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Rappel WJ, Baykaner T, Zaman J, Ganesan P, Rogers AJ, Narayan SM. Spatially Conserved Spiral Wave Activity During Human Atrial Fibrillation. Circ Arrhythm Electrophysiol 2024; 17:e012041. [PMID: 38348685 PMCID: PMC10950516 DOI: 10.1161/circep.123.012041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 01/17/2024] [Indexed: 03/21/2024]
Abstract
BACKGROUND Atrial fibrillation is the most common cardiac arrhythmia in the world and increases the risk for stroke and morbidity. During atrial fibrillation, the electric activation fronts are no longer coherently propagating through the tissue and, instead, show rotational activity, consistent with spiral wave activation, focal activity, collision, or partial versions of these spatial patterns. An unexplained phenomenon is that although simulations of cardiac models abundantly demonstrate spiral waves, clinical recordings often show only intermittent spiral wave activity. METHODS In silico data were generated using simulations in which spiral waves were continuously created and annihilated and in simulations in which a spiral wave was intermittently trapped at a heterogeneity. Clinically, spatio-temporal activation maps were constructed using 60 s recordings from a 64 electrode catheter within the atrium of N=34 patients (n=24 persistent atrial fibrillation). The location of clockwise and counterclockwise rotating spiral waves was quantified and all intervals during which these spiral waves were present were determined. For each interval, the angle of rotation as a function of time was computed and used to determine whether the spiral wave returned in step or changed phase at the start of each interval. RESULTS In both simulations, spiral waves did not come back in phase and were out of step." In contrast, spiral waves returned in step in the majority (68%; P=0.05) of patients. Thus, the intermittently observed rotational activity in these patients is due to a temporally and spatially conserved spiral wave and not due to ones that are newly created at the onset of each interval. CONCLUSIONS Intermittency of spiral wave activity represents conserved spiral wave activity of long, but interrupted duration or transient spiral activity, in the majority of patients. This finding could have important ramifications for identifying clinically important forms of atrial fibrillation and in guiding treatment.
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Affiliation(s)
| | - Tina Baykaner
- Department of Medicine, Stanford University, Palo Alto
| | - Junaid Zaman
- Department of Cardiovascular Medicine, University of Southern California, Los Angeles, CA
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Tyree TJ, Murphy P, Rappel WJ. Annihilation dynamics during spiral defect chaos revealed by particle models. ArXiv 2024:arXiv:2402.10308v1. [PMID: 38410644 PMCID: PMC10896354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Pair-annihilation events are ubiquitous in a variety of spatially extended systems and are often studied using computationally expensive simulations. Here we develop an approach in which we simulate the pair-annihilation of spiral wave tips in cardiac models using a computationally efficient particle model. Spiral wave tips are represented as particles with dynamics governed by diffusive behavior and short-ranged attraction. The parameters for diffusion and attraction are obtained by comparing particle motion to the trajectories of spiral wave tips in cardiac models during spiral defect chaos. The particle model reproduces the annihilation rates of the cardiac models and can determine the statistics of spiral wave dynamics, including its mean termination time. We show that increasing the attraction coefficient sharply decreases the mean termination time, making it a possible target for pharmaceutical intervention. Many physical systems exhibit annihilation events during which pairs of objects collide and are removed from the system. These events occur in a number of soft-matter and active-matter systems that exhibit spatiotemporal patterning. For example, topological defects in nematic liquid crystals can develop motile topological defects that annihilate when they meet 1,2. Pair-wise annihilation of defects or singularities also plays a role in a number of biological systems. In bacterial biofilms, for instance, imperfect cell alignment results in point-like defects that carry half-integer topological charge and can annihilate in pairs. These topological defects explain the formation of layers and have been proposed as a model for the buckling of biofilms in colonies of nematically ordered cells3,4.
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Affiliation(s)
- Timothy J Tyree
- Department of Physics, University of California, San Diego, CA
| | - Patrick Murphy
- Department of Mathematics and Statistics, San Jose State University, San Jose, CA
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3
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Azoulay-Shemer T, Schulze S, Nissan-Roda D, Bosmans K, Shapira O, Weckwerth P, Zamora O, Yarmolinsky D, Trainin T, Kollist H, Huffaker A, Rappel WJ, Schroeder JI. A role for ethylene signaling and biosynthesis in regulating and accelerating CO 2 - and abscisic acid-mediated stomatal movements in Arabidopsis. New Phytol 2023; 238:2460-2475. [PMID: 36994603 DOI: 10.1111/nph.18918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 03/05/2023] [Indexed: 05/19/2023]
Abstract
Little is known about long-distance mesophyll-driven signals that regulate stomatal conductance. Soluble and/or vapor-phase molecules have been proposed. In this study, the involvement of the gaseous signal ethylene in the modulation of stomatal conductance in Arabidopsis thaliana by CO2 /abscisic acid (ABA) was examined. We present a diffusion model which indicates that gaseous signaling molecule/s with a shorter/direct diffusion pathway to guard cells are more probable for rapid mesophyll-dependent stomatal conductance changes. We, therefore, analyzed different Arabidopsis ethylene-signaling and biosynthesis mutants for their ethylene production and kinetics of stomatal responses to ABA/[CO2 ]-shifts. According to our research, higher [CO2 ] causes Arabidopsis rosettes to produce more ethylene. An ACC-synthase octuple mutant with reduced ethylene biosynthesis exhibits dysfunctional CO2 -induced stomatal movements. Ethylene-insensitive receptor (gain-of-function), etr1-1 and etr2-1, and signaling, ein2-5 and ein2-1, mutants showed intact stomatal responses to [CO2 ]-shifts, whereas loss-of-function ethylene receptor mutants, including etr2-3;ein4-4;ers2-3, etr1-6;etr2-3 and etr1-6, showed markedly accelerated stomatal responses to [CO2 ]-shifts. Further investigation revealed a significantly impaired stomatal closure to ABA in the ACC-synthase octuple mutant and accelerated stomatal responses in the etr1-6;etr2-3, and etr1-6, but not in the etr2-3;ein4-4;ers2-3 mutants. These findings suggest essential functions of ethylene biosynthesis and signaling components in tuning/accelerating stomatal conductance responses to CO2 and ABA.
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Affiliation(s)
- Tamar Azoulay-Shemer
- Division of Biological Sciences, Cell and Developmental Biology Section, University of California San Diego, La Jolla, CA, 92093-0116, USA
- Fruit Tree Sciences, Agricultural Research Organization (ARO), The Volcani Center, Newe Ya'ar Research Center, Ramat Yishay, 30095, Israel
| | - Sebastian Schulze
- Division of Biological Sciences, Cell and Developmental Biology Section, University of California San Diego, La Jolla, CA, 92093-0116, USA
| | - Dikla Nissan-Roda
- Fruit Tree Sciences, Agricultural Research Organization (ARO), The Volcani Center, Newe Ya'ar Research Center, Ramat Yishay, 30095, Israel
| | - Krystal Bosmans
- Division of Biological Sciences, Cell and Developmental Biology Section, University of California San Diego, La Jolla, CA, 92093-0116, USA
| | - Or Shapira
- Fruit Tree Sciences, Agricultural Research Organization (ARO), The Volcani Center, Newe Ya'ar Research Center, Ramat Yishay, 30095, Israel
| | - Philipp Weckwerth
- Division of Biological Sciences, Cell and Developmental Biology Section, University of California San Diego, La Jolla, CA, 92093-0116, USA
| | - Olena Zamora
- Plant Signal Research Group, Institute of Technology, University of Tartu, Nooruse 1, Tartu, 50411, Estonia
| | - Dmitry Yarmolinsky
- Plant Signal Research Group, Institute of Technology, University of Tartu, Nooruse 1, Tartu, 50411, Estonia
| | - Taly Trainin
- Fruit Tree Sciences, Agricultural Research Organization (ARO), The Volcani Center, Newe Ya'ar Research Center, Ramat Yishay, 30095, Israel
| | - Hannes Kollist
- Plant Signal Research Group, Institute of Technology, University of Tartu, Nooruse 1, Tartu, 50411, Estonia
| | - Alisa Huffaker
- Division of Biological Sciences, Cell and Developmental Biology Section, University of California San Diego, La Jolla, CA, 92093-0116, USA
| | - Wouter-Jan Rappel
- Department of Physics, University of California San Diego, La Jolla, CA, 92093-0116, USA
| | - Julian I Schroeder
- Division of Biological Sciences, Cell and Developmental Biology Section, University of California San Diego, La Jolla, CA, 92093-0116, USA
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4
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Ganesan P, Deb B, Feng R, Rodrigo M, Ruiperez-Campillo S, Rogers AJ, Clopton P, Wang PJ, Zeemering S, Schotten U, Rappel WJ, Narayan SM. Quantifying a spectrum of clinical response in atrial tachyarrhythmias using spatiotemporal synchronization of electrograms. Europace 2023; 25:euad055. [PMID: 36932716 PMCID: PMC10227659 DOI: 10.1093/europace/euad055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 02/09/2023] [Indexed: 03/19/2023] Open
Abstract
AIMS There is a clinical spectrum for atrial tachyarrhythmias wherein most patients with atrial tachycardia (AT) and some with atrial fibrillation (AF) respond to ablation, while others do not. It is undefined if this clinical spectrum has pathophysiological signatures. This study aims to test the hypothesis that the size of spatial regions showing repetitive synchronized electrogram (EGM) shapes over time reveals a spectrum from AT, to AF patients who respond acutely to ablation, to AF patients without acute response. METHODS AND RESULTS We studied n = 160 patients (35% women, 65.0 ± 10.4 years) of whom (i) n = 75 had AF terminated by ablation propensity matched to (ii) n = 75 without AF termination and (iii) n = 10 with AT. All patients had mapping by 64-pole baskets to identify areas of repetitive activity (REACT) to correlate unipolar EGMs in shape over time. Synchronized regions (REACT) were largest in AT, smaller in AF termination, and smallest in non-termination cohorts (0.63 ± 0.15, 0.37 ± 0.22, and 0.22 ± 0.18, P < 0.001). Area under the curve for predicting AF termination in hold-out cohorts was 0.72 ± 0.03. Simulations showed that lower REACT represented greater variability in clinical EGM timing and shape. Unsupervised machine learning of REACT and extensive (50) clinical variables yielded four clusters of increasing risk for AF termination (P < 0.01, χ2), which were more predictive than clinical profiles alone (P < 0.001). CONCLUSION The area of synchronized EGMs within the atrium reveals a spectrum of clinical response in atrial tachyarrhythmias. These fundamental EGM properties, which do not reflect any predetermined mechanism or mapping technology, predict outcome and offer a platform to compare mapping tools and mechanisms between AF patient groups.
