Coarse graining the dynamics of nano-confined solutes: the case of ions in clays

We investigate the possibility of describing by a continuous solvent model the dynamics of solutes confined down to the molecular scale. We derive a generalised Langevin equation (GLE) for the generic motion of a solute in an external potential using the Mori–Zwanzig formalism. We then compute the corresponding memory function from molecular simulations, in the case of cesium ions confined in the interlayer porosity of montmorillonite clays, with a very low water content (only six solvent molecules per ion). Previous attempts to describe the dynamics of cesium in this system by a simple Langevin equation were unsuccessful. The purpose of this work is not to carry out GLE simulations using the memory function from molecular simulations, but rather to analyse the separation of time scales between the confined ions and solvent. We show that such a separation is not achieved and discuss the relative contribution of the ion–surface, ion–solvent and ion–ion interactions to the dynamics. On the picosecond time scale, the ion oscillates in a surface-and-solvent cage, which relaxes on much longer time scales extending to several nanoseconds. The resulting overall dynamics resembles that of glasses or diffusion inside a solid by site-to-site hopping.     

On the Modularity of the Intrinsic Flexibility of the μ Opioid Receptor: A Computational Study

The µ opioid receptor (µOR), the principal target to control pain, belongs to the G protein-coupled receptors (GPCRs) family, one of the most highlighted protein families due to their importance as therapeutic targets. The conformational flexibility of GPCRs is one of their essential characteristics as they take part in ligand recognition and subsequent activation or inactivation mechanisms. It is assessed that the intrinsic mechanical properties of the µOR, more specifically its particular flexibility behavior, would facilitate the accomplishment of specific biological functions, at least in their first steps, even in the absence of a ligand or any chemical species usually present in its biological environment. The study of the mechanical properties of the µOR would thus bring some indications regarding the highly efficient ability of the µOR to transduce cellular message. We therefore investigate the intrinsic flexibility of the µOR in its apo-form using all-atom Molecular Dynamics simulations at the sub-microsecond time scale. We particularly consider the µOR embedded in a simplified membrane model without specific ions, particular lipids, such as cholesterol moieties, or any other chemical species that could affect the flexibility of the µOR. Our analyses highlighted an important local effect due to the various bendability of the helices resulting in a diversity of shape and volume sizes adopted by the µOR binding site. Such property explains why the µOR can interact with ligands presenting highly diverse structural geometry. By investigating the topology of the µOR binding site, a conformational global effect is depicted: the correlation between the motional modes of the extra- and intracellular parts of µOR on one hand, along with a clear rigidity of the central µOR domain on the other hand. Our results show how the modularity of the µOR flexibility is related to its pre-ability to activate and to present a basal activity.     

Tracking Mouse Bone Marrow Monocytes In Vivo

Real time multiphoton imaging provides a great opportunity to study cell trafficking and cell-to-cell interactions in their physiological 3-dimensionnal environment. Biological activities of immune cells mainly rely on their motility capacities. Blood monocytes have short half-life in the bloodstream; they originate in the bone marrow and are constitutively released from it. In inflammatory condition, this process is enhanced, leading to blood monocytosis and subsequent infiltration of the peripheral inflammatory tissues. Identifying the biomechanical events controlling monocyte trafficking from the bone marrow towards the vascular network is an important step to understand monocyte physiopathological relevance. We performed in vivo time-lapse imaging by two-photon microscopy of the skull bone marrow of the Csf1r-Gal4VP16/UAS-ECFP (MacBlue) mouse. The MacBlue mouse expresses the fluorescent reporters enhanced cyan fluorescent protein (ECFP) under the control of a myeloid specific promoter ¹, in combination with vascular network labelling. We describe how this approach enables the tracking of individual medullar monocytes in real time to further quantify the migratory behaviour within the bone marrow parenchyma and the vasculature, as well as cell-to-cell interactions. This approach provides novel insights into the biology of the bone marrow monocyte subsets and allows to further address how these cells can be influenced in specific pathological conditions.     

