Use of molecular dynamics simulations to study the interactions between barley allelochemicals and plant plasma membrane

Gramine and hordenine, two alkaloids produced by barley, were shown to inhibit the growth of a common weed (Matricaria recutita L.). This feature could be useful in order to reach a more sustainable weeds management. In vitro experiments have proven that both molecules do interact with lipid bilayers (made of a phosphatidylglycerol (PG) lipid) mimicking plant plasma membranes and are able to modify some of their properties. Moreover, gramine was shown to be more effective than hordenine in both inhibiting weeds growth and altering lipid bilayers properties, suggesting that interactions with membranes could be linked to their mode of action. Molecular dynamics (MD) simulations are carried out in order to get an insight into the molecular mechanisms that underlie these interactions with model membranes and to discriminate between gramine behavior and hordenine behavior

Translating lung function genome-wide association study (GWAS) findings: new insights for lung biology

Chronic respiratory diseases are a major cause of worldwide mortality and morbidity. Although hereditary severe deficiency of α1 antitrypsin (A1AD) has been established to cause emphysema, A1AD accounts for only ∼1% of Chronic Obstructive Pulmonary Disease (COPD) cases. Genome-wide association studies (GWAS) have been successful at detecting multiple loci harboring variants predicting the variation in lung function measures and risk of COPD. However, GWAS are incapable of distinguishing causal from noncausal variants. Several approaches can be used for functional translation of genetic findings. These approaches have the scope to identify underlying alleles and pathways that are important in lung function and COPD. Computational methods aim at effective functional variant prediction by combining experimentally generated regulatory information with associated region of the human genome. Classically, GWAS association follow-up concentrated on manipulation of a single gene. However association data has identified genetic variants in >50 loci predicting disease risk or lung function. Therefore there is a clear precedent for experiments that interrogate multiple candidate genes in parallel, which is now possible with genome editing technology. Gene expression profiling can be used for effective discovery of biological pathways underpinning gene function. This information may be used for informed decisions about cellular assays post genetic manipulation. Investigating respiratory phenotypes in human lung tissue and specific gene knockout mice is a valuable in vivo approach that can complement in vitro work. Herein, we review state-of-the-art in silico, in vivo, and in vitro approaches that may be used to accelerate functional translation of genetic findings

Identification of a new gene regulatory circuit involving B cell receptor activated signaling using a combined analysis of experimental, clinical and global gene expression data

To discover new regulatory pathways in B lymphoma cells, we performed a combined analysis of experimental, clinical and global gene expression data. We identified a specific cluster of genes that was coherently expressed in primary lymphoma samples and suppressed by activation of the B cell receptor (BCR) through aIgM treatment of lymphoma cells in vitro. This gene cluster, which we called BCR. 1, includes numerous cell cycle regulators. A reduced expression of BCR. 1 genes after BCR activation was observed in different cell lines and also in CD10(+) germinal center B cells. We found that BCR activation led to a delayed entry to and progression of mitosis and defects in metaphase. Cytogenetic changes were detected upon long-term aIgM treatment. Furthermore, an inverse correlation of BCR. 1 genes with c-Myc co-regulated genes in distinct groups of lymphoma patients was observed. Finally, we showed that the BCR. 1 index discriminates activated B cell-like and germinal centre B cell-like diffuse large B cell lymphoma supporting the functional relevance of this new regulatory circuit and the power of guided clustering for biomarker discovery

Growth And The Growth Hormone-Insulin Like Growth Factor 1 Axis In Children With Chronic Inflammation:Current Evidence, Gaps In Knowledge And Future Directions

Growth failure is frequently encountered in children with chronic inflammatory conditions like juvenile idiopathic arthritis, inflammatory bowel disease and cystic fibrosis. Delayed puberty and attenuated pubertal growth spurt is often seen during adolescence. The underlying inflammatory state mediated by pro-inflammatory cytokines, prolonged use of glucocorticoid and suboptimal nutrition contribute to growth failure and pubertal abnormalities. These factors can impair growth by their effects on the growth hormone-insulin like growth factor axis and also directly at the level of the growth plate via alterations in chondrogenesis and local growth factor signaling. Recent studies on the impact of cytokines and glucocorticoid on the growth plate studies further advanced our understanding of growth failure in chronic disease and provided a biological rationale of growth promotion. Targeting cytokines using biologic therapy may lead to improvement of growth in some of these children but approximately one third continue to grow slowly. There is increasing evidence that the use of relatively high dose recombinant human growth hormone may lead to partial catch up growth in chronic inflammatory conditions, although long term follow-up data is currently limited. In this review, we comprehensively review the growth abnormalities in children with juvenile idiopathic arthritis, inflammatory bowel disease and cystic fibrosis, systemic abnormalities of the growth hormone-insulin like growth factor axis and growth plate perturbations. We also systematically reviewed all the current published studies of recombinant human growth hormone in these conditions and discuss the role of recombinant human insulin like growth factor-1