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Affiliation(s)
- Prasanth Ganesan
- Division of Cardiovascular Medicine, Stanford Cardiovascular Institute, Stanford University, 453 Quarry Road, Palo Alto, CA 94304, USA
| | - Brototo Deb
- Division of Cardiovascular Medicine, Stanford Cardiovascular Institute, Stanford University, 453 Quarry Road, Palo Alto, CA 94304, USA
| | - Ruibin Feng
- Division of Cardiovascular Medicine, Stanford Cardiovascular Institute, Stanford University, 453 Quarry Road, Palo Alto, CA 94304, USA
| | - Miguel Rodrigo
- Electronic Engineering Department, Universitat de Valencia, Av. de Blasco Ibáñez, 13, 46010 València, Spain
| | - Samuel Ruiperez-Campillo
- Electronic Engineering Department, Universitat de Valencia, Av. de Blasco Ibáñez, 13, 46010 València, Spain
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA
| | - Albert J Rogers
- Division of Cardiovascular Medicine, Stanford Cardiovascular Institute, Stanford University, 453 Quarry Road, Palo Alto, CA 94304, USA
| | - Paul Clopton
- Division of Cardiovascular Medicine, Stanford Cardiovascular Institute, Stanford University, 453 Quarry Road, Palo Alto, CA 94304, USA
| | - Paul J Wang
- Division of Cardiovascular Medicine, Stanford Cardiovascular Institute, Stanford University, 453 Quarry Road, Palo Alto, CA 94304, USA
| | - Stef Zeemering
- Department of Physiology, Maastricht University, 6211 LK Maastricht, 616 6200, Netherlands
| | - Ulrich Schotten
- Department of Physiology, Maastricht University, 6211 LK Maastricht, 616 6200, Netherlands
| | - Wouter-Jan Rappel
- Department of Physics, University of California, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Sanjiv M Narayan
- Division of Cardiovascular Medicine, Stanford Cardiovascular Institute, Stanford University, 453 Quarry Road, Palo Alto, CA 94304, USA
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5
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Kappel C, Reiss M, Rodrigo M, Ganesan P, Narayan SM, Rappel WJ. Predicting acute termination and non-termination during ablation of human atrial fibrillation using quantitative indices. Front Physiol 2022; 13:939350. [PMID: 36483297 PMCID: PMC9725096 DOI: 10.3389/fphys.2022.939350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 11/10/2022] [Indexed: 11/23/2022] Open
Abstract
Background: Termination of atrial fibrillation (AF), the most common arrhythmia in the United States, during catheter ablation is an attractive procedural endpoint, which has been associated with improved long-term outcome in some studies. It is not clear, however, whether it is possible to predict termination using clinical data. We developed and applied three quantitative indices in global multielectrode recordings of AF prior to ablation: average dominant frequency (ADF), spectral power index (SPI), and electrogram quality index (EQI). Methods: In N = 42 persistent AF patients (65 ± 9 years, 14% female) we collected unipolar electrograms from 64-pole baskets (Abbott, CA). We studied N = 17 patients in whom AF terminated during ablation ("Term") and N = 25 in whom it did not ("Non-term"). For each index, we determined its ability to predict ablation by computing receiver operating characteristic (ROC) and calculated the area under the curve (AUC). Results: The ADF did not differ for Term and Non-term patients at 5.28 ± 0.82 Hz and 5.51 ± 0.81 Hz, respectively (p = 0.34). Conversely, the SPI for these two groups was. 0.85 (0.80-0.92) and 0.97 (0.93-0.98) and the EQI was 0.61 (0.58-0.64) and 0.56 (0.55-0.59) (p < 0.0001). The AUC for predicting AF termination for the SPI was 0.85 ([0.68, 0.95] 95% CI), and for the EQI, 0.86 ([0.72, 0.95] 95% CI). Conclusion: Both the EQI and the SPI may provide a useful clinical tool to predict procedural ablation outcome in persistent AF patients. Future studies are required to identify which physiological features of AF are revealed by these indices and hence linked to AF termination or non-termination.
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Affiliation(s)
- Cole Kappel
- Department of Physics, UC Irvine, Irvine, CA, United States
| | - Michael Reiss
- Department of Physics, UC San Diego, La Jolla, CA, United States
| | - Miguel Rodrigo
- CoMMLab, Electronic Engineering Department, Universitat de Valencia, Valencia, Spain
| | - Prasanth Ganesan
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, United States
| | - Sanjiv M. Narayan
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, United States
| | - Wouter-Jan Rappel
- Department of Physics, UC San Diego, La Jolla, CA, United States,*Correspondence: Wouter-Jan Rappel,
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Ganesan P, Rogers AJ, Deb B, Feng R, Ruiperez-Campillo S, Tjong FV, Bhatia N, Clopton P, Rappel WJ, Narayan SM. Novel electrogram featurization reveals a spectrum of response to ablation from atrial tachycardia to types of atrial fibrillation. Eur Heart J 2022. [DOI: 10.1093/eurheartj/ehac544.471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Although atrial tachycardia (AT) may interconvert with fibrillation (AF) in many patients, it is undefined if this represents a pathophysiological spectrum of organization, or whether it indicates that AF will respond better to ablation.
Objective
To test the hypothesis that the spatial area within which electrograms (EGMs) repeat in synchronized fashion over time indicates a spectrum from AT, in which areas span the entire atria, to AF, in which areas are limited. We further hypothesized that repetitive areas would be larger in AF patients with acute termination than in those with poor response to ablation.
Methods
We studied N=234 patients (47% women, 64±10Y), of whom (i) N=10 had AT, (ii) N=120 had AF that terminated with ablation (“Term”), (ii) N=104 had AF that did not terminate (“Non-term”). All patients had global left atrial mapping by 64 pole baskets (Abbott, IL). Spatial areas of repetitive activity (REACT) were calculated by correlating unipolar EGMs in 2x2 grids for 4 sec, repeated for the entire atria (Figure 1A, B). We quantified global organization by averaging the REACT map for each patient.
Results
Figure 1C shows progressively decreasing areas of repetitive EGM from AT to AF Term to AF Non-term (p<0.001, ANOVA). Figure 1D shows a case of AT in a 71 YO male and global REACT >0.90, a case of AF REACT 0.45 in a 65 YO male with termination by ablation, and a case of AF with REACT 0.19 in an 85 YO male that did not terminate. Further, ROC analysis of REACT analysis in AF cases predicted termination with an AUC of 0.71.
Conclusion
Spatial areas of repeating electrogram shapes indicates a spectrum from AT to AF with good and AF with poor acute response to ablation. Future studies should investigate whether REACT areas can be identified non-invasively, such as by body surface ECG, to guide ablation or prognosis.
Funding Acknowledgement
Type of funding sources: Public grant(s) – National budget only. Main funding source(s): US National Institutes of Health
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Affiliation(s)
- P Ganesan
- Stanford University School of Medicine , Palo Alto , United States of America
| | - A J Rogers
- Stanford University School of Medicine , Palo Alto , United States of America
| | - B Deb
- Stanford University School of Medicine , Palo Alto , United States of America
| | - R Feng
- Stanford University School of Medicine , Palo Alto , United States of America
| | | | - F V Tjong
- Stanford University School of Medicine , Palo Alto , United States of America
| | - N Bhatia
- Emory University , Atlanta , United States of America
| | - P Clopton
- Stanford University School of Medicine , Palo Alto , United States of America
| | - W J Rappel
- University of California San Diego , San Diego , United States of America
| | - S M Narayan
- Stanford University School of Medicine , Palo Alto , United States of America
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7
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Ganesan P, Rogers AJ, Deb B, Feng R, Rodrigo M, Ruiperez-Campillo S, Tjong FV, Bhatia N, Clopton P, Rappel WJ, Narayan SM. Spatiotemporal signatures of response to atrial fibrillation ablation. Eur Heart J 2022. [DOI: 10.1093/eurheartj/ehac544.601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Atrial fibrillation (AF) can have organized regions, in the form of consistent dominant frequency sites, focal or reentrant sites, but it is unclear how these overlap with or differ from focal atrial tachycardias (AT) or potential drivers. We set out to develop an intuitive method based on fundamental electrogram shape and timing to separate types of AF.
Objective
To test the hypothesis that spatial regions of electrogram (EGM) in AF that show similar shapes over time based on cross-correlation analysis may separate patients with differing response to ablation.
Methods
We recruited N=133 patients (63.8±12.1 Y, 32% women), (i) N=10 had AT, (ii) N=122 AF that was or was not terminated by ablation, and (iii) N=1 pacing. All patients had left atrial mapping by 64 pole baskets. We applied repetitive activity (REACT) mapping that correlates EGMs in contiguous 2x2 regions (Fig. 1A) over 4sec. To calibrate REACT, we introduced simulated variations in shape (gaussian noise) and timing (gaussian delay) to pacing EGMs and computed nomograph over 100 random trials (Fig. 1C).
Results
Fig. 1B shows that REACT in a 71-year-old man with AT is more organized than in a 65 YO man with AF (100% vs 40% mapped field). Overall, REACT was higher in AT than AF (0.63±0.15 vs 0.36±0.22, p<0.001). There were 24 cases in which global REACT between AF and AT groups had the overlapping range of values, indicating organized “islands” in AF analogous to AT. From nomograph in Fig. 1C we identified that this overlap reflects 15 ms variation in cycle length and 20% variation in EGM shape (labelled “x” in Fig. 1C).
Conclusion
Basic electrogram properties in AF of similar shapes in spatial areas over time can separate response to ablation and may represent “islands” of AT. Future studies should investigate the mechanisms for such islands and whether they may be targeted for therapy.
Funding Acknowledgement
Type of funding sources: Public grant(s) – National budget only. Main funding source(s): US National Institutes of Health
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Affiliation(s)
- P Ganesan
- Stanford University School of Medicine , Palo Alto , United States of America
| | - A J Rogers
- Stanford University School of Medicine , Palo Alto , United States of America
| | - B Deb
- Stanford University School of Medicine , Palo Alto , United States of America
| | - R Feng
- Stanford University School of Medicine , Palo Alto , United States of America
| | - M Rodrigo
- University of Valencia , Valencia , Spain
| | | | - F V Tjong
- Stanford University School of Medicine , Palo Alto , United States of America
| | - N Bhatia
- Emory University , Atlanta , United States of America
| | - P Clopton
- Stanford University School of Medicine , Palo Alto , United States of America
| | - W J Rappel
- University of California San Diego , San Diego , United States of America
| | - S M Narayan
- Stanford University School of Medicine , Palo Alto , United States of America
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Abstract
The global burden caused by cardiovascular disease is substantial, with heart disease representing the most common cause of death around the world. There remains a need to develop better mechanistic models of cardiac function in order to combat this health concern. Heart rhythm disorders, or arrhythmias, are one particular type of disease which has been amenable to quantitative investigation. Here we review the application of quantitative methodologies to explore dynamical questions pertaining to arrhythmias. We begin by describing single-cell models of cardiac myocytes, from which two and three dimensional models can be constructed. Special focus is placed on results relating to pattern formation across these spatially-distributed systems, especially the formation of spiral waves of activation. Next, we discuss mechanisms which can lead to the initiation of arrhythmias, focusing on the dynamical state of spatially discordant alternans, and outline proposed mechanisms perpetuating arrhythmias such as fibrillation. We then review experimental and clinical results related to the spatio-temporal mapping of heart rhythm disorders. Finally, we describe treatment options for heart rhythm disorders and demonstrate how statistical physics tools can provide insights into the dynamics of heart rhythm disorders.
