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Shah SI, Demuro A, Mak DOD, Parker I, Pearson JE, Ullah G. TraceSpecks: A Software for Automated Idealization of Noisy Patch-Clamp and Imaging Data. Biophys J 2019; 115:9-21. [PMID: 29972815 DOI: 10.1016/j.bpj.2018.06.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 05/15/2018] [Accepted: 06/04/2018] [Indexed: 10/28/2022] Open
Abstract
Experimental records of single molecules or ion channels from fluorescence microscopy and patch-clamp electrophysiology often include high-frequency noise and baseline fluctuations that are not generated by the system under investigation and have to be removed. Moreover, multiple channels or conductance levels can be present at a time in the data that need to be quantified to accurately understand the behavior of the system. Manual procedures for removing these fluctuations and extracting conducting states or multiple channels are laborious, prone to subjective bias, and likely to hinder the processing of often very large data sets. We introduce a maximal likelihood formalism for separating signal from a noisy and drifting background such as fluorescence traces from imaging of elementary Ca2+ release events called puffs arising from clusters of channels, and patch-clamp recordings of ion channels. Parameters such as the number of open channels or conducting states, noise level, and background signal can all be optimized using the expectation-maximization algorithm. We implement our algorithm following the Baum-Welch approach to expectation-maximization in the portable Java language with a user-friendly graphical interface and test the algorithm on both synthetic and experimental data from the patch-clamp electrophysiology of Ca2+ channels and fluorescence microscopy of a cluster of Ca2+ channels and Ca2+ channels with multiple conductance levels. The resulting software is accurate, fast, and provides detailed information usually not available through manual analysis. Options for visual inspection of the raw and processed data with key parameters are provided, in addition to a range of statistics such as the mean open probabilities, mean open times, mean close times, dwell-time distributions for different number of channels open or conductance levels, amplitude distribution of all opening events, and number of transitions between different number of open channels or conducting levels in asci format with a single click.
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Affiliation(s)
| | - Angelo Demuro
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, California
| | - Don-On Daniel Mak
- Department of Physiology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ian Parker
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, California; Department of Physiology and Biophysics, University of California, Irvine, Irvine, California
| | - John E Pearson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Ghanim Ullah
- Department of Physics, University of South Florida, Tampa, Florida.
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Toglia P, Demuro A, Mak DOD, Ullah G. Data-driven modeling of mitochondrial dysfunction in Alzheimer's disease. Cell Calcium 2018; 76:23-35. [PMID: 30248575 DOI: 10.1016/j.ceca.2018.09.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 09/02/2018] [Accepted: 09/03/2018] [Indexed: 02/06/2023]
Abstract
Intracellular accumulation of oligomeric forms of β amyloid (Aβ) are now believed to play a key role in the earliest phase of Alzheimer's disease (AD) as their rise correlates well with the early symptoms of the disease. Extensive evidence points to impaired neuronal Ca2+ homeostasis as a direct consequence of the intracellular Aβ oligomers. However, little is known about the downstream effects of the resulting Ca2+ rise on the many intracellular Ca2+-dependent pathways. Here we use multiscale modeling in conjunction with patch-clamp electrophysiology of single inositol 1,4,5-trisphosphate (IP3) receptor (IP3R) and fluorescence imaging of whole-cell Ca2+ response, induced by exogenously applied intracellular Aβ42 oligomers to show that Aβ42 inflicts cytotoxicity by impairing mitochondrial function. Driven by patch-clamp experiments, we first model the kinetics of IP3R, which is then extended to build a model for the whole-cell Ca2+ signals. The whole-cell model is then fitted to fluorescence signals to quantify the overall Ca2+ release from the endoplasmic reticulum by intracellular Aβ42 oligomers through G-protein-mediated stimulation of IP3 production. The estimated IP3 concentration as a function of intracellular Aβ42 content together with the whole-cell model allows us to show that Aβ42 oligomers impair mitochondrial function through pathological Ca2+ uptake and the resulting reduced mitochondrial inner membrane potential, leading to an overall lower ATP and increased production of reactive oxygen species and H2O2. We further show that mitochondrial function can be restored by the addition of Ca2+ buffer EGTA, in accordance with the observed abrogation of Aβ42 cytotoxicity by EGTA in our live cells experiments.
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Affiliation(s)
- Patrick Toglia
- Department of Physics, University of South Florida, Tampa, FL 33620, USA
| | - Angelo Demuro
- Department of Neurobiology and Behavior and Physiology and Biophysics, University of California, Irvine, CA 92697, USA
| | - Don-On Daniel Mak
- Department of Physiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ghanim Ullah
- Department of Physics, University of South Florida, Tampa, FL 33620, USA.
