Time-encoded electrical detection of trace RNA biomarker by integrating programmable molecular amplifier on chip.

One of the serious challenges facing modern point-of-care (PoC) molecular diagnostic platforms relate to reliable detection of low concentration biomarkers such as nucleic acids or proteins in biological samples. Non-specific analyte-receptor interactions due to competitive binding in the presence of abundant molecules, inefficient mass transport and very low number of analyte molecules in sample volume, in general pose critical hurdles for successful implementation of such PoC platforms for clinical use. Focusing on these specific challenges, this work reports a unique PoC biosensor that combines the advantages of nanoscale biologically-sensitive field-effect transistor arrays (BioFET-arrays) realized in a wafer-scale top-down nanofabrication as high sensitivity electrical transducers with that of sophisticated molecular programs (MPs) customized for selective recognition of analyte miRNAs and amplification resulting in an overall augmentation of signal transduction strategy. The MPs realize a programmable universal molecular amplifier (PUMA) in fluidic matrix on chip and provide a biomarker-triggered exponential release of small nucleic acid sequences easily detected by receptor-modified BioFETs. A common miRNA biomarker LET7a was selected for successful demonstration of this novel biosensor, achieving limit of detection (LoD) down to 10 fM and wide dynamic ranges (10 pM-10 nM) in complex physiological solutions. As the determination of biomarker concentration is implemented by following the electrical signal related to analyte-triggered PUMA in time-domain instead of measuring the threshold shifts of BioFETs, and circumvents direct hybridization of biomarkers at transducer surface, this new strategy also allows for multiple usage (>3 times) of the biosensor platform suggesting exceptional cost-effectiveness for practical use.

Correction: Diamond nanowires modified with poly[3-(pyrrolyl)carboxylic acid] for the immobilization of histidine-tagged peptides.

Correction for 'Diamond nanowires modified with poly[3-(pyrrolyl)carboxylic acid] for the immobilization of histidine-tagged peptides' by Palaniappan Subramanian et al., Analyst, 2014, 139, 4343-4349, https://doi.org/10.1039/C4AN00146J.

Structural plasticity for neuromorphic networks with electropolymerized dendritic PEDOT connections.

Neural networks are powerful tools for solving complex problems, but finding the right network topology for a given task remains an open question. Biology uses neurogenesis and structural plasticity to solve this problem. Advanced neural network algorithms are mostly relying on synaptic plasticity and learning. The main limitation in reconciling these two approaches is the lack of a viable hardware solution that could reproduce the bottom-up development of biological neural networks. Here, we show how the dendritic growth of PEDOT:PSS-based fibers through AC electropolymerization can implement structural plasticity during network development. We find that this strategy follows Hebbian principles and is able to define topologies that leverage better computing performances with sparse synaptic connectivity for solving non-trivial tasks. This approach is validated in software simulation, and offers up to 61% better network sparsity on classification and 50% in signal reconstruction tasks.

Single-Cell Electrochemical Aptasensor Array.

Despite several demonstrations of electrochemical devices with limits of detection (LOD) of 1 cell/mL, the implementation of single-cell bioelectrochemical sensor arrays has remained elusive due to the challenges of scaling up. In this study, we show that the recently introduced nanopillar array technology combined with redox-labeled aptamers targeting epithelial cell adhesion molecule (EpCAM) is perfectly suited for such implementation. Combining nanopillar arrays with microwells determined for single cell trapping directly on the sensor surface, single target cells are successfully detected and analyzed. This first implementation of a single-cell electrochemical aptasensor array, based on Brownian-fluctuating redox species, opens new opportunities for large-scale implementation and statistical analysis of early cancer diagnosis and cancer therapy in clinical settings.

Electropolymerization processing of side-chain engineered EDOT for high performance microelectrode arrays.

