AntiMalarial Mode of Action (AMMA) Database: Data Selection, Verification and Chemical Space Analysis.

This paper presents the effort of collecting and curating a data set of 15461 molecules tested against the malaria parasite, with robust activity and mode of action annotations. The set is compiled from in-house experimental data and the public ChEMBL database subsets. We illustrate the usefulness of the dataset by building QSAR models for antimalarial activity and QSPR models for modes of actions, as well as by the analysis of the chemical space with the Generative Topographic Mapping method.

A fluorine scan of a tubulin polymerization inhibitor isocombretastatin A-4: Design, synthesis, molecular modelling, and biological evaluation.

A novel series of tubulin polymerization inhibitors, based on fluorinated derivatives of isocombretastatin A-4 was synthesized with the goal of evaluating the effect of these compounds on the proliferative activity. The introduction of fluorine atom was performed on the phenyl ring or at the linker between the two aromatic rings. The modification of isoCA-4 by introduction of difluoromethoxy group at the para-position (3i) and substitution of the two protons of the linker by two fluorine atoms (3m), produced the most active compounds in the series, with IC values of 0.

Influence of the anatase/rutile ratio on the charge transport properties of TiO-NTs arrays studied by dual wavelength opto-electrochemical impedance spectroscopy.

The modification of photo-generated charge transport properties in aligned titanium dioxide nanotubes (TiO-NTs) regarding the anatase/rutile ratio was studied by photo-electrochemical methods. TiO-NTs obtained by anodization were thermally treated under air flux at different temperatures to significantly modify the proportion of TiO anatase and rutile phases in the tubular structure. Material characterisation methods (XRD, SEM, UV-visible spectroscopy) were used to determine the characteristics of the different TiO-NT electrodes in terms of dimensions, proportion of each phase and optical properties.

Nonuniform Sampling Acquisition of Two-Dimensional Fourier Transform Ion Cyclotron Resonance Mass Spectrometry for Increased Mass Resolution of Tandem Mass Spectrometry Precursor Ions.

Obtaining the full MS/MS map for fragments and precursors of complex mixtures without hyphenation with chromatographic separation by a data-independent acquisition is a challenge in mass spectrometry which is solved by two-dimensional (2D) Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS). Until now 2D FTICR MS afforded only a moderate resolution for precursor ion since this resolution is limited by the number of evolution interval steps to which the number of scans, the acquisition time, and the sample consumption are proportional. An overnight acquisition is already required to reach a quadrupole mass filter-like unit mass resolution.

fMRI capture of auditory hallucinations: Validation of the two-steps method.

Our purpose was to validate a reliable method to capture brain activity concomitant with hallucinatory events, which constitute frequent and disabling experiences in schizophrenia. Capturing hallucinations using functional magnetic resonance imaging (fMRI) remains very challenging. We previously developed a method based on a two-steps strategy including (1) multivariate data-driven analysis of per-hallucinatory fMRI recording and (2) selection of the components of interest based on a post-fMRI interview.

Generative Topographic Mapping of Conformational Space.

Herein, Generative Topographic Mapping (GTM) was challenged to produce planar projections of the high-dimensional conformational space of complex molecules (the 1LE1 peptide). GTM is a probability-based mapping strategy, and its capacity to support property prediction models serves to objectively assess map quality (in terms of regression statistics). The properties to predict were total, non-bonded and contact energies, surface area and fingerprint darkness.

Mappability of drug-like space: towards a polypharmacologically competent map of drug-relevant compounds.

Intuitive, visual rendering--mapping--of high-dimensional chemical spaces (CS), is an important topic in chemoinformatics. Such maps were so far dedicated to specific compound collections--either limited series of known activities, or large, even exhaustive enumerations of molecules, but without associated property data. Typically, they were challenged to answer some classification problem with respect to those same molecules, admired for their aesthetical virtues and then forgotten--because they were set-specific constructs.

Water-induced local ordering of chitosan polymer chains in thin layer films.