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Affiliation(s)
- Wouter-Jan Rappel
- Department of Physics, University of California San Diego, La Jolla, CA 92037
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9
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Ganesan P, Deb B, Feng R, Rodrigo M, Ruiperez-Campillo S, Bhatia NK, Rogers AJ, Clopton P, Rappel WJ, Narayan SM. TARGETING SYNCHRONIZED ELECTROGRAM ISLANDS WITHIN ATRIAL FIBRILLATION FOR ABLATION. J Am Coll Cardiol 2022. [DOI: 10.1016/s0735-1097(22)00994-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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10
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Rappel WJ, Krummen DE, Baykaner T, Zaman J, Donsky A, Swarup V, Miller JM, Narayan SM. Stochastic termination of spiral wave dynamics in cardiac tissue. Front Netw Physiol 2022; 2:809532. [PMID: 36187938 PMCID: PMC9524168 DOI: 10.3389/fnetp.2022.809532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Rotating spiral waves are self-organized features in spatially extended excitable media and may play an important role in cardiac arrhythmias including atrial fibrillation (AF). In homogeneous media, spiral wave dynamics are perpetuated through spiral wave breakup, leading to the continuous birth and death of spiral waves, but have a finite probability of termination. In non-homogeneous media, however, heterogeneities can act as anchoring sources that result in sustained spiral wave activity. It is thus unclear how and if AF may terminate following the removal of putative spiral wave sources in patients. Here, we address this question using computer simulations in which a stable spiral wave is trapped by an heterogeneity and is surrounded by spiral wave breakup. We show that, following ablation of spatial heterogeneity to render that region of the medium unexcitable, termination of spiral wave dynamics is stochastic and Poisson-distributed. Furthermore, we show that the dynamics can be accurately described by a master equation using birth and death rates. To validate these predictions in vivo, we mapped spiral wave activity in patients with AF and targeted the locations of spiral wave sources using radiofrequency ablation. Targeted ablation was indeed able to terminate AF, but only after a variable delay of up to several minutes. Furthermore, and consistent with numerical simulations, termination was not accompanied by gradual temporal or spatial organization. Our results suggest that spiral wave sources and tissue heterogeneities play a critical role in the maintenance of AF and that the removal of sources results in spiral wave dynamics with a finite termination time, which could have important clinical implications.
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Affiliation(s)
| | | | - Tina Baykaner
- Department of Medicine and Cardiovascular Institute, Stanford University, Palo Alto, California
| | - Junaid Zaman
- Department of Medicine, Division of Cardiology, University of Southern California, Los Angeles, California
| | | | - Vijay Swarup
- Arizona Heart Rhythm Institute, Phoenix, Arizona
| | - John M Miller
- Krannert Institute, Indiana University, Indianapolis, Indiana
| | - Sanjiv M Narayan
- Department of Medicine and Cardiovascular Institute, Stanford University, Palo Alto, California
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11
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Karanam A, Rappel WJ. Boolean modelling in plant biology. Quant Plant Biol 2022; 3:e29. [PMID: 37077966 PMCID: PMC10095905 DOI: 10.1017/qpb.2022.26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 10/24/2022] [Accepted: 11/16/2022] [Indexed: 05/03/2023]
Abstract
Signalling and genetic networks underlie most biological processes and are often complex, containing many highly connected components. Modelling these networks can provide insight into mechanisms but is challenging given that rate parameters are often not well defined. Boolean modelling, in which components can only take on a binary value with connections encoded by logic equations, is able to circumvent some of these challenges, and has emerged as a viable tool to probe these complex networks. In this review, we will give an overview of Boolean modelling, with a specific emphasis on its use in plant biology. We review how Boolean modelling can be used to describe biological networks and then discuss examples of its applications in plant genetics and plant signalling.
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Affiliation(s)
- Aravind Karanam
- Department of Physics, University of California, San Diego, La Jolla, California92093, USA
| | - Wouter-Jan Rappel
- Department of Physics, University of California, San Diego, La Jolla, California92093, USA
- Author for correspondence: W.-J. Rappel, E-mail:
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12
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Abstract
Spiral waves are found in many excitable systems and are thought to play a role in the incoherent electrical activation that underlies cardiac arrhythmias. It is well-known that spiral waves can be permanently trapped by local heterogeneities. In this paper, we demonstrate that spiral waves can also be intermittently trapped by such heterogeneities. Using simulations of a cardiac model in two dimensions, we show that a tissue heterogeneity of sufficient strength or size can result in a spiral wave that is trapped for a few rotations, after which it dislodges and meanders away from the heterogeneity. We also show that these results can be captured by a particle model in which the particle represents the spiral wave tip. For both models, we construct a phase diagram which quantifies which parameter combinations of heterogeneity size and strength result in permanent, intermittent, or no trapping. Our results are consistent with clinical observations in patients with atrial fibrillation that showed that spiral wave reentry can be intermittent.
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13
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Karanam A, He D, Hsu PK, Schulze S, Dubeaux G, Karmakar R, Schroeder JI, Rappel WJ. Boolink: a graphical interface for open access Boolean network simulations and use in guard cell CO2 signaling. Plant Physiol 2021; 187:2311-2322. [PMID: 34618035 PMCID: PMC8644243 DOI: 10.1093/plphys/kiab344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 06/30/2021] [Indexed: 05/02/2023]
Abstract
Signaling networks are at the heart of almost all biological processes. Most of these networks contain large number of components, and often either the connections between these components are not known or the rate equations that govern the dynamics of soluble signaling components are not quantified. This uncertainty in network topology and parameters can make it challenging to formulate detailed mathematical models. Boolean networks, in which all components are either on or off, have emerged as viable alternatives to detailed mathematical models that contain rate constants and other parameters. Therefore, open-source platforms of Boolean models for community use are desirable. Here, we present Boolink, a freely available graphical user interface that allows users to easily construct and analyze existing Boolean networks. Boolink can be applied to any Boolean network. We demonstrate its application using a previously published network for abscisic acid (ABA)-driven stomatal closure in Arabidopsis spp. (Arabidopsis thaliana). We also show how Boolink can be used to generate testable predictions by extending the network to include CO2 regulation of stomatal movements. Predictions of the model were experimentally tested, and the model was iteratively modified based on experiments showing that ABA effectively closes Arabidopsis stomata at near-zero CO2 concentrations (1.5-ppm CO2). Thus, Boolink enables public generation and the use of existing Boolean models, including the prior developed ABA signaling model with added CO2 signaling components.
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Affiliation(s)
- Aravind Karanam
- Physics Department, University of California, San Diego, La Jolla, California 92093, USA
| | - David He
- Physics Department, University of California, San Diego, La Jolla, California 92093, USA
| | - Po-Kai Hsu
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093-0116, USA
| | - Sebastian Schulze
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093-0116, USA
| | - Guillaume Dubeaux
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093-0116, USA
| | - Richa Karmakar
- Physics Department, University of California, San Diego, La Jolla, California 92093, USA
| | - Julian I Schroeder
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093-0116, USA
| | - Wouter-Jan Rappel
- Physics Department, University of California, San Diego, La Jolla, California 92093, USA
- Author for communication:
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14
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Dubeaux G, Hsu PK, Ceciliato PHO, Swink KJ, Rappel WJ, Schroeder JI. Deep dive into CO2-dependent molecular mechanisms driving stomatal responses in plants. Plant Physiol 2021; 187:2032-2042. [PMID: 35142859 PMCID: PMC8644143 DOI: 10.1093/plphys/kiab342] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/30/2021] [Indexed: 05/04/2023]
Abstract
Recent advances are revealing mechanisms mediating CO2-regulated stomatal movements in Arabidopsis, stomatal architecture and stomatal movements in grasses, and the long-term impact of CO2 on growth.
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Affiliation(s)
- Guillaume Dubeaux
- Division of Biological Sciences, Cell and Developmental Biology Section, University of California San Diego, La Jolla, California 92093-0116, USA
| | - Po-Kai Hsu
- Division of Biological Sciences, Cell and Developmental Biology Section, University of California San Diego, La Jolla, California 92093-0116, USA
| | - Paulo H O Ceciliato
- Division of Biological Sciences, Cell and Developmental Biology Section, University of California San Diego, La Jolla, California 92093-0116, USA
| | - Kelsey J Swink
- Division of Biological Sciences, Cell and Developmental Biology Section, University of California San Diego, La Jolla, California 92093-0116, USA
| | - Wouter-Jan Rappel
- Physics Department, University of California San Diego, La Jolla, California 92093-0116, USA
| | - Julian I Schroeder
- Division of Biological Sciences, Cell and Developmental Biology Section, University of California San Diego, La Jolla, California 92093-0116, USA
- Author for communication:
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15
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Ganesan P, Kumar Bhatia N, Ravi N, Rogers AJ, Krummen DE, Wang PJ, Clopton P, Rappel WJ, Narayan SM. B-PO03-091 LARGER ATRIAL AREAS WITH 1:1 ELECTROGRAM LOCKING PREDICT TERMINATION OF ATRIAL FIBRILLATION BY ABLATION. Heart Rhythm 2021. [DOI: 10.1016/j.hrthm.2021.06.565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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16
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Ganesan P, Bhatia N, Rogers AJ, Krummen D, Wang P, Clopton P, Rappel WJ, Narayan S. Extent of atrium with 1:1 electrogram activation predicts response to ablation of atrial fibrillation. Europace 2021. [DOI: 10.1093/europace/euab116.260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Funding Acknowledgements
Type of funding sources: Public grant(s) – National budget only. Main funding source(s): US National Institutes of Health
Background
Mechanisms associated with successful termination of persistent atrial fibrillation (AF) are still under debate. We sought to study the association between spatial extent of atrium with organized conduction and AF ablation success. We hypothesized that patients with large areas of atrium having 1:1 electrogram activation akin to ‘atrial tachycardia’ may have a higher likelihood of AF termination by ablation.
Methods
In n = 40 AF patients, n = 20 had termination by ablation ("Term"), and the remaining did not have AF termination by ablation ("Non-term"). Basket catheters (64 poles) were used to record unipolar electrograms (EGMs) in one or both atrium. Ablation targeted localized rotational/focal regions, after which pulmonary vein isolation was performed. Unipolar EGMs of 4sec duration at each 2x2 electrode neighborhood within 8x8 catheter grid were processed using a statistical correlation technique to identify the duration of 1:1 activations. Any EGM activation cycle that had a correlation above 80% was considered to be 1:1. Duration of contiguous 1:1 cycles was determined as percentage of total duration (4 sec).
Results
Spatial area of atrium (percentage of mapping field) and the corresponding 1:1 durations were assessed for patients in Term and Non-term groups. Fig A shows spatial 1:1 maps of a Term and a Non-term patient. Fig B shows examples of 1:1 and non-1:1 EGMs. Patients in Term group had higher average 1:1 atrial area than non-term group for any 1:1 duration (Fig C, 15 ± 22% vs 2 ± 4% with ≥70% 1:1 duration, p = 0.03). Positive and negative predictive values of duration≥70% for AF termination were 64.7%, and 75%, with specificity 60% and sensitivity 78.6%, exceeding clinical risk scores.
Conclusion
Persistent AF atrium shows areas of organized 1:1 conduction. Larger 1:1 atrial areas were identified in patients in whom AF terminated by ablation. Future studies should investigate mechanistic bases of organized conduction in AF. Abstract Figure.
