scholarly journals CellSpecks: A Software for Automated Detection and Analysis of Calcium Channels in Live Cells

2018 ◽  
Author(s):  
S I Shah ◽  
M Smith ◽  
D Swaminathan ◽  
I Parker ◽  
G Ullah ◽  
...  
Keyword(s):  
Ion Channels ◽  
Patch Clamp ◽  
Nicotinic Acetylcholine Receptors ◽  
High Throughput Screening ◽  
Single Channel ◽  
Video Recording ◽  
Synthetic Data ◽  
Live Cells ◽  
Patch Clamp Recording ◽  
Additional Advantage

ABSTRACTTo couple the fidelity of patch-clamp recording with a more high-throughput screening capability, we pioneered a novel approach to single channel recording that we named “optical patch clamp”. By using highly-sensitive fluorescent Ca2+ indicator dyes in conjunction with total internal fluorescence microscopy techniques, we monitor Ca2+ flux through individual Ca2+-permeable channels. This approach provides information about channel gating analogous to patch-clamp recording at time resolution of ~ 2 ms, with the additional advantage of being massively parallel, providing simultaneous and independent recording from thousands of channels in native environment. However, manual analysis of the data generated by this technique presents severe challenges as a video recording can include many thousands of frames. To overcome this bottleneck, we developed an image processing and analysis framework called CellSpecks, capable of detecting and fully analyzing the kinetics of ion channels within a video sequence. By using a randomly generated synthetic data, we tested the ability of CellSpecks to rapidly and efficiently detect and analyze the activity of thousands of ion channels, including openings for a few milliseconds. Here, we report the use of CellSpecks for the analysis of experimental data acquired by imaging muscle nicotinic acetylcholine receptors and the Alzheimer’s disease-associated amyloid beta pores with multiconductance levels in the plasma membrane of Xenopus laevis oocytes. We show that CellSpecks can accurately and efficiently generate location maps, create raw and processed fluorescence time-traces, histograms of mean open times, mean close times, open probabilities, durations, and maximum amplitudes, and a ‘channel chip’ showing the activity of all channels as a function of time. Although we specifically illustrate the application of CellSpecks for analyzing data from Ca2+ channels, it can be easily customized to analyze other spatially and temporally localized signals.

scholarly journals A Novel Membrane Potential-Sensitive Fluorescent Dye Improves Cell-Based Assays for Ion Channels

2002 ◽  
Vol 7 (1) ◽  
pp. 79-85 ◽  
Author(s):  
Deborah F. Baxter ◽  
Martin Kirk ◽  
Amy F. Garcia ◽  
Alejandra Raimondi ◽  
Mats H. Holmqvist ◽  
...  
Keyword(s):  
Membrane Potential ◽  
Ion Channels ◽  
Patch Clamp ◽  
High Throughput Screening ◽  
Fluorescent Dye ◽  
Patch Clamp Recording ◽  
Whole Cell ◽  
Cell Patch Clamp ◽  
Whole Cell Patch Clamp ◽  
Electrophysiological Studies

The study of ion channel-mediated changes in membrane potential using the conventional bisoxonol fluorescent dye DiBAC4(3) has several limitations, including a slow onset of response and multistep preparation, that limit both the fidelity of the results and the throughput of membrane potential assays. Here, we report the characterization of the FLIPR Membrane Potential Assay Kit (FMP) in cells expressing voltage- and ligand-gated ion channels. The steady-state and kinetics fluorescence properties of FMP were compared with those of DiBAC4(3), using both FLIPR and whole-cell patch-clamp recording. Our experiments with the voltage-gated K+ channel, hElk-1, revealed that FMP was 14-fold faster than DiBAC4(3) in response to depolarization. On addition of 60 mM KCl, the kinetics of fluorescence changes of FMP using FLIPR were identical to those observed in the electrophysiological studies using whole-cell current clamp. In addition, KCl concentration-dependent increases in FMP fluorescence correlated with the changes of membrane potential recorded in whole-cell patch clamp. In studies examining vanilloid receptor-1, a ligand-gated nonselective cation channel, FMP was superior to DiBAC4(3) with respect to both kinetics and amplitude of capsaicin-induced fluorescence changes. FMP has also been used to measure the activation of KATP1 and hERG.2 Thus this novel membrane potential dye represents a powerful tool for developing high-throughput screening assays for ion channels.

Persistence: a new statistic for characterizing ion-channel activity

1995 ◽  
Vol 350 (1334) ◽  
pp. 353-367 ◽  
Keyword(s):  
Patch Clamp ◽  
Ion Channel ◽  
Single Channel ◽  
Statistical Technique ◽  
Channel Activity ◽  
Patch Clamp Recording ◽  
Conductance Level

We introduce and illustrate by examples a new statistical technique, the persistence function, for characterizing ion-channel activity in a single-channel patch-clamp recording. Persistence is a function of both current and time. It is the probability that the current is at a given level (conditional on it having been at that level at an earlier time). Viewed as a function of current it exhibits the prominent conductance levels present in the recording, and viewed as a function of time for a conductance level it portrays the kinetics at that level.

scholarly journals A generalized kinetic model describes ion-permeation mechanisms in various ion channels

2021 ◽  
Author(s):  
Di Wu
Keyword(s):  
Ion Channels ◽  
Kinetic Model ◽  
Patch Clamp ◽  
Cellular Responses ◽  
Ion Permeation ◽  
Patch Clamp Recording ◽  
Boltzmann Factor ◽  
Current Voltage ◽  
Test Voltage ◽  
Generalized Kinetic Model

Ion channels conduct various ions across biological membranes to maintain the membrane potential, to transmit the electrical signals, and to elicit the subsequent cellular responses by the signaling ions. Ion channels differ in their capabilities to select and conduct ions, which can be studied by the patch-clamp recording method that compares the current traces responding to the test voltage elicited at different conditions. In these experiments, the current-voltage curves are usually fitted by a sigmoidal function containing the Boltzmann factor. This equation is quite successful in fitting the experimental data in many cases, but it also fails in several others. Regretfully, some useful information may be lost in these data, which otherwise can reveal the ion-permeation mechanisms. Here we present a generalized kinetic model that captures the essential features of the current-voltage relations and describes the simple mechanism of the ion permeation through different ion channels. We demonstrate that this model is capable to fit various types of the patch-clamp data and explain their ion-permeation mechanisms.