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Wang JB, Gu Y, Zhang MX, Yang S, Wang Y, Wang W, Li XR, Zhao YT, Wang HT. High expression of type I inositol 1,4,5-trisphosphate receptor in the kidney of rats with hepatorenal syndrome. World J Gastroenterol 2018; 24:3273-3280. [PMID: 30090007 PMCID: PMC6079285 DOI: 10.3748/wjg.v24.i29.3273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 06/19/2018] [Accepted: 06/27/2018] [Indexed: 02/06/2023] Open
Abstract
AIM To detect the expression of type I inositol 1,4,5-trisphosphate receptor (IP3RI) in the kidney of rats with hepatorenal syndrome (HRS). METHODS One hundred and twenty-five Sprague-Dawley rats were randomly divided into four groups to receive an intravenous injection of D-galactosamine (D-GalN) plus lipopolysaccharide (LPS; group G/L, n = 50), D-GalN alone (group G, n = 25), LPS alone (group L, n = 25), and normal saline (group NS, n = 25), respectively. At 3, 6, 9, 12, and 24 h after injection, blood, liver, and kidney samples were collected. Hematoxylin-eosin staining of liver tissue was performed to assess hepatocyte necrosis. Electron microscopy was used to observe ultrastructural changes in the kidney. Western blot analysis and real-time PCR were performed to detect the expression of IP3RI protein and mRNA in the kidney, respectively. RESULTS Hepatocyte necrosis was aggravated gradually, which was most significant at 12 h after treatment with D-galactosamine/lipopolysaccharide, and was characterized by massive hepatocyte necrosis. At the same time, serum levels of biochemical indicators including liver and kidney function indexes were all significantly changed. The structure of the renal glomerulus and tubules was normal at all time points. Western blot analysis indicated that IP3RI protein expression began to rise at 3 h (P < 0.05) and peaked at 12 h (P < 0.01). Real-time PCR demonstrated that IP3RI mRNA expression began to rise at 3 h (P < 0.05) and peaked at 9 h (P < 0.01). CONCLUSION IP3RI protein expression is increased in the kidney of HRS rats, and may be regulated at the transcriptional level.
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MESH Headings
- Animals
- Disease Models, Animal
- Galactosamine/toxicity
- Hepatocytes/pathology
- Hepatorenal Syndrome/chemically induced
- Hepatorenal Syndrome/pathology
- Humans
- Inositol 1,4,5-Trisphosphate Receptors/genetics
- Inositol 1,4,5-Trisphosphate Receptors/metabolism
- Kidney/blood supply
- Kidney/cytology
- Kidney/pathology
- Kidney/ultrastructure
- Lipopolysaccharides/toxicity
- Liver/cytology
- Liver/drug effects
- Liver/pathology
- Male
- Microscopy, Electron
- Muscle, Smooth, Vascular/cytology
- Muscle, Smooth, Vascular/pathology
- Myocytes, Smooth Muscle/pathology
- Myocytes, Smooth Muscle/ultrastructure
- Necrosis
- RNA, Messenger/metabolism
- Rats
- Rats, Sprague-Dawley
- Specific Pathogen-Free Organisms
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Affiliation(s)
- Jing-Bo Wang
- Liver Cirrhosis Ward, the Sixth People’s Hospital of Shenyang, Shenyang 110006, Liaoning Province, China
| | - Ye Gu
- Liver Cirrhosis Ward, the Sixth People’s Hospital of Shenyang, Shenyang 110006, Liaoning Province, China
| | - Ming-Xiang Zhang
- Liver Cirrhosis Ward, the Sixth People’s Hospital of Shenyang, Shenyang 110006, Liaoning Province, China
| | - Shun Yang
- Liaoning Cancer Hospital & Institute, Shenyang 110042, Liaoning Province, China
| | - Yan Wang
- Liver Cirrhosis Ward, the Sixth People’s Hospital of Shenyang, Shenyang 110006, Liaoning Province, China
| | - Wei Wang
- Liver Cirrhosis Ward, the Sixth People’s Hospital of Shenyang, Shenyang 110006, Liaoning Province, China
| | - Xi-Ran Li
- Liver Cirrhosis Ward, the Sixth People’s Hospital of Shenyang, Shenyang 110006, Liaoning Province, China
| | - Yi-Tong Zhao
- Liver Cirrhosis Ward, the Sixth People’s Hospital of Shenyang, Shenyang 110006, Liaoning Province, China
| | - Hai-Tao Wang
- Department of General Surgery, the Second Affiliated Hospital of Shenyang Medical College, Shenyang 110002, Liaoning Province, China
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King JR, Ullah A, Bak E, Jafri MS, Kabbani N. Ionotropic and Metabotropic Mechanisms of Allosteric Modulation of α7 Nicotinic Receptor Intracellular Calcium. Mol Pharmacol 2018; 93:601-611. [PMID: 29588343 PMCID: PMC11033947 DOI: 10.1124/mol.117.111401] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 03/23/2018] [Indexed: 12/13/2022] Open
Abstract