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Affiliation(s)
- P Ganesan
- Stanford University School of Medicine, Palo Alto, United States of America
| | - N Bhatia
- Emory University, Atlanta, United States of America
| | - AJ Rogers
- Stanford University School of Medicine, Palo Alto, United States of America
| | - D Krummen
- University of California San Diego, San Diego, United States of America
| | - P Wang
- Stanford University School of Medicine, Palo Alto, United States of America
| | - P Clopton
- Stanford University School of Medicine, Palo Alto, United States of America
| | - WJ Rappel
- University of California San Diego, San Diego, United States of America
| | - S Narayan
- Stanford University School of Medicine, Palo Alto, United States of America
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17
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Rodrigo M, Baykaner T, Rappel WJ, Narayan S. NON-INVASIVE TRACKING OF ATRIAL FIBRILLATION PREDICTS ACUTE TERMINATION BY ABLATION. J Am Coll Cardiol 2021. [DOI: 10.1016/s0735-1097(21)01639-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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18
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Ganesan P, Bhatia N, Beck TC, Ravi N, Rogers A, Krummen D, Wang P, Rappel WJ, Narayan S. CONSISTENT SPATIOTEMPORAL VECTORS IN ATRIAL FIBRILLATION PREDICT RESPONSE TO ABLATION. J Am Coll Cardiol 2021. [DOI: 10.1016/s0735-1097(21)01693-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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19
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Abad R, Collart O, Ganesan P, Rogers AJ, Alhusseini MI, Rodrigo M, Narayan SM, Rappel WJ. Three dimensional reconstruction to visualize atrial fibrillation activation patterns on curved atrial geometry. PLoS One 2021; 16:e0249873. [PMID: 33836026 PMCID: PMC8034734 DOI: 10.1371/journal.pone.0249873] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 03/26/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The rotational activation created by spiral waves may be a mechanism for atrial fibrillation (AF), yet it is unclear how activation patterns obtained from endocardial baskets are influenced by the 3D geometric curvature of the atrium or 'unfolding' into 2D maps. We develop algorithms that can visualize spiral waves and their tip locations on curved atrial geometries. We use these algorithms to quantify differences in AF maps and spiral tip locations between 3D basket reconstructions, projection onto 3D anatomical shells and unfolded 2D surfaces. METHODS We tested our algorithms in N = 20 patients in whom AF was recorded from 64-pole baskets (Abbott, CA). Phase maps were generated by non-proprietary software to identify the tips of spiral waves, indicated by phase singularities. The number and density of spiral tips were compared in patient-specific 3D shells constructed from the basket, as well as 3D maps from clinical electroanatomic mapping systems and 2D maps. RESULTS Patients (59.4±12.7 yrs, 60% M) showed 1.7±0.8 phase singularities/patient, in whom ablation terminated AF in 11/20 patients (55%). There was no difference in the location of phase singularities, between 3D curved surfaces and 2D unfolded surfaces, with a median correlation coefficient between phase singularity density maps of 0.985 (0.978-0.990). No significant impact was noted by phase singularities location in more curved regions or relative to the basket location (p>0.1). CONCLUSIONS AF maps and phase singularities mapped by endocardial baskets are qualitatively and quantitatively similar whether calculated by 3D phase maps on patient-specific curved atrial geometries or in 2D. Phase maps on patient-specific geometries may be easier to interpret relative to critical structures for ablation planning.
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Affiliation(s)
- Ricardo Abad
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, United States of America
| | - Orvil Collart
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, United States of America
| | - Prasanth Ganesan
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, United States of America
| | - A. J. Rogers
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, United States of America
| | - Mahmood I. Alhusseini
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, United States of America
| | - Miguel Rodrigo
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, United States of America
- Universitat Politècnica de València, Valencia, Spain
| | - Sanjiv M. Narayan
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail: (SMN); (WJR)
| | - Wouter-Jan Rappel
- Department of Physics, UC San Diego, La Jolla, California, United States of America
- * E-mail: (SMN); (WJR)
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20
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Karmakar R, Tang MH, Yue H, Lombardo D, Karanam A, Camley BA, Groisman A, Rappel WJ. Cellular memory in eukaryotic chemotaxis depends on the background chemoattractant concentration. Phys Rev E 2021; 103:012402. [PMID: 33601617 DOI: 10.1103/physreve.103.012402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 12/16/2020] [Indexed: 01/17/2023]
Abstract
Cells of the social amoeba Dictyostelium discoideum migrate to a source of periodic traveling waves of chemoattractant as part of a self-organized aggregation process. An important part of this process is cellular memory, which enables cells to respond to the front of the wave and ignore the downward gradient in the back of the wave. During this aggregation, the background concentration of the chemoattractant gradually rises. In our microfluidic experiments, we exogenously applied periodic waves of chemoattractant with various background levels. We find that increasing background does not make detection of the wave more difficult, as would be naively expected. Instead, we see that the chemotactic efficiency significantly increases for intermediate values of the background concentration but decreases to almost zero for large values in a switch-like manner. These results are consistent with a computational model that contains a bistable memory module, along with a nonadaptive component. Within this model, an intermediate background level helps preserve directed migration by keeping the memory activated, but when the background level is higher, the directional stimulus from the wave is no longer sufficient to activate the bistable memory, suppressing directed migration. These results suggest that raising levels of chemoattractant background may facilitate the self-organized aggregation in Dictyostelium colonies.
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Affiliation(s)
- Richa Karmakar
- Department of Physics, University of California, San Diego, La Jolla, California 92093, USA
| | - Man-Ho Tang
- Department of Physics, University of California, San Diego, La Jolla, California 92093, USA
| | - Haicen Yue
- Courant Institute for Mathematical Sciences, New York University, New York, New York 10012, USA
| | - Daniel Lombardo
- Department of Physics, University of California, San Diego, La Jolla, California 92093, USA
| | - Aravind Karanam
- Department of Physics, University of California, San Diego, La Jolla, California 92093, USA
| | - Brian A Camley
- Department of Physics & Astronomy, Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Alex Groisman
- Department of Physics, University of California, San Diego, La Jolla, California 92093, USA
| | - Wouter-Jan Rappel
- Department of Physics, University of California, San Diego, La Jolla, California 92093, USA
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21
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Krummen DE, Ho G, Hoffmayer KS, Schweis FN, Baykaner T, Rogers AJ, Han FT, Hsu JC, Viswanathan MN, Wang PJ, Rappel WJ, Narayan SM. Electrical Substrate Ablation for Refractory Ventricular Fibrillation: Results of the AVATAR Study. Circ Arrhythm Electrophysiol 2021; 14:e008868. [PMID: 33550811 DOI: 10.1161/circep.120.008868] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- David E Krummen
- University of California, San Diego (D.E.K., G.H., K.S.H., F.N.S., F.T.H., J.C.H., W.-J.R.).,Veterans Affairs San Diego Healthcare System, CA (D.E.K., G.H., K.S.H., F.T.H.)
| | - Gordon Ho
- University of California, San Diego (D.E.K., G.H., K.S.H., F.N.S., F.T.H., J.C.H., W.-J.R.).,Veterans Affairs San Diego Healthcare System, CA (D.E.K., G.H., K.S.H., F.T.H.)
| | - Kurt S Hoffmayer
- University of California, San Diego (D.E.K., G.H., K.S.H., F.N.S., F.T.H., J.C.H., W.-J.R.).,Veterans Affairs San Diego Healthcare System, CA (D.E.K., G.H., K.S.H., F.T.H.)
| | - Franz N Schweis
- University of California, San Diego (D.E.K., G.H., K.S.H., F.N.S., F.T.H., J.C.H., W.-J.R.)
| | - Tina Baykaner
- Stanford University, Palo Alto, CA (T.B., A.J.R., M.N.V., P.J.W., S.M.N.)
| | - A J Rogers
- Stanford University, Palo Alto, CA (T.B., A.J.R., M.N.V., P.J.W., S.M.N.)
| | - Frederick T Han
- University of California, San Diego (D.E.K., G.H., K.S.H., F.N.S., F.T.H., J.C.H., W.-J.R.).,Veterans Affairs San Diego Healthcare System, CA (D.E.K., G.H., K.S.H., F.T.H.)
| | - Jonathan C Hsu
- University of California, San Diego (D.E.K., G.H., K.S.H., F.N.S., F.T.H., J.C.H., W.-J.R.)
| | | | - Paul J Wang
- Stanford University, Palo Alto, CA (T.B., A.J.R., M.N.V., P.J.W., S.M.N.)
| | - Wouter-Jan Rappel
- University of California, San Diego (D.E.K., G.H., K.S.H., F.N.S., F.T.H., J.C.H., W.-J.R.)
| | - Sanjiv M Narayan
- Stanford University, Palo Alto, CA (T.B., A.J.R., M.N.V., P.J.W., S.M.N.)
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22
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Rappel WJ, Ghabache E, Cao Y, Miao Y, Groisman A, Devreotes PN. Different Cell Migration Modes: Insights from Traction Force Microscopy and Modeling. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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23
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Dai W, Guo X, Cao Y, Mondo JA, Campanale JP, Montell BJ, Burrous H, Streichan S, Gov N, Rappel WJ, Montell DJ. Tissue topography steers migrating Drosophila border cells. Science 2021; 370:987-990. [PMID: 33214282 DOI: 10.1126/science.aaz4741] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 05/11/2020] [Accepted: 09/28/2020] [Indexed: 12/16/2022]
Abstract
Moving cells can sense and respond to physical features of the microenvironment; however, in vivo, the significance of tissue topography is mostly unknown. Here, we used Drosophila border cells, an established model for in vivo cell migration, to study how chemical and physical information influences path selection. Although chemical cues were thought to be sufficient, live imaging, genetics, modeling, and simulations show that microtopography is also important. Chemoattractants promote predominantly posterior movement, whereas tissue architecture presents orthogonal information, a path of least resistance concentrated near the center of the egg chamber. E-cadherin supplies a permissive haptotactic cue. Our results provide insight into how cells integrate and prioritize topographical, adhesive, and chemoattractant cues to choose one path among many.
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Affiliation(s)
- Wei Dai
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
| | - Xiaoran Guo
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
| | - Yuansheng Cao
- Department of Physics, University of California, San Diego, CA 92093, USA
| | - James A Mondo
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
| | - Joseph P Campanale
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
| | | | - Haley Burrous
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
| | - Sebastian Streichan
- Department of Physics, University of California, Santa Barbara, CA 93106, USA
| | - Nir Gov
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Wouter-Jan Rappel
- Department of Physics, University of California, San Diego, CA 92093, USA
| | - Denise J Montell
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA.