Carbon-13 NMR (CP-MAS and FSLG (1)H-(13)C HETCOR) have been applied to chitosan salt films synthesized in acetic acid and exposed to different relative humidity environments (32% or 75%) at 20°C for 1 month. It gives insight in the relationship between structure and functional properties according to the hydration level of this biomaterial as a film. The acetate ions trapped in the chitosan act as structuring agents between chitosan chains for the low hydration state.

The dog mummy, the ticks and the louse fly: Archaeological report of severe ectoparasitosis in Ancient Egypt.

The authors report the first archaeological case of dog ectoparasitosis in Ancient Egypt. The study of a mummified young dog dated to the Roman period suggests a significant infestation by two blood sucking ectoparasites, respectively the brown dog tick Rhipicephalus sanguineus Latreille, 1806 (Acari: Ixodidae), the louse fly Hippobosca longipennis Fabricius, 1805 (Diptera: Hippoboscidae) as well as puparia of sarcosaprophagous flies (Diptera: Sarcophagidae and Calliphoridae), a potential source of myiasis. All of these species are known to be potential vectors of different pathogens which may be responsible for the premature death of the dog.

A dual flowing continuum approach to model denitrification experiments in porous media colonized by biofilms.

We present a modeling exercise of solute transport and biodegradation in a coarse porous medium widely colonized by a biofilm phase. Tracer tests in large laboratory columns using both conservative (fluorescein) and biodegradable (nitrate) solutes are simulated by means of a dual flowing continuum approach. The latter clearly distinguishes concentrations in a flowing porous phase from concentrations conveyed in the biofilm.

Specificity of Ocimum basilicum geraniol synthase modified by its expression in different heterologous systems.

Numerous aromatic plant species produce high levels of monoterpenols, using geranyl diphosphate (GPP) as a precursor. Sweet basil (Ocimum basilicum) geraniol synthase (GES) was used to evaluate the monoterpenol profiles arising from heterologous expressions in various plant models. Grapevine (Vitis vinifera) calli were transformed using Agrobacterium tumefasciens and the plants were regenerated.

Identification of a lysine residue important for the catalytic activity of yeast farnesyl diphosphate synthase.

The Saccharomyces cerevisiae ERG20 gene (encoding farnesyl diphosphate synthase) has been subjected to a set of mutations at the catalytic site, at position K254 to determine the in vivo impact. The mutated strains have been shown to exhibit various growth rates, sterol profiles and monoterpenol producing capacities. The results obtained suggest that K at position 254 helps to stabilize one of the three Mg(2+) forming a bridge between the enzyme and DMAPP, and demonstrate that destabilizing two of the three Mg(2+) ions, by introducing a double mutation at positions K197 and K254, results in a loss of FPPS activity and a lethal phenotype.

Impact of Quillaja saponaria saponins on grapevine ecosystem organisms.

The control of grapevine pathogens is a rising concern in Vitis vinifera culture. The current international trend is toward banning chemicals that are highly toxic to the environment and human workers, and adopting tighter regulations. We evaluated the impact of saponins on three kinds of organisms found in grapevine culture.

Metabolic engineering of monoterpene synthesis in yeast.

Terpenoids are one of the largest and most diverse families of natural compounds. They are heavily used in industry, and the trend is toward engineering modified microorganisms that produce high levels of specific terpenoids. Most studies have focused on creating specific heterologous pathways for sesquiterpenes in Escherichia coli or yeast.

Primary tumour genetic alterations and intra-tumoral heterogeneity are maintained in xenografts of human colon cancers showing chromosome instability.

Evaluation of the role of clonal heterogeneity in colon tumour sensitivity/resistance to drugs and/or in conferring metastatic potential requires an adequate experimental model in which the tumour cells maintain the initial genetic alterations and intra-tumoral heterogeneity through maintenance of the genetic clones present in the initial tumour. Therefore, we xenografted subcutaneously into nude mice seven human colonic tumours (from stages B1 to D) that showed chromosome instability and transplanted them sequentially for up to 14 passages. Maintenance after xenografting of the genetic alterations present in the initial tumours was scored by allelotype studies targeting 45 loci localized on 18 chromosomes.