Altimetry for the future: Building on 25 years of progress

In 2018 we celebrated 25 years of development of radar altimetry, and the progress achieved by this methodology in the fields of global and coastal oceanography, hydrology, geodesy and cryospheric sciences. Many symbolic major events have celebrated these developments, e.g., in Venice, Italy, the 15th (2006) and 20th (2012) years of progress and more recently, in 2018, in Ponta Delgada, Portugal, 25 Years of Progress in Radar Altimetry. On this latter occasion it was decided to collect contributions of scientists, engineers and managers involved in the worldwide altimetry community to depict the state of altimetry and propose recommendations for the altimetry of the future. This paper summarizes contributions and recommendations that were collected and provides guidance for future mission design, research activities, and sustainable operational radar altimetry data exploitation. Recommendations provided are fundamental for optimizing further scientific and operational advances of oceanographic observations by altimetry, including requirements for spatial and temporal resolution of altimetric measurements, their accuracy and continuity. There are also new challenges and new openings mentioned in the paper that are particularly crucial for observations at higher latitudes, for coastal oceanography, for cryospheric studies and for hydrology. The paper starts with a general introduction followed by a section on Earth System Science including Ocean Dynamics, Sea Level, the Coastal Ocean, Hydrology, the Cryosphere and Polar Oceans and the ‘‘Green” Ocean, extending the frontier from biogeochemistry to marine ecology. Applications are described in a subsequent section, which covers Operational Oceanography, Weather, Hurricane Wave and Wind Forecasting, Climate projection. Instruments’ development and satellite missions’ evolutions are described in a fourth section. A fifth section covers the key observations that altimeters provide and their potential complements, from other Earth observation measurements to in situ data. Section 6 identifies the data and methods and provides some accuracy and resolution requirements for the wet tropospheric correction, the orbit and other geodetic requirements, the Mean Sea Surface, Geoid and Mean Dynamic Topography, Calibration and Validation, data accuracy, data access and handling (including the DUACS system). Section 7 brings a transversal view on scales, integration, artificial intelligence, and capacity building (education and training). Section 8 reviews the programmatic issues followed by a conclusion

Altimetry for the future: building on 25 years of progress

In 2018 we celebrated 25 years of development of radar altimetry, and the progress achieved by this methodology in the fields of global and coastal oceanography, hydrology, geodesy and cryospheric sciences. Many symbolic major events have celebrated these developments, e.g., in Venice, Italy, the 15th (2006) and 20th (2012) years of progress and more recently, in 2018, in Ponta Delgada, Portugal, 25 Years of Progress in Radar Altimetry. On this latter occasion it was decided to collect contributions of scientists, engineers and managers involved in the worldwide altimetry community to depict the state of altimetry and propose recommendations for the altimetry of the future. This paper summarizes contributions and recommendations that were collected and provides guidance for future mission design, research activities, and sustainable operational radar altimetry data exploitation. Recommendations provided are fundamental for optimizing further scientific and operational advances of oceanographic observations by altimetry, including requirements for spatial and temporal resolution of altimetric measurements, their accuracy and continuity. There are also new challenges and new openings mentioned in the paper that are particularly crucial for observations at higher latitudes, for coastal oceanography, for cryospheric studies and for hydrology. The paper starts with a general introduction followed by a section on Earth System Science including Ocean Dynamics, Sea Level, the Coastal Ocean, Hydrology, the Cryosphere and Polar Oceans and the “Green” Ocean, extending the frontier from biogeochemistry to marine ecology. Applications are described in a subsequent section, which covers Operational Oceanography, Weather, Hurricane Wave and Wind Forecasting, Climate projection. Instruments’ development and satellite missions’ evolutions are described in a fourth section. A fifth section covers the key observations that altimeters provide and their potential complements, from other Earth observation measurements to in situ data. Section 6 identifies the data and methods and provides some accuracy and resolution requirements for the wet tropospheric correction, the orbit and other geodetic requirements, the Mean Sea Surface, Geoid and Mean Dynamic Topography, Calibration and Validation, data accuracy, data access and handling (including the DUACS system). Section 7 brings a transversal view on scales, integration, artificial intelligence, and capacity building (education and training). Section 8 reviews the programmatic issues followed by a conclusion