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24
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Rogers AJ, Selvalingam A, Alhusseini MI, Krummen DE, Corrado C, Abuzaid F, Baykaner T, Meyer C, Clopton P, Giles W, Bailis P, Niederer S, Wang PJ, Rappel WJ, Zaharia M, Narayan SM. Machine Learned Cellular Phenotypes in Cardiomyopathy Predict Sudden Death. Circ Res 2020; 128:172-184. [PMID: 33167779 DOI: 10.1161/circresaha.120.317345] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
RATIONALE Susceptibility to VT/VF (ventricular tachycardia/fibrillation) is difficult to predict in patients with ischemic cardiomyopathy either by clinical tools or by attempting to translate cellular mechanisms to the bedside. OBJECTIVE To develop computational phenotypes of patients with ischemic cardiomyopathy, by training then interpreting machine learning of ventricular monophasic action potentials (MAPs) to reveal phenotypes that predict long-term outcomes. METHODS AND RESULTS We recorded 5706 ventricular MAPs in 42 patients with coronary artery disease and left ventricular ejection fraction ≤40% during steady-state pacing. Patients were randomly allocated to independent training and testing cohorts in a 70:30 ratio, repeated K=10-fold. Support vector machines and convolutional neural networks were trained to 2 end points: (1) sustained VT/VF or (2) mortality at 3 years. Support vector machines provided superior classification. For patient-level predictions, we computed personalized MAP scores as the proportion of MAP beats predicting each end point. Patient-level predictions in independent test cohorts yielded c-statistics of 0.90 for sustained VT/VF (95% CI, 0.76-1.00) and 0.91 for mortality (95% CI, 0.83-1.00) and were the most significant multivariate predictors. Interpreting trained support vector machine revealed MAP morphologies that, using in silico modeling, revealed higher L-type calcium current or sodium-calcium exchanger as predominant phenotypes for VT/VF. CONCLUSIONS Machine learning of action potential recordings in patients revealed novel phenotypes for long-term outcomes in ischemic cardiomyopathy. Such computational phenotypes provide an approach which may reveal cellular mechanisms for clinical outcomes and could be applied to other conditions.
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Affiliation(s)
- Albert J Rogers
- Department of Medicine and Cardiovascular Institute (A.J.R., A.S., M.I.A., T.B., P.C., P.J.W., S.M.N.), Stanford University
| | - Anojan Selvalingam
- Department of Medicine and Cardiovascular Institute (A.J.R., A.S., M.I.A., T.B., P.C., P.J.W., S.M.N.), Stanford University.,Department of Cardiology, University Medical Center Hamburg-Eppendorf, Germany (A.S., C.M.)
| | - Mahmood I Alhusseini
- Department of Medicine and Cardiovascular Institute (A.J.R., A.S., M.I.A., T.B., P.C., P.J.W., S.M.N.), Stanford University
| | - David E Krummen
- Department of Medicine (D.E.K.), University of California, San Diego
| | - Cesare Corrado
- Department of Biomedical Engineering, King's College London, United Kingdom (C.C., S.N.)
| | - Firas Abuzaid
- Department of Computer Sciences (F.A., M.Z., P.B.), Stanford University
| | - Tina Baykaner
- Department of Medicine and Cardiovascular Institute (A.J.R., A.S., M.I.A., T.B., P.C., P.J.W., S.M.N.), Stanford University
| | - Christian Meyer
- Department of Cardiology, University Medical Center Hamburg-Eppendorf, Germany (A.S., C.M.)
| | - Paul Clopton
- Department of Medicine and Cardiovascular Institute (A.J.R., A.S., M.I.A., T.B., P.C., P.J.W., S.M.N.), Stanford University
| | - Wayne Giles
- Department of Physiology and Pharmacology, University of Calgary, Canada (W.G.)
| | - Peter Bailis
- Department of Computer Sciences (F.A., M.Z., P.B.), Stanford University
| | - Steven Niederer
- Department of Biomedical Engineering, King's College London, United Kingdom (C.C., S.N.)
| | - Paul J Wang
- Department of Medicine and Cardiovascular Institute (A.J.R., A.S., M.I.A., T.B., P.C., P.J.W., S.M.N.), Stanford University
| | - Wouter-Jan Rappel
- Department of Physics (W.-J.R.), University of California, San Diego
| | - Matei Zaharia
- Department of Computer Sciences (F.A., M.Z., P.B.), Stanford University
| | - Sanjiv M Narayan
- Department of Medicine and Cardiovascular Institute (A.J.R., A.S., M.I.A., T.B., P.C., P.J.W., S.M.N.), Stanford University
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25
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Karmakar R, Schich C, Kamprad N, Scheller V, Gutierrez E, Groisman A, Rappel WJ, Tarantola M. Novel micropatterning technique reveals dependence of cell-substrate adhesion and migration of social amoebas on parental strain, development, and fluorescent markers. PLoS One 2020; 15:e0236171. [PMID: 32702047 PMCID: PMC7377449 DOI: 10.1371/journal.pone.0236171] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 06/30/2020] [Indexed: 02/07/2023] Open
Abstract
Cell-substrate adhesion of the social amoeba Dictyostelium discoideum, a model organism often used for the study of chemotaxis, is non-specific and does not involve focal adhesion complexes. Therefore, micropatterned substrates where adherent Dictyostelium cells are constrained to designated microscopic regions are difficult to make. Here we present a micropatterning technique for Dictyostelium cells that relies on coating the substrate with an ∼1μm thick layer of polyethylene glycol (PEG) gel. We show that, when plated on a substrate with narrow parallel stripes of PEG-gel and glass, Dictyostelium cells nearly exclusive adhere to and migrate along the glass stripes, thus providing a model system to study one-dimensional migration of amoeboid cells. Surprisingly, we find substantial differences in the adhesion to PEG-gel and glass stripes between vegetative and developed cells and between two different axenic laboratory strains of Dictyostelium, AX2 and AX4. Even more surprisingly, we find that the distribution of Dictyostelium cells between PEG-gel and glass stripes is significantly affected by the expression of several fluorescent protein markers of the cytoskeleton. We carry out atomic force microscopy based single cell force spectroscopy measurements that confirm that the force of adhesion to PEG-gel substrate can be significantly different between vegetative and developed cells, AX2 and AX4 cells, and cells with and without fluorescent markers. Thus, the choice of parental background, the degree of development, and the expression of fluorescent protein markers can all have a profound effect on cell-substrate adhesion and should be considered when comparing migration of cells and when designing micropatterned substrates.
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Affiliation(s)
- Richa Karmakar
- Department of Physics, University of California, San Diego, La Jolla, California, United States of America
| | | | - Nadine Kamprad
- Institute for Dynamics of Complex Systems, Goettingen, Germany.,Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
| | | | - Edgar Gutierrez
- Department of Physics, University of California, San Diego, La Jolla, California, United States of America
| | - Alex Groisman
- Department of Physics, University of California, San Diego, La Jolla, California, United States of America
| | - Wouter-Jan Rappel
- Department of Physics, University of California, San Diego, La Jolla, California, United States of America
| | - Marco Tarantola
- Institute for Dynamics of Complex Systems, Goettingen, Germany.,Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
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Alhusseini MI, Abuzaid F, Rogers AJ, Zaman JAB, Baykaner T, Clopton P, Bailis P, Zaharia M, Wang PJ, Rappel WJ, Narayan SM. Machine Learning to Classify Intracardiac Electrical Patterns During Atrial Fibrillation: Machine Learning of Atrial Fibrillation. Circ Arrhythm Electrophysiol 2020; 13:e008160. [PMID: 32631100 DOI: 10.1161/circep.119.008160] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
BACKGROUND Advances in ablation for atrial fibrillation (AF) continue to be hindered by ambiguities in mapping, even between experts. We hypothesized that convolutional neural networks (CNN) may enable objective analysis of intracardiac activation in AF, which could be applied clinically if CNN classifications could also be explained. METHODS We performed panoramic recording of bi-atrial electrical signals in AF. We used the Hilbert-transform to produce 175 000 image grids in 35 patients, labeled for rotational activation by experts who showed consistency but with variability (kappa [κ]=0.79). In each patient, ablation terminated AF. A CNN was developed and trained on 100 000 AF image grids, validated on 25 000 grids, then tested on a separate 50 000 grids. RESULTS In the separate test cohort (50 000 grids), CNN reproducibly classified AF image grids into those with/without rotational sites with 95.0% accuracy (CI, 94.8%-95.2%). This accuracy exceeded that of support vector machines, traditional linear discriminant, and k-nearest neighbor statistical analyses. To probe the CNN, we applied gradient-weighted class activation mapping which revealed that the decision logic closely mimicked rules used by experts (C statistic 0.96). CONCLUSIONS CNNs improved the classification of intracardiac AF maps compared with other analyses and agreed with expert evaluation. Novel explainability analyses revealed that the CNN operated using a decision logic similar to rules used by experts, even though these rules were not provided in training. We thus describe a scaleable platform for robust comparisons of complex AF data from multiple systems, which may provide immediate clinical utility to guide ablation. Registration: URL: https://www.clinicaltrials.gov; Unique identifier: NCT02997254. Graphic Abstract: A graphic abstract is available for this article.
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Affiliation(s)
- Mahmood I Alhusseini
- Department of Medicine (M.I.A., A.J.R., J.A.B.Z., T.B., P.C., P.J.W., S.M.N.), Stanford University
| | - Firas Abuzaid
- Department of Computer Science (F.A., P.B., M.Z.), Stanford University
| | - Albert J Rogers
- Department of Medicine (M.I.A., A.J.R., J.A.B.Z., T.B., P.C., P.J.W., S.M.N.), Stanford University
| | - Junaid A B Zaman
- Department of Medicine (M.I.A., A.J.R., J.A.B.Z., T.B., P.C., P.J.W., S.M.N.), Stanford University
| | - Tina Baykaner
- Department of Medicine (M.I.A., A.J.R., J.A.B.Z., T.B., P.C., P.J.W., S.M.N.), Stanford University
| | - Paul Clopton
- Department of Medicine (M.I.A., A.J.R., J.A.B.Z., T.B., P.C., P.J.W., S.M.N.), Stanford University
| | - Peter Bailis
- Department of Computer Science (F.A., P.B., M.Z.), Stanford University
| | - Matei Zaharia
- Department of Computer Science (F.A., P.B., M.Z.), Stanford University
| | - Paul J Wang
- Department of Medicine (M.I.A., A.J.R., J.A.B.Z., T.B., P.C., P.J.W., S.M.N.), Stanford University
| | - Wouter-Jan Rappel
- Department of Physics, University of California, San Diego (W.-J.R.)
| | - Sanjiv M Narayan
- Department of Medicine (M.I.A., A.J.R., J.A.B.Z., T.B., P.C., P.J.W., S.M.N.), Stanford University
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27
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Bhatia NK, Rogers AJ, Krummen DE, Hossainy S, Sauer W, Miller JM, Alhusseini MI, Peszek A, Armenia E, Baykaner T, Brachmann J, Turakhia MP, Clopton P, Wang PJ, Rappel WJ, Narayan SM. Termination of persistent atrial fibrillation by ablating sites that control large atrial areas. Europace 2020; 22:897-905. [PMID: 32243508 PMCID: PMC7273336 DOI: 10.1093/europace/euaa018] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 01/06/2020] [Indexed: 11/14/2022] Open
Abstract
AIMS Persistent atrial fibrillation (AF) has been explained by multiple mechanisms which, while they conflict, all agree that more disorganized AF is more difficult to treat than organized AF. We hypothesized that persistent AF consists of interacting organized areas which may enlarge, shrink or coalesce, and that patients whose AF areas enlarge by ablation are more likely to respond to therapy. METHODS AND RESULTS We mapped vectorial propagation in persistent AF using wavefront fields (WFF), constructed from raw unipolar electrograms at 64-pole basket catheters, during ablation until termination (Group 1, N = 20 patients) or cardioversion (Group 2, N = 20 patients). Wavefront field mapping of patients (age 61.1 ± 13.2 years, left atrium 47.1 ± 6.9 mm) at baseline showed 4.6 ± 1.0 organized areas, each separated by disorganization. Ablation of sites that led to termination controlled larger organized area than competing sites (44.1 ± 11.1% vs. 22.4 ± 7.0%, P < 0.001). In Group 1, ablation progressively enlarged unablated areas (rising from 32.2 ± 15.7% to 44.1 ± 11.1% of mapped atrium, P < 0.0001). In Group 2, organized areas did not enlarge but contracted during ablation (23.6 ± 6.3% to 15.2 ± 5.6%, P < 0.0001). CONCLUSION Mapping wavefront vectors in persistent AF revealed competing organized areas. Ablation that progressively enlarged remaining areas was acutely successful, and sites where ablation terminated AF were surrounded by large organized areas. Patients in whom large organized areas did not emerge during ablation did not exhibit AF termination. Further studies should define how fibrillatory activity is organized within such areas and whether this approach can guide ablation.
