On the affinity regulation of the metal-ion-dependent adhesion sites in integrins

Density functional theory and a polarizable continuum model are used to (i) understand the affinity modulating mechanisms of the interaction between the metal-ion-dependent adhesion site (MIDAS) of a selected integrin, lymphocyte function-associated antigen-1 (LFA-1) and a ligand mimetic acetate molecule and to (ii) propose a new, promising family of inhibitors to block the interaction of the integrin with intercellular adhesion molecule-1 (ICAM-1). We quantify the effect of isolated factors, such as the metal coordination, the nature of the ligand or the cation present on the MIDAS, and the effect of the permittivity of the media. We show that the affinity for ligand decreases when metal coordination changes from the open conformation to the closed conformation. In addition, Mn2+ and Zn2+ showed to be good competitors for the octahedrically coordinated Mg2+ and yielded excellent affinity values, whereas Ca2+ in an octahedric environment would decrease the affinity for the ligand. Our affinity studies of the open MIDAS showed that nitronate-derived or carboxylic acid-containing ligands may represent new promising scaffolds of future inhibitors. Finally, we show that affinities are always highly favored by low-dielectric environments, which explains the propensity of MIDAS motifs to be surrounded by hydrophobic residues in integrins and highlights the importance of including hydrophobic groups in the inhibitors.     

Theoretical study of Cu(I)Y zeolite: structure and electronic properties

The structural and electronic properties of the accessible Cu(I) site of a faujasite-type zeolite have been studied, by use of large cluster models and a density functional theory-based methodology. We demonstrate that the local ideal C(3) symmetry of the Cu(I) site II is broken. The Cu(I) cation is bonded to the zeolite framework by one bond of about 2.26 A and two shorter ones of 2.07 A. We demonstrate that only one cation position exists at this site. This result is also confirmed by a molecular electrostatic potential analysis. We show that local properties at site II, as well as the global properties of the solid (frontier orbitals), do not depend on the Al and cation distribution and only slightly on the cocation nature. Taking into account the present results and well-known experimental data, we propose that specific catalytic behaviors are correlated with local response properties, such as the local acid strength or, in other reactions, specific local architecture or confinement.     

Whole-cell spectroscopy is a convenient tool to assist molecular identification of cultivatable marine bacteria and to investigate their adaptive metabolism

Recent developments in whole-cell spectroscopic methods allow rapid characterization of microorganisms of interest to human health, but have yet to be widely applied to marine microbiological studies. In this study of bacteria associated with the kelp Laminaria digitata, we have isolated 18 epiphytic bacterial strains from several thalli, sequenced their 16S rDNA, built corresponding phylogenetic trees, and characterized them using spectroscopic methods. Molecular taxonomy revealed Gram⁺Actinobacteria and Gram⁻Alphaproteobacteria, Gammaproteobacteria and Bacteroidetes. Twelve marine reference strains (Gram⁺Firmicutes, and Gram⁻Alphaproteobacteria, Gammaproteobacteria and Bacteroidetes) were treated accordingly. Whole-cell MALDI-TOF MS spectral profiles of 29 of the 30 strains were built into a database against which 16 replicate spectra of each strain were compared and categorized into groups. The proton HR-MAS NMR stack plots allowed visual delineation into taxonomic groups according to their most common peaks, in agreement with identifiable compounds from corresponding D₂O solution spectra. With both methods, these groups corresponded to taxa identified by 16S rDNA sequences, MALDI-TOF MS being more discriminative than HR-MAS NMR. Culture age did not influence the spectral signatures in both approaches. Most cells grown under minimal conditions (VNSS medium) afforded HR-MAS NMR profiles markedly different to those grown in enriched conditions (ZoBell medium), indicating different adaptive metabolic responses between the two media. Spectral signatures obtained under strictly controlled conditions can be used as rapid and reliable tools for taxonomic purposes and as markers of physiological status.     

Complex Networks: from Graph Theory to Biology

The aim of this text is to show the central role played by networks in complex system science. A remarkable feature of network studies is to lie at the crossroads of different disciplines, from mathematics (graph theory, combinatorics, probability theory) to physics (statistical physics of networks) to computer science (network generating algorithms, combinatorial optimization) to biological issues (regulatory networks). New paradigms recently appeared, like that of ‘scale-free networks’ providing an alternative to the random graph model introduced long ago by Erdös and Renyi. With the notion of statistical ensemble and methods originally introduced for percolation networks, statistical physics is of high relevance to get a deep account of topological and statistical properties of a network. Then their consequences on the dynamics taking place in the network should be investigated. Impact of network theory is huge in all natural sciences, especially in biology with gene networks, metabolic networks, neural networks or food webs. I illustrate this brief overview with a recent work on the influence of network topology on the dynamics of coupled excitable units, and the insights it provides about network emerging features, robustness of network behaviors, and the notion of static or dynamic motif.     