Microelectrode Arrays (MEAs) are popular tools for in vitro extracellular recording. They are often optimized by surface engineering to improve affinity with neurons and guarantee higher recording quality and stability. Recently, PEDOT:PSS has been used to coat microelectrodes due to its good biocompatibility and low impedance, which enhances neural coupling. Herein, we investigate on electro-co-polymerization of EDOT with its triglymated derivative to control valence between monomer units and hydrophilic functions on a conducting polymer. Molecular packing, cation complexation, dopant stoichiometry are governed by the glycolation degree of the electro-active coating of the microelectrodes. Optimal monomer ratio allows fine-tuning the material hydrophilicity and biocompatibility without compromising the electrochemical impedance of microelectrodes nor their stability while interfaced with a neural cell culture. After incubation, sensing readout on the modified electrodes shows higher performances with respect to unmodified electropolymerized PEDOT, with higher signal-to-noise ratio (SNR) and higher spike counts on the same neural culture. Reported SNR values are superior to that of state-of-the-art PEDOT microelectrodes and close to that of state-of-the-art 3D microelectrodes, with a reduced fabrication complexity. Thanks to this versatile technique and its impact on the surface chemistry of the microelectrode, we show that electro-co-polymerization trades with many-compound properties to easily gather them into single macromolecular structures. Applied on sensor arrays, it holds great potential for the customization of neurosensors to adapt to environmental boundaries and to optimize extracted sensing features.

Precision of neuronal localization in 2D cell cultures by using high-performance electropolymerized microelectrode arrays correlated with optical imaging.

Recently, the development of electronic devices to extracellularly record the simultaneous electrical activities of numerous neurons has been blooming, opening new possibilities to interface and decode neuronal activity. In this work, we tested how the use of EDOT electropolymerization to tune post-fabrication materials could optimize the cell/electrode interface of such devices. Our results showed an improved signal-to-noise ratio, better biocompatibility, and a higher number of neurons detected in comparison with gold electrodes. Then, using such enhanced recordings with 2D neuronal cultures combined with fluorescent optical imaging, we checked the extent to which the positions of the recorded neurons could be estimated solely via their extracellular signatures. Our results showed that assuming neurons behave as monopoles, positions could be estimated with a precision of approximately tens of micrometers.

Development of nanomaterial enabling highly sensitive surface-assisted laser desorption/ionization mass spectrometry peptide analysis.

RATIONALE: Surface-assisted laser desorption/ionization mass spectrometry (SALDI-MS) is an approach derived from matrix-assisted laser desorption/ionization (MALDI)-MS which overcomes the drawbacks associated with the use of organic matrices required to co-crystallize with the analytes. Indeed, nanomaterials commonly used in SALDI-MS as inert surfaces to promote desorption/ionization (D/I) ensure straightforward direct deposition of samples while providing mass spectra with ions only related to the compound of interest. The objective of this study was to develop a novel SALDI-MS approach based on steel plates that are surfaces very rapidly and easily tuned to perform the most efficient peptide detection as possible. To compare the SALDI efficacy of such metal substrates, D/I efficiency and deposit homogeneity were evaluated according to steel plate fabrication processes. METHODS: The studied surfaces were nanostructured steel plates that were chemically modified by perfluorosilane and textured according to different frequencies and laser writing powers. The capacity of each tested 100 surfaces was demonstrated by comparative analyses of a mixture of standard peptides (m/z 600-3000) performed with a MALDI-TOF instrument enabling MALDI, SALDI and imaging experiments. RESULTS: A peptide mix was used to screen the different surfaces depending on their D/I efficiency and their ability to ensure homogeneous deposit of the samples. For that purpose, deposition homogeneity was visualized owing to reconstructed ionic images from all protonated or sodiated ions of the 10 peptides constituting the standard mix. CONCLUSIONS: Seven surfaces were then selected satisfying the required D/I efficiency and deposit homogeneity criteria. Results obtained with these optimal surfaces were then compared with those recorded by MALDI-MS analyses used as references.

Theoretical modeling of dendrite growth from conductive wire electro-polymerization.

Electropolymerization is a bottom-up materials engineering process of micro/nano-scale that utilizes electrical signals to deposit conducting dendrites morphologies by a redox reaction in the liquid phase. It resembles synaptogenesis in the brain, in which the electrical stimulation in the brain causes the formation of synapses from the cellular neural composites. The strategy has been recently explored for neuromorphic engineering by establishing link between the electrical signals and the dendrites' shapes. Since the geometry of these structures determines their electrochemical properties, understanding the mechanisms that regulate polymer assembly under electrically programmed conditions is an important aspect. In this manuscript, we simulate this phenomenon using mesoscale simulations, taking into account the important features of spatial-temporal potential mapping based on the time-varying signal, the motion of charged particles in the liquid due to the electric field, and the attachment of particles on the electrode. The study helps in visualizing the motion of the charged particles in different electrical conditions, which is not possible to probe experimentally. Consistent with the experiments, the higher AC frequency of electrical activities favors linear wire-like growth, while lower frequency leads to more dense and fractal dendrites' growth, and voltage offset leads to asymmetrical growth. We find that dendrites' shape and growth process systematically depend on particle concentration and random scattering. We discover that the different dendrites' architectures are associated with different Laplace and diffusion fields, which govern the monomers' trajectory and subsequent dendrites' growth. Such unconventional engineering routes could have a variety of applications from neuromorphic engineering to bottom-up computing strategies.