Etude des interactions de molécules phytotoxiques avec des modèles membranaires inspirés de la membrane plasmique végétale

L’agriculture se trouve actuellement face à un double défi : produire suffisamment et produire durablement. Ces dernières décennies, l’accent a essentiellement été mis sur les rendements, tirés vers le haut notamment via l’usage massif d’herbicides synthétiques permettant de gérer les adventices. Leur efficacité est cependant menacée par le développement de résistances parmi les adventices, lié au faible renouvellement de leurs modes d’action. De nombreuses études pointent en outre les risques associés à l’usage de ce type de produits tant pour l’environnement que pour la santé humaine. De nouveaux outils de lutte contre les adventices sont donc activement recherchés afin de rencontrer ces deux enjeux. L’allélopathie, qui désigne le phénomène par lequel certaines plantes affectent le développement des plantes voisines en émettant des composés (allélo)chimiques dans l’environnement, représente une piste prometteuse à cet égard. Il paraît toutefois nécessaire d’identifier au préalable les composés allélochimiques impliqués dans de telles interactions et d’élucider leur mode d’action afin d’en faire une exploitation sécurisée, maîtrisée et optimisée. Plus largement, de nombreuses molécules d’origine végétale s’avèrent phytotoxiques, et pourraient donc servir d’herbicides naturels présentant potentiellement des modes d’action nouveaux et une biodégradabilité plus élevée que les herbicides synthétiques traditionnels. L’objet de cette thèse consiste à étudier certaines molécules phytotoxiques d’origine végétale sous un angle original : leurs interactions avec des modèles membranaires inspirés de la membrane plasmique de plante. Cette perspective est intéressante car la membrane plasmique est à la fois le site d’interaction initial d’un composé toxique avec une cellule et le siège de nombreux processus cruciaux pour le bon fonctionnement cellulaire, et apparaît donc comme une cible potentielle. Des bicouches lipidiques artificielles composées de lipides retrouvés dans la membrane plasmique de plante ont été utilisées pour étudier le comportement de molécules phytotoxiques d’origine végétale en présence d’un tel environnement. Deux types de structures moléculaires ont été étudiés dans ce contexte : des petits composés aromatiques amphiphiles et des composés possédant une chaîne hydrocarbonée. Dans un premier temps, deux alcaloïdes de l’orge, la gramine et l’hordénine, ont été considérés. Il s’agit de composés caractérisés par une petite structure aromatique et amphiphile. Leur phytotoxicité a été évaluée via des essais biologiques réalisés sur Matricaria recutita L., la camomille, une adventice commune d’Europe. Les deux composés ont induit une réduction de la longueur racinaire chez cette espèce, mais la gramine s’est révélée nettement plus toxique que l’hordénine. Les interactions de ces molécules avec des bicouches lipidiques ont ensuite été investiguées grâce à des techniques de biophysique. Des titrages calorimétriques isothermes ont permis de montrer que l’affinité de la gramine pour des bicouches lipidiques est supérieure à celle de l’hordénine. Des expériences en spectroscopie infrarouge ont mis en évidence l’impact de ces alcaloïdes sur une propriété importante des bicouches lipidiques : leur température de transition de phase. A nouveau, l’effet de la gramine sur ce paramètre s’est avéré plus important que celui de l’hordénine. Les mécanismes moléculaires sous-jacents ont été explorés par le biais de simulations de dynamique moléculaire. Les résultats des expériences de biophysique sont discutés, de même que leur possible corrélation avec les résultats des tests biologiques. Dans un deuxième temps, des molécules avec un autre type de structures, incluant une chaîne hydrocarbonée, ont été étudiées. L’acide nonanoïque, la sarmentine et la sorgoléone ont été choisis. Leur impact sur l’ordre et la fluidité de bicouches lipidiques a été étudié par fluorimétrie. L’utilisation du 1,6-diphenyl-1,3,5-hexatriène (DPH) et du laurdan, deux sondes fluorescentes, a ainsi permis de mettre en évidence l’augmentation d’ordre et l’augmentation de la température de transition de phase d’une bicouche lipidique induite par la présence de sorgoléone. L’acide nonanoïque et la sarmentine ont en revanche semblé n’avoir qu’un impact minime ou inexistant sur ces mêmes paramètres. Grâce à des titrages calorimétriques isothermes, l’affinité des trois molécules pour les bicouches lipidiques a pu être mesurée, et classée comme suit : sorgoléone >> sarmentine > acide nonanoïque. Des simulations en dynamique moléculaire ont enfin été réalisées afin d’obtenir des détails concernant la localisation préférentielle des composés au sein d’une bicouche lipidique. Une analyse du paramètre d’ordre des chaînes hydrophobes des lipides basée sur ces simulations a confirmé l’effet rigidifiant de la sorgoléone et suggéré la présence d’une possible influence subtile de l’acide nonanoïque et de la sarmentine sur la stabilité des bicouches lipidiques. Les résultats sont discutés par rapport à leur implication potentielle quant à la phytotoxicité des composés. Une discussion générale revient sur les principaux résultats obtenus dans le cadre de la thèse, leur apport à l’état des connaissances et les limites de leur signification. L’impact de certains traits structuraux présentés par des molécules phytotoxiques susceptibles d’interagir avec des bicouches lipidiques est discuté. Finalement, des perspectives à partir de cette thèse sont évoquées, en soulignant notamment l’importance des recherches à mener pour mieux comprendre le fonctionnement de la membrane plasmique et le rôle de sa composante lipidique