Analytical developments for multi-omics analysis by liquid chromatography coupled to mass spectrometry

L’analyse de biomolécules en santé ou en environnement nécessite l’utilisation d’outils analytiques de grande précision ainsi que des méthodes d’acquisition de données adaptées. De nombreux verrous scientifiques peuvent être rencontrés comme le suivi limité d’un grand nombre de molécules en spectrométrie de masse ciblée, les variations d’ionisation ou bien l’analyse simultanée de biomolécules de propriétés physico-chimiques différentes. Les enjeux de cette thèse ont été d’optimiser et d’améliorer l’acquisition des données dans les sciences omiques comme la protéomique, la lipidomique et la métabolomique dans un contexte environnemental. Le premier axe de recherche a été d’améliorer les capacités de multiplexage via un nouveau mode d’acquisition en spectrométrie de masse ciblée, appelé Scout-MRM tout en permettant de s’affranchir du temps de rétention. Ce développement innovant a été appliqué pour l’étude de G. fossarum, espèce sentinelle en écotoxicologie, via le suivi en protéomique ciblée d’un grand multiplex constitué d’un panel de 157 protéines clés. Afin de faciliter le développement de méthodes ciblées en lipidomique et dans une approche de type « plug-and-play », Scout-MRM a été employé sur différentes matrices biologiques. Le deuxième axe de recherche a été de développer un protocole biphasique pour l’extraction simultanée des protéines, des lipides et des métabolites d’un même échantillon. Cette approche multi-omique a permis de mettre en exergue des signatures moléculaires au cours du développement chez les gammarides femelles. Le troisième axe de recherche a été d’explorer les potentialités de la chromatographie liquide bidimensionnelle ainsi que différentes configurations d’orthogonalité couplée à la spectrométrie de masse de haute résolution pour l’analyse des lipides.The analysis of biomolecules in health or in environment requires the use of high precision analytical instruments and adapted data acquisition methods. Several scientific challenges can be met such as the limited monitoring of a large number of molecules in targeted mass spectrometry, ionization variations or the simultaneous analysis of biomolecules with different physico-chemical properties. The main objective of this thesis was to optimize and improve data acquisition in the omics field such as proteomics, lipidomics and metabolomics in an environmental context. The first research axis was to improve the multiplexing capabilities via a new acquisition mode called Scout-MRM, in targeted mass spectrometry, free from retention time. This innovative development has been applied to the study of G. fossarum, a sentinel species widely used in ecotoxicology, via the monitoring in targeted proteomics of a large multiplex composed of a panel of 157 key proteins. To facilitate the development of targeted methods in lipidomics and in a "plug-and-play" philosophy, Scout-MRM was used on different biological matrices. The second research axis was to develop a biphasic protocol for the simultaneous extraction of proteins, lipids, and metabolites from the same sample. This multi-omics approach highlighted molecular signatures during the development cycle of female gammarids. The third research axis was to explore the capabilities of two-dimensional liquid chromatography as well as different orthogonality configurations coupled with high resolution mass spectrometry for lipid analysis

Développements analytiques pour l’analyse multi-omique en chromatographie liquide couplée à la spectrométrie de masse