Recording of single γ-aminobutyrate- and acetylcholine-activated receptor channels translated by exogenous mRNA in Xenopus oocytes

1983 ◽  
Vol 218 (1213) ◽  
pp. 481-484 ◽  
Keyword(s):  
High Resolution ◽  
Patch Clamp ◽  
Xenopus Oocytes ◽  
Optic Lobe ◽  
Single Channel ◽  
Patch Clamp Recording ◽  
Chick Optic Lobe ◽  
Single Channel Currents ◽  
Channel Currents

High resolution (‘giga-seal’) patch clamp recording in Xenopus oocytes was used to measure single channel currents from ACh- and GABA-activated receptors. The proteins that make up these receptors had been translated from mRNA derived from, respectively, denervated cat muscle and chick optic lobe.

scholarly journals Application of Machine-Learning Methods to Recognize mitoBK Channels from Different Cell Types Based on the Experimental Patch-Clamp Results

2021 ◽  
Vol 22 (2) ◽  
pp. 840
Author(s):  
Monika Richter-Laskowska ◽  
Paulina Trybek ◽  
Piotr Bednarczyk ◽  
Agata Wawrzkiewicz-Jałowiecka
Keyword(s):  
Machine Learning ◽  
Patch Clamp ◽  
Single Channel ◽  
Conformational Dynamics ◽  
Cell Types ◽  
Inner Mitochondrial Membrane ◽  
Patch Clamp Recording ◽  
K Nearest Neighbors ◽  
Channel Protein ◽  
Different Cell Types

(1) Background: In this work, we focus on the activity of large-conductance voltage- and Ca2+-activated potassium channels (BK) from the inner mitochondrial membrane (mitoBK). The characteristic electrophysiological features of the mitoBK channels are relatively high single-channel conductance (ca. 300 pS) and types of activating and deactivating stimuli. Nevertheless, depending on the isoformal composition of mitoBK channels in a given membrane patch and the type of auxiliary regulatory subunits (which can be co-assembled to the mitoBK channel protein) the characteristics of conformational dynamics of the channel protein can be altered. Consequently, the individual features of experimental series describing single-channel activity obtained by patch-clamp method can also vary. (2) Methods: Artificial intelligence approaches (deep learning) were used to classify the patch-clamp outputs of mitoBK activity from different cell types. (3) Results: Application of the K-nearest neighbors algorithm (KNN) and the autoencoder neural network allowed to perform the classification of the electrophysiological signals with a very good accuracy, which indicates that the conformational dynamics of the analyzed mitoBK channels from different cell types significantly differs. (4) Conclusion: We displayed the utility of machine-learning methodology in the research of ion channel gating, even in cases when the behavior of very similar microbiosystems is analyzed. A short excerpt from the patch-clamp recording can serve as a “fingerprint” used to recognize the mitoBK gating dynamics in the patches of membrane from different cell types.

Stretch-activated ion channels in tissue-cultured chick heart

1993 ◽  
Vol 264 (3) ◽  
pp. H960-H972 ◽  
Author(s):  
A. Ruknudin ◽  
F. Sachs ◽  
J. O. Bustamante
Keyword(s):  
Ion Channels ◽  
Single Channel ◽  
Inward Rectifier ◽  
Channel Noise ◽  
Patch Clamp Recording ◽  
Alkali Cations ◽  
Channel Expression ◽  
Inward Currents ◽  
Extracellular Ions ◽  
Stretch Activated Ion Channels

With use of single-channel patch-clamp recording, we found five distinct types of stretch-activated ion channels (SACs) in tissue-cultured embryonic chick cardiac myocytes. With 140 mM K+ saline in the pipette, four channels had linear conductances of approximately equal to 25, 50, 100, and 200 pS and other channel was an inward rectifier of approximately equal to 25 pS at 0 mV membrane potential. The 100- and 200-pS channels were K+ selective, whereas the others passed alkali cations and Ca2+. From reversal potentials, the permeability ratio of K+/Na+, PK/PNa, was 3–7 for nonselective channels and 7–16 for K(+)-selective channels. Channel density was approximately equal to 0.3/microns2 for linear conductances and approximately equal to 0.1/microns2 for inward rectifier. Open-channel noise was a function of pipette filling solution with root-mean-square (RMS) noise increasing in the order K+ < isosmotic sucrose (plus trace ions) < Na+, probably reflecting short-lived block by extracellular ions. All channels were blocked by 20 microM Gd3+. The 25-pS linear channel was also blocked by 12.5 microM tetrodotoxin and 10 microM diltiazem, but the others were insensitive at these concentrations. Extracellular Cs+ and tetraethylammonium chloride did not block any channels. We saw no SAC activity in cells grown without embryo extract (EE), which demonstrates that channel expression, or some necessary cofactor, is under control of growth factors. Basic fibroblast growth factor (FGF) could replace EE in supporting channel expression. The presence of SACs capable of generating inward currents might explain how stretch increases automaticity in the heart. Because some SACs were permeable to Ca2+, they could contribute to the Starling curve and perhaps to initiating stretch-induced hypertrophy.

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