Étude et développement d'une plateforme microfluidique pour l'imagerie électrochimique

Ce mémoire traite la conception, la microfabrication et la caractérisation d’une matrice de microélectrodes dans une architecture microfluidique pour l’analyse par imagerie électrochimique des substances biochimique. Un nouveau procédé de microfabrication des moules des canaux microfluidiques a été développé en utilisant un procédé de photolithographie d’une résine photosensible sèche et solide. Le microcanal est fabriqué à partir de 2 substrats collés par plasma avec une matrice de 200 microélectrodes (ME). Les dimensions de chaque électrode sont de 340 μm x 340 μm fabriqués sur un circuit imprimé (PCB : printed circuit bord). La surface des électrodes a été modifiée par électrodéposition du nickel et de l’Au pour améliorer les courbes cyclo voltamétriques. Une caractérisation électro-analytique du micro-dispositif est réalisée par voltamétrie cyclique en écoulement laminaire. Le nouveau dispositif proposé nous a permis d’obtenir des images électrochimiques en pixélisant le microcanal avec la MME. Cette pixellisation du microcanal est une cartographie de l’intensité du courant et donc de la concentration des molécules dans le microcanal. Des simulations numériques 2D de la vitesse, pression ainsi que de la diffusion chimique ont été réalisées en utilisant un logiciel de modélisation par éléments finis (COMSOL). Des images microscopiques ont été aussi analysées afin de localiser la distribution des molécules à l’intérieur du canal microfluidique. Mots Clés : Microélectrodes, microfluidique, laboratoire sur puce, analyse électrochimique, circuit imprimé, oxydoréduction.In this project we present a complete microfluidic platform with integrated 200 electrodes for in situ screening and imaging of biochemical samples through a lab-on-chip system. We incorporated electrochemical sensor arrays (20x10) connected to a PCB into a 200 μm tall microfluidic channel. The micro-channel contains three inlets, two of which where used to introduce phosphate buffer saline (PBS), which confined a central stream of ferrocynide solution. A custom multiplexer and potentiostat were used to sequentially perform cyclic voltammetry on each electrode. The behaviour of the system was linear in term of variation of current versus concentration. A pseudo real-time interface collected currents from each electrode. It was then analyzed to detect different species and their concentrations at different locations on-chip. An electrochemical image was generated presenting the concentration distribution inside the microfluidic device. A numerical calculation with COMSOL was achieved to solve Navier-Stocks equation to confirm experimental results, finally microscopic image analyzed to show the position of the confined flow. Key words : Microelectrodes, microfluidics, lab-on-a-chip, electrochemical analysis, printed circuit board, redox reaction

The BioGRID interaction database: 2013 update

The Biological General Repository for Interaction Datasets (BioGRID: http//thebiogrid.org) is an open access archive of genetic and protein interactions that are curated from the primary biomedical literature for all major model organism species. As of September 2012, BioGRID houses more than 500 000 manually annotated interactions from more than 30 model organisms. BioGRID maintains complete curation coverage of the literature for the budding yeast Saccharomyces cerevisiae, the fission yeast Schizosaccharomyces pombe and the model plant Arabidopsis thaliana. A number of themed curation projects in areas of biomedical importance are also supported. BioGRID has established collaborations and/or shares data records for the annotation of interactions and phenotypes with most major model organism databases, including Saccharomyces Genome Database, PomBase, WormBase, FlyBase and The Arabidopsis Information Resource. BioGRID also actively engages with the text-mining community to benchmark and deploy automated tools to expedite curation workflows. BioGRID data are freely accessible through both a user-defined interactive interface and in batch downloads in a wide variety of formats, including PSI-MI2.5 and tab-delimited files. BioGRID records can also be interrogated and analyzed with a series of new bioinformatics tools, which include a post-translational modification viewer, a graphical viewer, a REST service and a Cytoscape plugin

The BioGRID interaction database: 2015 update

The Biological General Repository for Interaction Datasets (BioGRID: http://thebiogrid.org) is an open access database that houses genetic and protein interactions curated from the primary biomedical literature for all major model organism species and humans. As of September 2014, the BioGRID contains 749 912 interactions as drawn from 43 149 publications that represent 30 model organisms. This interaction count represents a 50% increase compared to our previous 2013 BioGRID update. BioGRID data are freely distributed through partner model organism databases and meta-databases and are directly downloadable in a variety of formats. In addition to general curation of the published literature for the major model species, BioGRID undertakes themed curation projects in areas of particular relevance for biomedical sciences, such as the ubiquitin-proteasome system and various human disease-associated interaction networks. BioGRID curation is coordinated through an Interaction Management System (IMS) that facilitates the compilation interaction records through structured evidence codes, phenotype ontologies, and gene annotation. The BioGRID architecture has been improved in order to support a broader range of interaction and post-translational modification types, to allow the representation of more complex multi-gene/protein interactions, to account for cellular phenotypes through structured ontologies, to expedite curation through semi-automated text-mining approaches, and to enhance curation quality control

