non-photochemical quenching during low-waves was found to be dependent on electron transport to oxygen during the preceding flash. Moreover, in conditions in which low-waves were observed in the light-adapted state, the fluorescence induction kinetics in the first minute of lighting after dark-adaptation presented also a reversible strong drop. Nevertheless, at the stationary state, oxygen production and photochemical yield of photosystem II were not affected. Providing a better understanding of the processes underlying low-waves, our work also draws attention on the effect of CO2 concentration on the onset of photosynthesis. [less ▲]

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See detailInflorescence development in tomato: gene functions within a zigzag model.
Périlleux, Claire ULg; Lobet, Guillaume ULg; Tocquin, Pierre ULg

in Frontiers in Plant Science (2014), 5

Tomato is a major crop plant and several mutants have been selected for breeding but also for isolating important genes that regulate flowering and sympodial growth. Besides, current research in ... [more ▼]

Tomato is a major crop plant and several mutants have been selected for breeding but also for isolating important genes that regulate flowering and sympodial growth. Besides, current research in developmental biology aims at revealing mechanisms that account for diversity in inflorescence architectures. We therefore found timely to review the current knowledge of the genetic control of flowering in tomato and to integrate the emerging network into modeling attempts. We developped a kinetic model of the tomato inflorescence development where each meristem was represented by its ‘vegetativeness’ (V), reflecting its maturation state towards flower initiation. The model followed simple rules: maturation proceeded continuously at the same rate in every meristem (dV); floral transition and floral commitment occurred at threshold levels of V; lateral meristems were initiated with a gain of V (ΔV) relative to the V level of the meristem from which they derived. This last rule created a link between successive meristems and gave to the model its zigzag shape. We next exploited the model to explore the diversity of morphotypes that could be generated by varying dV and ΔV and matched them with existing mutant phenotypes. This approach, focused on the development of the primary inflorescence, allowed us to elaborate on the genetic regulation of the kinetic model of inflorescence development. We propose that the lateral inflorescence meristem fate in tomato is closer to an immature flower meristem than to the inflorescence meristem of Arabidopsis. In the last part of our paper, we extend our thought to spatial regulators that should be integrated in a next step for unraveling the relationships between the different meristems that participate to sympodial growth. [less ▲]

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See detailThe hidden half of flowering
Bouché, Frédéric ULg; Mistiaen, Kevin ULg; D'Aloia, Maria ULg et al

Poster (2013, June)

Flowering is one of the most important developmental steps in plant life cycle and is therefore tightly controlled by environmental cues. The involvement of the aerial part of the plant in the molecular ... [more ▼]

Flowering is one of the most important developmental steps in plant life cycle and is therefore tightly controlled by environmental cues. The involvement of the aerial part of the plant in the molecular mechanisms leading to floral transition is well documented while participation of the roots received less attention. Nevertheless, the induction of flowering by photoperiod is known to involve systemic signals that move in phloem sap towards sinks, throughout the plants, including the roots. Transcriptomic analysis of roots tissues during the floral induction of flowering by a single long day of in Arabidopsis thaliana by a single long day allowed us to identify a large number of differentially expressed genes. How mutations We subsequently selected in some candidate genes affect plant development - including root architecture and flowering time - is being to analyze their flowering timefurther analyzed. Further analysis of those genes will permit us to unravel their role in the flowering induction process. [less ▲]

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See detailTowards the improvement of a rhizosecretion-based recombinant protein production system: Developing protease-depleted lines of Arabidopsis thaliana.
Lallemand, Jérôme ULg; Désiron, Carole ULg; Périlleux, Claire ULg et al

Poster (2013, June)

Besides traditional production systems, such as bacteria, yeasts and mammal cells, plants can now be used to produce eukaryotic recombinant proteins. Their advantages as hosts for protein production ... [more ▼]

