Molecular Diagnosis of Drug-Resistant Tuberculosis; A Literature Review

Drug-resistant tuberculosis is a global health problem that hinders the progress of tuberculosis eradication programs. Accurate and early detection of drug-resistant tuberculosis is essential for effective patient care, for preventing tuberculosis spread, and for limiting the development of drug-resistant strains. Culture-based drug susceptibility tests are the gold standard method for the detection of drug-resistant tuberculosis, but they are time-consuming and technically challenging, especially in low- and middle-income countries. Nowadays, different nucleic acid-based assays that detect gene mutations associated with resistance to drugs used to treat tuberculosis are available. These tests vary in type and number of targets and in sensitivity and specificity. In this review, we will describe the available molecular tests for drug-resistant tuberculosis detection and discuss their advantages and limitations

Développement d'un outil d'analyse d'interactions moléculaires basé sur la résonance plasmonique de surface (SPRi)

Ces dernières décennies, on a assisté à l augmentation du nombre de technologies et de concepts permettant l analyse des interactions intermoléculaires. Dans ce contexte, les puces à fluorescence restent les plus fréquemment utilisées. Cependant, cette technologie bien que très sensible et multiplexée, ne permet pas d avoir accès aux paramètres cinétiques, indispensables au calcul des constantes d affinité et la recherche de systèmes alternatifs s impose. Dans cette optique, la résonance plasmonique de surface par imagerie (SPRi) est considérée comme une véritable option. Cette technologie se caractérise par l absence de marquage et permet de suivre en temps réel d infimes variations de masses consécutives à des interactions intermoléculaires sur la surface du prisme. L obtention de constantes d affinité est ainsi possible. En revanche, la SPRi présente un certain nombre de limites, principalement au niveau de la sensibilité et du multiplexage. Les objectifs de la thèse ont ainsi consisté à combler en partie ces différentes limites. La chimie de greffage basée sur l utilisation d oligonucléotides modifiés par un thiol a permis d améliorer le multiplexage et de déposer plus de 1000 spots par cm sur la surface d or du prisme. Dans le même temps, la modification de la surface avec des colloïdes d or et des dendrimères a permis pour des interactions ADN/ADN, d atteindre une limite de détection de 2 nM (d où un gain de 200%). En parallèle de ces travaux, diverses applications biologiques ont été effectuées. Une première étude a consisté à rechercher des ligands spécifiques des structures G-quadruplex des télomères. Une seconde étude s est portée sur le complexe de partition bactérien. Par des études de criblage les bases impliquées dans l interaction avec une protéine indispensable à la partition du plasmide F chez E.coli ont été identifiées. L ensemble de ces travaux ont montré le fort potentiel de la SPRi et les applications potentielles qui en découlent sont nombreuses.During the last decades a large number of technologies have been developed to analyze intermolecular interactions. In this context, the fluorescence biochips remain the most frequently used. Although this technology is very sensitive and multiplexed, it does not allow access to the kinetic parameters, essential to the calculation of the constants of affinity. Therefore, the research for alternative systems is essential. In this way, the Surface Plasmon Resonance imaging (SPRi) is considered as an opportunity. It is an optical detection process that can occur when a polarized light hits a prism covered by a thin metal layer. Under certain conditions free electrons at the surface of the biochip absorb incident light photons and convert them into surface plasmon waves. Perturbations at the surface of the biochip, such as an interaction between probes immobilized on the chip and targets, induce a modification of resonance conditions which can be measured. It is a label free technology which allows intermolecular interactions in real time and gives access to the kinetics parameters. However, SPRi is limited in sensitivity and multiplexing. The objectives of my PhD were to circumvent these various limits. Thus, we validated the immobilization of DNA probes on gold surface using thiol-modified oligonucleotide probes. Deposition carried out on non-modified gold surface, does not require electrical stimulation and expensive specific robotic devices. The thiol modification of the probes was shown to be very stable at room temperature, contrary to pyrrole and diazonium probes that need to be prepared just prior to their spotting. We demonstrate that thiol-modified oligonucleotide probes spotted on a gold surface of the SPRi-prisms are very robust and reproducible. We also demonstrated that this simple chemistry is compatible with high density arrays fabrication bearing more than 1000 spots using a classical spotter. Furthermore, the modification of the prism surface with gold colloids and dendrimers allowed for DNA/DNA interactions, to reach a detection limit of 2 nM. In parallel of this work, various biological applications were carried out and validate our previous developments. A first study was to screen G-quadruplex specific ligands to inhibit telomerase activity. We demonstrated that SPRi technology is particularly well adapted to the screening of interaction of small molecules with DNA probes and is sensitive enough to permit distinction between interactions with different DNA structures. The second study was on the bacterial partition complex. We study the DNA binding requirement involved in SopB-sopC specific interactions and analysed at the nucleotide level the bases involved in the binding efficiency and essential for the partition All this PhD work improved the SPRi technology and demonstrated its great potential in biological applications.TOULOUSE-INSA-Bib. electronique (315559905) / SudocSudocFranceF

Pharmacovigilance des essais cliniques en France suite à l'harmonisation européenne

CAEN-BU Médecine pharmacie (141182102) / SudocLYON1-BU Santé (693882101) / SudocSudocFranceF

High-Resolution Chromatin Immunoprecipitation: ChIP-Sequencing.

