Dynamic clamp with StdpC software

Dynamic clamp is a powerful method that allows the introduction of artificial electrical components into target cells to simulate ionic conductances and synaptic inputs. This method is based on a fast cycle of measuring the membrane potential of a cell, calculating the current of a desired simulated component using an appropriate model and injecting this current into the cell. Here we present a dynamic clamp protocol using free, fully integrated, open-source software (StdpC, for spike timing-dependent plasticity clamp). Use of this protocol does not require specialist hardware, costly commercial software, experience in real-time operating systems or a strong programming background. The software enables the configuration and operation of a wide range of complex and fully automated dynamic clamp experiments through an intuitive and powerful interface with a minimal initial lead time of a few hours. After initial configuration, experimental results can be generated within minutes of establishing cell recording

Single Molecule Conformational Memory Extraction: P5ab RNA Hairpin

Extracting kinetic models from single molecule data is an important route to mechanistic insight in biophysics, chemistry, and biology. Data collected from force spectroscopy can probe discrete hops of a single molecule between different conformational states. Model extraction from such data is a challenging inverse problem because single molecule data are noisy and rich in structure. Standard modeling methods normally assume (i) a prespecified number of discrete states and (ii) that transitions between states are Markovian. The data set is then fit to this predetermined model to find a handful of rates describing the transitions between states. We show that it is unnecessary to assume either (i) or (ii) and focus our analysis on the zipping/unzipping transitions of an RNA hairpin. The key is in starting with a very broad class of non-Markov models in order to let the data guide us toward the best model from this very broad class. Our method suggests that there exists a folding intermediate for the P5ab RNA hairpin whose zipping/unzipping is monitored by force spectroscopy experiments. This intermediate would not have been resolved if a Markov model had been assumed from the onset. We compare the merits of our method with those of others

Minimal state models for ionic channels involved in glucagon secretion

Pancreatic alpha cells synthesize and release glucagon. This hormone along with insulin, preserves blood glucose levels within a physiological range. During low glucose levels, alpha cells exhibit electrical activity related to glucagon secretion. In this paper, we introduce minimal state models for those ionic channels involved in this electrical activity in mice alpha cells. For estimation of model parameters, we use Monte Carlo algorithms to fit steadystate channel currents. Then, we simulate dynamic ionic currents following experimental protocols. Our aims are 1) To understand the individual ionic channel functioning and modulation that could affect glucagon secretion, and 2) To simulate ionic currents actually measured in voltage-clamp alpha-cell experiments in mice. Our estimations indicate that alpha cells are highly permeable to sodium and potassium which mainly manage action potentials. We have also found that our estimated N-type calcium channel population and density in alpha cells is in good agreement to those reported for L-type calcium channels in beta cells. This finding is strongly relevant since both, L-type and N-type calcium channels, play a main role in insulin and glucagon secretion, respectively

Identification of IKr Kinetics and Drug Binding in Native Myocytes

Determining the effect of a compound on IKr is a standard screen for drug safety. Often the effect is described using a single IC50 value, which is unable to capture complex effects of a drug. Using verapamil as an example, we present a method for using recordings from native myocytes at several drug doses along with qualitative features of IKr from published studies of HERG current to estimate parameters in a mathematical model of the drug effect on IKr. IKr was recorded from canine left ventricular myocytes using ruptured patch techniques. A voltage command protocol was used to record tail currents at voltages from −70 to −20 mV, following activating pulses over a wide range of voltages and pulse durations. Model equations were taken from a published IKr Markov model and the drug was modeled as binding to the open state. Parameters were estimated using a combined global and local optimization algorithm based on collected data with two additional constraints on IKrI–V relation and IKr inactivation. The method produced models that quantitatively reproduce both the control IKr kinetics and dose dependent changes in the current. In addition, the model exhibited use and rate dependence. The results suggest that: (1) the technique proposed here has the practical potential to develop data-driven models that quantitatively reproduce channel behavior in native myocytes; (2) the method can capture important drug effects that cannot be reproduced by the IC50 method. Although the method was developed for IKr, the same strategy can be applied to other ion channels, once appropriate channel-specific voltage protocols and qualitative features are identified

Spray coating polymer substrates from a green solvent to enhance desalination performances of thin film composites

Toxic solvents like n,n-dimethylformamide (DMF), n,n-dimethylethanamide (DMAc), and 1-methyl-2-pyrrolidone (NMP) are commonly used to fabricate polymer support membranes. Replacing these toxic solvents with green solvents such as Cyrene™ can imbue sustainability into membrane fabrication, but at the expense of poor membrane separation performances. Here we overcome this limitation by spray coating Cyrene™-based polymer dope solutions to form highly porous asymmetric membranes. The pure water permeance of spray-coated polyethersulfone (PES) membranes reached 68.9 L m−2 h−1 bar−1, 7-fold higher than knife cast membranes. This significant increase in permeance was ascribed to a porous, thin skin layer and macrovoids interconnected with finger-like pores in spray-coated PES films. However, this did not impact on the ability to yield thin film composites (TFCs) with high separation performances. Through interfacial polymerisation, we deposited a polyamide selective layer on to the surface of spray-coated PES films to yield TFCs for desalination of a 2000 ppm NaCl solution. The salt rejection rate and permeance of such TFCs reached 93% and 1.76 L m−2 h−1 bar−1, respectively. This desalination performance was similar to knife cast membranes produced from DMF-, NMP- and DMAc-based polymer dope solutions, but fabricated here in a more sustainable manner. This indicated that spray coating can overcome the trade-off between poor membrane separation performance and sustainability. © 2023 The Royal Society of Chemistry

The role of surface functionality of sustainable mesoporous materials Starbon® on the adsorption of toxic ammonia and sulphur gasses

The interest in adsorbing toxic gases nowadays is primarily due to their short- and long-term adverse health effects. It is generally accepted that the pore morphology and the surface nature play key roles in the adsorption mechanism of any molecules. The interactions between the adsorbate and adsorbent are affected by their polarity, where nonpolar surfaces would be attracted to a non-polar adsorbate, while polar surfaces have a higher affinity for polar molecules. The primary issue is access to a controllable set of materials with multiple functionalities that provide both polar and nonpolar surfaces for adsorption, which would present an advantage over single-phase adsorbents. Recently this has become available thanks to a novel class of bio-based carbonaceous materials (Starbon®). The functionality of these materials can be easily controlled by their temperature of preparation. The present work studies the nature of the surface chemistry and porosity of bio-based mesoporous materials Starbon and the role this plays in the adsorption of toxic volatile molecules such as ammonia, as a basic adsorptive and two acidic gasses (hydrogen sulphide and sulphur dioxide) using an InfraSorp optical calorimeter. Both hydrogen sulphide and sulphur dioxide adsorb better onto a hydrophobic surface, while ammonia adsorbs best onto a hydrophilic surface. The results showed that in both cases, Starbon significantly outperformed the industrially available powdered Norit® activated carbon (AC) and reacted chemically with the gasses to some extent