electronic-tongue-generating-continuous-recognition-patterns-for

Electronic Tongue Generating Continuous Recognition Patterns for Protein Analysis

In current protocol, a combinatorial approach has been developed to simplify the design and production of sensing materials for the construction of ...

Institut Nanosciences et Cryogénie, CEA-Grenoble

We investigate the current-phase relation of S/F/S junctions near the crossover between the 0 and the pi ground states. We use Nb/CuNi/Nb junctions where this crossover is driven both by thickness and temperature. For a certain thickness a nonzero minimum of critical current is observed at the crossover temperature. We analyze this residual supercurrent by applying a high frequency excitation and observe the formation of half-integer Shapiro steps. We attribute these fractional steps to a doubling of the Josephson frequency due to a sin((2phi) current-phase relation. This phase dependence is explained by the splitting of the energy levels in the ferromagnetic exchange field.

Half-integer Shapiro steps at the 0-pi crossover of a ferromagnetic Josephson junction.

This work establishes the compatibility of surface plasmon resonance imaging (SPR-i) with the visualization of localized electropolymerization. The "writing" of polypyrrole and polypyrrole-oligonucleotide patterns onto thin gold films is demonstrated using scanning electrochemical microcopy (SECM), while an optical method, SPR-i, simultaneously detected the formed micropatterns. The combination of these two methods, SECM/SPR-i, has the advantage of not only controlling the patterning process but also providing unique information on the micropattern formation. The influence of the pulsing time and the monomer concentration on the spot size and its characteristics has been investigated in detail using SPR-i. Fluorescence microscopy and atomic force microscopy have also been used to support the data obtained by SPR-i.

New approach to writing and simultaneous reading of micropatterns: combining surface plasmon resonance imaging with scanning electrochemical microscopy (SECM).

Developing rapid, high-throughput assays for detecting and characterizing protein-protein interactions is a great challenge in the postgenomic era. We have developed a new method that allows parallel analysis of multiple analytes in biological fluids and is suitable for biological and medical studies.

Clinically related protein-peptide interactions monitored in real time on novel peptide chips by surface plasmon resonance imaging.

We constructed multi-channel hybrid bilayer membrane (HBM) biochips and characterized them by surface plasmon resonance imaging. Each channel in the biochip was prepared using vesicles with different proportions of negative, neutral, and positive lipids. The HBM surfaces were tested by interaction with two globular proteins that recognize surfaces covered with opposite charges. Spots modified with the same HBM show responses within a relative standard deviation of 10% or smaller. These devices were also used to study in detail the interaction between cytochrome-c (cyt-c) and HBMs. Cooperative binding between cyt-c and negative HBMs was demonstrated. Using an adaptation of the Hill model, we calculated a Hill coefficient of 5 and a 10-fold increase in the binding constant with the increase in cyt-c concentration. We propose that this treatment can be used to evaluate the cooperative binding of surface proteins to membranes.

Construction of hybrid bilayer membrane (HBM) Biochips and characterization of the cooperative binding between cytochrome-c and HBM.

We demonstrate the use of SPR imaging for the detection of site-specific binding of either B or T lymphocyte populations on an electrochemically-grafted antibody array.

Real-time detection of lymphocytes binding on an antibody chip using SPR imaging.

Base excision repair (BER) is the major mechanism for the correction of damaged nucleobases resulting from the alkylation and oxidation of DNA. The first step in the BER pathway consists of excision of the abnormal base by several specific DNA N-glycosylases. A decrease in BER activity was found to be related to an increased risk of carcinogenesis and aging. To investigate BER activities we set up a new device for DNA repair analysis based on surface plasmon resonance imaging (SPRi). Oligonucleotides bearing an abnormal nucleoside, namely 8-oxo-7,8-dihydro-2'-deoxyguanosine and (5'S)-5',8-cyclopurine-2'-deoxynucleoside, were grafted by a pyrrole electro-copolymerization process on a glass prism coated with a gold layer. The latter label-free DNA sensor chip permits the detection of N-glycosylase/AP-lyase activity as well as the binding of repair proteins to DNA damage without cleavage activity. Thus, the Fapy DNA N-glycosylase (Fpg) protein is shown as expected to bind and then cleave its natural substrate, namely 8-oxo-7,8-dihydro-guanine, together with the resulting abasic site. Using the current SPR imaging-based DNA array we observed an original binding activity of Fpg towards the (5'S)-5',8-cyclodAdenosine residue. These results altogether show that SPR imaging may be used to simultaneously and specifically detect recognition and excision of several damaged DNA nucleobases, and constitutes an interesting technique to screen inhibitors of DNA repair proteins.