Pedigree-Free Estimates of Heritability in the Wild: Promising Prospects for Selfing Populations

Estimating the genetic variance available for traits informs us about a population’s ability to evolve in response to novel selective challenges. In selfing species, theory predicts a loss of genetic diversity that could lead to an evolutionary dead-end, but empirical support remains scarce. Genetic variability in a trait is estimated by correlating the phenotypic resemblance with the proportion of the genome that two relatives share identical by descent (‘realized relatedness’). The latter is traditionally predicted from pedigrees (Φ_A: expected value) but can also be estimated using molecular markers (average number of alleles shared). Nevertheless, evolutionary biologists, unlike animal breeders, remain cautious about using marker-based relatedness coefficients to study complex phenotypic traits in populations. In this paper, we review published results comparing five different pedigree-free methods and use simulations to test individual-based models (hereafter called animal models) using marker-based relatedness coefficients, with a special focus on the influence of mating systems. Our literature review confirms that Ritland’s regression method is unreliable, but suggests that animal models with marker-based estimates of relatedness and genomic selection are promising and that more testing is required. Our simulations show that using molecular markers instead of pedigrees in animal models seriously worsens the estimation of heritability in outcrossing populations, unless a very large number of loci is available. In selfing populations the results are less biased. More generally, populations with high identity disequilibrium (consanguineous or bottlenecked populations) could be propitious for using marker-based animal models, but are also more likely to deviate from the standard assumptions of quantitative genetics models (non-additive variance).     

Age-Related Wayfinding Differences in Real Large-Scale Environments: Detrimental Motor Control Effects during Spatial Learning Are Mediated by Executive Decline?

The aim of this study was to evaluate motor control activity (active vs. passive condition) with regards to wayfinding and spatial learning difficulties in large-scale spaces for older adults. We compared virtual reality (VR)-based wayfinding and spatial memory (survey and route knowledge) performances between 30 younger and 30 older adults. A significant effect of age was obtained on the wayfinding performances but not on the spatial memory performances. Specifically, the active condition deteriorated the survey measure in all of the participants and increased the age-related differences in the wayfinding performances. Importantly, the age-related differences in the wayfinding performances, after an active condition, were further mediated by the executive measures. All of the results relative to a detrimental effect of motor activity are discussed in terms of a dual task effect as well as executive decline associated with aging.     

Feeding Performance in Heterochronic Alpine Newts is Consistent with Trophic Niche and Maintenance of Polymorphism

The feeding performances of two heterochronic morphs of the Alpine newt Triturus alpestris were investigated in laboratory experiments. Although both morphs are able to feed in the aquatic habitat, the hydrodynamics of prey capture differ between morphs. In paedomorphs water sucked with prey is expelled behind the mouth through gill bars. In metamorphs, water is expelled by the mouth as gill slits are closed. Feeding performance was better in paedomorphs than in metamorphs when foraging on aquatic crustaceans, but paedomorphs were less successful when foraging on terrestrial invertebrates caught at the water surface. These differences in prey capture success related to prey type allow the two morphs to use specific resources in their aquatic habitat. These results are consistent with previous studies that showed diet differentiation between morphs in natural populations. Such resource partitioning is a factor favouring the maintenance of facultative paedomorphosis in natural populations.     

FGF3 from Xenopus laevis.

Fibroblast growth factor 3 (FGF3) was first identified as the product of a cellular oncogene activated by mouse mammary tumour virus but its normal role appears to be in the developing embryo. To gain further insights into its function, we have isolated sequences encoding the FGF3 homologue in Xenopus laevis, XFGF3. COS-1 cells transfected with XFGF3 cDNA express a 31 kDa product, p31, generated by signal peptide cleavage and Asn-linked glycosylation at the single consensus site. This product is secreted and becomes associated with the cell surface and extracellular matrix. Proteolytic cleavage of p31 in the extracellular compartment results in an amino-terminally truncated product, p27, that is also glycosylated. Both p31 and p27 bind quantitatively to heparin-Sepharose and can be displaced from the cell surface and extracellular matrix by soluble heparin. Conditioned medium containing these two proteins is capable of inducing transient morphological transformation of NIH3T3 cells and of stimulating DNA synthesis in quiescent C57MG and BALB/MK cells which express different isoforms of FGF receptors 1 and 2. Since XFGF3 behaves very differently from its mouse counterpart, we constructed chimeras in which amino-terminal sequences from XFGF3 were fused with carboxy-terminal sequences from mouse FGF3. Increasing the contribution from mouse FGF3 led to a more restricted host range for the chimeric ligand.     

