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Araujo R, Brumley D, Cursons J, Day K, Faria M, Flegg JA, Germano D, Hunt H, Hunter P, Jenner A, Johnston S, McCaw JM, Maini P, Miller C, Muskovic W, Osborne J, Pan M, Rajagopal V, Shahidi N, Siekmann I, Stumpf M, Zanca A. Frontiers of Mathematical Biology: A workshop honouring Professor Edmund Crampin. Math Biosci 2023; 359:109007. [PMID: 37062447 DOI: 10.1016/j.mbs.2023.109007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/28/2023] [Accepted: 04/02/2023] [Indexed: 04/18/2023]
Affiliation(s)
- Robyn Araujo
- School of Mathematical Sciences, Queensland University of Technology, Australia
| | - Douglas Brumley
- School of Mathematics and Statistics, The University of Melbourne, Australia
| | | | - Karen Day
- Bio21 Institute, The University of Melbourne, Australia
| | - Matthew Faria
- Department of Biomedical Engineering, The University of Melbourne, Australia
| | - Jennifer A Flegg
- School of Mathematics and Statistics, The University of Melbourne, Australia
| | - Domenic Germano
- School of Mathematics and Statistics, The University of Melbourne, Australia
| | - Hilary Hunt
- Department of Biology, University of Oxford, United Kingdom
| | - Peter Hunter
- Auckland Bioengineering Institute, University of Auckland, New Zealand
| | - Adrianne Jenner
- School of Mathematical Sciences, Queensland University of Technology, Australia
| | - Stuart Johnston
- School of Mathematics and Statistics, The University of Melbourne, Australia
| | - James M McCaw
- School of Mathematics and Statistics, The University of Melbourne, Australia; Melbourne School of Population and Global Health, The University of Melbourne, Australia.
| | - Philip Maini
- Mathematical Institute, University of Oxford, United Kingdom
| | - Claire Miller
- Auckland Bioengineering Institute, University of Auckland, New Zealand
| | | | - James Osborne
- School of Mathematics and Statistics, The University of Melbourne, Australia
| | - Michael Pan
- School of Mathematics and Statistics, The University of Melbourne, Australia
| | - Vijay Rajagopal
- Department of Biomedical Engineering, The University of Melbourne, Australia
| | - Niloofar Shahidi
- Auckland Bioengineering Institute, University of Auckland, New Zealand
| | - Ivo Siekmann
- School of Computer Science and Mathematics, Liverpool John Moores University, United Kingdom
| | - Michael Stumpf
- School of Mathematics and Statistics, The University of Melbourne, Australia; Melbourne Integrative Genomics, The University of Melbourne, Australia
| | - Adriana Zanca
- School of Mathematics and Statistics, The University of Melbourne, Australia
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Affiliation(s)
- Philip K Maini
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, OX2 6GG, UK.
| | - Peter J Hunter
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Peter J Gawthrop
- Systems Biology Laboratory, Department of Biomedical Engineering, Faculty of Engineering and Information Technology, University of Melbourne, Victoria, 3010, Australia
- Systems Biology Laboratory, School of Mathematics and Statistics, University of Melbourne, Victoria, 3010, Australia
| | - Nic P Smith
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
- Queensland University of Technology, Brisbane, Australia
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Siems T, Hellmuth M, Liebscher V. Simultaneous Credible Regions for Multiple Changepoint Locations. J Comput Graph Stat 2018. [DOI: 10.1080/10618600.2018.1513366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Tobias Siems
- aDepartment of Mathematics and Computer Science, University of Greifswald, Greifswald, Germany
| | - Marc Hellmuth
- aDepartment of Mathematics and Computer Science, University of Greifswald, Greifswald, Germany
| | - Volkmar Liebscher
- aDepartment of Mathematics and Computer Science, University of Greifswald, Greifswald, Germany
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Hwang W, Lee IB, Hong SC, Hyeon C. Decoding Single Molecule Time Traces with Dynamic Disorder. PLoS Comput Biol 2016; 12:e1005286. [PMID: 28027304 PMCID: PMC5226833 DOI: 10.1371/journal.pcbi.1005286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 01/11/2017] [Accepted: 12/07/2016] [Indexed: 12/11/2022] Open
Abstract
Single molecule time trajectories of biomolecules provide glimpses into complex folding landscapes that are difficult to visualize using conventional ensemble measurements. Recent experiments and theoretical analyses have highlighted dynamic disorder in certain classes of biomolecules, whose dynamic pattern of conformational transitions is affected by slower transition dynamics of internal state hidden in a low dimensional projection. A systematic means to analyze such data is, however, currently not well developed. Here we report a new algorithm—Variational Bayes-double chain Markov model (VB-DCMM)—to analyze single molecule time trajectories that display dynamic disorder. The proposed analysis employing VB-DCMM allows us to detect the presence of dynamic disorder, if any, in each trajectory, identify the number of internal states, and estimate transition rates between the internal states as well as the rates of conformational transition within each internal state. Applying VB-DCMM algorithm to single molecule FRET data of H-DNA in 100 mM-Na+ solution, followed by data clustering, we show that at least 6 kinetic paths linking 4 distinct internal states are required to correctly interpret the duplex-triplex transitions of H-DNA. We have developed a new algorithm to better decode single molecule data with dynamic disorder. Our new algorithm, which represents a substantial improvement over other methodologies, can detect the presence of dynamic disorder in each trajectory and quantify the kinetic characteristics of underlying energy landscape. As a model system, we applied our algorithm to the single molecule FRET time traces of H-DNA. While duplex-triplex transitions of H-DNA are conventionally interpreted in terms of two-state kinetics, slowly varying dynamic patterns corresponding to hidden internal states can also be identified from the individual time traces. Our algorithm reveals that at least 4 distinct internal states are required to correctly interpret the data.