The analysis of biomolecules in health or in environment requires the use of high precision analytical instruments and adapted data acquisition methods. Several scientific challenges can be met such as the limited monitoring of a large number of molecules in targeted mass spectrometry, ionization variations or the simultaneous analysis of biomolecules with different physico-chemical properties. The main objective of this thesis was to optimize and improve data acquisition in the omics field such as proteomics, lipidomics and metabolomics in an environmental context. The first research axis was to improve the multiplexing capabilities via a new acquisition mode called Scout-MRM, in targeted mass spectrometry, free from retention time. This innovative development has been applied to the study of G. fossarum, a sentinel species widely used in ecotoxicology, via the monitoring in targeted proteomics of a large multiplex composed of a panel of 157 key proteins. To facilitate the development of targeted methods in lipidomics and in a "plug-and-play" philosophy, Scout-MRM was used on different biological matrices. The second research axis was to develop a biphasic protocol for the simultaneous extraction of proteins, lipids, and metabolites from the same sample. This multi-omics approach highlighted molecular signatures during the development cycle of female gammarids. The third research axis was to explore the capabilities of two-dimensional liquid chromatography as well as different orthogonality configurations coupled with high resolution mass spectrometry for lipid analysis.L’analyse de biomolécules en santé ou en environnement nécessite l’utilisation d’outils analytiques de grande précision ainsi que des méthodes d’acquisition de données adaptées. De nombreux verrous scientifiques peuvent être rencontrés comme le suivi limité d’un grand nombre de molécules en spectrométrie de masse ciblée, les variations d’ionisation ou bien l’analyse simultanée de biomolécules de propriétés physico-chimiques différentes. Les enjeux de cette thèse ont été d’optimiser et d’améliorer l’acquisition des données dans les sciences omiques comme la protéomique, la lipidomique et la métabolomique dans un contexte environnemental. Le premier axe de recherche a été d’améliorer les capacités de multiplexage via un nouveau mode d’acquisition en spectrométrie de masse ciblée, appelé Scout-MRM tout en permettant de s’affranchir du temps de rétention. Ce développement innovant a été appliqué pour l’étude de G. fossarum, espèce sentinelle en écotoxicologie, via le suivi en protéomique ciblée d’un grand multiplex constitué d’un panel de 157 protéines clés. Afin de faciliter le développement de méthodes ciblées en lipidomique et dans une approche de type « plug-and-play », Scout-MRM a été employé sur différentes matrices biologiques. Le deuxième axe de recherche a été de développer un protocole biphasique pour l’extraction simultanée des protéines, des lipides et des métabolites d’un même échantillon. Cette approche multi-omique a permis de mettre en exergue des signatures moléculaires au cours du développement chez les gammarides femelles. Le troisième axe de recherche a été d’explorer les potentialités de la chromatographie liquide bidimensionnelle ainsi que différentes configurations d’orthogonalité couplée à la spectrométrie de masse de haute résolution pour l’analyse des lipides

From shotgun to targeted proteomics: rapid Scout-MRM assay development for monitoring potential immunomarkers in Dreissena polymorpha

This work benefitted from the French GDR "Aquatic Ecotoxicology" framework which is aimed at fostering stimulating scientific discussions and collaborations for more integrative approaches.International audienc

Regiocontrolled syntheses of FAHFAs and LC-MS/MS differentiation of regioisomers

International audienceAn efficient regiospecific total synthesis of several branched fatty acyl hydroxyl-fatty acids (FAHFA) has been achieved from available terminal alkenes and alkynes. The key steps feature a boron trifluoride mediated epoxide ring opening with acetylide carbanions, followed by hydrogenation of the alkyne function. The carboxylic acid of the hydroxylated chains is introduced at the last step of the synthesis to allow the esterification of the branched hydroxyl group by fatty acids beforehand. The chemical syntheses of a “linear” FAHFA and a branched FAHFA analog containing a Z-olefin in the hydroxyl-fatty acid chain are also reported. A LC-MS/MS method has been developed. Several reversed phase columns were compared. Regioisomers were separated

Development of a multi-omics extraction method for ecotoxicology: investigation of the reproductive cycle of Gammarus fossarum