Analog programing of conducting-polymer dendritic interconnections and control of their morphology.

Although materials and processes are different from biological cells', brain mimicries led to tremendous achievements in parallel information processing via neuromorphic engineering. Inexistent in electronics, we emulate dendritic morphogenesis by electropolymerization in water, aiming in operando material modification for hardware learning. Systematic study of applied voltage-pulse parameters details on tuning independently morphological aspects of micrometric dendrites': fractal number, branching degree, asymmetry, density or length. Growths time-lapse image processing shows spatial features to be dynamically dependent, and expand distinctively before and after conductive bridging with two electro-generated dendrites. Circuit-element analysis and impedance spectroscopy confirms their morphological control in temporal windows where growth kinetics is finely perturbed by the input frequency and duty cycle. By the emulation of one's most preponderant mechanisms for brain's long-term memory, its implementation in vicinity of sensing arrays, neural probes or biochips shall greatly optimize computational costs and recognition required to classify high-dimensional patterns from complex environments.

Dendritic Organic Electrochemical Transistors Grown by Electropolymerization for 3D Neuromorphic Engineering.

One of the major limitations of standard top-down technologies used in today's neuromorphic engineering is their inability to map the 3D nature of biological brains. Here, it is shown how bipolar electropolymerization can be used to engineer 3D networks of PEDOT:PSS dendritic fibers. By controlling the growth conditions of the electropolymerized material, it is investigated how dendritic fibers can reproduce structural plasticity by creating structures of controllable shape. Gradual topologies evolution is demonstrated in a multielectrode configuration. A detailed electrical characterization of the PEDOT:PSS dendrites is conducted through DC and impedance spectroscopy measurements and it is shown how organic electrochemical transistors (OECT) can be realized with these structures. These measurements reveal that quasi-static and transient response of OECTs can be adjusted by controlling dendrites' morphologies. The unique properties of organic dendrites are used to demonstrate short-term, long-term, and structural plasticity, which are essential features required for future neuromorphic hardware development.

A critical review on surface modifications mitigating dairy fouling.

Thermal treatments performed in food processing industries generate fouling. This fouling deposit impairs heat transfer mechanism by creating a thermal resistance, thus leading to regular shutdown of the processes. Therefore, periodic and harsh cleaning-in-place (CIP) procedures are implemented. This CIP involves the use of chemicals and high amounts of water, thus increasing environmental burden. It has been estimated that 80% of production costs are owed to dairy fouling deposit. Since the 1970s, different types of surface modifications have been performed either to prevent fouling deposition (anti-fouling) or to facilitate removal (fouling-release). This review points out the impacts of surface modification on type A dairy fouling and on cleaning behaviors under batch and continuous flow conditions. Both types of anti-fouling and fouling-release coatings are reported as well as the different techniques used to modify stainless steel surface. Finally, methods for testing and characterising the effectiveness of coatings in mitigating dairy fouling are discussed.

Influence of buried oxide layers of nanostructured SOI surfaces on matrix-free LDI-MS performances.

In this paper, we report on the nanostructuration of the silicon crystalline top layer of different "home-made" SOI substrates presenting various buried oxide (BOx) layer thicknesses. The nanostructuration was achieved via a one-step metal assisted chemical etching (MACE) procedure. The etched N-SOI substrate surfaces were then characterized by AFM, SEM and photoluminescence. To investigate their laser desorption/ionization mass spectrometry performances, the different surfaces have been assessed towards peptide mixtures. We have shown that the matrix-free LDI process occurred from surface heating after laser irradiation and was fostered by thermal confinement in the thin nanostructured Si surface layer. This thermal confinement was enhanced with the increase of the buried oxide layer thickness until an optimal thickness of 200 nm for which the best results in terms of signal intensities, peptide discrimination and spot to spot and surface to surface variations were found.

Fast and facile preparation of nanostructured silicon surfaces for laser desorption/ionization mass spectrometry of small compounds.

