scholarly journals Unsupervised idealization of ion channel recordings by Minimum Description Length: Application to human PIEZO1-channels

2017 ◽  
Author(s):  
Radhakrishnan Gnanasambandam ◽  
Morten Schak Nielsen ◽  
Christopher Nicolai ◽  
Frederick Sachs ◽  
Johannes Pauli Hofgaard ◽  
...  
Keyword(s):  
Ion Channels ◽  
Ion Channel ◽  
Markov Models ◽  
Single Channel ◽  
Minimum Description Length ◽  
Simulated Data ◽  
Multiple Channels ◽  
Electrophysiological Recordings ◽  
Single Channel Currents ◽  
Channel Currents

AbstractResearchers can investigate the mechanistic and molecular basis of many physiological phenomena in cells by analyzing the fundamental properties of single ion channels. These analyses entail recording single channel currents and measuring current amplitudes and transition rates between conductance states. Since most electrophysiological recordings contain noise, the data analysis can proceed by idealizing the recordings to isolate the true currents from the noise. This de-noising can be accomplished with threshold crossing algorithms and Hidden Markov Models, but such procedures generally depend on inputs and supervision by the user, thus requiring some prior knowledge of underlying processes. Channels with unknown gating and/or functional sub-states and the presence in the recording of currents from uncorrelated background channels present substantial challenges to unsupervised analyses.Here we describe and characterize an idealization algorithm based on Rissanen’s Minimum Description Length (MDL) Principle. This method uses minimal assumptions and idealizes ion channel recordings without requiring a detailed user input or a priori assumptions about channel conductance and kinetics.. Furthermore, we demonstrate that correlation analysis of conductance steps can resolve properties of single ion channels in recordings contaminated by signals from multiple channels. We first validated our methods on simulated data defined with a range of different signal-to-noise levels, and then showed that our algorithm can recover channel currents and their substates from recordings with multiple channels, even under conditions of high noise. We then tested the MDL algorithm on real experimental data from human PIEZO1 channels and found that our method revealed the presence of substates with alternate conductances.

Ion channels and disease

2020 ◽  
pp. 246-255
Author(s):  
Frances Ashcroft ◽  
Paolo Tammaro
Keyword(s):  
Ion Channels ◽  
Ion Channel ◽  
Single Channel ◽  
Cell Types ◽  
Channel Structure ◽  
Channel Proteins ◽  
Channel Function ◽  
Ion Channel Proteins ◽  
Single Channel Currents ◽  
Channel Currents

Ion channels are membrane proteins that act as gated pathways for the movement of ions across cell membranes. They are found in both surface and intracellular membranes and play essential roles in the physiology of all cell types. An ever-increasing number of human diseases are now known to be caused by defects in ion channel function. To understand how ion channel defects give rise to disease, it is helpful to understand how the ion channel proteins work. This chapter therefore considers what is known of ion channel structure, explains the properties of the single ion channel, and shows how single-channel currents give rise to action potentials and synaptic potentials.

On the stochastic properties of single ion channels

1981 ◽  
Vol 211 (1183) ◽  
pp. 205-235 ◽  
Keyword(s):  
Ion Channels ◽  
Single Channel ◽  
The State ◽  
Agonist Action ◽  
Agonist Concentration ◽  
Relaxation Experiments ◽  
Flow Through ◽  
Single Channel Currents ◽  
Stochastic Properties ◽  
Channel Currents

It is desirable to be able to predict, from a specified mechanism, the appearance of currents that flow through single ion channels ( a ) to enable interpretation of experiments in which single channel currents are observed, and ( b ) to allow physical meaning to be attached to the results observed in kinetic (noise and relaxation) experiments in which the aggregate of many single channel currents is observed. With this object, distributions (and their means) are derived for the length of the sojourn in any specified subset of states (e. g. all shut states). In general these are found to depend not only on the state in which the sojourn starts, but also on the state that immediately follows the sojourn. The methods described allow derivation of the distribution of, for example, ( a ) the number of openings, and total length of the burst of openings, that may occur during a single occupancy, and ( b ) the apparent gap between such bursts. The methods are illustrated by their application to two simple theories of agonist action. The Castillo-Katz (non-cooperative) mechanism predicts, for example, that the number of openings per occupancy, and the apparent burst length, are independent of agonist concentration whereas a simple cooperative mechanism predicts that both will increase with agonist concentration.

scholarly journals The nature and origin of spontaneous noise in G protein-gated ion channels.

1991 ◽  
Vol 97 (6) ◽  
pp. 1279-1293 ◽  
Author(s):  
K Okabe ◽  
A Yatani ◽  
A M Brown
Keyword(s):  
Ion Channels ◽  
G Protein ◽  
Single Channel ◽  
Coupled Systems ◽  
Dependent Manner ◽  
Protein Receptor ◽  
Spontaneous Noise ◽  
Single Channel Currents ◽  
Channel Currents ◽  
Inside Out

Arrival of agonist is generally thought to initiate the signal transduction process in G protein-receptor coupled systems. However, the muscarinic atrial K+ (K+[ACh]) channel opens spontaneously in the absence of applied agonist, giving a noisy appearance to the current records. We investigated the nature and origin of the noise by measuring single channel currents in cell-attached or excised, inside-out membrane patches. Guanosine triphosphate (GTP) produced identical single channel currents in a concentration- and Mg(2+)-dependent manner in the presence or absence of carbachol, but the requirements for GTP were greater in the absence of agonist. Hence the agonist-independent currents appeared to be produced by an endogenous G protein, Gk. This prediction was confirmed when an affinity-purified, sequence-specific Gi-3 alpha antibody or pertussis toxin (PTX) blocked the agonist-independent currents. Candidate endogenous agonists were ruled out by the lack of effect of their corresponding antagonists. Thus agonist-independent currents had the same nature as agonist-dependent K+[ACh] currents and seemed to originate in the same way. We have developed a hypothesis in which agonist-free, empty receptors prime Gk with GTP and Gk activates atrial K+ [ACh] channels producing basal currents or noise. Agonist-independent activation by G proteins of effectors including ion channels appears to be a common occurrence.