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Affiliation(s)
- Wonseok Hwang
- Korea Institute for Advanced Study, Seoul, Republic of Korea
| | - Il-Buem Lee
- Department of Physics, Korea University, Seoul, Republic of Korea
| | - Seok-Cheol Hong
- Korea Institute for Advanced Study, Seoul, Republic of Korea
- Department of Physics, Korea University, Seoul, Republic of Korea
| | - Changbong Hyeon
- Korea Institute for Advanced Study, Seoul, Republic of Korea
- * E-mail:
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Emergence of ion channel modal gating from independent subunit kinetics. Proc Natl Acad Sci U S A 2016; 113:E5288-97. [PMID: 27551100 DOI: 10.1073/pnas.1604090113] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Many ion channels exhibit a slow stochastic switching between distinct modes of gating activity. This feature of channel behavior has pronounced implications for the dynamics of ionic currents and the signaling pathways that they regulate. A canonical example is the inositol 1,4,5-trisphosphate receptor (IP3R) channel, whose regulation of intracellular Ca(2+) concentration is essential for numerous cellular processes. However, the underlying biophysical mechanisms that give rise to modal gating in this and most other channels remain unknown. Although ion channels are composed of protein subunits, previous mathematical models of modal gating are coarse grained at the level of whole-channel states, limiting further dialogue between theory and experiment. Here we propose an origin for modal gating, by modeling the kinetics of ligand binding and conformational change in the IP3R at the subunit level. We find good agreement with experimental data over a wide range of ligand concentrations, accounting for equilibrium channel properties, transient responses to changing ligand conditions, and modal gating statistics. We show how this can be understood within a simple analytical framework and confirm our results with stochastic simulations. The model assumes that channel subunits are independent, demonstrating that cooperative binding or concerted conformational changes are not required for modal gating. Moreover, the model embodies a generally applicable principle: If a timescale separation exists in the kinetics of individual subunits, then modal gating can arise as an emergent property of channel behavior.
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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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Multiscale modelling of saliva secretion. Math Biosci 2014; 257:69-79. [PMID: 25014770 DOI: 10.1016/j.mbs.2014.06.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 06/18/2014] [Accepted: 06/26/2014] [Indexed: 01/28/2023]
Abstract
We review a multiscale model of saliva secretion, describing in brief how the model is constructed and what we have so far learned from it. The model begins at the level of inositol trisphosphate receptors (IPR), and proceeds through the cellular level (with a model of acinar cell calcium dynamics) to the multicellular level (with a model of the acinus), finally to a model of a saliva production unit that includes an acinus and associated duct. The model at the level of the entire salivary gland is not yet completed. Particular results from the model so far include (i) the importance of modal behaviour of IPR, (ii) the relative unimportance of Ca(2+) oscillation frequency as a controller of saliva secretion, (iii) the need for the periodic Ca(2+) waves to be as fast as possible in order to maximise water transport, (iv) the presence of functional K(+) channels in the apical membrane increases saliva secretion, (v) the relative unimportance of acinar spatial structure for isotonic water transport, (vi) the prediction that duct cells are highly depolarised, (vii) the prediction that the secondary saliva takes at least 1mm (from the acinus) to reach ionic equilibrium. We end with a brief discussion of future directions for the model, both in construction and in the study of scientific questions.
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