International audienceOmics study exemplified by proteomics, lipidomics or metabolomics, provides the opportunity to get insight of the molecular modifications occurring in living organisms in response to contaminants or in different physiological conditions. However, individual omics discloses only a single layer of information leading to a partial image of the biological complexity. Multiplication of samples preparation and processing can generate analytical variations resulting from several extractions and instrumental runs. To get all the -omics information at the proteins, metabolites and lipids level coming from a unique sample, a specific sample preparation must be optimized. In this study, we streamlined a biphasic extraction procedure based on a MTBE/Methanol mixture to provide the simultaneous extraction of polar (proteins, metabolites) and apolar compounds (lipids) for multi-omics analyses from a unique biological sample by a liquid chromatography (LC)/mass spectrometry (MS)/MS-based targeted approach. We applied the methodology for the study of female amphipod Gammarus fossarum during the reproductive cycle. Multivariate data analyses including Partial Least Squares Discriminant Analysis and multiple factor analysis were applied for the integration of the multi-omics data sets and highlighted molecular signatures, specific to the different stages

High-multiplexed monitoring of protein biomarkers in the sentinel Gammarus fossarum by targeted scout-MRM assay, a new vision for ecotoxicoproteomics

International audienceEcotoxicoproteomics employs mass spectrometry-based approaches centered on proteins of sentinel organisms to assess for instance, chemical toxicity in fresh water. In this study, we combined proteogenomics experiments and a novel targeted proteomics approach free from retention time scheduling called Scout-MRM. This methodology will enable the measurement of simultaneously changes in the relative abundance of multiple proteins involved in key physiological processes and potentially impacted by contaminants in the freshwater sentinel Gammarus fossarum. The development and validation of the assay were performed to target 157 protein biomarkers of this non-model organism. We carefully chose and validated the transitions to monitor using conventional parameters (linearity, repeatability, LOD, LOQ). Finally, the potential of the methodology is illustrated by measuring 277peptide-plex assay (831 transitions) in sentinel animals exposed in natura to different agricultural sites potentially exposed to pesticide contamination. Multivariate data analyses highlighted the modulation of several key proteins involved in feeding and molting. This multiplex-targeted proteomics assay paves the way for the discovery and the use of a large panel of novel protein biomarkers in emergent ecotoxicological models for environmental monitoring in the future.Biological significance: The study contributed to the development of Scout-MRM for the high-throughput quantitation of a large panel of proteins in the Gammarus fossarum freshwater sentinel. Increasing the number of markers in ecotoxicoproteomics is of most interest to assess the impact of pollutants in freshwater organisms. The development and validation of the assay enabled the monitoring of a large panel of reporter peptides of exposed gammarids. To illustrate the applicability of the methodology, animals from different agricultural sites were analysed. The application of the assay highlighted the modulation of some biomarker proteins involved in key physiological pathways, such as molting, feeding and general stress response. Increasing multiplexing capabilities and field test will provide the development of diagnostic protein biomarkers for emergent ecotoxicological models in future environmental biomonitoring programs

Evaluation of different bone markers in hemodialyzed patients

Background: Routinely, nephrologists rely on different biochemical markers like intact PTH (iPTH), bone-specific alkaline phosphatase (BALP), plasmatic calcium and phosphate. The aim of the present study was to evaluate different other bone markers like N-terminal propeptide of type I procollagen (PINP), active isoform 5b of the tartrate-resistant acid phosphatase (TRAP 5b) and beta-crossLaps (R) (CTXS) as well as full-length PTH (wPTH), presumed non-(1-84) PTH, and their ratio in the diagnosis of renal osteodystrophy with high and low turnover. We also determined 25 hydroxyvitamin D (25VTD), 1-25 dihydroxyvitamin D and homocystein (HCY). Methods: We performed those parameters on 73 patients with end-stage renal disease according to the manufacturers' instructions. Results: There were very strong correlations between the bone markers concentrations, particularly between BALP and PINP (r=0.953). We did not observe any correlation between the ratio whole PTH/non-(1-84) PTH and any of the usual bone markers. This ratio was significantly (p < 0.05) higher in low and high bone turnover patients than in normal patients according to the K/DOQI. We found a correlation between low levels of 25VTD and high levels of HCY Conclusions: BALP offers the best clinical and analytical profile as the easier marker of choice in hemodiallyzed patients for the diagnosis of bone disease. (c) 2006 Elsevier B.V All rights reserved