AC amplification gain in organic electrochemical transistors for impedance-based single cell sensors

Research on electrolyte-gated and organic electrochemical transistor (OECT) architectures is motivated by the prospect of a highly biocompatible interface capable of amplifying bioelectronic signals at the site of detection. Despite many demonstrations in these directions, a quantitative model for OECTs as impedance biosensors is still lacking. We overcome this issue by introducing a model experiment where we simulate the detection of a single cell by the impedance sensing of a dielectric microparticle. The highly reproducible experiment allows us to study the impact of transistor geometry and operation conditions on device sensitivity. With the data we rationalize a mathematical model that provides clear guidelines for the optimization of OECTs as single cell sensors, and we verify the quantitative predictions in an in-vitro experiment. In the optimized geometry, the OECT-based impedance sensor allows to record single cell adhesion and detachment transients, showing a maximum gain of 20.2±0.9 dB with respect to a single electrode-based impedance sensor

Optimized pipeline of MuTect and GATK tools to improve the detection of somatic single nucleotide polymorphisms in whole- exome sequencing data

Background: Detecting somatic mutations in whole exome sequencing data of cancer samples has become a popular approach for profiling cancer development, progression and chemotherapy resistance. Several studies have proposed software packages, filters and parametrizations. However, many research groups reported low concordance among different methods. We aimed to develop a pipeline which detects a wide range of single nucleotide mutations with high validation rates. We combined two standard tools – Genome Analysis Toolkit (GATK) and MuTect – to create the GATK-LODN method. As proof of principle, we applied our pipeline to exome sequencing data of hematological (Acute Myeloid and Acute Lymphoblastic Leukemias) and solid (Gastrointestinal Stromal Tumor and Lung Adenocarcinoma) tumors. We performed experiments on simulated data to test the sensitivity and specificity of our pipeline. Results: The software MuTect presented the highest validation rate (90 %) for mutation detection, but limited number of somatic mutations detected. The GATK detected a high number of mutations but with low specificity. The GATK-LODN increased the performance of the GATK variant detection (from 5 of 14 to 3 of 4 confirmed variants), while preserving mutations not detected by MuTect. However, GATK-LODN filtered more variants in the hematological samples than in the solid tumors. Experiments in simulated data demonstrated that GATK-LODN increased both specificity and sensitivity of GATK results. Conclusion: We presented a pipeline that detects a wide range of somatic single nucleotide variants, with good validation rates, from exome sequencing data of cancer samples. We also showed the advantage of combining standard algorithms to create the GATK-LODN method, that increased specificity and sensitivity of GATK results. This pipeline can be helpful in discovery studies aimed to profile the somatic mutational landscape of cancer genomes

Hypoxia Depresses Synaptic Transmission in the Primary Motor Cortex of the Infant Rat—Role of Adenosine A1 Receptors and Nitric Oxide

The acute and long-term consequences of perinatal asphyxia have been extensively investigated, but only a few studies have focused on postnatal asphyxia. In particular, electrophysiological changes induced in the motor cortex by postnatal asphyxia have not been examined so far, despite the critical involvement of this cortical area in epilepsy. In this study, we exposed primary motor cortex slices obtained from infant rats in an age window (16–18 day-old) characterized by high incidence of hypoxia-induced seizures associated with epileptiform motor behavior to 10 min of hypoxia. Extracellular field potentials evoked by horizontal pathway stimulation were recorded in layers II/III of the primary motor cortex before, during, and after the hypoxic event. The results show that hypoxia reversibly depressed glutamatergic synaptic transmission and neuronal excitability. Data obtained in the presence of specific blockers suggest that synaptic depression was mediated by adenosine acting on pre-synaptic A1 receptors to decrease glutamate release, and by a nitric oxide (NO)/cGMP postsynaptic pathway. These effects are neuroprotective because they limit energy failure. The present findings may be helpful in the preclinical search for therapeutic strategies aimed at preventing acute and long-term neurological consequences of postnatal asphyxia

Biological applications of conductive polymers

Starting from the last decade, conductive polymers have been employed to realize a wide variety of devices applied in biological research, thanks to their favourable electrical, mechanical and biocompatibility properties in respect to traditional inorganic semiconductors. In this abstract, a few examples that illustrate the coupling between organic electronics and biology are considered, with a particular regard to poly(3,4-ethylenedioxytiophene) (PEDOT) based devices