Besides traditional production systems, such as bacteria, yeasts and mammal cells, plants can now be used to produce eukaryotic recombinant proteins. Their advantages as hosts for protein production include correct post-translational modifications, low cost of maintenance and no risk of contamination by human pathogens. Targeting heterologous proteins to the extracellular space is required for the correct folding of complex proteins and makes harvesting and purification easier. However, the quantity and the quality of recombinant proteins have been proved to be reduced by the action of endogenous co-secreted proteases. In this study, we aimed at identifying active root-secreted (rhizosecreted) proteases in the model plant Arabidopsis thaliana. Their activity was assayed by in vitro degradation of a target protein (Bovine Serum Albumine, BSA) in a range of pH. The protease classes involved in BSA degradation were evaluated by inhibitor-based assays that revealed serine proteases as the major class involved in this degradation in any tested conditions. As a first step towards identification, and subsequent silencing, of the most active members of this class, rhizosecreted proteases are being analyzed by the “Activity-Based Protein Profiling” approach. [less ▲]

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See detailTowards identification of active root-secreted proteases of Arabidopsis thaliana.
Lallemand, Jérôme ULg; Désiron, Carole ULg; Périlleux, Claire ULg et al

Poster (2013, April 18)

Besides traditional production systems, such as bacteria, yeasts and mammal cells, plants can now be used to produce eukaryotic recombinant proteins. Their advantages as hosts for proteins production ... [more ▼]

Besides traditional production systems, such as bacteria, yeasts and mammal cells, plants can now be used to produce eukaryotic recombinant proteins. Their advantages as hosts for proteins production include correct post-translational modifications, low cost of maintenance and no risk of contamination by human pathogens. Targeting heterologous proteins to the extracellular space is required for the correct folding of complex proteins and makes harvesting and purification easier. However, the quantity and the quality of recombinant proteins have been proved to be reduced by the action of endogenous co-secreted proteases. In this study, we characterized root-secreted proteases in the model plant Arabidopsis thaliana, at the activity and expression levels. Their activity was analyzed by in vitro degradation of a target protein (Bovine Serum Albumine, BSA) in a range of pH and in the presence of several proteases inhibitors. Serine proteases were identified as the major protease class involved in the degradation of BSA under all tested conditions. As a first step towards the identification of the key players, the expression level of selected members of this class was analyzed by quantitative RT-PCR in roots and leaves. [less ▲]

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See detailMolecular analysis of root medium impact on Arabidopsis thaliana development
Bouché, Frédéric ULg; André, Julie; Tocquin, Pierre ULg et al

Poster (2013, April 18)

Hydroponics and soil are the most common media used for plant growth. Hydroponics has the main advantage of providing easy access to the root system and is therefore commonly used for gene expression ... [more ▼]

Hydroponics and soil are the most common media used for plant growth. Hydroponics has the main advantage of providing easy access to the root system and is therefore commonly used for gene expression analyses in molecular studies of the model plant Arabidopsis thaliana. However, the impact of root substrate on plant growth remains poorly documented. Here we show that hydroponics accelerates both shoot growth and developmental phases as compared with culture on soil. In order to identify molecular changes in the roots that could account for these medium effects, a transcriptomic comparison was performed by microarray analysis. This experiment revealed that more than 20% of the genes were differentially expressed in hydroponics vs soil. Among them, the flowering time gene FLOWERING LOCUS C and two clades of microRNA targeted genes. To further assess the role of these genes in roots, artificial microRNAs were designed for root specific expression in transgenic Arabidopsis plants. [less ▲]

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See detailA root chicory MADS-box sequence and the Arabidopsis flowering repressor FLC share common features that suggest conserved function in vernalization and devernalization responses
Périlleux, Claire ULg; Pieltain, Alexandra; Jacquemin, Guillaume et al

in Plant Journal (The) (2013), 75

Root chicory (Cichorium intybus var. sativum) is a biennial crop, but is harvested for root inulin at the end of the first growing season before flowering. However, cold temperatures might vernalize seeds ... [more ▼]

