Les documents scientifiques informels: un patrimoine peu exploré, témoin de la construction des savoirs

L'objectif du projet ECRITO était de contribuer à préserver et à valoriser les documents scientifiques produits quotidiennement par les chercheurs de Midi-Pyrénées, en amont des publications formelles : non seulement les articles, communications ou monographies, qui constituent la partie visible de la recherche, mais aussi tous les matériaux et informations accumulés par les chercheurs, et sur la base desquels se construit leur travail. Ces matériaux sont de types très divers : littérature " grise " (rapports, mémoires, documentation techniques...), documents textuels " informels " (carnets, notes, brouillons, correspondances, cahiers de laboratoires), corpus visuels, sonores ou multimédia (campagnes photographiques, campagnes d'enquêtes, enregistrements audio ou vidéo), données électroniques (bases de données, fichiers informatiques), etc. Le projet visait également à prolonger, de manière exploratoire, le questionnement sur le patrimoine scientifique à partir des traces matérielles produites quotidiennement par les chercheurs dans leurs activités de recherche. Ces traces représentent en effet une fenêtre irremplaçable sur la science en train de se construire : elles permettent de rendre visible et compréhensible le processus habituellement dissimulé de production de la science, ce qui constitue un enjeu scientifique et pédagogique fondamental

TRY plant trait database – enhanced coverage and open access

Plant traits - the morphological, anatomical, physiological, biochemical and phenological characteristics of plants - determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait‐based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits - almost complete coverage for ‘plant growth form’. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait–environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives

The Plasma Oxylipin Signature Provides a Deep Phenotyping of Metabolic Syndrome Complementary to the Clinical Criteria

Metabolic syndrome (MetS) is a complex condition encompassing a constellation of cardiometabolic abnormalities. Oxylipins are a superfamily of lipid mediators regulating many cardiometabolic functions. Plasma oxylipin signature could provide a new clinical tool to enhance the phenotyping of MetS pathophysiology. A high-throughput validated mass spectrometry method, allowing for the quantitative profiling of over 130 oxylipins, was applied to identify and validate the oxylipin signature of MetS in two independent nested case/control studies involving 476 participants. We identified an oxylipin signature of MetS (coined OxyScore), including 23 oxylipins and having high performances in classification and replicability (cross-validated AUCROC of 89%, 95% CI: 85–93% and 78%, 95% CI: 72–85% in the Discovery and Replication studies, respectively). Correlation analysis and comparison with a classification model incorporating the MetS criteria showed that the oxylipin signature brings consistent and complementary information to the clinical criteria. Being linked with the regulation of various biological processes, the candidate oxylipins provide an integrative phenotyping of MetS regarding the activation and/or negative feedback regulation of crucial molecular pathways. This may help identify patients at higher risk of cardiometabolic diseases. The oxylipin signature of patients with metabolic syndrome enhances MetS phenotyping and may ultimately help to better stratify the risk of cardiometabolic diseases

Validation inter-laboratoires d’une méthode de profilage lipidomique des oxylipines dans le cadre du projet JPI-HDHL OXYGENATE

communication flash posterActuellement 20 à 25% de la population adulte mondiale présente un syndromecardiométabolique (CardMet) qui se caractérise par des troubles métaboliques, cardiovasculaires et inflammatoires amenant au développement du diabète de type II et des maladies cardiovasculaires. Cependant le diagnostic de ce syndrome n’est pas satisfaisant car pas assez intégratif et précoce pour permettre une prise en charge nutritionnelle. Les oxylipines sont des médiateurs lipidiques impliqués dans la régulation de processus biologiques liés à ce syndrome et dont la biosynthèse est modulée par le statut CardMet et aussi par l’alimentation. Le projet OXYGENATE a pour but d’identifier et de valider des oxylipines discriminant le statut CardMet et la qualité de l’alimentation. Pour cela, il est nécessaire d’avoir une méthode fiable de profilage quantitatif des oxylipines permettant d’obtenir des profils comparables entre différents laboratoires. Nous avons donc réalisé une comparaison inter-laboratoires de notre méthode afin d’estimer les variabilités analytiques et d’identifier les oxylipines critiques. Cinq laboratoires ont préparé (en triplicat et sur 2 jours différents) et analysé 7 plasmas présentant des profils d’oxylipines très contrastés. Les variabilités intra- et inter-jour ainsi que la part de variabilité attribuable à la préparation et à l’appareillage sont évalués. Au-delà de l’intérêt pour le projet OXYGENATE, cette comparaison inter-laboratoires unique permettra d’harmoniser les profils d’oxylipines réalisés par l’ensemble de la communauté scientifique

Comparaison des différents conditionnements à base d'irradiation corporelle totale, en hématologie pédiatrique maligne (étude rétrospective de 702 patients à partir du registre de la Société française de greffe de moelle et thérapie cellulaire)

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

Contribution de la radiographie à l'étude du mobilier archéologique (méthodologie pour la mise en valeur de l'information (réalisation, interprétation, traitement graphique des clichés))

TOULOUSE2-BUC Mirail (315552102) / SudocSudocFranceF

In silico prediction of metabolism as a tool to identify new metabolites of dietary monoterpenes