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Affiliation(s)
- Neal K Bhatia
- Department of Medicine and Cardiovascular Institute, Stanford University, 780 Welch Road, MC 5773, Stanford, CA 94305, USA
- Department of Medicine, Emory University, Atlanta, GA, USA
| | - Albert J Rogers
- Department of Medicine and Cardiovascular Institute, Stanford University, 780 Welch Road, MC 5773, Stanford, CA 94305, USA
| | - David E Krummen
- Department of Medicine, University of California, San Diego, CA, USA
| | - Samir Hossainy
- Department of Medicine and Cardiovascular Institute, Stanford University, 780 Welch Road, MC 5773, Stanford, CA 94305, USA
| | - William Sauer
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - John M Miller
- Department of Medicine, University of Indiana, Indianapolis, IN, USA
| | - Mahmood I Alhusseini
- Department of Medicine and Cardiovascular Institute, Stanford University, 780 Welch Road, MC 5773, Stanford, CA 94305, USA
| | - Adam Peszek
- Department of Medicine, University of Colorado, Denver, CO, USA
| | - Erin Armenia
- Department of Medicine, University of Rochester, Rochester, NY, USA
| | - Tina Baykaner
- Department of Medicine and Cardiovascular Institute, Stanford University, 780 Welch Road, MC 5773, Stanford, CA 94305, USA
| | | | - Mintu P Turakhia
- Department of Medicine, Veterans Affairs Palo Alto, Palo Alto, CA, USA
| | - Paul Clopton
- Department of Medicine and Cardiovascular Institute, Stanford University, 780 Welch Road, MC 5773, Stanford, CA 94305, USA
| | - Paul J Wang
- Department of Medicine and Cardiovascular Institute, Stanford University, 780 Welch Road, MC 5773, Stanford, CA 94305, USA
| | | | - Sanjiv M Narayan
- Department of Medicine and Cardiovascular Institute, Stanford University, 780 Welch Road, MC 5773, Stanford, CA 94305, USA
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28
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Ravi N, Rogers AJ, Bhatia N, Tung JS, Krummen D, Sauer W, Alhusseini M, Baykaner T, Wang P, Rappel WJ, Narayan S. LARGER ORGANIZED AREAS IN PERSISTENT ATRIAL FIBRILLATION PREDICTS TERMINATION DURING ABLATION. J Am Coll Cardiol 2020. [DOI: 10.1016/s0735-1097(20)30906-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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29
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Ghabache E, Miao Y, Devreotes PN, Rappel WJ. Diverse Modes of Motion of Dictyostelium Discoideum Cells: Correlating Cytoskeleton Organization and Generation of Traction Forces. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.1151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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30
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Abstract
Diverse interactions among species within bacterial colonies lead to intricate spatiotemporal dynamics, which can affect their growth and survival. Here, we describe the emergence of complex structures in a colony grown from mixtures of motile and non-motile bacterial species on a soft agar surface. Time-lapse imaging shows that non-motile bacteria 'hitchhike' on the motile bacteria as the latter migrate outward. The non-motile bacteria accumulate at the boundary of the colony and trigger an instability that leaves behind striking flower-like patterns. The mechanism of the front instability governing this pattern formation is elucidated by a mathematical model for the frictional motion of the colony interface, with friction depending on the local concentration of the non-motile species. A more elaborate two-dimensional phase-field model that explicitly accounts for the interplay between growth, mechanical stress from the motile species, and friction provided by the non-motile species, fully reproduces the observed flower-like patterns.
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Affiliation(s)
- Liyang Xiong
- Department of PhysicsUniversity of California, San DiegoLa JollaUnited States
- BioCircuits InstituteUniversity of California, San DiegoLa JollaUnited States
| | - Yuansheng Cao
- Department of PhysicsUniversity of California, San DiegoLa JollaUnited States
| | - Robert Cooper
- BioCircuits InstituteUniversity of California, San DiegoLa JollaUnited States
| | - Wouter-Jan Rappel
- Department of PhysicsUniversity of California, San DiegoLa JollaUnited States
| | - Jeff Hasty
- BioCircuits InstituteUniversity of California, San DiegoLa JollaUnited States
- The San Diego Center for Systems BiologySan DiegoUnited States
- Molecular Biology Section, Division of Biological SciencesUniversity of California, San DiegoLa JollaUnited States
- Department of BioengineeringUniversity of California, San DiegoLa JollaUnited States
| | - Lev Tsimring
- BioCircuits InstituteUniversity of California, San DiegoLa JollaUnited States
- The San Diego Center for Systems BiologySan DiegoUnited States
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31
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Cao Y, Ghabache E, Miao Y, Niman C, Hakozaki H, Reck-Peterson SL, Devreotes PN, Rappel WJ. A minimal computational model for three-dimensional cell migration. J R Soc Interface 2019; 16:20190619. [PMID: 31847757 DOI: 10.1098/rsif.2019.0619] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
During migration, eukaryotic cells can continuously change their three-dimensional morphology, resulting in a highly dynamic and complex process. Further complicating this process is the observation that the same cell type can rapidly switch between different modes of migration. Modelling this complexity necessitates models that are able to track deforming membranes and that can capture the intracellular dynamics responsible for changes in migration modes. Here we develop an efficient three-dimensional computational model for cell migration, which couples cell mechanics to a simple intracellular activator-inhibitor signalling system. We compare the computational results to quantitative experiments using the social amoeba Dictyostelium discoideum. The model can reproduce the observed migration modes generated by varying either mechanical or biochemical model parameters and suggests a coupling between the substrate and the biomechanics of the cell.
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Affiliation(s)
- Yuansheng Cao
- Department of Physics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Elisabeth Ghabache
- Department of Physics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yuchuan Miao
- Department of Biological Chemistry, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Cassandra Niman
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Hiroyuki Hakozaki
- National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA 92093, USA
| | - Samara L Reck-Peterson
- Department of Cellular and Molecular Medicine, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Peter N Devreotes
- Department of Cell Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Wouter-Jan Rappel
- Department of Physics, University of California, San Diego, La Jolla, CA 92093, USA
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32
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Bhatia NK, Rappel WJ, Narayan SM. Response by Bhatia et al to Letter Regarding Article, "Wavefront Field Mapping Reveals a Physiologic Network Between Drivers Where Ablation Terminates Atrial Fibrillation". Circ Arrhythm Electrophysiol 2019; 12:e008022. [PMID: 31726861 PMCID: PMC7365521 DOI: 10.1161/circep.119.008022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Neal K Bhatia
- Cardiovascular Institute and Department of Medicine/Division of Cardiology, Stanford University, CA (N.K.B., S.M.N.)
| | - Wouter-Jan Rappel
- Department of Physics, University of California, San Diego (W.-J.R.)
| | - Sanjiv M Narayan
- Cardiovascular Institute and Department of Medicine/Division of Cardiology, Stanford University, CA (N.K.B., S.M.N.)
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33
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Zhang J, De-Oliveira-Ceciliato P, Takahashi Y, Schulze S, Dubeaux G, Hauser F, Azoulay-Shemer T, Tõldsepp K, Kollist H, Rappel WJ, Schroeder JI. Insights into the Molecular Mechanisms of CO 2-Mediated Regulation of Stomatal Movements. Curr Biol 2019; 28:R1356-R1363. [PMID: 30513335 DOI: 10.1016/j.cub.2018.10.015] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Plants must continually balance the influx of CO2 for photosynthesis against the loss of water vapor through stomatal pores in their leaves. This balance can be achieved by controlling the aperture of the stomatal pores in response to several environmental stimuli. Elevation in atmospheric [CO2] induces stomatal closure and further impacts leaf temperatures, plant growth and water-use efficiency, and global crop productivity. Here, we review recent advances in understanding CO2-perception mechanisms and CO2-mediated signal transduction in the regulation of stomatal movements, and we explore how these mechanisms are integrated with other signaling pathways in guard cells.
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Affiliation(s)
- Jingbo Zhang
- Division of Biological Sciences, Cell and Developmental Biology Section, University of California San Diego, La Jolla, CA 92093, USA
| | - Paulo De-Oliveira-Ceciliato
- Division of Biological Sciences, Cell and Developmental Biology Section, University of California San Diego, La Jolla, CA 92093, USA
| | - Yohei Takahashi
- Division of Biological Sciences, Cell and Developmental Biology Section, University of California San Diego, La Jolla, CA 92093, USA
| | - Sebastian Schulze
- Division of Biological Sciences, Cell and Developmental Biology Section, University of California San Diego, La Jolla, CA 92093, USA
| | - Guillaume Dubeaux
- Division of Biological Sciences, Cell and Developmental Biology Section, University of California San Diego, La Jolla, CA 92093, USA
| | - Felix Hauser
- Division of Biological Sciences, Cell and Developmental Biology Section, University of California San Diego, La Jolla, CA 92093, USA
| | - Tamar Azoulay-Shemer
- Division of Biological Sciences, Cell and Developmental Biology Section, University of California San Diego, La Jolla, CA 92093, USA
| | - Kadri Tõldsepp
- Institute of Technology, University of Tartu, Tartu 50411, Estonia
| | - Hannes Kollist
- Institute of Technology, University of Tartu, Tartu 50411, Estonia
| | - Wouter-Jan Rappel
- Physics Department, University of California San Diego, La Jolla, CA 92093, USA
| | - Julian I Schroeder
- Division of Biological Sciences, Cell and Developmental Biology Section, University of California San Diego, La Jolla, CA 92093, USA.
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Abstract
Eukaryotic cells can migrate using different modes, ranging from amoeboid-like, during which actin filled protrusions come and go, to keratocyte-like, characterized by a stable morphology and persistent motion. How cells can switch between these modes is not well understood but waves of signaling events are thought to play an important role in these transitions. Here we present a simple two-component biochemical reaction-diffusion model based on relaxation oscillators and couple this to a model for the mechanics of cell deformations. Different migration modes, including amoeboid-like and keratocyte-like, naturally emerge through transitions determined by interactions between biochemical traveling waves, cell mechanics and morphology. The model predictions are explicitly verified by systematically reducing the protrusive force of the actin network in experiments using Dictyostelium discoideum cells. Our results indicate the importance of coupling signaling events to cell mechanics and morphology and may be applicable in a wide variety of cell motility systems.