Interactions between natural herbicides and lipid bilayers mimicking the plant plasma membrane

Natural phytotoxic compounds could become an alternative to traditional herbicides in the framework of sustainable agriculture. Nonanoic acid, sarmentine and sorgoleone are such molecules extracted from plants and able to inhibit the growth of various plant species. However, their mode of action is not fully understood and despite clues indicating that they could affect the plant plasma membrane, molecular details of such phenomenon are lacking. In this paper, we investigate the interactions between those natural herbicides and artificial bilayers mimicking the plant plasma membrane. First, their ability to affect lipid order and fluidity is evaluated by means of fluorescence measurements. It appears that sorgoleone has a clear ordering effect on lipid bilayers, while nonanoic acid and sarmentine induce no or little change to these parameters. Then, a thermodynamic characterization of interactions of each compound with lipid vesicles is obtained with isothermal titration calorimetry, and their respective affinity for bilayers is found to be ranked as follows: sorgoleone > sarmentine > nonanoic acid. Finally, molecular dynamics simulations give molecular details about the location of each compound within a lipid bilayer and confirm the rigidifying effect of sorgoleone. Data also suggest that mismatch in alkyl chain length between nonanoic acid or sarmentine and lipid hydrophobic tails could be responsible for bilayer destabilization. Results are discussed regarding their implications for the phytotoxicity of these compounds

Mucoviscidose : le kinésithérapeute face au risque infectieux

Introduction Respiratory infections play a deleterious role in the progression of patients suffering from cystic fibrosis. Cross infections and epidemics have been documented in these patients, justifying a rigorous prevention regime. Background This prevention regime concerns all health workers and rests on various recommendations. Segregation of patients and hand hygiene are important factors. Respiratory equipment and, more specifically, nebulisers represent a potential source of bacterial contamination requiring special attention. In the same perspective the risks related to the health care environment, particularly the lung function laboratory, should not be ignored. The modalities of prevention sometimes have a significant psychological impact that may often be reduced by careful explanation. Conclusions In view of the time spent in contact with these patients the physiotherapists are naturally involved in this prevention regime which is an integral part of their treatment

Interactions of allelochemicals with plant plasma membrane: a case study with alkaloids from barley

Allelopathy is defined as “any direct or indirect harmful effect by one plant on another through production of chemical compounds that escape into the environment” (Rice, 1974).This phenomenon is seen as a potential tool for weeds management within the framework of sustainable agriculture. While many studies investigated the mode of action of various allelochemicals (molecules emitted by allelopathic plants), little attention was given to their initial contact with the plant plasma membrane. In our work, this key step is explored for two alkaloids, gramine and hordenine, that are allelochemicals produced by barley

Molecular dynamics study of micelle proeprties according to their size

Surfactants are molecules able to spontaneously self-assemble to form aggregates with well-defined properties, such as spherical micelles, planar bilayers, cylindrical micelles or vesicles. Micelles have notably several applications in many domains, such as drug delivery or membrane protein solubilization. In this context, the study of micelle formation in relation with the structural and physico-chemical properties of surfactants is of great interest to better control their use in the different application fields. In this work, we use the MD approach developed by Yoshii et al. and extend it to surfactants with different structures. We aim to systematically investigate different micellar properties as a function of the aggregates size by a molecular dynamics approach, to get an insight into the micellar organization and to collect some relevant descriptors about micelle formation. For this, we perform short MD simulations of preformed micelles of various sizes and analyze three parameters for each micelle size, namely the eccentricity of the micelles, the hydrophobic/hydrophilic surface ratio and the hydrophobic tails hydration. If these parameters are known descriptors of micelles, they were not yet studied in this way by MD. We show that eccentricity, used as “validator” parameter, exhibits minimal values when the aggregate size is close to the experimental aggregation number for surfactants that are known to form spherical micelles. This hence indicates that our methodology gives consistent results. The evolution of the two descriptors follows another scheme, with a sharp increase and decrease, respectively, followed by a leveling-off. The aggregate sizes at which this stabilization starts to occur are close to the respective aggregation number of each surfactant. In our approach, we validate the use of these descriptors to follow micelle formation by MD, from “simple” surfactants to more complex structures, like lipopeptides. Our calculations also suggest that some peculiar behavior, like that of TPC, can be highlighted by our approach. In the context of peptidic surfactants, our methodology could further help to improve computer simulations combined to molecular thermodynamic models to predict micellar properties of those more complex amphiphilic molecules