Dietary terpenes have been little studied, despite the fact that they are well absorbed and display a range of biological properties. Better knowledge about their metabolism will help understanding the health effects of plant foods, herbs and spices and may provide new biomarkers of food intake. As part of the FoodBAll project we are investigating the metabolism of terpenes, identifying metabolites and biotransformations involved in their metabolism.PhytoHub (database that compiles all known metabolites of dietary phytochemicals, including terpenes) and Nexus Meteor (in silico prediction of metabolism), were used to identify biotransformations involved in the metabolism of monoterpenoids. Selected biotransformations were used to predict the metabolism of camphene, camphor, carvacrol, carvone, caryophyllene, 1,4-cineole, 1,8-cineole, citral, citronellal, cuminaldehyde, p-cymene, fenchone, geraniol, limonene, linalool, menthol, myrcene, nootkatone, perillyl alcohol, pinene, pulegone, terpinen-4-ol and thymol. Wistar rats received a chemically defined diet with or without 0.05% of the referred compounds. Before and after 5 days of the exposure to the dietary monoterpenes, urine was collected and untargeted metabolomics analysis performed using high-resolution mass spectrometry (UPLC-QToF). We identified twenty-two enzymatic reactions involved in the metabolism of monoterpenoids leading to the synthesis of monoterpenoid metabolites described in the literature. In average, 10 metabolites per compound were identified in rat urine, including new and known ones. Identification of metabolites was based on monoisotopic mass and formula match, presence of adducts and specific mass losses indicative of glucuronidation and conjugation to amino acids. Validation of identification is being done using orbitrap MS/MS and hydrogen-deuterium exchange experiments.The combination of in silico prediction and in vivo experiment allowed the identification of known and new metabolites of different dietary terpenoids. Predicted metabolites of terpenes will be added in PhytoHub to complement the database of known metabolites

MS-based lipidomic profiling of oxylipins supports mild inflammation in dysmetabolic iron overload syndrome affected patients

Topical Area: Energy and Macronutrient Metabolism, ObesityInsulin resistance-associated hepatic iron overload, referred as dysmetabolic iron overload syndrome (DIOS) associates a mild increase of both liver and body iron stores and various components of the metabolic syndrome (MetS). DIOS occurrence is frequent and concerns up to 20% of patients with MetS. The causes and clinical relevance of DIOS are still misunderstood. Oxylipins refer to a large family of signaling lipids notably involved in the regulation of inflammation. We hypothesized that iron overload in DIOS could be associated with an altered oxylipin profile reflecting the dysregulation of inflammatory and oxidative stress status.Methods : This case-control study involved 20 subjects with DIOS (DIOS), 20 subjects with metabolic syndrome without iron overload (MetS) and 20 healthy control subjects (Healthy). Oxylipin profiling was performed in plasma of each participant using mass spectrometry (MS)-based lipidomic profiling.Results : Univariate analysis identified eleven oxylipins significantly higher in the DIOS group in comparison with MetS and healthy subjects. These include (i) prostaglandin D2 which is produced from arachidonic acid (AA) via the cylcooxygenase action, (ii) 8-hydroxy fatty acids including 5-HETE and 15-HETE, well known mediators of inflammation derived from AA via the lipooxygenase pathway, and (iii) two oxylipins of the cytochrome P450 pathways, namely 14,15-EET and 5,6-DiHETE. Of notes, PGD2 as well as 5- and 15-HETE are mediators of inflammation. Multivariate analysis including hierarchical cluster analysis and PCA did not discriminate subjects from the different groups.Conclusions : Iron overload in DIOS was associated with moderate alterations of the oxylipin profile suggesting a mild inflammation, but larger sample size would be necessary to confirm results from this pilot study.Funding Sources : This study was funded by the University Hospital of Clermont-Ferrand and by the French Society of Internal Medicine

Stability of total oxylipins – influence of plasma generation and long-term storage

International audienc

In silico prediction of metabolism as a tool to identify new metabolites of dietary terpenes

Dietary terpenes have been little studied, despite the fact that they are well absorbed and display a range of biological properties. Better knowledge about their metabolism will help understanding the health effects of plant foods, herbs and spices and may provide new biomarkers of food intake. As part of the FoodBAll project we are investigating the metabolism of terpenes, identifying metabolites and biotransformations involved in their metabolism.PhytoHub (database that compiles all known metabolites of dietary phytochemicals, including terpenes) and Nexus Meteor (in silico prediction of metabolism), were used to identify biotransformations involved in the metabolism of monoterpenoids. Selected biotransformations were used to predict the metabolism of camphene, camphor, carvacrol, carvone, caryophyllene, 1,4-cineole, 1,8-cineole, citral, citronellal, cuminaldehyde, p-cymene, fenchone, geraniol, limonene, linalool, menthol, myrcene, nootkatone, perillyl alcohol, pinene, pulegone, terpinen-4-ol and thymol. Wistar rats received a chemically defined diet with or without 0.05% of the referred compounds. Before and after 5 days of the exposure to the dietary monoterpenes, urine was collected and untargeted metabolomics analysis performed using high-resolution mass spectrometry (UPLC-QToF). We identified twenty-two enzymatic reactions involved in the metabolism of monoterpenoids leading to the synthesis of monoterpenoid metabolites described in the literature. In average, 10 metabolites per compound were identified in rat urine, including new and known ones. Identification of metabolites was based on monoisotopic mass and formula match, presence of adducts and specific mass losses indicative of glucuronidation and conjugation to amino acids. Validation of identification is being done using orbitrap MS/MS and hydrogen-deuterium exchange experiments.The combination of in silico prediction and in vivo experiment allowed the identification of known and new metabolites of different dietary terpenoids. Predicted metabolites of terpenes will be added in PhytoHub to complement the database of known metabolites