Root chicory (Cichorium intybus var. sativum) is a biennial crop, but is harvested for root inulin at the end of the first growing season before flowering. However, cold temperatures might vernalize seeds or plantlets, leading to incidental early flowering and hence understanding the molecular basis of vernalization is important. A MADS-box sequence was isolated by RT-PCR and named FLC-LIKE1 (CiFL1) because of its phylogenetic positioning within the same clade as the floral repressor Arabidopsis FLOWERING LOCUS C (AtFLC). Moreover, overexpression of CiFL1 in Arabidopsis caused late flowering and prevented up-regulation of the AtFLC target FLOWERING LOCUS T gene by photoperiod, suggesting functional conservation between root chicory and Arabidopsis. Like AtFLC in Arabidopsis, CiFL1 was repressed during vernalization of seeds or plantlets of chicory, but repression of CiFL1 was unstable whether the post-vernalization temperature was favorable to flowering or whether it devernalized the plants. Instability of CiFL1 repression might be linked to bienniality of root chicory versus the annual life cycle of Arabidopsis. However, reactivation of AtFLC was also observed in Arabidopsis when a high temperature treatment was given straight after seed vernalization, erasing the promotive effect of cold on flowering. Cold-induced downregulation of a MADS-box floral repressor and its reactivation by high temperature thus appear as conserved features of the vernalization and devernalization responses in distant species.This article is protected by copyright. All rights reserved. [less ▲]

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See detailOptimization of an Haematococcus pluvialis medium by a Genetic Algorithm-based strategy
Fratamico, Anthony ULg; Tocquin, Pierre ULg; Franck, Fabrice ULg

Poster (2012, June 14)

The successful use of living organisms for the production of biomass or metabolites requires a careful control and optimization over growing conditions. However the range of interacting parameters makes ... [more ▼]

The successful use of living organisms for the production of biomass or metabolites requires a careful control and optimization over growing conditions. However the range of interacting parameters makes full optimization difficult and time-consuming. In this context, Genetic Algorithm-based (GA) methods emerge as promising strategies for optimization of biotechnological processes. However, the potential of GA in the microalgae field remains, today, poorly explored. As a proof-of-concept, we evaluated how GA could be applied for the optimization of a medium for high yield photoautotrophic growth of Haematoccocus pluvialis. [less ▲]

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See detailRooting the flowering process
D'Aloia, Maria ULg; Bouché, Frédéric ULg; Tamseddak, Karim et al

Poster (2012, May)

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See detailDegradation of recombinant IgG by root-secreted proteases of Arabidopsis thaliana and Nicotiana tabacum
Désiron, Carole ULg; Lallemand, Jérôme ULg; Périlleux, Claire ULg et al

Poster (2012, April 18)

Plants are promising hosts for the production of complex recombinant pharmaceuticals, such as antibodies (mAbs), because they offer an inexpensive and safer alternative to traditional production systems ... [more ▼]

Plants are promising hosts for the production of complex recombinant pharmaceuticals, such as antibodies (mAbs), because they offer an inexpensive and safer alternative to traditional production systems. The plant-based production of mAbs, which are multimeric glycoproteins, require their targeting to the secretory pathaway where they are properly folded and matured. However, co-secretion of endogenous proteases, which can represent up to 10% of the extracellular proteins (secretome), is known to significantly alter the yield and quality of secreted mAbs. In this study, we analyzed the proteolytic activities in root-secretome of Arabidopsis thaliana and Nicotiana tabacum. Root-secretomes were recovered by salt extraction and the protease activity was assayed in vitro or by zymography, in a range of pH. The relative contribution of protease classes was evaluated with specific inhibitors. [less ▲]

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See detailOptimization of recombinant root-secreted IgGs production in Arabidopsis thaliana by screening cell wall mutants
Boulanger, Benoit ULg; Périlleux, Claire ULg; Tocquin, Pierre ULg

Poster (2012, April 18)

The production of complex heterologous proteins (e.g. monoclonal antibodies, mAbs) in plants has several advantages animal based systems such as low cost, scalability and limited risk of contamination by ... [more ▼]

The production of complex heterologous proteins (e.g. monoclonal antibodies, mAbs) in plants has several advantages animal based systems such as low cost, scalability and limited risk of contamination by human pathogens. mAbs are glycoproteins that require to be targeted to the plant secretory pathway in order to be properly folded and matured. They are ultimately delivered in the cell wall and are expected to be freely released in the extracellular space and the external medium, which would greatly simplify downstream processing. However, a significant part of plant produced and secreted mAbs remains bound to the cell wall, therefore hindering recovery. In this study, we evaluated the extra-cellular release of root-secreted proteins of wild-type plants and cell wall mutants of Arabidopsis thaliana. Recovered protein were either analyzed by SDS-PAGE for full proteome profiling or by gelatin zymography to reveal the activity of cell wall-bound proteases. The production, secretion and release of recombinant IgG will be eventually studied in transgenic hairy-roots generated from selected mutants. [less ▲]