SPR imaging for label-free multiplexed analyses of DNA N-glycosylase interactions with damaged DNA duplexes.

In molecular biology, formamide (FA) is a commonly used denaturing agent for DNA. Although its influence on DNA duplex stability in solution is well established, little is known about immobilized DNA on microarrays. We measured thermal denaturation curves for oligonucleotides immobilized by two standard protocols: thiol self-assembling and pyrrole electrospotting. A decrease of the DNA denaturation temperature with increasing FA fraction of the solvent was observed on sequences with mutations for both surface chemistries. The average dissociation temperature decrease was found to be -0.58+/-0.05 degrees C/% FA (v/v) independently of grafting chemistry and probe sequence.

Effects of formamide on the thermal stability of DNA duplexes on biochips.

The possibility to detect low abundant DNA point mutations is essential for early cancer diagnosis and/or prognosis. Furthermore, in order to be less invasive, the somatic mutations are not only sought in tumor extract samples but also from body fluids or stools rendering their content even more diluted compared to the wild type sequences. In this short communication, we propose two protocols based on temperature scans or cycles for the enrichment of the mutation strands hybridized on microarrays. We predict numerically and confirm experimentally a 10-fold increase in the fraction of mutated DNA hybridized on the microarray compared to the sample content. Coupled to more standard solution phase enrichment techniques, it would be possible to lower by one order of magnitude the current detection limit with the advantage of multiple mutation detections offered by the microarray technology.

Temperature scans/cycles for the detection of low abundant DNA point mutations on microarrays.

Continuous evolution profiles for electronic-tongue-based analysis.

Microbial culture continues to be the most common protocol for bacterial detection and identification in medicine and agronomics. Using this process may take days to identify a specific pathogen for most bacterial strains. Surface Plasmon Resonance (SPR) detection is an emerging alternative technology that can be used for the detection of bacteria using protein microarrays although typical limits of detection are in the range of 10(3)-10(6) cfu mL(-1), which is not compatible with most Food Safety regulation requirements. In this work, we combine concomitant "on-chip" microbial culture with sensitive SPR detection of bacteria thus allowing rapid specific detection of bacteria pathogens - including Salmonella enterica serovar Enteritidis, Streptococcus pneumoniae and Escherichia coli O157:H7 - cultured on a protein microarray. This Culture-Capture-Measure (CCM) approach significantly decreases both the number of processing steps and the overall assay time for bacterial detection. Signal analysis of SPR responses allowed the fast and quantitative assessment of bacterial concentrations initially present in the sample as low as 2.8 ± 19.6 cfu per milliliter. Altogether, our results show how simple, easy-to-operate, fluidic-less and lo-tec microarrays can be used with unprocessed samples and yield - in a single assay - both qualitative and quantitative information regarding bacterial contamination.

On-chip microbial culture for the specific detection of very low levels of bacteria.

Hepatitis C virus infection leads to liver disease whose severity can range from mild to serious lifelong illness. However the parameters involved in the evolution of the disease are still unknown. Among other factors, the virus-elicited antibody profile is suspected to play a role in the outcome of the disease. Analysis of the relationship between anti-virus antibodies and disease state requires the analysis of a large number of serums from patients (hepatitis C virus+) and of epitopes from the viral proteins. Such a study would benefit from microarray-based screening systems that are appropriate for high-throughput assays. We used a method combining peptide chips and surface plasmon resonance imaging previously shown to be suitable for analyzing complex mediums and detecting peptide-protein interactions. 56 peptides covering the entire viral proteome were grafted on chips and their interaction with antibodies present in the 68 injected serums from infected and non-infected donors was measured. Statistical analyses were conducted to determine a possible relationship between antibodies (specificity and amount) and disease states. A good discrimination between infected and non-infected donors validated our approach, and several correlations between antibodies profiles and clinical parameters have been identified. In particular, we demonstrated that ratios between particular antibodies levels allow for accurate discrimination of patients according to their pathologic states.

Relationship between humoral response against hepatitis C virus and disease overcome.

