In Ssarch of new anti-bacterial target genes: a comparative/structural genomics approach

We outline a joint academic/industrial (CNRS/AVENTIS) functional genomics project aiming at the discovery of new anti-bacterial gene targets. Starting from all publicly available bacterial genomes, a subset of the most evolutionary conserved protein-coding genes has been identified. We retained genes with clear homolog in E. coli and at least one gram-positive bacterium among B.subtilis, M. tuberculosis, L. lactis or S. pyogenes. This subset was further reduced to genes encoding non-membrane proteins of unknown or hypothetical functions. The 221 E. coli Open Reading Frames (ORFs) identified through this comprehensive bioinformatic analysis are now submitted to a systematic 3-D structure determination protocol including cloning, protein expression and purification, crystallisation and X-ray diffraction. Our strategy was designed to focus on promising wide-spectrum targets as well as original biochemical pathways. Bioinformatics is used throughout all phases of project, including the initial large-scale comparative genomics analyses, the purification/expression and crystallisation stages for the detection of helpful sequence-specific features (e.g. cofactor binding motifs, non-structured N- or C- term extremities, etc ), and finally for the interpretation of the structures in conjunction with multiple sequence alignments for the identification of key residues, interaction areas on molecular surfaces, and overall function predictions.     

Mono-, di-, and trinuclear luminescent silver(I) and gold(I) N-heterocyclic carbene complexes derived from the picolyl-substituted methylimidazolium salt: 1-methyl-3-(2-pyridinylmethyl)-1H-imidazolium tetrafluoroborate

The N-heterocyclic carbene (NHC) precursor, 1-methyl-3-(2-pyridinylmethyl)-1H-imidazolium tetrafluoroborate, [HCH3im(CH2py)]BF4, reacted with AgBF4 in the presence of aqueous NaOH to produce the silver complex [Ag(CH3im(CH2py))2]BF4 (1) which was then reacted with Au(tht)Cl to form the corresponding gold(I) complex, [Au(CH3im(CH2py))2]BF4 (2). Complex 2 reacted with 1 equiv of AgBF4 to produce the mixed-metal species [AuAg(CH3im(CH2py))2](BF4)2 (3). The reaction of 2 with 1 equiv of Au(tht)Cl followed by metathesis with NaBF4 produces the dimetallic gold complex [Au2(CH3im(CH2py))2](BF4)2 (4). The reaction of [Ag(CH3im(CH2py))2]BF4 (1) with 1 equiv of AgBF4 produces the trinuclear [Ag3(CH3im(CH2py))3(NCCH3)2](BF4)3 (5) complex, which appears to dissociate into a dimetallic complex in solution. Complexes 1-5 were characterized by 1H NMR, 13C NMR, UV-vis, luminescence spectroscopy, elemental analysis, mass spectrometry, and X-ray crystallography. The CH3im(CH2py) ligands in 3 are arranged in a head-to-head fashion spanning a Au-Ag separation of 3.0318(5) A with the carbene portion of the ligand remaining coordinated to the Au(I) center. In 4, the ligands are arranged in a head-to-tail fashion with an Au-Au separation of 3.1730(5) A. In 5, the ligands bridge the nearly symmetrical Ag3 triangular core with short Ag-Ag separations of 2.7765(8), 2.7832(8), and 2.7598(8) A. All of these complexes, including the ligand precursor, are intensely luminescent in solution and the solid state.     

Synthesis of some heterocyclic skeletons via organoiron complexes. Crystal and molecular structure of (5a,6,7,8,9,9a-η6-1,4-benzoxathiino[3,2-b]pyridine)(η5-cyclopentadienyl)iron hexafluorophosphate

Synthesis of the heterocyclic skeletons of some biologically active compounds from (η⁶-o-dichlorobenzene)(η⁵-cyclopentadienyrl)iron hexafluorophosphate in a two step procedure is described. Cyclopentadienyliron hexafluorophosphate complexes of 1,4-benzodioxino[2,3-b]pyridine, 1,4-benzoxathiino[3,2-b]pyridine, 10H-pyrido[3,2-b]benzoxazine, benzo[b]naphtho[2,3-e][1,4]dioxin, 4-methylbenzo[b]benzopyran-2-one[7,6-e][1,4]dioxin and benzo[b]anthracen-9,10-diono[1,2-e][1,4]dioxin were isolated and characterized. Upon pyrolytic sublimation of these complexes the free heterocycles were obtained and characterized. (η⁶-1,4-Benzoxathiino[3,2-b]pyridine)(η⁵-cyclopentadienyl)iron hexafluorophosphate crystalizes in the orthothombic system, space group Pbca; the dihedral angle between the planes of outer rings was found to be 176.8 (1).     

Synthesis and characterization of mannosyl mimetic derivatives based on a beta-cyclodextrin core

The synthesis of branched beta-cyclodextrins substituted with mannosyl mimetic derivatives at one primary hydroxy group is described. It was shown that the self-inclusion phenomenon observed for the target compounds in water did not preclude the inclusion properties of the cyclodextrin moiety.     