Water compartmentalization, cell viability and morphology changes monitored under stress by 1H-NMR relaxometry and phase contrast optical microscopy

The quasi-continuous distributions of spin-lattice (T1) and spin-spin (T2) relaxation times of a population of cells kept under stress conditions for about 400 h has been obtained by 1H-NMR relaxometry. The comparison with the results obtained from the analysis of cell viability and morphological variations by phase contrast optical microscopy and performed with acquisition times, duration and conditions matching those of the relaxometry experiments allowed us to identify three main phases of the processes related to the exchanges of water and remodeling of cellular compartments: between 0 and 40 h the intra- and extra-cellular compartments are characterized by a T2 of ~250 ms and of ~2 s respectively and the cell population halflife has been experimentally evaluated to be ~45 h; after 40 and until 100 h cells NMR parameter changes suggest that the confined water is increasing according to the progressive fragmentation of the cells membrane; over 100 h almost all cells are non-viable and the constancy of the main NMR parameters reflects the reaching of the final equilibrium of the system. In conclusion our observations validated the use of NMR as a non-destructive, noninvasive powerful technique for monitoring the progression of cellular processes involving compartments water exchange and reorganization

BK channel overexpression on plasma membrane of fibroblasts from Hutchinson-Gilford progeria syndrome

Hutchinson-Gilford progeria syndrome (HGPS) is an extremely rare genetic disorder wherein symptoms resembling aspects of aging are manifested at a very early age. It is a genetic condition that occurs due to a de novo mutation in the LMNA gene encoding for the nuclear structural protein lamin A. The lamin family of proteins are thought to be involved in nuclear stability, chromatin structure and gene expression and this leads to heavy effects on the regulation and functionality of the cell machinery. The functional role of the large-conductance calcium-activated potassium channels (BKCa) is still unclear, but has been recently described a strong relationship with their membrane expression, progerin nuclear levels and the ageing process. In this study, we found that: i) the outward potassium membrane current amplitude and the fluorescence intensity of the BKCa channel probe showed higher values in human dermal fibroblast obtained from patients affected by HGPS if compared to that from healthy young subjects; ii) this result appears to correlate with a basic cellular activity such as the replicative boost. We suggest that studying the HGPS also from the electrophysiological point of view might reveal new clues about the normal process of aging

Galvanotactic phenomenon induced by non-contact electrostatic field: Investigation in a scratch assay

Non-contact galvanotaxis as a way to drive the cells migration could be a promising tool for a variety of biomedical applications, such as wound healing control, avoiding the interaction between electrodes and cell cultures. To this regard, the efficacy of this electrical stimulus application has to be deeper studied to control physiological migratory phenomena in a remote way.Aim of this work is to provide an experimental investigation on the mobility of cells exposed to a static electric field in a "noncontact" mode, supported by a suitable modeling of the electric field distribution inside the experimental setup. In particular, scratch assays have been carried out placing the electrodes outside the cells medium support and changing the cells holder to study more than one configuration.Clinical Relevance— In this study the in vitro experiments on the non-contact galvanotaxis, together with the numerical simulations of the exposure setup, provide a way to investigate the effects that could affect an electrically drive cell migration

Electrically Controlled \u201cSponge Effect\u201d of PEDOT:PSS Governs Membrane Potential and Cellular Growth

ABSTRACT: PEDOT:PSS is a highly conductive material with good thermal and chemical stability and enhanced biocompatibility that make it suitable for bioengineering applications. The electrical control of the oxidation state of PEDOT:PSS films allows modulation of peculiar physical and chemical properties of the material, such as topography, wettability, and conductivity, and thus offers a possible route for controlling cellular behavior. Through the use of (i) the electrophysiological response of the plasma membrane as a biosensor of the ionic availability; (ii) relative abundance around the cells via Xray spectroscopy; and (iii) atomic force microscopy to monitor PEDOT:PSS film thickness relative to its oxidation state, we demonstrate that redox processes confer to PEDOT:PSS the property to modify the ionic environment at the film 12liquid interface through a \u201csponge-like\u201d effect on ions. Finally, we show how this property offers the capability to electrically control central cellular properties such as viability, substrate adhesion, and growth, paving the way for novel bioelectronics and biotechnological applications