Unsupervised Idealization of Ion Channel Recordings by Minimum Description Length: Application to Human PIEZO1-Channels.

Researchers 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 such 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.

Estimation of the effective intercellular diffusion coefficient in cell monolayers coupled by gap junctions.

OBJECTIVE: A recently developed dye-based assay to study gap junction permeability is analysed. The assay is based on electroporation of dye into a large number of connexin 43 expressing cells, grown to confluency on electrically conductive slides. The subsequent intercellular spread of dye to non-electroporated parts of the monolayer enables estimation of the intercellular coupling. So far, the extent of dye spread has been analyzed in qualitative terms only and not in a manner based directly on the physics of the underlying diffusion process. METHODS: We apply a continuum approximation assuming that the observed dye spread can be described by Fick's law of diffusion. Deduced from Fick's law, new measures are presented which directly relate the observed spread of dye to the diffusion coefficient. RESULTS: The theoretical framework enables the estimation of an effective diffusion coefficient from Fick's law independently of the specific indicator substance used in the assay. For Lucifer Yellow, diffusion stops within few minutes after the electroporation. Therefore only an order-of-magnitude estimate of the diffusion coefficient can be given for this dye. CONCLUSION: In terms of the underlying diffusion coefficient, the hitherto used measures give a relatively poor degree of quantification. In contrast, the present methods may yield direct information on the effective intercellular diffusion coefficient and hence provide additional and more precise information as to the permeability modulating effect of various substances.

Norepinephrine inhibits intercellular coupling in rat cardiomyocytes by ubiquitination of connexin43 gap junctions.

UNLABELLED: Gαq-stimulation reduces intercellular coupling within 10 min via a decrease in the membrane lipid phosphatidylinositol-4,5-bisphosphate (PIP2), but the mechanism is unknown. Here we show that uncoupling in rat cardiomyocytes after stimulation of α-adrenergic Gαq-coupled receptors with norepinephrine is prevented by proteasomal and lysosomal inhibitors, suggesting that internalization and possibly degradation of connexin43 (Cx43) is involved. Uncoupling was accompanied by increased Triton X-100 solubility of Cx43, which is considered a measure of the non-junctional pool of Cx43. However, inhibition of the proteasome and lysosome further increased solubility while preserving coupling, suggesting that communicating gap junctions can be part of the soluble fraction. Ubiquitination of Cx43 was also increased, and Cx43 co-immunoprecipitated with the ubiquitin ligase Nedd4. CONCLUSIONS: Norepinephrine increases ubiquitination of Cx43 in cardiomyocytes, possibly via Nedd4. We suggest that Cx43 is subsequently internalized, which is preceded by acquired solubility in Triton X-100, which does not lead to uncoupling per se.

Quantification of gap junctional intercellular communication based on digital image analysis.

Intercellular communication via gap junction channels can be quantified by several methods based on diffusion of fluorescent dyes or metabolites. Given the variation in intercellular coupling of cells, even under untreated control conditions, it is of essence to quantify the coupling between numerous cells to obtain reliable estimates of metabolic coupling. Quantification is often based on manual counting of fluorescent cells, which is time consuming and may include some degree of subjectivity. In this report, we introduce a technique based on digital image analysis, and the software for the analysis is presented together with a detailed protocol in the online supplemental material (http://bmi.ku.dk/matlab_program/). Fluorescent dye was introduced in connexin 43-expressing C6 glioma cells by in situ electroporation, and fluorescence intensity was measured in the electroporated cells and in cells receiving dye by intercellular diffusion. The analysis performed is semiautomatic, and comparison with traditional cell counting shows that this method reliably determines the effect of uncoupling by several interventions. This new method of analysis yields a rapid and objective quantification process with a high degree of reproducibility.

Phosphatidylinositol-bisphosphate regulates intercellular coupling in cardiac myocytes.

Changes in the lipid composition of cardiac myocytes have been reported during cardiac hypertrophy, cardiomyopathy, and infarction. Because a recent study indicates a relation between low phosphatidylinositol-bisphosphate (PIP(2)) levels and reduced intercellular coupling, we tested the hypothesis that agonist-induced changes in PIP(2) can result in a reduction of the functional coupling of cardiomyocytes and, consequently, in changes in conduction velocity. Intercellular coupling was measured by Lucifer Yellow dye transfer in cultured neonatal rat cardiomyocytes. Conduction velocity was measured in cardiomyocytes grown on microelectrode arrays. Intercellular coupling was reduced by angiotensin II (43.7 +/- 9.3%, N = 11) and noradrenaline (58.0 +/- 10.7%, N = 11). To test if reduced intercellular coupling after agonist stimulation was caused by PIP(2)-depletion, myocytes were stimulated by angiotensin II (57.3 +/- 5.7%, N = 14) and then allowed to recover in medium with or without wortmannin (an inhibitor of PIP(2) synthesis). Intercellular coupling fully recovered in control medium (102.1 +/- 8.9%, N = 10), whereas no recovery occurred in the presence of wortmannin (69.3 +/- 7.8%, N = 12). Inhibition of PKC, calmodulin, or arachidonic acid production did not affect the response to either angiotensin II or noradrenaline. Furthermore, decreasing or increasing PIP(2) also decreased and increased intercellular coupling, respectively. This supports the role of PIP(2) in the regulation of intercellular coupling. In beating myocytes, conduction velocity was reduced by angiotensin II stimulation, and recovery after wash out was prevented by inhibition of PIP(2) production. Reductions in PIP(2) inhibit intercellular coupling in cardiomyocytes, and stimulation by physiologically relevant agonists reduces intercellular coupling by this mechanism. The reduction in intercellular coupling lowered conduction velocity.

Protection by 6-aminonicotinamide against oxidative stress in cardiac cells.

Oxidative stress at the time of reperfusion is a major aspect of ischemia-reperfusion injury in heart as well as in other organs. There is a continuing interest in development of pharmacological approaches to alleviate this injury. 6-Aminonicotinamide (6AN) has been shown to diminish myocardial necrosis following global ischemia in an isolated rat heart, apparently by limiting the oxidative injury component. We therefore explored the antioxidative potential of 6AN in a model using H9C2(2-1) rat cardiac myoblasts exposed to H2O2 stress. Dependent on the specific protocol, 6AN pretreatment for 6-23 h resulted in a strongly increased cell survival: from 11% to 16% in untreated cells to 56-75% following 6AN treatment. This 6AN-mediated protection was associated with a modest increase (up to 55%) of the cytosolic free Ca2+, and was blocked by ryanodine, but not by verapamil or nifedipine. The protective effect of 6AN was associated with a decrease in total cell content of the reduced glutathione (GSH) by 15-44%, indicative of an oxidative shift in the GSH/GSSG system redox potential. We propose that this redox shift caused an increased Ca2+ leak through ryanodine receptors, reflecting their known sensitivity to redox modulation. In turn, this Ca2+ redistribution appeared to trigger a state of an enhanced antioxidative resistance, somewhat analogous to the phenomenon of Ca2+ preconditioning. Similar to some of the cases of Ca2+ preconditioning, this protected state involved the activity of Ca2+ -independent, but not of Ca2+ -dependent, isoform(s) of protein kinase C.