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See detailScreening for a low-cost Haematococcus pluvialis medium reveals an unexpected impact of a low N:P ratio on vegetative growth
Tocquin, Pierre ULg; Fratamico, Anthony ULg; Franck, Fabrice ULg

in Journal of Applied Phycology (2012), 24(3), 365-373

Haematococcus pluvialis is the current better source of natural astaxanthin, a high-value carotenoid. Traditionally, the production process of astaxanthin by this algae is achieved by a two-stage system ... [more ▼]

Haematococcus pluvialis is the current better source of natural astaxanthin, a high-value carotenoid. Traditionally, the production process of astaxanthin by this algae is achieved by a two-stage system: during the first stage, vegetative “green” cells are produced and then converted, in the second stage, into cysts that accumulate astaxanthin. In this work, a medium screening strategy based on the mixing of a 3-component hydroponic fertilizer was applied to identify a new formulation optimized for the vegetative stage. A maximal and high cell density of 2 x 106 cells mL−1 was obtained in a medium containing a high level of phosphate relative to nitrate, resulting in a N:P ratio much lower than commonly used media for H. pluvialis. In this medium, cells remained at the vegetative and motile stage during a prolonged period of time. Both high cell density culture and motile stage persistence was proved to be related to the N:P feature of this medium. We conclude that the macrozoid stage of H. pluvialis is favored under high-P and low-N supply and that low-cost hydroponic fertilizers can be successfully used for achieving high density cultures of vegetative cells of H. pluvialis. [less ▲]

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See detailAnalysis of Root Secreted Proteases in Arabidopsis thaliana and Nicotiana tabacum
Désiron, Carole ULg; De Lemos Esteves, Frédéric ULg; Natalis, Lucie et al

Poster (2011, June 09)

Plants are promising tools to produce complex recombinant proteins like antibodies. When host plants are grown on hydroponics, the production of recombinant proteins that are secreted by the roots ... [more ▼]

Plants are promising tools to produce complex recombinant proteins like antibodies. When host plants are grown on hydroponics, the production of recombinant proteins that are secreted by the roots ('rhizosecretion') greatly simplifies harvest and purification of the product, during whole plant life. However, proteases represent up to 10% of the naturally secreted proteins and are known to significantly decrease the yield of production by rhizosecretion. In this study, we analyzed the rhizosecreted proteases of Arabidopsis thaliana and Nicotiana tabacum. Total rhizosecreted proteins were recovered by salt extraction and the protease activity was assayed in vitro or by zymography. The relative contribution of major protease families to total activity was evaluated with specific inhibitors and revealed significant differences between the two species. The degradation capacity of the root-secreted proteases was further characterized against selected target proteins: BSA and human IgGs. [less ▲]

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See detailTranscriptomic analysis of Arabidopsis roots during floral induction by photoperiod
D'Aloia, Maria ULg; Lamoureux, Thibaut ULg; Tocquin, Pierre ULg et al

Poster (2011, June)

Contribution of the root system to the flowering process remains poorly studied. Part of the problem resides in its difficult isolation from the substrate, especially on adult plants. We used an ... [more ▼]

Contribution of the root system to the flowering process remains poorly studied. Part of the problem resides in its difficult isolation from the substrate, especially on adult plants. We used an hydroponic device that allows synchronous growth and flowering of Arabidopsis and performed global transcript profiling of roots. Samples were harvested during the extension period of a single long day (LD), and in non inductive short day. Microarray data were validated by real-time RT-PCR, and the expression patterns of selected probes were further analyzed in shoots and roots. Some of the genes that were differentially expressed in the roots during the inductive LD did not show the same variations in the shoot, indicating that root transcriptome undergoes specific changes at floral transition. These genes include, for example, GIGANTEA. T-DNA mutants from selected candidate genes are being studied. Both the expression analysis and the reverse genetic approach provide new insights into the contribution of the roots to the flowering process. [less ▲]

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