Time-resolved ultraviolet laser-induced breakdown spectroscopy for organic material analysis

Ultraviolet pulses (266 nm) delivered by a quadrupled Nd:YAG laser were used to analyze organic samples with laser-induced breakdown spectroscopy (LIBS). We present characteristics of the spectra obtained from organic samples with special attentions on the emissions of organic elements, O and N, and molecular bonds CN. The choice of these atomic or molecular species is justified on one hand, by the importance of these species to specify organic or biological materials; and on the other hand by the possible interferences with ambient air when laser ablation takes place in the atmosphere. Time-resolved LIBS was used to determine the time-evolution of line intensity emitted from these species. We demonstrate different kinetic behaviors corresponding to different origins of emitters: native atomic or molecular species directly vaporized from the sample or those generated through dissociation or recombination due to interaction between laser-induced plasma and air molecules. Our results show the ability of time-resolved UV-LIBS for detection and identification of native atomic or molecular species from an organic sample.     

Stability in Colloidal Mixtures Containing Particles with a Large Disparity in Size

An experimental approach, based on turbidity measurements, is proposed for studies of the stability in colloidal mixtures containing particles with large disparity in size. The main advantage of this approach is that it permits investigations even under conditions of comparable particle number concentrations of the two colloidal populations. Binary mixtures containing a poly(vinyl acetate) (PVAc) latex and a Ludox AS-40 silica sol were investigated. The silica particles were much smaller than the latex ones. The experimental stability factors were compared with the theoretical values computed on the basis of the Kihira-Ryde-Matijevic model (J. Chem. Soc., Faraday Trans. 88(16), 2379 (1992)) for interaction between spherical particles with unevenly distributed surface charges. All the experimental results support the idea that, even when both sols are negatively charged, the small silica particles are adsorbed onto the latex surface. Under these conditions, the heteroaggregates, which are composed of PVAc cores surrounded with silica particles, can be modeled as PVAc particles having "modified" surface characteristics (i.e., average Stern potential and varying extents of the surface charge segregation). Copyright 2001 Academic Press.     

Structural aspects of the metal-insulator transitions in V0.985Al0.015O2

The crystal structure of V_0.985Al_0.015O₂ has been refined from single-crystal X-ray data at four temperatures. At 373°K it has the tetragonal rutile structure. At 323°K, which is below the first metal-insulator transition, it has the monoclinic M₂ structure, where half of the vanadium atoms are paired with alternating short (2.540 Å) and long (3.261 Å) V-V separations. The other half of the vanadium atoms form equally spaced (2.935 Å) zigzag V chains. At 298°K, which is below the second electric and magnetic transition, V_0.985Al_0.015O₂ has the triclinic T structure where both vanadium chains contain V-V bonds, V(1)-V(1) = 2.547 Å and V(2)-V(2) = 2.819 Å. At 173°K the pairing of the V(1) chain remains constant: V(1)-V(1) = 2.545 Å, whereas that of the V(2) chain decreases: V(2)-V(2) = 2.747 Å. From the variation of the lattice parameters as a function of temperature it seems that these two short V-V distances will not become equal at lower temperatures. The effective charges as calculated from the bond strengths at 298 and 173°K show that a cation disproportionation has taken place between these two temperatures. About 20% of the V⁴⁺ cations of the V(1) chains have become V³⁺ and correspondingly 20% of the V⁴⁺ cations of the V(2) chains have become V⁵⁺. This disproportionation process would explain the difference between the two short V-V distances. Also it would explain why the T → M₁ transition does not take at lower temperatures.     

Comprehensive two-dimensional liquid chromatography for the characterization of functional acrylate polymers

Comprehensive two-dimensional liquid chromatography-size-exclusion chromatography (LC x SEC) was investigated as a tool for the characterization of functional poly(methyl methacrylate) (PMMA) polymers. Ultraviolet-absorbance and evaporative light-scattering detection (ELSD) were used. A simple method to quantify ELSD data is presented. Each data point from the ELSD chromatogram can be converted into a mass concentration using experimental calibration curves. The qualitative and quantitative information obtained on two representative samples is used to demonstrate the applicability of LC x SEC for determining the mutually dependent molar-mass distributions (MMD) and functionality-type distributions (FTD) of functional polymers. The influence of the molar mass on the retention behavior in LC was investigated using LC x SEC for hydroxyl-functional PMMA polymers. The critical conditions, at which retention is--by definition--independent of molar mass, were not exactly the same for PMMA series with different end-groups. Our observations are in close agreement with theoretical curves reported in the literature. However, for practical applications of LC x SEC it is not strictly necessary to work at the exact critical solvent composition. Near-critical conditions are often sufficient to determine the mutually dependent distributions (MMD and FTD) of functional polymers.     

Interaction of nonionic surfactants with copolymer microgel particles of NIPAM and acrylic acid

Binding of the nonionic surfactants Triton X-100 and Triton X-405 onto linear copolymers of N-isopropylacrylamide (NIPAM) and acrylic acid and to cross-linked microgel particles of similar composition but differing in their cross-link densities has been studied. The binding capacities vary for each of these polymeric systems, being smallest for the linear copolymer. The binding is also significantly less in all cases for the more hydrophilic surfactant, namely, Triton X-405. By comparing estimates of the pore or "cage" size within the microgel particles with the dimensions of the free micelles in solution, it is concluded that micelles of Triton X-100 form within the microgel particles more readily for the lower cross-linked microgel particles. However, micelles do not form as easily inside either microgel for Triton X-405. The swelling/deswelling behavior of each of the two microgels, in the presence of the surfactants, has been explained in terms of their relative binding behavior and how this contributes to the osmotic pressure difference inside and outside the microgel particles and also in terms of micelle "bridging" of the polymer network, causing shrinkage.