Caution on the storage of waters and aqueous solutions in plastic containers for hydrogen and oxygen stable isotope analysis

RATIONALE The choice of containers for storage of aqueous samples between their collection, transport and water hydrogen (2H) and oxygen (18O) stable isotope analysis is a topic of concern for a wide range of fields in environmental, geological, biomedical, food, and forensic sciences. The transport and separation of water molecules during water vapor or liquid uptake by sorption or solution and the diffusive transport of water molecules through organic polymer material by permeation or pervaporation may entail an isotopic fractionation. An experiment was conducted to evaluate the extent of such fractionation. METHODS Sixteen bottle-like containers of eleven different organic polymers, including low and high density polyethylene (LDPE and HDPE), polypropylene (PP), polycarbonate (PC), polyethylene terephthalate (PET), and perfluoroalkoxy-Teflon (PFA), of different wall thickness and size were completely filled with the same mineral water and stored for 659?days under the same conditions of temperature and humidity. Particular care was exercised to keep the bottles tightly closed and prevent loss of water vapor through the seals. RESULTS Changes of up to +5 parts per thousand for d2H values and +2.0 parts per thousand for d18O values were measured for water after more than 1?year of storage within a plastic container, with the magnitude of change depending mainly on the type of organic polymer, wall thickness, and container size. The most important variations were measured for the PET and PC bottles. Waters stored in glass bottles with Polyseal (TM) cone-lined PP screw caps and thick-walled HDPE or PFA containers with linerless screw caps having an integrally molded inner sealing ring preserved their original d2H and d18O values. The carbon, hydrogen, and oxygen stable isotope compositions of the organic polymeric materials were also determined. CONCLUSIONS The results of this study clearly show that for precise and accurate measurements of the water stable isotope composition in aqueous solutions, rigorous sampling and storage procedures are needed both for laboratory standards and for unknown samples. Copyright (c) 2012 John Wiley & Sons, Ltd.

Nucleic acid-binding properties of the RRM-containing protein RDM1.

RDM1 (RAD52 Motif 1) is a vertebrate protein involved in the cellular response to the anti-cancer drug cisplatin. In addition to an RNA recognition motif, RDM1 contains a small amino acid motif, named RD motif, which it shares with the recombination and repair protein, RAD52. RDM1 binds to single- and double-stranded DNA, and recognizes DNA distortions induced by cisplatin adducts in vitro. Here, we have performed an in-depth analysis of the nucleic acid-binding properties of RDM1 using gel-shift assays and electron microscopy. We show that RDM1 possesses acidic pH-dependent DNA-binding activity and that it binds RNA as well as DNA, and we present evidence from competition gel-shift experiments that RDM1 may be capable of discrimination between the two nucleic acids. Based on reported studies of RAD52, we have generated an RDM1 variant mutated in its RD motif. We find that the L119GF --> AAA mutation affects the mode of RDM1 binding to single-stranded DNA.

Molecular modeling study of the binding and signaling properties of the TCRpMHC complex

