Biochip and Bionanotechnogy

Véronique LE BERRE, head of the team Biochip and Bionanotechnology

veronique.leberre@insa-toulouse.fr - +335 61 55 94 71

 

A new team dedicated to the Biochip and Bionanotechnogy

 

Founded in 2010, the team Biochip - bionanotechnology was built based on the expertise developed by the Biochips platform with the ambition to lead a cutting-edge research to develop new generations of biochips. This group is specialized in the production, analysis and development of DNA or proteins microarrays, next generation sequencing for different applications (de novo sequencing, RNAseq, small RNA-seq, ampli-seq…) and analysis of interactions between biomolecules in real time. Current researches are carried out within a multidisciplinary team (biologists, chemists, physicists, computer scientist, bioinformatics and statistician). This activity has led to 5 patents and 21 publications from 2010, and the materialization of a spin-off: DendriS. The group is also involved in the PEPI IBIS (Ingénierie BioInformatique et Statistiques pour les données haut débit) and in the CATI BIOS4BIOL.

 

 

Nanobiotechnology, Surface functionalization and Surface Plasmon resonance: developments for the next Biochip generation


The EAD2 develops R&D activities around two principal axes:

1- Development of new microarrays diagnostic tools and

2- Biomolecule interaction analyses


First axe: Development of new microarrays diagnostic tools

  • INNODIAG: Labeled by the Pôle Cancer-Bio-Santé and funded by the ANR,  INNODIAG try to developed an vitro molecular diagnostics for the prognosis of breast cancer using the latest developments in Nanotechnology. This project involves several research laboratories, Institut Claudius Regaud and two SMEs Dendris and Innopsys and will follow the recurrence of breast cancer using conventional chip or diffraction. A patent has been deposit for a "macrotimbre", a new spotting technique and a scanner recording the diffraction is being developed by the company Innopsys. This project will be in a strategic context for the integration of converging technologies BIO-NANO-INFO in the field of Life Sciences in making the best use of potential public and private research for economic development regionally and nationally.. This project is now supported by the Région Midi Pyrénées (OncoSan’Tech 2013) with the Oncograde project.
  • PHYTOCHIP: a new tool to study the toxic phytoplankton diversity in the bay of Seine. The aims of this project in partnership with IFREMER is to develop a new molecular tool as alternative means to provide fast, safe and complete identification of HAB species. Monitoring of phytoplankton is actually based on the microscopic identification and counting of the cells of interests. It is time consuming, tedious and no challenging. Trained people in algal taxonomy are required to carry out these analyses. Accurate and rapid methods for phytoplankton identification, such as DNA microarray, are highly needed for environmental monitoring. A Phytochip dedicated to toxic species determination is developed for sanitary purposes and to study the communities of the French coast in English Channel. The novel Phytochip allows us 1) to discriminate various toxic species within the Pseudo-nitzschia, Alexandrium, Dinophysis and Karenia genera and 2) to estimate dynamic and distribution of these species in the Bay of Seine.
  • CAZyChip Carbohydrate Active enZymes bioChip for high throughput exploration of microbial lignocellulolytic competence. In this project we propose to develop a robust and generic tool, the CAZyChip, to analyze expression of a large variety of GH and quickly explore the enzymatic arsenal of microorganisms (biodiversity) to isolate new efficient enzymatic cocktails.
  • SECURIDIAL: Detection of food-borne pathogens using DNA technology.
  • ALLERGOCHIP and DIAGALA: Food allergy diagnosis with microarrays. in collaboration with Pharma-DEV team (Annick Barre, Pierre Rougé). Funded by PRES University of Toulouse. The aim of Allergochip is to produce a protein based biochip for the detection of allergies.

 

Second axe Biomolecule interaction analyses

  • BactMit: Molecular interactions involved in bacterial mitosis. The segregation of plasmid F of Escherichia coli is highly reliable. The molecular mechanism that drives active chromosome segregation is still not yet understood at the molecular level. In order to define precisely the interactions involved in the assembly of partition complexes on chromosomes we use Surface Plasmon Resonance Imaging (SPRi-Plex) technique, which allows analysis in parallel of more than hundred interactions in real time. This full range analysis at a level never undertaken for DNA-protein interactions on centromeric DNA sequences in bacteria is the “raison d’être” of our partnership with the LMGM laboratory: “Motor of genome segregation: mechanism and diversity” team. The Sop partition locus, responsible for this stable maintenance, is composed of two genes, sopA and sopB and a centromere, sopC. We have investigated the requirements for specific SopB–sopC interactions using a surface plasmon resonance imaging technique. Surface Plasmon Resonance imaging (SPRi) is a label free technique typically used to follow biomolecular interactions in real time. The selectivity of the detection of protein-DNA interactions we tested several functionalization of the gold surface. We demonstrated that using this dendrimer G4-functionalized surface, the specificity of the SPRi response was significantly improved allowing discrimination between protein-DNA interactions of different strength.
  • We obtained a PhD grant for the next 3 years from the APR ComUE Université de Toulouse 2014 to follow the ANR BactMiT (2010-2014) on the molecular characterization of the nucleoid segregation by NGS approaches.
  • Conventional techniques of DNA microarrays fabrication are tentatively replaced by alternative technology such as soft lithography to produce new generation of biochips by developing a label free detection method based on optical diffraction. A patented nanostructured chemical layer was elaborated to generate glass slides with gratings of periodic nanometric lines. These gratings efficiently diffract light from a laser beam and were used as anchor for covalent immobilization of DNA probes, thus creating multiple diffracted DNA gratings. Hybridization between DNA probes and their complementary targets induced a variation in diffracted intensities of the gratings that was translated into a quantitative detection signal. These results were obtained using a custom scanner system, developed by Innopsys Company, able to monitor the diffracted intensities. Based on this principle, this simple-multiplexed-low cost- technology was successfully applied for the identification of bacterial species in biological samples.

 

Multidisciplinary and Industrial collaborations

Because of its themes and the close link with the transcriptomics Biochips Platform (GeT-Biochip) of the Genopole Toulouse, the EAD2 is involved in numerous projects connecting research and industry. Based on our experience, a start up called ‘DendriS’ has been created in 2010, by Prof Jean M François (INSA), Dr JP Majoral (LCC-CNRS) and Dr Richard Fabre (Biopole) from the patent of our group, dedicated to application of phosphorous dendrimers for functionalization of surface and fabrication of biochips. We currently collaborate with this company on the development of new microarrays for diagnosis.
The team is particularly associated in different projects concerning the “pôles de compétitivité”, especialy “Pôle Cancer-Bio-Santé” and “Pôle Agrimip Innovation en Midi-Pyrénées”.