International audienceChromatin immunoprecipitation (ChIP) coupled with next-generation sequencing (NGS) is widely used for studying the nucleoprotein components that are involved in the various cellular processes required for shaping the bacterial nucleoid. This methodology, termed ChIP-sequencing (ChIP-seq), enables the identification of the DNA targets of DNA binding proteins across genome-wide maps. Here, we describe the steps necessary to obtain short, specific, high-quality immunoprecipitated DNA prior to DNA library construction for NGS and high-resolution ChIP-seq data

Characterization and functional properties of the α-amylase inhibitor (α-AI) from kidney bean (Phaseolus vulgaris) seeds

International audienceAlpha-amylase inhibitor (alpha-AI) from kidney bean (Phaseolus vulgaris L. cv Tendergreen) seeds has been purified to homogeneity by heat treatment in acidic medium, ammonium sulphate fractionation, chromatofocusing and gel filtration. Two isoforms, alpha-AI1 and alpha-AI1', of 43 kDa have been isolated which differ from each other by their isoelectric points and neutral sugar contents. The major isoform alpha-AI1 inhibited human and porcine pancreatic alpha-amylases (PPA) but was devoid of activity on alpha-amylases of bacterial or fungal origins. As shown on the Lineweaver-Burk plots, the nature of the inhibition is explained by a mixed non-competitive inhibition mechanism. Alpha-AI1 formed a 1:2 stoichiometric complex with PPA which showed an optimum pH of 4.5 at 30 degrees C. Owing to the low optimum pH found for alpha-AI activity, inhibitor-containing diets such as beans or transgenic plants expressing alpha-AI should be devoid of any harmful effect on human health

Investigating the caffeine effects in the yeast Saccharomyces cerevisiae brings new insights into the connection between TOR, PKC and Ras/cAMP signalling pathways

International audienc

Plasma membrane coating with cationic silica particles and osmotic shock alters the morphology of bovine aortic endothelial cells

International audienceWe have used a published method of membrane preparation based on the precoating of the apical membrane of aortic endothelial cells with cationic silica microbeads (with or without polyacrylic acid) in combination with an osmotic shock and mechanical shearing to isolate the apical from the basal plasma membranes of these cells, in vitro. After labeling of the plasma membrane of adherent endothelial cells with a fluorescent derivative of phosphatidylcholine and by using laser confocal fluorescence scanning microscopy, we found that this method of membrane isolation rapidly induced invaginations of the basal plasma membrane to an extent which makes this method unsuitable for further membrane lipid analysis. Morphological analysis of the cells and fluorescence recovery after photobleaching experiments on the plasma membranes were performed at each step of the purification procedure and showed that only hypotonic shock and mechanical shearing of the cells enabled the basal plasma membranes to be purified without significant morphological changes.

Cantilever-based microsystem for contact and non-contact deposition of picoliter biological samples

International audienceThis paper describes a cantilever-based microsystem that permits the deposition of picoliter biological samples using a contact or non-contact method. Arrays of silicon-based cantilevers have been used to produce DNA microarrays. An electrowetting-on-dielectric (EWOD) principle is applied for the loading of the liquid by controlling surface tension. Deposition is achieved by direct contact between cantilevers and the surface by capillary transport. A non-contact deposition method has also been developed. It consists in an electric-field applied between the cantilevers and a conductive surface. The results obtained demonstrate that our system meets the need for producing high-density DNA, protein and cell chips

An Approach to the Study of Gene Expression in Hepatocarcinogenesis Initiation

International audienceIn carcinogenesis, determination of gene and protein expression profiles is important for prevention and treatment. Caffeic acid phenethyl ester (CAPE) in a single dose administered before carcinogenic initiation induced by diethyl-nitrosamine (DEN) prevents the appearance of preneoplastic lesions. On the basis of this approach, the main purpose of this work was to compare the gene expression profiles induced by DEN or a previously administered single dose of CAPE. Using a modified hepatocarcinogenesis-resistant hepatocyte model, male Fischer-344 rats were administered with one intraperitoneal dose of CAPE (20 mg/kg) 12 hours before DEN administration (200 mg/kg). Livers were removed and processed for microarray analysis and reverse transcription-polymerase chain reaction 12 hours after CAPE dosing and 24 hours after DEN administration with or without CAPE. CAPE alone did not alter the expression profile. DEN treatment modified the expression of 665 genes, and CAPE plus DEN induced changes in 1371 genes. DEN treatment increased the expression of genes associated with oxidative stress such as glutathione reductase, genes involved in cell cycle regulation including p53, and modified cytochrome P450. CAPE plus DEN diminished the expression of cytochrome involved in DEN bioactivation such as CYP2B1 as well as the expression of regulators of oxidative stress such as glutathione reductase, GST-κ and GST-θ, and cell cycle regulators such as p53. Using CAPE as a tool, we uncovered new approaches for studying the altered expression of reactive genes and identifying proteins that will help to propose well-sustained and concrete hypothesis of DEN mechanism of hepato-carcinogenesis initiation

Molecular diagnosis of drug-resistant Ttuberculosis : a literature review

International audienceDrug-resistant tuberculosis is a global health problem that hinders the progress of tuberculosis eradication programs. Accurate and early detection of drug-resistant tuberculosis is essential for effective patient care, for preventing tuberculosis spread, and for limiting the development of drug-resistant strains. Culture-based drug susceptibility tests are the gold standard method for the detection of drug-resistant tuberculosis, but they are time-consuming and technically challenging, especially in low- and middle-income countries. Nowadays, different nucleic acid-based assays that detect gene mutations associated with resistance to drugs used to treat tuberculosis are available. These tests vary in type and number of targets and in sensitivity and specificity. In this review, we will describe the available molecular tests for drug-resistant tuberculosis detection and discuss their advantages and limitations