The activation of the specific immune response against tumor cells is based on the recognition by the CD8+ Cytotoxic Τ Lymphocytes (CTL), of antigenic peptides (p) presented at the surface of the cell by the class I major histocompatibility complex (MHC). The ability of the so-called T-Cell Receptors (TCR) to discriminate between self and non-self peptides constitutes the most important specific control mechanism against infected cells. The TCR/pMHC interaction has been the subject of much attention in cancer therapy since the design of the adoptive transfer approach, in which Τ lymphocytes presenting an interesting response against tumor cells are extracted from the patient, expanded in vitro, and reinfused after immunodepletion, possibly leading to cancer regression. In the last decade, major progress has been achieved by the introduction of engineered lypmhocytes. In the meantime, the understanding of the molecular aspects of the TCRpMHC interaction has become essential to guide in vitro and in vivo studies. In 1996, the determination of the first structure of a TCRpMHC complex by X-ray crystallography revealed the molecular basis of the interaction. Since then, molecular modeling techniques have taken advantage of crystal structures to study the conformational space of the complex, and understand the specificity of the recognition of the pMHC by the TCR. In the meantime, experimental techniques used to determine the sequences of TCR that bind to a pMHC complex have been used intensively, leading to the collection of large repertoires of TCR sequences that are specific for a given pMHC. There is a growing need for computational approaches capable of predicting the molecular interactions that occur upon TCR/pMHC binding without relying on the time consuming resolution of a crystal structure. This work presents new approaches to analyze the molecular principles that govern the recognition of the pMHC by the TCR and the subsequent activation of the T-cell. We first introduce TCRep 3D, a new method to model and study the structural properties of TCR repertoires, based on homology and ab initio modeling. We discuss the methodology in details, and demonstrate that it outperforms state of the art modeling methods in predicting relevant TCR conformations. Two successful applications of TCRep 3D that supported experimental studies on TCR repertoires are presented. Second, we present a rigid body study of TCRpMHC complexes that gives a fair insight on the TCR approach towards pMHC. We show that the binding mode of the TCR is correctly described by long-distance interactions. Finally, the last section is dedicated to a detailed analysis of an experimental hydrogen exchange study, which suggests that some regions of the constant domain of the TCR are subject to conformational changes upon binding to the pMHC. We propose a hypothesis of the structural signaling of TCR molecules leading to the activation of the T-cell. It is based on the analysis of correlated motions in the TCRpMHC structure. - L'activation de la réponse immunitaire spécifique dirigée contre les cellules tumorales est basée sur la reconnaissance par les Lymphocytes Τ Cytotoxiques (CTL), d'un peptide antigénique (p) présenté à la suface de la cellule par le complexe majeur d'histocompatibilité de classe I (MHC). La capacité des récepteurs des lymphocytes (TCR) à distinguer les peptides endogènes des peptides étrangers constitue le mécanisme de contrôle le plus important dirigé contre les cellules infectées. L'interaction entre le TCR et le pMHC est le sujet de beaucoup d'attention dans la thérapie du cancer, depuis la conception de la méthode de transfer adoptif: les lymphocytes capables d'une réponse importante contre les cellules tumorales sont extraits du patient, amplifiés in vitro, et réintroduits après immunosuppression. Il peut en résulter une régression du cancer. Ces dix dernières années, d'importants progrès ont été réalisés grâce à l'introduction de lymphocytes modifiés par génie génétique. En parallèle, la compréhension du TCRpMHC au niveau moléculaire est donc devenue essentielle pour soutenir les études in vitro et in vivo. En 1996, l'obtention de la première structure du complexe TCRpMHC à l'aide de la cristallographie par rayons X a révélé les bases moléculaires de l'interaction. Depuis lors, les techniques de modélisation moléculaire ont exploité les structures expérimentales pour comprendre la spécificité de la reconnaissance du pMHC par le TCR. Dans le même temps, de nouvelles techniques expérimentales permettant de déterminer la séquence de TCR spécifiques envers un pMHC donné, ont été largement exploitées. Ainsi, d'importants répertoires de TCR sont devenus disponibles, et il est plus que jamais nécessaire de développer des approches informatiques capables de prédire les interactions moléculaires qui ont lieu lors de la liaison du TCR au pMHC, et ce sans dépendre systématiquement de la résolution d'une structure cristalline. Ce mémoire présente une nouvelle approche pour analyser les principes moléculaires régissant la reconnaissance du pMHC par le TCR, et l'activation du lymphocyte qui en résulte. Dans un premier temps, nous présentons TCRep 3D, une nouvelle méthode basée sur les modélisations par homologie et ab initio, pour l'étude de propriétés structurales des répertoires de TCR. Le procédé est discuté en détails et comparé à des approches standard. Nous démontrons ainsi que TCRep 3D est le plus performant pour prédire des conformations pertinentes du TCR. Deux applications à des études expérimentales des répertoires TCR sont ensuite présentées. Dans la seconde partie de ce travail nous présentons une étude de complexes TCRpMHC qui donne un aperçu intéressant du mécanisme d'approche du pMHC par le TCR. Finalement, la dernière section se concentre sur l'analyse détaillée d'une étude expérimentale basée sur les échanges deuterium/hydrogène, dont les résultats révèlent que certaines régions clés du domaine constant du TCR sont sujettes à un changement conformationnel lors de la liaison au pMHC. Nous proposons une hypothèse pour la signalisation structurelle des TCR, menant à l'activation du lymphocyte. Celle-ci est basée sur l'analyse des mouvements corrélés observés dans la structure du TCRpMHC.