The pharmacological targeting of the α7 nicotinic acetylcholine receptor (α7) is a promising strategy in the development of new drugs for neurologic diseases. Because α7 receptors regulate cellular calcium, we investigated how the prototypical type II-positive allosteric modulator PNU120596 affects α7-mediated calcium signaling. Live imaging experiments show that PNU120596 augments ryanodine receptor-driven calcium-induced calcium release (CICR), inositol-induced calcium release (IICR), and phospholipase C activation by the α7 receptor. Both influx of calcium through the α7 nicotinic acetylcholine receptor (nAChR) channel as well as the binding of intracellular G proteins were involved in the effect of PNU120596 on intracellular calcium. This is evidenced by the findings that chelation of extracellular calcium, expression of α7D44A or α7345-348A mutant subunits, or blockade of calcium store release compromised the ability of PNU120596 to increase intracellular calcium transients generated by α7 ligand activation. Spatiotemporal stochastic modeling of calcium transient responses corroborates these results and indicates that α7 receptor activation enables calcium microdomains locally and to lesser extent in the distant cytosol. From the model, allosteric modulation of the receptor activates CICR locally via ryanodine receptors and augments IICR through enhanced calcium influx due to prolonged α7 nAChR opening. These findings provide a new mechanistic framework for understanding the effect of α7 receptor allosteric modulation on both local and global calcium dynamics.
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Affiliation(s)
- Justin R King
- Interdisciplinary Program in Neuroscience (J.R.K., M.S.J., N.K.) and School of Systems Biology (A.U., E.B., M.S.J., N.K.), George Mason University, Fairfax, Virginia
| | - Aman Ullah
- Interdisciplinary Program in Neuroscience (J.R.K., M.S.J., N.K.) and School of Systems Biology (A.U., E.B., M.S.J., N.K.), George Mason University, Fairfax, Virginia
| | - Ellen Bak
- Interdisciplinary Program in Neuroscience (J.R.K., M.S.J., N.K.) and School of Systems Biology (A.U., E.B., M.S.J., N.K.), George Mason University, Fairfax, Virginia
| | - M Saleet Jafri
- Interdisciplinary Program in Neuroscience (J.R.K., M.S.J., N.K.) and School of Systems Biology (A.U., E.B., M.S.J., N.K.), George Mason University, Fairfax, Virginia
| | - Nadine Kabbani
- Interdisciplinary Program in Neuroscience (J.R.K., M.S.J., N.K.) and School of Systems Biology (A.U., E.B., M.S.J., N.K.), George Mason University, Fairfax, Virginia
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Toglia P, Ullah G, Pearson JE. Analyzing optical imaging of Ca 2+ signals via TIRF microscopy: The limits on resolution due to chemical rates and depth of the channels. Cell Calcium 2017; 67:65-73. [PMID: 29029792 DOI: 10.1016/j.ceca.2017.08.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 08/22/2017] [Accepted: 08/23/2017] [Indexed: 11/17/2022]
Abstract
High resolution total internal reflection (TIRF) microscopy (TIRFM) together with detailed computational modeling provides a powerful approach towards the understanding of a wide range of Ca2+ signals mediated by the ubiquitous inositol 1,4,5-trisphosphate (IP3) receptor (IP3R) channel. Exploiting this fruitful collaboration further requires close agreement between the models and observations. However, elementary Ca2+ release events, puffs, imaged through TIRFM do not show the rapid single-channel openings and closings during and between puffs as are present in simulated puffs using data-driven single channel models. TIRFM also shows a rapid equilibration of 10ms after a channel opens or closes which is not achievable in simulation using standard Ca2+ diffusion coefficients and reaction rates between indicator dye and Ca2+. Furthermore, TIRFM imaging cannot decipher the depth of the channel with respect to the microscope, which will affect the change in fluorescence that the microscope detects, thereby affecting its sensitivity to fast single-channel activity. Using the widely used Ca2+ diffusion coefficients and reaction rates, our simulations show equilibration rates that are eight times slower than TIRFM imaging. We show that to get equilibrium rates consistent with observed values, the diffusion coefficients and reaction rates have to be significantly higher than the values reported in the literature, and predict the channel depth to be 200-250nm. Finally, we show that with the addition of noise, short events due to 1-2ms opening and closing of channels that are observed in computational models can be missed in TIRFM.
