Rate-distortion tradeoff to optimize high-throughput phenotyping systems. Application to X-ray images of seeds

In the context of high-throughput plant phenotyping, measurements are carried out on large populations of plants and produce large amounts of data to be analyzed and stored. The need for automated phenotyping in plant biology opens new fields of application for image acquisition and compression algorithms. In this report, we focus on X-ray imaging for high-throughput analysis of seeds. A practical tradeoff between the tolerated distortion on images and image acquisition rates is demonstrated for measurement, visual inspection or pattern recognition. In these contexts, using the same methodology, we quantify the highest acquisition and compression rates achievable while preserving all the useful biological information with standard lossy compression formats. Using a study case, we quantitatively demonstrate the interest of considering the final biological task as a priori knowledge to optimize the design of phenotyping systems

Molecular cloning and characterization of a novel tomato xylosyltransferase specific for gentisic acid

The importance of salicylic acid (SA) in the signal transduction pathway of plant disease resistance has been well documented in many incompatible plant–pathogen interactions, but less is known about signalling in compatible interactions. In this type of interaction, tomato plants have been found to accumulate high levels of 2,5-dihydroxybenzoic acid (gentisic acid, GA), a metabolic derivative of SA. Exogenous GA treatments induce in tomato plants a set of PR proteins that differ from those induced by salicylic acid. While SA accumulates in tomato plants mainly as 2-O-β-D-glucoside, GA has only been found as 5-O-β-D-xyloside. To characterize this step of the GA signalling pathway further, the present work focuses on the study of the GA-conjugating activity in tomato plants. A gentisate glycosyltransferase (GAGT) cDNA has been isolated and overexpressed in Pichia pastoris, and GA-conjugating activity was confirmed by detecting the xylosylated GA. The purified plant protein is highly specific for GA, showing no activity toward many other phenolic compounds, including SA. In addition, it shows an outstanding selectivity for UDP-xylose as the sugar donor, which differentiates this enzyme from most glycosyltransferases. Both the GA-conjugating activity and the corresponding mRNA show a strong, rapid, and transient induction upon treatment of tomato plants with GA or SA. Furthermore, its expression is rapidly induced by compatible infections. However, neither the gene nor the activity seems to respond to incompatible infections or wounding. The unique properties of this new glycosyltransferase suggest a specific role in regulating the free GA levels in compatible plant–pathogen interactions

Metabolomic, Transcriptional, Hormonal, and Signaling Cross-Talk in Superroot2

Auxin homeostasis is pivotal for normal plant growth and development. The superroot2 (sur2) mutant was initially isolated in a forward genetic screen for auxin overproducers, and SUR2 was suggested to control auxin conjugation and thereby regulate auxin homeostasis. However, the phenotype was not uniform and could not be described as a pure high auxin phenotype, indicating that knockout of CYP83B1 has multiple effects. Subsequently, SUR2 was identified as CYP83B1, a cytochrome P450 positioned at the metabolic branch point between auxin and indole glucosinolate metabolism. To investigate concomitant global alterations triggered by knockout of CYP83B1 and the countermeasures chosen by the mutant to cope with hormonal and metabolic imbalances, 10-day-old mutant seedlings were characterized with respect to their transcriptome and metabolome profiles. Here, we report a global analysis of the sur2 mutant by the use of a combined transcriptomic and metabolomic approach revealing pronounced effects on several metabolic grids including the intersection between secondary metabolism, cell wall turnover, hormone metabolism, and stress responses. Metabolic and transcriptional cross-talks in sur2 were found to be regulated by complex interactions between both positively and negatively acting transcription factors. The complex phenotype of sur2 may thus not only be assigned to elevated levels of auxin, but also to ethylene and abscisic acid responses as well as drought responses in the absence of a water deficiency. The delicate balance between these signals explains why minute changes in growth conditions may result in the non-uniform phenotype. The large phenotypic variation observed between and within the different surveys may be reconciled by the complex and intricate hormonal balances in sur2 seedlings decoded in this study

Multi-substrate flavonol O-glucosyltransferases from strawberry (Fragaria×ananassa) achene and receptacle