Molecular determinants of vesicular storage and release of the gliotransmitter D-serine from cortical astrocytes

Neuron-astrocyte reciprocal communication at synapses has emerged as a novel signalling pathway in brain function. Astrocytes sense the level of synaptic activity and, in turn, influence its efficacy through the regulated release of 'gliotransmitters' such as glutamate, ATP or D-serine. A calcium-dependent exocytosis is proposed to drive the release of gliotransmitters but its existence is still debated. Over the last years, we have been studying the molecular determinants governing D-serine release from glia using different approaches. Using a novel bioassay for D-serine, we have been able to show that D-serine release occurs mainly through a calcium- and SNARE proteindependent mechanism just supporting the idea that this amino acid is released by exocytosis from glia. We next have pursued our exploration by confocal imaging and tracking of the exocytotic routes for Dserine- mediated gliotransmission and have shown that D-serine releasable pools are confined to synaptobrevin2/cellubrevin-bearing vesicles. To shed light onto the mechanisms controlling the storage and the release of gliotransmitters and namely D-serine, we have developed a new method for the immunoisolation of synaptobrevin 2- positive vesicles from rat cortical astrocytes in culture while preserving their content in gliotransmitters. The purified organelles are clear round shape vesicles of excellent purity with homogeneous size (40 nm) as judged by electron microscopy. Immunoblotting analysis revealed that isolated vesicles contain most of the major proteins already described for neuron-derived vesicles like synaptic vesicle protein 2 (SV2) and the proton pump H?-ATPase. In addition, we have analyzed the content for various amino acids of these vesicles by means of chiral capillary electrophoresis coupled to laser-induced fluorescence detection. The purified vesicles contain large amount of D-serine. We also detect peaks corresponding to unidentified compounds that may correspond to others amino acids. Postembedding immunogold labelling of the rat neocortex further revealed the expression of D-serine in astrocytes processes contacting excitatory synapses. Finally, we have examined the uptake properties for Dserine and glutamate inside the isolated glial vesicles. Our results provide significant support for the existence of an uptake system for D-serine in secretory glial vesicles and for the storage of chemical substances like D-serine and glutamate. 11th International Congress on Amino Acids, Peptides and Proteins 763 123

The stable hydrogen and oxygen isotope variation of water stored in polyethylene terephthalate (PET) bottles

A set of bottled waters from a single natural spring distributed worldwide in polyethylene terephthalate (PET) bottles has been used to examine the effects of storage in plastic polymer material on the isotopic composition (delta(18)O and delta(2)H values) of the water. All samples analyzed were subjected to the same packaging procedure but experienced different conditions of temperature and humidity during storage. Water sorption and the diffusive transfer of water and water vapor through the wall of the PET bottle may cause isotopic exchange between water within the bottle and water vapor in air near the PET-water interface. Changes of about +4 parts per thousand for delta(2)H and +0.7 parts per thousand for delta(18)O have been measured for water after 253 days of storage within the PET bottle. The results of this study clearly indicate the need to use glass bottles for storing water samples for isotopic studies. It is imperative to transfer PET-bottled natural waters to glass bottles for their use as calibration material or potential international working standards. Copyright (C) 2008 John Wiley & Sons, Ltd.