Electrochemical imaging for microfluidics : a full-system approach

Electrochemistry is developed as a new chemical imaging modality for microfluidics. The technique is based on multipoint voltammetry using an embedded 20 × 10 miniature electrode array implemented on a customized printed circuit board. Electrode durability was enhanced by chemical modification of the electrode surfaces, which enabled continuous, stable use for over 2 months. A system-level approach enables automatic calibration, data acquisition and data processing through a graphical user interface. Following data processing, redox currents and peak positions are extracted from location-specific voltammograms and converted into pixels of an “electrochemical image”. The system is validated by imaging steady-state and dynamic laminar flow patterns of flow-confined solutions of the redox pairs FeIJCN)6 3−/4− or multi-redox environments that include coflowing RuIJNH3)6 2+/3+ solutions. The images obtained are compared with flow simulations and optical images for validation. A strategy to achieve measurements with spatial resolution smaller than the individual electrodes is also demonstrated as an avenue to enhance image spatial resolution. It is expected that this new approach to chemical imaging will expand the applicability of microfluidics in certain areas of chemistry and biology without requiring expertise in electrochemistr

Towards a Multifunctional Electrochemical Sensing and Niosome Generation Lab-on-Chip Platform Based on a Plug-and-Play Concept

In this paper, we present a new modular lab on a chip design for multimodal neurotransmitter (NT) sensing and niosome generation based on a plug-and-play concept. This architecture is a first step toward an automated platform for an automated modulation of neurotransmitter concentration to understand and/or treat neurodegenerative diseases. A modular approach has been adopted in order to handle measurement or drug delivery or both measurement and drug delivery simultaneously. The system is composed of three fully independent modules: three-channel peristaltic micropumping system, a three-channel potentiostat and a multi-unit microfluidic system composed of pseudo-Y and cross-shape channels containing a miniature electrode array. The system was wirelessly controlled by a computer interface. The system is compact, with all the microfluidic and sensing components packaged in a 5 cm × 4 cm × 4 cm box. Applied to serotonin, a linear calibration curve down to 0.125 mM, with a limit of detection of 31 μ M was collected at unfunctionalized electrodes. Added sensitivity and selectivity was achieved by incorporating functionalized electrodes for dopamine sensing. Electrode functionalization was achieved with gold nanoparticles and using DNA and o-phenylene diamine polymer. The as-configured platform is demonstrated as a central component toward an “intelligent” drug delivery system based on a feedback loop to monitor drug delivery

Use of the BioGRID Database for Analysis of Yeast Protein and Genetic Interactions

The BioGRID database is an extensive repository of curated genetic and protein interactions for the budding yeast Saccharomyces cerevisiae, the fission yeast Schizosaccharomyces pombe, and the yeast Candida albicans SC5314, as well as for several other model organisms and humans. This protocol describes how to use the BioGRID website to query genetic or protein interactions for any gene of interest, how to visualize the associated interactions using an embedded interactive network viewer, and how to download data files for either selected interactions or the entire BioGRID interaction data set

BioGRID: A Resource for Studying Biological Interactions in Yeast: Table 1.

The Biological General Repository for Interaction Datasets (BioGRID) is a freely available public database that provides the biological and biomedical research communities with curated protein and genetic interaction data. Structured experimental evidence codes, an intuitive search interface, and visualization tools enable the discovery of individual gene, protein, or biological network function. BioGRID houses interaction data for the major model organism species—including yeast, nematode, fly, zebrafish, mouse, and human—with particular emphasis on the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe as pioneer eukaryotic models for network biology. BioGRID has achieved comprehensive curation coverage of the entire literature for these two major yeast models, which is actively maintained through monthly curation updates. As of September 2015, BioGRID houses approximately 335,400 biological interactions for budding yeast and approximately 67,800 interactions for fission yeast. BioGRID also supports an integrated posttranslational modification (PTM) viewer that incorporates more than 20,100 yeast phosphorylation sites curated through its sister database, the PhosphoGRID