Epoxide configuration in 3β-acetoxy-7α-hydroxy-14,15-epoxy-apotirucallane prepared from tirucalla-7,24-dien-3-one : X-ray analysis

Epoxidation of 3β - Acetoxy - 7α - hydroxy - Δ¹⁴ - apotirucallane, prepared from Δ7-tirucallone, afforded the corresponding 14α,15α epoxide. The α-configuration of the epoxide function has been established by single-crystal X-ray analysis, representing the first such study of a tirucallol derivative with an intact side-chain. Epoxidation of Apotirucalla - 3,7 - dione gave the corresponding 14α,15α - epoxide as well. Eight new tirucallol derivatives were described.     

Determination of acephate and its degradation product methamidophos in soil and water by solid-phase extraction (SPE) and GC-MS

Acephate and its metabolite, methamidophos, are both highly polar organophosphorus pesticides (OPs) and are therefore highly soluble in water, which leads to difficulties when traditional methods of extraction, such as LLE (liquid–liquid extraction), are used. Solid-phase extraction (SPE) is a relatively new, highly versatile method, which has proven successful in many cases that were considered problematic in the past. In this study, several adsorbents (polymeric and silica based) and parameters are considered and modified to obtain maximum recovery. Maximum recoveries for acephate and methamidophos were found to be 90–95% and 85–90% respectively with Oasis HLB cartridges and methylene chloride as the elution solvent. In order to establish applicability and reliability, the matrix effect of several real water and solid (compost and soil) samples was evaluated. A 20–30% diminution of recovery is noted for some samples with a complex matrix containing a high amount of dissolved organic matter.     

Trace determination of tamoxifen and 5-fluorouracil in hospital and urban wastewaters

Tamoxifen and 5-fluorouracil are widely used in cancer therapy. They are highly toxic (teratogenic, mutagenic, etc.), as are most of the anticancer drugs. Two methods were set up to analyse these drugs in wastewaters to evaluate the potential for environmental contamination by cytostatic agents. Liquid–liquid extraction followed by purification on OASIS® MCX cartridge and gas chromatography with mass spectrometry detection (GC-MS) was used for the analysis of tamoxifen. 5-Fluorouracil was extracted with an ENV+?(Isolute) cartridge (solid-phase extraction), derivatized with pentafluorobenzyl bromide (PFBBr) and detected by GC-MS. Both methods showed good recoveries (>70%), repeatability (RSD<10%) and limits of detection (LOD 6–15?ng/L). Wastewaters from a residential area, a hospital, and sewage-treatment plants (STPs) were analysed using the analytical methods developed in this study. Tamoxifen was detected in wastewaters of the hospital, residential area, and influent of STPs, but not in treated wastewaters. 5-Fluorouracil in all wastewaters was below the LOD of the analytical method.     

An efficient spectra processing method for metabolite identification from 1H-NMR metabolomics data

The spectra processing step is crucial in metabolomics approaches, especially for proton NMR metabolomics profiling. During this step, noise reduction, baseline correction, peak alignment and reduction of the 1D ¹H-NMR spectral data are required in order to allow biological information to be highlighted through further statistical analyses. Above all, data reduction (binning or bucketing) strongly impacts subsequent statistical data analysis and potential biomarker discovery. Here, we propose an efficient spectra processing method which also provides helpful support for compound identification using a new data reduction algorithm that produces relevant variables, called buckets. These buckets are the result of the extraction of all relevant peaks contained in the complex mixture spectra, rid of any non-significant signal. Taking advantage of the concentration variability of each compound in a series of samples and based on significant correlations that link these buckets together into clusters, the method further proposes automatic assignment of metabolites by matching these clusters with the spectra of reference compounds from the Human Metabolome Database or a home-made database. This new method is applied to a set of simulated ¹H-NMR spectra to determine the effect of some processing parameters and, as a proof of concept, to a tomato ¹H-NMR dataset to test its ability to recover the fruit extract compositions. The implementation code for both clustering and matching steps is available upon request to the corresponding author.

Influence of steric interactions and random side chain variations on the mesomorphic properties of bowlic mesogens

The effect of structural variations on the mesomorphic nature of columnar liquid crystals of general structure I is studied. X-ray crystal structure analyses of compounds la and 2a reveal the columnar organization of the macrocyclic cores in the solid state. The up and down asymmetry of the cores is resolved in an alternating sequence of up-up and down-down intermolecular contacts. Specific interactions between the R substituents are present, which influence the stacking distance between the cores in the down-down intermolecular contacts. Statistical incorporation of different side chains on the same macrocyclic core produces, when the difference in length between the alkyl chains is appropriate, random mixtures having wide mesomorphic ranges. The increase of disorder associated with the statistical side chain distribution on the core and with the structural heterogeneity of each component of the mixture have the effect of depressing mainly the crystal-mesophase transition temperature.