RATIONALE: Many important biological processes rely on specific biomarkers (such as metabolites, drugs, proteins or peptides, carbohydrates, lipids, ...) that need to be monitored in various fluids (blood, plasma, urine, cell cultures, tissue homogenates, …). Although mass spectrometry (MS) hyphenated to liquid chromatography (LC) is widely accepted as a 'gold-standard' method for identifying such synthetic chemicals or biological products, their robust fast sensitive detection from complex matrices still constitutes a highly challenging matter. METHODS: In order to circumvent the constraints intrinsic to LC/MS technology in terms of prior sample treatment, analysis time and overall method development to optimize ionization efficiency affecting the detection threshold, we investigated laser desorption/ionization mass spectrometry (LDI-MS) by directly depositing the sample under study onto cheap inert nanostructures made of silicon to perform straightforward sensitive and rapid screening of targeted low mass biomarkers on a conventional MALDI platform. RESULTS: The investigated silicon nanostructures were found to act as very efficient ion-promoting surfaces exhibiting high performance for the detection of different classes of organic compounds, including glutathione, glucose, peptides and antibiotics. Achieving such broad detection was compulsory to develop a SALDI-MS-based pre-screening tool. CONCLUSIONS: The key contribution of the described analytical strategy consists of designing inert surfaces that are fast (minute preparation) and cheap to produce, easy to handle and able to detect small organic compounds in matrix-free LDI-MS prerequisite for biomarkers pre-screening from body fluids without the recourse of any separation step.

Spatiotemporal control of DNA-based chemical reaction network via electrochemical activation in microfluidics.

In recent years, DNA computing frameworks have been developed to create dynamical systems which can be used for information processing. These emerging synthetic biochemistry tools can be leveraged to gain a better understanding of fundamental biology but can also be implemented in biosensors and unconventional computing. Most of the efforts so far have focused on changing the topologies of DNA molecular networks or scaling them up. Several issues have thus received little attention and remain to be solved to turn them into real life technologies. In particular, the ability to easily interact in real-time with them is a key requirement. The previous attempts to achieve this aim have used microfluidic approaches, such as valves, which are cumbersome. We show that electrochemical triggering using DNA-grafted micro-fabricated gold electrodes can be used to give instructions to these molecular systems. We demonstrate how this approach can be used to release at specific times and locations DNA- based instructions. In particular, we trigger reaction-diffusion autocatalytic fronts in microfluidic channels. While limited by the stability of the Au-S bond, this easy to implement, versatile and scalable technique can be used in any biology laboratory to provide new ways to interact with any DNA-based computing framework.

Comparison of Ti-Based Coatings on Silicon Nanowires for Phosphopeptide Enrichment and Their Laser Assisted Desorption/Ionization Mass Spectrometry Detection.

We created different TiO2-based coatings on silicon nanowires (SiNWs) by using either thermal metallization or atomic layer deposition (ALD). The fabricated surfaces were characterized by X-ray photoelectron spectroscopy (XPS), energy dispersive X-ray spectroscopy (EDX), and reflectivity measurements. Surfaces with different TiO2 based coating thicknesses were then used for phosphopeptide enrichment and subsequent detection by laser desorption/ionization mass spectrometry (LDI-MS). Results showed that the best enrichment and LDI-MS detection were obtained using the silicon nanowires covered with 10 nm of oxidized Ti deposited by means of thermal evaporation. This sample was also able to perform phosphopeptide enrichment and MS detection from serum.

Antifouling Biomimetic Liquid-Infused Stainless Steel: Application to Dairy Industrial Processing.

Fouling is a widespread and costly issue, faced by all food-processing industries. Particularly, in the dairy sector, where thermal treatments are mandatory to ensure product safety, heat-induced fouling represents up to 80% of the total production costs. Significant environmental impacts, due the massive consumption of water and energy, are also to deplore. Fouling control solutions are thus desperately needed, as they would lead to substantial financial gains as well as tremendous progress toward eco-responsible processes. This work aims at presenting a novel and very promising dairy fouling-mitigation strategy, inspired by nature, and to test its antifouling performances in real industrial conditions. Slippery liquid-infused surfaces were successfully designed directly on food grade stainless steel, via femtosecond laser ablation, followed by fluorosilanization and impregnation with an inert perfluorinated oil. Resulting hydrophobic surfaces (water contact angle of 112°) exhibited an extremely slippery nature (contact angle hysteresis of 0.6°). Outstanding fouling-release performances were obtained for these liquid-infused surfaces as absolutely no trace of dairy deposit was found after 90 min of pasteurization test in pilot-scale equipment followed by a short water rinse.