In an effort to characterize fruit ripening-related genes functionally, two glucosyltransferases, FaGT6 and FaGT7, were cloned from a strawberry (Fragaria×ananassa) cDNA library and the full-length open reading frames were amplified by rapid amplification of cDNA ends. FaGT6 and FaGT7 were expressed heterologously as fusion proteins in Escherichia coli and target protein was purified using affinity chromatography. Both recombinant enzymes exhibited a broad substrate tolerance in vitro, accepting numerous flavonoids, hydroxycoumarins, and naphthols. FaGT6 formed 3-O-glucosides and minor amounts of 7-O-, 4′-O-, and 3′-O-monoglucosides and one diglucoside from flavonols such as quercetin. FaGT7 converted quercetin to the 3-O-glucoside and 4′-O-glucoside and minor levels of the 7- and 3′-isomers but formed no diglucoside. Gene expression studies showed that both genes are strongly expressed in achenes of small-sized green fruits, while the expression levels were generally lower in the receptacle. Significant levels of quercetin 3-O-, 7-O-, and 4′-O-glucosides, kaempferol 3-O- and 7-O-glucosides, as well as isorhamnetin 7-O-glucoside, were identified in achenes and the receptacle. In the receptacle, the expression of both genes is negatively controlled by auxin which correlates with the ripening-related gene expression in this tissue. Salicylic acid, a known signal molecule in plant defence, induces the expression of both genes. Thus, it appears that FaGT6 and FaGT7 are involved in the glucosylation of flavonols and may also participate in xenobiotic metabolism. The latter function is supported by the proven ability of strawberries to glucosylate selected unnatural substrates injected in ripe fruits. This report presents the first biochemical characterization of enzymes mainly expressed in strawberry achenes and provides the foundation of flavonoid metabolism in the seeds

Rôle de glycosyltransférases du métabolisme secondaire au cours des interactions plantes-agents pathogènes chez Arabidopsis thaliana

Les métabolites secondaires jouent des rôles importants dans les réponses de défense des plantes aux agents pathogènes. La conjugaison à un sucre est l'une des modifications les plus répandues qui contribuent à la grande diversité et à la réactivité de ces substances naturelles. Les réactions de glycosylation assurées par les glycosyltransférases (UGTs) sont impliquées dans des voies métaboliques, dans la régulation de signaux endogènes et dans le transport de métabolites. Chez Arabidopsis thaliana, les UGTs du métabolisme secondaire sont codées par 120 gènes, organisés en 14 groupes (A-N). Les UGTs du groupe D sont exprimées de manière différentielle au cours de la réaction d'hypersensibilité (HR) d'A. thaliana à une souche avirulente de Pseudomonas syringae pv. tomato et après traitement par des molécules de signalisation impliquées dans les réponses de défense. Au sein de ce groupe, nous avons identifié deux gènes d'intérêt, UGT73B3 et UGT73B5, fortement induits au cours de la HR et après traitement par l'acide salicylique et le peroxyde d'hydrogène. Les lignées d'insertion d'ADN-T, ugt73b3 et ugt73b5, présentent une perte de résistance à la souche avirulente de P. syringae. Une approche de profilage métabolique a été développée pour identifier les substrats de ces deux enzymes in planta. Bien que la nature de ces substrats n'ait pas été identifiée, les résultats suggèrent que les mutants ugt73b3 et ugt73b5 sont affectés au niveau de composés pariétaux. La similarité de séquence d'UGT73B3 et UGT73B5 avec une UGT de tabac intervenant dans la gestion du burst oxydatif au cours de la HR, suggère une implication de ces deux UGTs dans le maintien de l'homéostasie redox cellulaire.Secondary metabolites play important roles in plant defense against pathogens. Conjugaison to sugar moiety is one of the most widespread modifications that contribute to the great diversity and reactivity of these natural products. Glycosylation ensured by glycosyltransferases (UGTs) is involved in metabolic pathways, endogenous signal regulation and metabolite transport. In Arabidopsis thaliana, secondary metabolism UGTs are encoded by 120 genes, organised into 14 groups (A-N). Group D UGTs are differentially expressed during the hypersensitive response (HR) of A. thaliana to an avirulent strain of Pseudomonas syringae pv. tomato and after treatements with defense related signaling molecules. Within this group, we identified two genes, UGT73B3 and UGT73B5, which were highly induced during HR and after salicylic acid and hydrogen peroxide treatements. ugt73b3 and ugt73b5 T-DNA insertion lines, exhibit a loss of resistance to P. syringae avirulent strain. A metabolic profiling approach was carried out to identify UGT73B3 and UGT73B5 substrates in planta. Although the nature of the substrates has not been identified, the results indicate that ugt73b3 and ugt73b5 differ from wild type plants in cell wall-bound compounds. UGT73B3 and UGT73B5 are closely related to a tobacco UGT involved in the control of oxidative burst during HR, suggesting that these two UGTs may also be involved in the maintenance of cellular redox homeostasis.ORSAY-PARIS 11-BU Sciences (914712101) / SudocSudocFranceF

Etude descriptive des examens cliniques du pédiatre en suites de couches

LILLE2-BU Santé-Recherche (593502101) / SudocPARIS-BIUM (751062103) / SudocSudocFranceF