PROTEOMICS OF OXIDATIVE LESIONS OCCURRING DURING TRANSFUSION-PURPOSED STORAGE OF ERYTHROCYTE CONCENTRATES

Erythrocyte concentrates (ECs) are the major labile blood product being transfused worldwide, aiming at curing anemia of diverse origins. In Switzerland, ECs are stored at 4 °C up to 42 days in saline-adenine-glucose-mannitol (SAGM). Such storage induces cellular lesions, altering red blood cells (RBCs) metabolism, protein content and rheological properties. A hot debate exists regarding the impact of the storage lesions, thus the age of ECs on transfusion-related clinical adverse outcomes. Several studies tend to show that poorer outcomes occur in patients receiving older blood products. However, no clear association was demonstrated up to date. While metabolism and early rheological changes are reversible through transfusion of the blood units, oxidized proteins cannot be repaired, and it is likely such irreversible damages would affect the quality of the blood product and the efficiency of the transfusion. In vivo, RBCs are constantly exposed to oxygen fluxes, and are thus well equipped to deal with oxidative challenges. Moreover, functional 20S proteasome complexes allow for recognition and proteolysis of fairly oxidized protein, and some proteins can be eliminated from RBCs by the release of microvesicles. The present PhD thesis is involved in a global research project which goal is to characterize the effect of processing and storage on the quality of ECs. Assessing protein oxidative damages during RBC storage is of major importance to understand the mechanisms of aging of stored RBCs. To this purpose, redox proteomic-based investigations were conducted here. In a first part, cysteine oxidation and protein carbonylation were addressed via 2D-DIGE and derivatization-driven immunodetection approaches, respectively. Then, the oxidized sub- proteomes were characterized through LC-MS/MS identification of proteins in spots of interest (cysteine oxidation) or affinity-purified carbonylated proteins. Gene ontology annotation allowed classifying targets of oxidation according to their molecular functions. In a third part, the P20S activity was evaluated throughout the storage period of ECs, and its susceptibility to highly oxidized environment was investigated. The potential defensive role of microvesiculation was also addressed through the quantification of eliminated carbonylated proteins. We highlighted distinct protein groups differentially affected by cysteine oxidation, either reversibly or irreversibly. In addition, soluble extracts showed a decrease in carbonylation at the beginning of the storage and membrane extracts revealed increasing carbonylation after 4 weeks of storage. Engaged molecular functions revealed that antioxidant (AO) are rather reversibly oxidized at their cysteine residue(s), but are irreversibly oxidized through carbonylation. In the meantime, the 20S proteasome activity is decreased by around 40 % at the end of the storage period. Incubation of fresh RBCs extracts with exogenous oxidized proteins showed a dose-dependent and protein-dependent inhibitory effect. Finally, we proved that the release of microvesicles allows the elimination of increasing quantities of carbonylated proteins. Taken together, these results revealed an oxidative pathway model of RBCs storage, on which further investigation towards improved storage conditions will be based. -- Les concentrés érythrocytaires (CE) sont le produit sanguin le plus délivré au monde, permettant de traiter différentes formes d'anémies. En Suisse, les CE sont stocké à 4 °C pendant 42 jours dans une solution saline d'adénine, glucose et mannitol (SAGM). Une telle conservation induit des lésions de stockage qui altèrent le métabolisme, les protéines et les propriétés rhéologique du globule rouge (GR). Un débat important concerne l'impact du temps de stockage des CE sur les risques de réaction transfusionnelles, certaines études tentant de démontrer que des transfusions de sang vieux réduiraient l'espérance de vie des patients. Cependant, aucune association concrète n'a été prouvée à ce jour. Alors que les modifications du métabolisme et changement précoces des propriétés rhéologiques sont réversibles suite à la transfusion du CE, les protéines oxydées ne peuvent être réparées, et il est probable que de telles lésions affectent la qualité et l'efficacité des produits sanguins. In vivo, les GR sont constamment exposés à l'oxygène, et sont donc bien équipés pour résister aux lésions oxydatives. De plus, les complexes fonctionnels de proteasome 20S reconnaissent et dégradent les protéines modérément oxydées, et certaines protéines peuvent être éliminées par les microparticules. Cette thèse de doctorat est imbriquée dans un projet de recherche global ayant pour objectif la caractérisation des effets de la préparation et du stockage sur la qualité des GR. Evaluer les dommages oxydatifs du GR pendant le stockage est primordial pour comprendre les mécanismes de vieillissement des produits sanguin. Dans ce but, des recherches orientées redoxomique ont été conduites. Dans une première partie, l'oxydation des cystéines et la carbonylation des protéines sont évaluées par électrophorèse bidimensionnelle différentielle et par immunodétection de protéines dérivatisées. Ensuite, les protéines d'intérêt ainsi que les protéines carbonylées, purifiées par affinité, sont identifiées par spectrométrie de masse en tandem. Les protéines cibles de l'oxydation sont classées selon leur fonction moléculaire. Dans une troisième partie, l'activité protéolytique du protéasome 20S est suivie durant la période de stockage. L'impact du stress oxydant sur cette activité a été évalué en utilisant des protéines exogènes oxydées in vitro. Le potentiel rôle défensif de la microvesiculation a également été étudié par la quantification des protéines carbonylées éliminées. Dans ce travail, nous avons observé que différents groupes de protéines sont affectés par l'oxydation réversible ou irréversible de leurs cystéines. De plus, une diminution de la carbonylation en début de stockage dans les extraits solubles et une augmentation de la carbonylation après 4 semaines dans les extraits membranaires ont été montrées. Les fonctions moléculaires engagées par les protéines altérées montrent que les défenses antioxydantes sont oxydées de façon réversible sur leurs résidus cystéines, mais sont également irréversiblement carbonylées. Pendant ce temps, l'activité protéolytique du protéasome 20S décroit de 40 % en fin de stockage. L'incubation d'extraits de GR en début de stockage avec des protéines oxydées exogènes montre un effet inhibiteur « dose-dépendant » et « protéine-dépendant ». Enfin, les microvésicules s'avèrent éliminer des quantités croissantes de protéines carbonylées. La synthèse de ces résultats permet de modéliser une voie oxydative du stockage des GRs, à partir de laquelle de futures recherches seront menées avec pour but l'amélioration des conditions de stockage.