scholarly journals Analysis of single ion channel data incorporating time-interval omission and sampling

2005 ◽  
Vol 3 (6) ◽  
pp. 87-97 ◽  
Author(s):  
Yu-Kai The ◽  
Jens Timmer
Keyword(s):  
Markov Models ◽  
Dead Time ◽  
Single Channel ◽  
Hidden Markov ◽  
Interval Length ◽  
Time Interval ◽  
Sampled Data ◽  
The Dead ◽  
Single Channel Currents ◽  
Channel Currents

Hidden Markov models are widely used to describe single channel currents from patch-clamp experiments. The inevitable anti-aliasing filter limits the time resolution of the measurements and therefore the standard hidden Markov model is not adequate anymore. The notion of time-interval omission has been introduced where brief events are not detected. The developed, exact solutions to this problem do not take into account that the measured intervals are limited by the sampling time. In this case the dead-time that specifies the minimal detectable interval length is not defined unambiguously. We show that a wrong choice of the dead-time leads to considerably biased estimates and present the appropriate equations to describe sampled data.

A vesicle preparation for resolving single-channel currents in tegument of male Schistosoma mansoni

Parasitology ◽  
1997 ◽  
Vol 115 (2) ◽  
pp. 183-192 ◽  
Author(s):  
A. P. ROBERTSON ◽  
R. J. MARTIN ◽  
J. R. KUSEL
Keyword(s):  
Electron Microscopy ◽  
Ion Channel ◽  
Schistosoma Mansoni ◽  
Adult Male ◽  
Single Channel ◽  
Patch Clamp Technique ◽  
Fluorescence Studies ◽  
Vesicle Preparation ◽  
Single Channel Currents ◽  
Channel Currents

A tegumental vesicle preparation from adult male Schistosoma mansoni was developed that allows the resolution of single ion-channel currents. Adult male schistosomes were exposed to a low pH (3·75) medium for a period of approximately 30 min at 37°C. During this period smooth vesicles formed from the tegument. Fluorescence microscopy following staining of the tegument with the dye, 5-N-[octadecanoyl]aminofluorescein (AF-18), transmission electron microscopy and scanning electron microscopy revealed that the vesicles were produced from the outer tegumental membrane. The fluorescence studies showed the presence of the double bilayer structure of the outer membrane in >41% of the vesicles. These studies suggested that the preparation is suitable for single-channel recording with the patch-clamp technique. Cell-attached and isolated inside-out patch recordings of ion-channel activity were obtained with giga-ohm resistance seals. Different types of ion-channel were recorded from tegumental vesicles from male schistosomes, illustrating the potential of the technique. The channels observed included: a non-selective cation channel (360 pS); a K+ channel (with a conductance of 115 pS in high bath-K conditions); and a Cl− selective channel (20 pS). The currents of these ion-channels may cross the double bilayer of the outer tegumental membrane.

scholarly journals TOK Homologue in Neurospora crassa: First Cloning and Functional Characterization of an Ion Channel in a Filamentous Fungus

2003 ◽  
Vol 2 (1) ◽  
pp. 181-190 ◽  
Author(s):  
Stephen K. Roberts
Keyword(s):  
Ion Channels ◽  
Ion Channel ◽  
Neurospora Crassa ◽  
Filamentous Fungus ◽  
Single Channel ◽  
Functional Characterization ◽  
Reversal Potential ◽  
Channel Activity ◽  
Biophysical Properties ◽  
Patch Clamp Technique

ABSTRACT In contrast to animal and plant cells, very little is known of ion channel function in fungal physiology. The life cycle of most fungi depends on the “filamentous” polarized growth of hyphal cells; however, no ion channels have been cloned from filamentous fungi and comparatively few preliminary recordings of ion channel activity have been made. In an attempt to gain an insight into the role of ion channels in fungal hyphal physiology, a homolog of the yeast K+ channel (ScTOK1) was cloned from the filamentous fungus, Neurospora crassa. The patch clamp technique was used to investigate the biophysical properties of the N. crassa K+ channel (NcTOKA) after heterologous expression of NcTOKA in yeast. NcTOKA mediated mainly time-dependent outward whole-cell currents, and the reversal potential of these currents indicated that it conducted K+ efflux. NcTOKA channel gating was sensitive to extracellular K+ such that channel activation was dependent on the reversal potential for K+. However, expression of NcTOKA was able to overcome the K+ auxotrophy of a yeast mutant missing the K+ uptake transporters TRK1 and TRK2, suggesting that NcTOKA also mediated K+ influx. Consistent with this, close inspection of NcTOKA-mediated currents revealed small inward K+ currents at potentials negative of EK. NcTOKA single-channel activity was characterized by rapid flickering between the open and closed states with a unitary conductance of 16 pS. NcTOKA was effectively blocked by extracellular Ca2+, verapamil, quinine, and TEA+ but was insensitive to Cs+, 4-aminopyridine, and glibenclamide. The physiological significance of NcTOKA is discussed in the context of its biophysical properties.

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