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Affiliation(s)
- Yuansheng Cao
- Department of PhysicsUniversity of California, San DiegoLa JollaUnited States
| | - Elisabeth Ghabache
- Department of PhysicsUniversity of California, San DiegoLa JollaUnited States
| | - Wouter-Jan Rappel
- Department of PhysicsUniversity of California, San DiegoLa JollaUnited States
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35
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Yue H, Camley BA, Rappel WJ. Minimal Network Topologies for Signal Processing during Collective Cell Chemotaxis. Biophys J 2019; 114:2986-2999. [PMID: 29925034 DOI: 10.1016/j.bpj.2018.04.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 03/30/2018] [Accepted: 04/10/2018] [Indexed: 01/08/2023] Open
Abstract
Cell-cell communication plays an important role in collective cell migration. However, it remains unclear how cells in a group cooperatively process external signals to determine the group's direction of motion. Although the topology of signaling pathways is vitally important in single-cell chemotaxis, the signaling topology for collective chemotaxis has not been systematically studied. Here, we combine mathematical analysis and simulations to find minimal network topologies for multicellular signal processing in collective chemotaxis. We focus on border cell cluster chemotaxis in the Drosophila egg chamber, in which responses to several experimental perturbations of the signaling network are known. Our minimal signaling network includes only four elements: a chemoattractant, the protein Rac (indicating cell activation), cell protrusion, and a hypothesized global factor responsible for cell-cell interaction. Experimental data on cell protrusion statistics allows us to systematically narrow the number of possible topologies from more than 40,000,000 to only six minimal topologies with six interactions between the four elements. This analysis does not require a specific functional form of the interactions, and only qualitative features are needed; it is thus robust to many modeling choices. Simulations of a stochastic biochemical model of border cell chemotaxis show that the qualitative selection procedure accurately determines which topologies are consistent with the experiment. We fit our model for all six proposed topologies; each produces results that are consistent with all experimentally available data. Finally, we suggest experiments to further discriminate possible pathway topologies.
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Affiliation(s)
- Haicen Yue
- Department of Physics, University of California, San Diego, La Jolla, California
| | - Brian A Camley
- Department of Physics and Astronomy, Johns Hopkins University, Baltimore, Maryland; Department of Biophysics, Johns Hopkins University, Baltimore, Maryland
| | - Wouter-Jan Rappel
- Department of Physics, University of California, San Diego, La Jolla, California.
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36
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Leef G, Shenasa F, Bhatia NK, Rogers AJ, Sauer W, Miller JM, Swerdlow M, Tamboli M, Alhusseini MI, Armenia E, Baykaner T, Brachmann J, Turakhia MP, Atienza F, Rappel WJ, Wang PJ, Narayan SM. Wavefront Field Mapping Reveals a Physiologic Network Between Drivers Where Ablation Terminates Atrial Fibrillation. Circ Arrhythm Electrophysiol 2019; 12:e006835. [PMID: 31352796 DOI: 10.1161/circep.118.006835] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
BACKGROUND Localized drivers are proposed mechanisms for persistent atrial fibrillation (AF) from optical mapping of human atria and clinical studies of AF, yet are controversial because drivers fluctuate and ablating them may not terminate AF. We used wavefront field mapping to test the hypothesis that AF drivers, if concurrent, may interact to produce fluctuating areas of control to explain their appearance/disappearance and acute impact of ablation. METHODS We recruited 54 patients from an international registry in whom persistent AF terminated by targeted ablation. Unipolar AF electrograms were analyzed from 64-pole baskets to reconstruct activation times, map propagation vectors each 20 ms, and create nonproprietary phase maps. RESULTS Each patient (63.6±8.5 years, 29.6% women) showed 4.0±2.1 spatially anchored rotational or focal sites in AF in 3 patterns. First, a single (type I; n=7) or, second, paired chiral-antichiral (type II; n=5) rotational drivers controlled most of the atrial area. Ablation of 1 to 2 large drivers terminated all cases of types I or II AF. Third, interaction of 3 to 5 drivers (type III; n=42) with changing areas of control. Targeted ablation at driver centers terminated AF and required more ablation in types III versus I (P=0.02 in left atrium). CONCLUSIONS Wavefront field mapping of persistent AF reveals a pathophysiologic network of a small number of spatially anchored rotational and focal sites, which interact, fluctuate, and control varying areas. Future work should define whether AF drivers that control larger atrial areas are attractive targets for ablation.
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Affiliation(s)
- George Leef
- Department of Medicine, Stanford University, California (G.L., F.S., N.K.B., A.J.R., M.S., M.T., M.I.A., T.B., P.J.W., S.M.N.)
| | - Fatemah Shenasa
- Department of Medicine, Stanford University, California (G.L., F.S., N.K.B., A.J.R., M.S., M.T., M.I.A., T.B., P.J.W., S.M.N.)
| | - Neal K Bhatia
- Department of Medicine, Stanford University, California (G.L., F.S., N.K.B., A.J.R., M.S., M.T., M.I.A., T.B., P.J.W., S.M.N.)
| | - Albert J Rogers
- Department of Medicine, Stanford University, California (G.L., F.S., N.K.B., A.J.R., M.S., M.T., M.I.A., T.B., P.J.W., S.M.N.)
| | - William Sauer
- Department of Medicine, University of Colorado, Denver (W.S., E.A.)
| | - John M Miller
- Department of Medicine, University of Indiana, Indianapolis (J.M.M.)
| | - Mark Swerdlow
- Department of Medicine, Stanford University, California (G.L., F.S., N.K.B., A.J.R., M.S., M.T., M.I.A., T.B., P.J.W., S.M.N.)
| | - Mallika Tamboli
- Department of Medicine, Stanford University, California (G.L., F.S., N.K.B., A.J.R., M.S., M.T., M.I.A., T.B., P.J.W., S.M.N.)
| | - Mahmood I Alhusseini
- Department of Medicine, Stanford University, California (G.L., F.S., N.K.B., A.J.R., M.S., M.T., M.I.A., T.B., P.J.W., S.M.N.)
| | - Erin Armenia
- Department of Medicine, University of Colorado, Denver (W.S., E.A.)
| | - Tina Baykaner
- Department of Medicine, Stanford University, California (G.L., F.S., N.K.B., A.J.R., M.S., M.T., M.I.A., T.B., P.J.W., S.M.N.)
| | | | - Mintu P Turakhia
- Department of Medicine, Veterans Affairs Palo Alto Health Care System, CA (M.P.T.)
| | - Felipe Atienza
- Departamento de Cardiologia, Hospital General Universitario Gregorio Maranon, Madrid, Spain (F.A.)
| | | | - Paul J Wang
- Department of Medicine, Stanford University, California (G.L., F.S., N.K.B., A.J.R., M.S., M.T., M.I.A., T.B., P.J.W., S.M.N.)
| | - Sanjiv M Narayan
- Department of Medicine, Stanford University, California (G.L., F.S., N.K.B., A.J.R., M.S., M.T., M.I.A., T.B., P.J.W., S.M.N.)
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37
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Abstract
Spiral waves have been observed in a variety of physical, chemical, and biological systems. They play a major role in cardiac arrhythmias, including fibrillation, where the observed irregular activation patterns are generally thought to arise from the continuous breakup of multiple unstable spiral waves. Using spatially extended simulations of different electrophysiological models of cardiac tissue, we show that a single spiral wave in the presence of heterogeneities can display chaotic tip trajectories, consistent with fibrillation. We also show that the simulated spiral tip dynamics, including chaotic trajectories, can be captured by a simple particle model which only describes the dynamics of the spiral tip. This shows that spiral wave breakup, or interactions with other waves, are not necessary to initiate chaos in spiral waves.
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Affiliation(s)
- Daniel M Lombardo
- Department of Physics, University of California San Diego, San Diego, California 92093, USA
| | - Wouter-Jan Rappel
- Department of Physics, University of California San Diego, San Diego, California 92093, USA
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38
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Bhatia NK, Hossainy S, Rogers A, Alhusseini M, Brodt C, Moosvi N, Baykaner T, Wang P, Rappel WJ, Narayan S. SITES THAT CONTROL LARGER AREAS DURING ATRIAL FIBRILLATION MAY DETERMINE TERMINATION DURING ABLATION. J Am Coll Cardiol 2019. [DOI: 10.1016/s0735-1097(19)31008-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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39
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Rogers AJ, Moosvi N, Singh A, Alhusseini M, Baykaner T, Clopton P, Rappel WJ, Wang P, Narayan S. INTRACLASS CORRELATIONS OF VOLTAGE, FRACTIONATED ELECTROGRAMS, AND DOMINANT FREQUENCY IN PATIENTS WHERE LOCALIZED ABLATION TERMINATED PERSISTENT ATRIAL FIBRILLATION. J Am Coll Cardiol 2019. [DOI: 10.1016/s0735-1097(19)31129-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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40
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Alhusseini M, Abuzaid F, Clopton P, Rogers A, Rodrigo M, Baykaner T, Wang P, Rappel WJ, Narayan S. MACHINE LEARNING IDENTIFIES SITES WHERE ABLATION TERMINATES PERSISTENT ATRIAL FIBRILLATION. J Am Coll Cardiol 2019. [DOI: 10.1016/s0735-1097(19)30909-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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41
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Cao Y, Karmakar R, Ghabache E, Gutierrez E, Zhao Y, Groisman A, Levine H, Camley BA, Rappel WJ. Cell motility dependence on adhesive wetting. Soft Matter 2019; 15:2043-2050. [PMID: 30724956 DOI: 10.1039/c8sm01832d] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Adhesive cell-substrate interactions are crucial for cell motility and are responsible for the necessary traction that propels cells. These interactions can also change the shape of the cell, analogous to liquid droplet wetting on adhesive substrates. To address how these shape changes affect cell migration and cell speed we model motility using deformable, 2D cross-sections of cells in which adhesion and frictional forces between cell and substrate can be varied separately. Our simulations show that increasing the adhesion results in increased spreading of cells and larger cell speeds. We propose an analytical model which shows that the cell speed is inversely proportional to an effective height of the cell and that increasing this height results in increased internal shear stress. The numerical and analytical results are confirmed in experiments on motile eukaryotic cells.
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Affiliation(s)
- Yuansheng Cao
- Department of Physics, University of California, San Diego, La Jolla, California 92093, USA.
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42
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Abstract
Spatially extended excitable systems can exhibit spiral defect chaos (SDC) during which spiral waves continuously form and disappear. To address how this dynamical state terminates using simulations can be computationally challenging, especially for large systems. To circumvent this limitation, we treat the number of spiral waves as a stochastic population with a corresponding birth-death equation and use techniques from statistical physics to determine the mean episode duration of SDC. Motivated by cardiac fibrillation, during which the heart's electrical activity becomes disorganized and shows fragmenting spiral waves, we use generic models of cardiac electrophysiology. We show that the duration can be computed in minimal computational time and that it depends exponentially on domain size. Therefore, the approach can result in efficient and accurate predictions of mean episode duration which may be extended to more complex geometries and models.