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Affiliation(s)
- Patrick Toglia
- Department of Physics, University of South Florida, Tampa, FL 33620, USA
| | - Ghanim Ullah
- Department of Physics, University of South Florida, Tampa, FL 33620, USA.
| | - John E Pearson
- T-6 Theoretical Biology and Biophysics Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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Cao P, Falcke M, Sneyd J. Mapping Interpuff Interval Distribution to the Properties of Inositol Trisphosphate Receptors. Biophys J 2017; 112:2138-2146. [PMID: 28538151 DOI: 10.1016/j.bpj.2017.03.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/14/2017] [Accepted: 03/24/2017] [Indexed: 01/24/2023] Open
Abstract
Tightly clustered inositol trisphosphate receptors (IP3Rs) control localized Ca2+ liberation from the endoplasmic reticulum to generate repetitive Ca2+ puffs. Distributions of the interpuff interval (IPI), i.e., the waiting time between successive puffs, are found to be well characterized by a probability density function involving only two parameters, λ and ξ, which represent the basal rate of puff generation and the recovery rate from refractoriness, respectively. However, how the two parameters depend on the kinetic parameters of single IP3Rs in a cluster is still unclear. In this article, using a stochastic puff model and a single-channel data-based IP3R model, we establish the dependencies of λ and ξ on two important IP3R model parameters, IP3 concentration ([IP3]) and the recovery rate from Ca2+ inhibition (rlow). By varying [IP3] and rlow in physiologically plausible ranges, we find that the ξ-λ plane is comprised of only two disjoint regions, a biologically impermissible region and a region where each parameter set (ξ, λ) can be caused by using two different combinations of [IP3] and rlow. The two combinations utilize very different mechanisms to maintain the same IPI distribution, and the mechanistic difference provides a way of identifying IP3R kinetic parameters by observing properties of the IPI.
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Affiliation(s)
- Pengxing Cao
- School of Mathematics and Statistics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Martin Falcke
- Mathematical Cell Physiology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - James Sneyd
- Department of Mathematics, The University of Auckland, Auckland, New Zealand.
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Siekmann I, Fackrell M, Crampin EJ, Taylor P. Modelling modal gating of ion channels with hierarchical Markov models. Proc Math Phys Eng Sci 2016; 472:20160122. [PMID: 27616917 PMCID: PMC5014102 DOI: 10.1098/rspa.2016.0122] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 07/22/2016] [Indexed: 11/12/2022] Open
Abstract
Many ion channels spontaneously switch between different levels of activity. Although this behaviour known as modal gating has been observed for a long time it is currently not well understood. Despite the fact that appropriately representing activity changes is essential for accurately capturing time course data from ion channels, systematic approaches for modelling modal gating are currently not available. In this paper, we develop a modular approach for building such a model in an iterative process. First, stochastic switching between modes and stochastic opening and closing within modes are represented in separate aggregated Markov models. Second, the continuous-time hierarchical Markov model, a new modelling framework proposed here, then enables us to combine these components so that in the integrated model both mode switching as well as the kinetics within modes are appropriately represented. A mathematical analysis reveals that the behaviour of the hierarchical Markov model naturally depends on the properties of its components. We also demonstrate how a hierarchical Markov model can be parametrized using experimental data and show that it provides a better representation than a previous model of the same dataset. Because evidence is increasing that modal gating reflects underlying molecular properties of the channel protein, it is likely that biophysical processes are better captured by our new approach than in earlier models.
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Affiliation(s)
- Ivo Siekmann
- Systems Biology Laboratory, Melbourne School of Engineering, University of Melbourne, Melbourne, Australia
- Centre for Systems Genomics, University of Melbourne, Melbourne, Australia
| | - Mark Fackrell
- School of Mathematics and Statistics, University of Melbourne, Melbourne, Australia
| | - Edmund J. Crampin
- Systems Biology Laboratory, Melbourne School of Engineering, University of Melbourne, Melbourne, Australia
- Centre for Systems Genomics, University of Melbourne, Melbourne, Australia
- School of Mathematics and Statistics, University of Melbourne, Melbourne, Australia
- School of Medicine, University of Melbourne, Melbourne, Australia
- Australian Research Council Centre of Excellence in Convergent Bio-Nano Science and Technology, Melbourne, Australia
| | - Peter Taylor
- School of Mathematics and Statistics, University of Melbourne, Melbourne, Australia
- Australian Research Council Centre of Excellence for Mathematical and Statistical Frontiers, Melbourne, Australia
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