Numerical analysis of wave-induced fluid flow effects on seismic data: Application to monitoring of CO2 storage at the Sleipner Field

In this work we analyze how patchy distributions of CO2 and brine within sand reservoirs may lead to significant attenuation and velocity dispersion effects, which in turn may have a profound impact on surface seismic data. The ultimate goal of this paper is to contribute to the understanding of these processes within the framework of the seismic monitoring of CO2 sequestration, a key strategy to mitigate global warming. We first carry out a Monte Carlo analysis to study the statistical behavior of attenuation and velocity dispersion of compressional waves traveling through rocks with properties similar to those at the Utsira Sand, Sleipner field, containing quasi-fractal patchy distributions of CO2 and brine. These results show that the mean patch size and CO2 saturation play key roles in the observed wave-induced fluid flow effects. The latter can be remarkably important when CO2 concentrations are low and mean patch sizes are relatively large. To analyze these effects on the corresponding surface seismic data, we perform numerical simulations of wave propagation considering reservoir models and CO2 accumulation patterns similar to the CO2 injection site in the Sleipner field. These numerical experiments suggest that wave-induced fluid flow effects may produce changes in the reservoir's seismic response, modifying significantly the main seismic attributes usually employed in the characterization of these environments. Consequently, the determination of the nature of the fluid distributions as well as the proper modeling of the seismic data constitute important aspects that should not be ignored in the seismic monitoring of CO2 sequestration problems.

TCRep 3D: an automated in silico approach to study the structural properties of TCR repertoires.

TCRep 3D is an automated systematic approach for TCR-peptide-MHC class I structure prediction, based on homology and ab initio modeling. It has been considerably generalized from former studies to be applicable to large repertoires of TCR. First, the location of the complementary determining regions of the target sequences are automatically identified by a sequence alignment strategy against a database of TCR Vα and Vβ chains. A structure-based alignment ensures automated identification of CDR3 loops. The CDR are then modeled in the environment of the complex, in an ab initio approach based on a simulated annealing protocol. During this step, dihedral restraints are applied to drive the CDR1 and CDR2 loops towards their canonical conformations, described by Al-Lazikani et. al. We developed a new automated algorithm that determines additional restraints to iteratively converge towards TCR conformations making frequent hydrogen bonds with the pMHC. We demonstrated that our approach outperforms popular scoring methods (Anolea, Dope and Modeller) in predicting relevant CDR conformations. Finally, this modeling approach has been successfully applied to experimentally determined sequences of TCR that recognize the NY-ESO-1 cancer testis antigen. This analysis revealed a mechanism of selection of TCR through the presence of a single conserved amino acid in all CDR3β sequences. The important structural modifications predicted in silico and the associated dramatic loss of experimental binding affinity upon mutation of this amino acid show the good correspondence between the predicted structures and their biological activities. To our knowledge, this is the first systematic approach that was developed for large TCR repertoire structural modeling.