MoS2/TiO2/SiNW surface as an effective substrate for LDI-MS detection of glucose and glutathione in real samples.

Here, we report for the first time, the use of molybdenum disulfide/titanium oxide/silicon nanowires (MoS2/TiO2/SiNW) surfaces for SALDI-MS detection as alternative to MALDI-MS method. Silicon nanowires were fabricated by the well-known metal-assisted chemical etching process followed by the deposition of TiO2 by atomic layer deposition. MoS2 deposition was achieved through hydrothermal treatment. The MoS2/TiO2/SiNW substrate has shown high performance for the detection of small compounds of different molecular weights, including glutathione, glucose, amino acids, antibiotics to name a few. All of the tested compounds, in pure or in mixed solutions were successfully detected in positive ion mode. Therefore, we have also attempted quantitative measurements of GSH and glucose in human blood serum.

Electrophoretic Approach for the Simultaneous Deposition and Functionalization of Reduced Graphene Oxide Nanosheets with Diazonium Compounds: Application for Lysozyme Sensing in Serum.

Electrophoretic deposition (EPD) of reduced graphene oxide nanosheets (rGO) offers several advantages over other surface coating approaches, including process simplicity, uniformity of the deposited films, and good control of the film thickness. The EPD conditions might also be of interest for the reduction of diazonium salts, which upon the release of N2 molecules and generation of radicals, can form covalent bonds with the sp2 hybridized carbon lattice atoms of rGO films. In this work, we report on the coating of gold electrodes in one step with rGO/polyethylenimine (PEI) thin films and their simultaneous modification using different phenyl (Ph) diazonium salt precursors bearing various functionalities such as -B(OH)2, -COOH, and -C≡CH. We show further the interest of such interfaces for designing highly sensitive sensing platforms. Azide-terminated lysozyme aptamers were clicked onto the rGO/PEI/Ph-alkynyl matrix and used for the sensing of lysozyme levels in patients suffering from inflammatory bowel disease (IBD), where lysozyme levels are up-regulated. The approach attained the required demand for the determination of lysozyme level in patients suffering from IBD with a 200 fM detection limit and a linear range up to 20 pM without signal amplification.

Characterization of peptide attachment on silicon nanowires by X-ray photoelectron spectroscopy and mass spectrometry.

In this paper, we report an original method to immobilize a model peptide on silicon nanowires (SiNWs) via a photolinker attached to the SiNWs' surface. The silicon nanowires were fabricated by a metal assisted chemical etching (MACE) method. Then, direct characterization of the peptide immobilization on SiNWs was performed either by X-ray photoelectron spectroscopy (XPS) or by laser-desorption/ionization mass spectrometry (LDI-MS). XPS allowed us to follow the peptide immobilization and its photorelease by recording the variation of the signal intensities of the different elements present on the SiNW surface. Mass spectrometry was performed without the use of an organic matrix and peptide ions were produced via a photocleavage mechanism. Indeed, thanks to direct photorelease achieved upon laser irradiation, a recorded predictable peak related to the molecular peptide ion has been detected, allowing the identification of the model peptide. Additional MS/MS experiments confirmed the photodissociation site and confirmed the N-terminal immobilization of the peptide on SiNWs.

Toxicity effect of graphene oxide on growth and photosynthetic pigment of the marine alga Picochlorum sp. during different growth stages.

Graphene oxide (GO), a recently discovered material, has been investigated for many applications in various fields. Thus, an immense awareness should be paid on the potential effects of the material on the environment as huge quantities of GO may get to the environment. Aquatic organisms, marine algae as an example, are exposed to such material when disposed to the environment. Accordingly, it is significant to assess the probable interactions of GO with algae in evaluating its possible environmental risks. In this study, we have examined the effect of different concentrations of GO on Picochlorum sp. during the different growth phases. The results showed that the toxicity of GO increases with increasing its concentration. The lowest concentration (0.5 mg L-1) was found to improve the algae growth and pigment content of Picochlorum sp. In contrast, higher GO concentrations had a negative consequence on the growth of algae and photosynthetic pigment concentration.