Molecular Cloning of a Gene on Chromosome 19q12 Coding for a Novel Intracellular Protein: Analysis of Expression in Human and Mouse Tissues and in Human Tumor Cells, Particularly Reed–Sternberg Cells in Hodgkin Disease

A novel protein, named NNX3, was molecularly characterized by cloning its cDNA, and its gene was mapped to chromosome 19q12. The equivalent mouse cDNA and gene were also cloned to allow us to analyze expression in murine in addition to human cells and tissues. Human and mouse NNX3 genes are composed of nine exons coding for proteins that are unrelated to any known protein. Signal peptides and hydrophobic domains are absent, corroborating their localization in the cytoplasm in transfected Cos cells. In Western blotting and immunoprecipitation, human NNX3 appeared as a doublet ofM_r64K–66K, while mouse NNX3 was a 70-kDa protein, both apparently much larger than the predicted 50 kDa, due in part to a stretch of 16–18 acidic residues hinging two nearly equally sized domains. In addition, phosphorylation of serine residues was demonstrated. Putative nuclear targeting signals were predicted, but NNX3 protein and two truncated versions remained localized in the cytoplasm of transfected Cos cells. NNX3 was expressed in embryonic and adult mouse tissues, particularly in brain, muscle, and lung. The expression of human NNX3 was most notable in human skeletal muscle and in ganglion cells and was also evident in human tumors and derived cell lines. This was confirmed by entries appearing in the GenBank EST database during the later phase of this study, representing partial NNX3 cDNA isolated from diverse neoplastic and developing tissues. Surprisingly, NNX3 was immunochemically detected in Reed–Sternberg cells of Hodgkin disease, in parallel with restin, a cytoplasmic protein we previously characterized (J. Delabieet al.,1993,Leuk. Lymphoma 12,21–26). The cloning and comprehensive molecular analysis of NNX3 as presented will form the basis for elucidating its function and, conversely, will constitute a marker for Reed–Sternberg cells in Hodgkin disease.     

Cytoplasmic acidification as an early phosphorylation-dependent response of tobacco cells to elicitors

Elicitor-induced cytoplasmic pH changes of tobacco (Nicotiana tabacum L. cv. Xanthi) cells grown in suspension cultures were explored under a variety of conditions by using a flexible technique based on the distribution of [¹⁴C] benzoic acid between the intracellular and extracellular compartments. Comparison of data obtained by this technique and by ³¹P-nuclear magnetic resonance spectrometry qualifies the benzoic acid distribution method as a convenient and reliable way to probe cytoplasmic pH variations. Various elicitors shown to induce several defense-related responses in tobacco cells, namely oligogalacturonides of degree of polymerization 7–20, pectolyase from Aspergillus japonicus, Phytophthora megasperma crude elicitors and purified cryptogein, triggered cytoplasmic acidifications differing in intensity and kinetics according to the signal molecule. In contrast, no changes in cytoplasmic protons and external pH were observed in cells treated with short galacturonide oligomers, or with soybean-specific hepta -glucoside from P. megasperma, which are devoid of elicitor activity in tobacco cells. The oligogalacturonide-induced cytoplasmic acidification was inhibited by two structurally unrelated protein kinase inhibitors, staurosporine and 6-dimethylaminopurine, which both reduced the external alkalinization response to the elicitor. The protein phosphatase inhibitor calyculin A alone behaved as an elicitormimicking molecule in triggering cytoplasmic acidification, again associated with extracellular alkalinization. These results indicate that the increase in the cytoplasmic concentration of protons may be considered as a common early intracellular response of tobacco cells to elicitors, associated with the extracellular alkalinization response and controlled by protein phosphorylation.Abbreviations BA(H) benzoic acid (protonated form) - 6-DMAP 6-dimethylaminopurine - DP degree of polymerization - Mes 2-(N-morpholino)ethanesulfonic acid - OG oligogalacturonide - pHc cytoplasmic pH - ³¹P-NMR nuclear magnetic resonance spectroscopy of ³¹P atoms The authors thank P. Albersheim (CCRC, Athens, Georgia, USA) for providing the purified oligogalacturonides and the hepta -glucoside and P. Ricci (INRA, Antibes, France) for providing the purified cryptogein.     

Structure et fonctionnement des écosystèmes du Haut-Rhône français

Many abandoned stream channels are provided alternatively by river water or groundwater from the interstitial flow. The cyclopoid populations from an abandoned channel of the Rhône river are compared with those from a neighbouring interstitial station. Among the 18 species of cyclopoids found during the present study, only 4 are common to both stations. During 3 years of sampling, the populations living in interstitial waters were rather stable, while the epigean populations were more fluctuating. The latter seem to be influenced by the origin of the water.