Lipid coating is a method highly used to improve the biocompatibility of nanoparticles (NPs), even though its effect on the NP properties is still object of investigation. Herein, silica NPs containing methylene blue, which is a photosensitizer used in a variety of biomedical applications, were coated with a phospholipid bilayer. Regarding the photophysical properties, lipid-coating did not cause significant changes since bare and lipid-coated NPs presented very similar absorption spectra and generated singlet oxygen with similar efficiencies. However, NP interaction with cells and membrane mimics was totally different for bare and lipid-coated NPs. Lipid-coated NPs were distributed through the cell cytoplasm whereas bare NPs were detected only in some vacuolar regions within the cells. Since cellular uptake and cytolocalization are influenced by NP adsorption on cell membranes, the interaction of lipid-coated and bare NPs were studied on a membrane mimic, i.e., Hybrid Bilayer Membranes (HBMs) made of different compositions of negatively charged and neutral lipids. Interactions of bare and lipid-coated NPs with HBMs were analyzed by Surface Plasmon Resonance Imaging. Bare NPs presented high adsorption and aggregation on HBMs independently of the surface charge. Conversely, lipid-coated NPs presented less aggregation on the membrane surface and the adsorption was dependent on the charges of the NPs and of the HBMs. Our results indicated that NPs aggregation on the membrane surface can be modulated by lipid coating, which affects the cytosolic distribution of the NPs.

Effect of lipid coating on the interaction between silica nanoparticles and membranes.

This work proposes a miniaturized system able to perform multiple cell capture followed by cell-type selective release from a biochip surface. Unlabelled lymphocytes were first specifically captured onto a DNA array by antibody-DNA conjugates. The immobilized cells were subsequently released under spatiotemporal control within local heating generated by intense Surface Plasmon Resonance (SPR) produced by laser illumination.

Photothermal effect for localized desorption of primary lymphocytes arrayed on an antibody/DNA-based biochip.

Electronic noses/tongues (eN/eT) have emerged as promising alternatives for analysis of complex mixtures in the domain of food and beverage quality control. We have recently developed an electronic tongue by combining surface plasmon resonance imaging (SPRi) with an array of non-specific and cross-reactive receptors prepared by simply mixing two small molecules in varying and controlled proportions and allowing the mixtures to self-assemble on the SPRi prism surface. The obtained eT generated novel and unique 2D continuous evolution profiles (CEPs) and 3D continuous evolution landscapes (CELs) based on which the differentiation of complex mixtures such as red wine, beer and milk were successful. The preliminary experiments performed for monitoring the deterioration of UHT milk demonstrated its potential for quality control applications. Furthermore, the eT exhibited good repeatability and stability, capable of operating after a minimum storage period of 5 months.

Article	Year
Half-integer Shapiro steps at the 0-pi crossover of a ferromagnetic Josephson junction. Physical review letters\| PubMed ID: 15245053	2004
New approach to writing and simultaneous reading of micropatterns: combining surface plasmon resonance imaging with scanning electrochemical microscopy (SECM). Langmuir : the ACS journal of surfaces and colloids\| PubMed ID: 15461512	2004
Clinically related protein-peptide interactions monitored in real time on novel peptide chips by surface plasmon resonance imaging. Clinical chemistry\| PubMed ID: 16339301	2006
Construction of hybrid bilayer membrane (HBM) Biochips and characterization of the cooperative binding between cytochrome-c and HBM. Langmuir : the ACS journal of surfaces and colloids\| PubMed ID: 17497811	2007
Real-time detection of lymphocytes binding on an antibody chip using SPR imaging. Lab on a chip\| PubMed ID: 17713622	2007
SPR imaging for label-free multiplexed analyses of DNA N-glycosylase interactions with damaged DNA duplexes. The Analyst\| PubMed ID: 18645645	2008
Effects of formamide on the thermal stability of DNA duplexes on biochips. Analytical biochemistry\| PubMed ID: 19796625	2010
Temperature scans/cycles for the detection of low abundant DNA point mutations on microarrays. Biosensors & bioelectronics\| PubMed ID: 22047974	2012
Continuous evolution profiles for electronic-tongue-based analysis. Angewandte Chemie (International ed. in English)\| PubMed ID: 22968809	2012
On-chip microbial culture for the specific detection of very low levels of bacteria. Lab on a chip\| PubMed ID: 23912527	2013
Relationship between humoral response against hepatitis C virus and disease overcome. SpringerPlus\| PubMed ID: 24516785	2014
Effect of lipid coating on the interaction between silica nanoparticles and membranes. Journal of biomedical nanotechnology\| PubMed ID: 24730247	2014
Photothermal effect for localized desorption of primary lymphocytes arrayed on an antibody/DNA-based biochip. Lab on a chip\| PubMed ID: 24789691	2014
SPR imaging based electronic tongue via landscape images for complex mixture analysis. Talanta\| PubMed ID: 25159378	2014

Roberto Calemczuk

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