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Affiliation(s)
- David Vidmar
- Department of Physics, University of California, San Diego, La Jolla, California 92093, USA
| | - Wouter-Jan Rappel
- Department of Physics, University of California, San Diego, La Jolla, California 92093, USA
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43
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Zhang J, Wang N, Miao Y, Hauser F, McCammon JA, Rappel WJ, Schroeder JI. Identification of SLAC1 anion channel residues required for CO 2/bicarbonate sensing and regulation of stomatal movements. Proc Natl Acad Sci U S A 2018; 115:11129-11137. [PMID: 30301791 PMCID: PMC6217375 DOI: 10.1073/pnas.1807624115] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Increases in CO2 concentration in plant leaves due to respiration in the dark and the continuing atmospheric [CO2] rise cause closing of stomatal pores, thus affecting plant-water relations globally. However, the underlying CO2/bicarbonate (CO2/HCO3-) sensing mechanisms remain unknown. [CO2] elevation in leaves triggers stomatal closure by anion efflux mediated via the SLAC1 anion channel localized in the plasma membrane of guard cells. Previous reconstitution analysis has suggested that intracellular bicarbonate ions might directly up-regulate SLAC1 channel activity. However, whether such a CO2/HCO3- regulation of SLAC1 is relevant for CO2 control of stomatal movements in planta remains unknown. Here, we computationally probe for candidate bicarbonate-interacting sites within the SLAC1 anion channel via long-timescale Gaussian accelerated molecular dynamics (GaMD) simulations. Mutations of two putative bicarbonate-interacting residues, R256 and R321, impaired the enhancement of the SLAC1 anion channel activity by CO2/HCO3- in Xenopus oocytes. Mutations of the neighboring charged amino acid K255 and residue R432 and the predicted gate residue F450 did not affect HCO3- regulation of SLAC1. Notably, gas-exchange experiments with slac1-transformed plants expressing mutated SLAC1 proteins revealed that the SLAC1 residue R256 is required for CO2 regulation of stomatal movements in planta, but not for abscisic acid (ABA)-induced stomatal closing. Patch clamp analyses of guard cells show that activation of S-type anion channels by CO2/HCO3-, but not by ABA, was impaired, indicating the relevance of R256 for CO2 signal transduction. Together, these analyses suggest that the SLAC1 anion channel is one of the physiologically relevant CO2/HCO3- sensors in guard cells.
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Affiliation(s)
- Jingbo Zhang
- Cell and Developmental Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0116
| | - Nuo Wang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093
| | - Yinglong Miao
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093;
- Center for Computational Biology, University of Kansas, Lawrence, KS 66047
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045
| | - Felix Hauser
- Cell and Developmental Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0116
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093
| | - Wouter-Jan Rappel
- Department of Physics, University of California, San Diego, La Jolla, CA 92093-0354
| | - Julian I Schroeder
- Cell and Developmental Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0116;
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44
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Vidmar D, Alhusseini MI, Narayan SM, Rappel WJ. Characterizing Electrogram Signal Fidelity and the Effects of Signal Contamination on Mapping Human Persistent Atrial Fibrillation. Front Physiol 2018; 9:1232. [PMID: 30237766 PMCID: PMC6135945 DOI: 10.3389/fphys.2018.01232] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 08/15/2018] [Indexed: 11/30/2022] Open
Abstract
Objective: Determining accurate intracardiac maps of atrial fibrillation (AF) in humans can be difficult, owing primarily to various sources of contamination in electrogram signals. The goal of this study is to develop a measure for signal fidelity and to develop methods to quantify robustness of observed rotational activity in phase maps subject to signal contamination. Methods: We identified rotational activity in phase maps of human persistent AF using the Hilbert transform of sinusoidally recomposed signals, where localized ablation at rotational sites terminated fibrillation. A novel measure of signal fidelity was developed to quantify signal quality. Contamination is then introduced to the underlying electrograms by removing signals at random, adding noise to computations of cycle length, and adding realistic far-field signals. Mean tip number N and tip density δ, defined as the proportion of time a region contains a tip, at the termination site are computed to compare the effects of contamination. Results: Domains of low signal fidelity correspond to the location of rotational cores. Removing signals and altering cycle length accounted for minor changes in tip density, while targeted removal of low fidelity electrograms can result in a significant increase in tip density and stability. Far-field contamination was found to obscure rotation at the termination site. Conclusion: Rotational activity in clinical AF can produce domains of low fidelity electrogram recordings at rotational cores. Observed rotational patterns in phase maps appear most sensitive to far-field activation. These results may inform novel methods to map AF in humans which can be tested directly in patients at electrophysiological study and ablation.
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Affiliation(s)
- David Vidmar
- Department of Physics, University of California, San Diego, San Diego, CA, United States
| | - Mahmood I. Alhusseini
- Division of Cardiology, Department of Medicine, Stanford University, Stanford, CA, United States
| | - Sanjiv M. Narayan
- Division of Cardiology, Department of Medicine, Stanford University, Stanford, CA, United States
| | - Wouter-Jan Rappel
- Department of Physics, University of California, San Diego, San Diego, CA, United States
- *Correspondence: Wouter-Jan Rappel
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45
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Tariqul Islam AFM, Yue H, Scavello M, Haldeman P, Rappel WJ, Charest PG. The cAMP-induced G protein subunits dissociation monitored in live Dictyostelium cells by BRET reveals two activation rates, a positive effect of caffeine and potential role of microtubules. Cell Signal 2018; 48:25-37. [PMID: 29698704 DOI: 10.1016/j.cellsig.2018.04.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/17/2018] [Accepted: 04/22/2018] [Indexed: 02/01/2023]
Abstract
To study the dynamics and mechanisms controlling activation of the heterotrimeric G protein Gα2βγ in Dictyostelium in response to stimulation by the chemoattractant cyclic AMP (cAMP), we monitored the G protein subunit interaction in live cells using bioluminescence resonance energy transfer (BRET). We found that cAMP induces the cAR1-mediated dissociation of the G protein subunits to a similar extent in both undifferentiated and differentiated cells, suggesting that only a small number of cAR1 (as expressed in undifferentiated cells) is necessary to induce the full activation of Gα2βγ. In addition, we found that treating cells with caffeine increases the potency of cAMP-induced Gα2βγ activation; and that disrupting the microtubule network but not F-actin inhibits the cAMP-induced dissociation of Gα2βγ. Thus, microtubules are necessary for efficient cAR1-mediated activation of the heterotrimeric G protein. Finally, kinetics analyses of Gα2βγ subunit dissociation induced by different cAMP concentrations indicate that there are two distinct rates at which the heterotrimeric G protein subunits dissociate when cells are stimulated with cAMP concentrations above 500 nM versus only one rate at lower cAMP concentrations. Quantitative modeling suggests that the kinetics profile of Gα2βγ subunit dissociation results from the presence of both uncoupled and G protein pre-coupled cAR1 that have differential affinities for cAMP and, consequently, induce G protein subunit dissociation through different rates. We suggest that these different signaling kinetic profiles may play an important role in initial chemoattractant gradient sensing.
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Affiliation(s)
- A F M Tariqul Islam
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721-0088, USA
| | - Haicen Yue
- Department of Physics, University of California-San Diego, La Jolla, CA 92093, USA
| | - Margarethakay Scavello
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721-0088, USA
| | - Pearce Haldeman
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721-0088, USA; Division of Biology and Biological Engineering, Joint Center for Transitional Medicine, California Institute of Technology, Pasadena, CA 91125, USA
| | - Wouter-Jan Rappel
- Department of Physics, University of California-San Diego, La Jolla, CA 92093, USA
| | - Pascale G Charest
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721-0088, USA.
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46
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Abstract
Adaptation refers to the biological phenomenon where living systems change their internal states in response to changes in their environments in order to maintain certain key functions critical for their survival and fitness. Adaptation is one of the most ubiquitous and arguably one of the most fundamental properties of living systems. It occurs throughout all biological scales, from adaptation of populations of species over evolutionary time to adaptation of a single cell to different environmental stresses during its life span. In this article, we review some of the recent progress made in understanding molecular mechanisms of cellular level adaptation. We take the minimalist (or the physicist) approach and study the simplest systems that exhibit generic adaptive behaviors. We focus on understanding the basic biochemical interaction networks in living matter that are responsible for adaptation dynamics. By combining theoretical modeling with quantitative experimentation, we demonstrate universal features in adaptation as well as important differences in different cellular systems, including chemotaxis in bacterium cells (Escherichia coli) and eukaryotic cells (Dictyostelium). Future work in extending the modeling framework to study adaptation in more complex systems such as sensory neurons are discussed.
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Affiliation(s)
- Yuhai Tu
- IBM T. J. Watson Research Center, Yorktown Heights, NY 10598
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47
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Lee RM, Yue H, Rappel WJ, Losert W. Inferring single-cell behaviour from large-scale epithelial sheet migration patterns. J R Soc Interface 2018; 14:rsif.2017.0147. [PMID: 28490603 DOI: 10.1098/rsif.2017.0147] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/13/2017] [Indexed: 12/22/2022] Open
Abstract
Cell migration plays an important role in a wide variety of biological processes and can incorporate both individual cell motion and collective behaviour. The emergent properties of collective migration are receiving increasing attention as collective motion's role in diseases such as metastatic cancer becomes clear. Yet, how individual cell behaviour influences large-scale, multi-cell collective motion remains unclear. In this study, we provide insight into the mechanisms behind collective migration by studying cell migration in a spreading monolayer of epithelial MCF10A cells. We quantify migration using particle image velocimetry and find that cell groups have features of motion that span multiple length scales. Comparing our experimental results to a model of collective cell migration, we find that cell migration within the monolayer can be affected in qualitatively different ways by cell motion at the boundary, yet it is not necessary to introduce leader cells at the boundary or specify other large-scale features to recapitulate this large-scale phenotype in simulations. Instead, in our model, collective motion can be enhanced by increasing the overall activity of the cells or by giving the cells a stronger coupling between their motion and polarity. This suggests that investigating the activity and polarity persistence of individual cells will add insight into the collective migration phenotypes observed during development and disease.
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Affiliation(s)
- Rachel M Lee
- Department of Physics, University of Maryland, College Park, MD, USA
| | - Haicen Yue
- Department of Physics, University of California, San Diego, CA, USA
| | | | - Wolfgang Losert
- Department of Physics, University of Maryland, College Park, MD, USA
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48
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Ho G, Hoffmayer KS, Villongco CT, Vidmar D, Rappel WJ, Krummen DE. Successful ventricular fibrillation functional substrate ablation via a single vascular access site. HeartRhythm Case Rep 2018; 4:173-176. [PMID: 29915711 PMCID: PMC6003783 DOI: 10.1016/j.hrcr.2017.12.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Gordon Ho
- Department of Medicine, University of California San Diego, La Jolla, California.,Veterans Affairs San Diego Healthcare System, San Diego, California
| | - Kurt S Hoffmayer
- Department of Medicine, University of California San Diego, La Jolla, California.,Veterans Affairs San Diego Healthcare System, San Diego, California
| | | | - David Vidmar
- Department of Physics, University of California San Diego, La Jolla, California
| | - Wouter-Jan Rappel
- Department of Physics, University of California San Diego, La Jolla, California
| | - David E Krummen
- Department of Medicine, University of California San Diego, La Jolla, California.,Veterans Affairs San Diego Healthcare System, San Diego, California
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49
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Zhang J, Wang N, Miao Y, Hauser F, Rappel WJ, McCammon JA, Schroeder J. Gaussian-Accelerated Molecular Dynamics Modeling Leads to Identification of SLAC1 Anion Channel Residues for CO2 Signaling in Arabidopsis Guard Cell. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.1717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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50
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Affiliation(s)
- David Vidmar
- Department of Physics, University of California, San Diego, La Jolla, California
| | - Wouter-Jan Rappel
- Department of Physics, University of California, San Diego, La Jolla, California.
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