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Lambert B, MacLean AL, Fletcher AG, Combes AN, Little MH, Byrne HM. Bayesian inference of agent-based models: a tool for studying kidney branching morphogenesis. J Math Biol 2018; 76:1673-1697. [PMID: 29392399 PMCID: PMC5906521 DOI: 10.1007/s00285-018-1208-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 01/02/2018] [Indexed: 12/11/2022]
Abstract
The adult mammalian kidney has a complex, highly-branched collecting duct epithelium that arises as a ureteric bud sidebranch from an epithelial tube known as the nephric duct. Subsequent branching of the ureteric bud to form the collecting duct tree is regulated by subcellular interactions between the epithelium and a population of mesenchymal cells that surround the tips of outgrowing branches. The mesenchymal cells produce glial cell-line derived neurotrophic factor (GDNF), that binds with RET receptors on the surface of the epithelial cells to stimulate several subcellular pathways in the epithelium. Such interactions are known to be a prerequisite for normal branching development, although competing theories exist for their role in morphogenesis. Here we introduce the first agent-based model of ex vivo kidney uretic branching. Through comparison with experimental data, we show that growth factor-regulated growth mechanisms can explain early epithelial cell branching, but only if epithelial cell division depends in a switch-like way on the local growth factor concentration; cell division occurring only if the driving growth factor level exceeds a threshold. We also show how a recently-developed method, "Approximate Approximate Bayesian Computation", can be used to infer key model parameters, and reveal the dependency between the parameters controlling a growth factor-dependent growth switch. These results are consistent with a requirement for signals controlling proliferation and chemotaxis, both of which are previously identified roles for GDNF.
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Affiliation(s)
- Ben Lambert
- Department of Zoology, University of Oxford, Oxford, UK.
| | - Adam L MacLean
- Mathematical Institute, University of Oxford, Andrew Wiles Building, Woodstock Road, Oxford, UK
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA
| | - Alexander G Fletcher
- School of Mathematics and Statistics, University of Sheffield, Hicks Building, Hounsfield Road, Sheffield, S3 7RH, UK
- Bateson Centre, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Alexander N Combes
- Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, VIC, 3010, Australia
- Murdoch Childrens Research Institute, Flemington Rd, Parkville, Melbourne, VIC, 3052, Australia
| | - Melissa H Little
- Murdoch Childrens Research Institute, Flemington Rd, Parkville, Melbourne, VIC, 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Helen M Byrne
- Mathematical Institute, University of Oxford, Andrew Wiles Building, Woodstock Road, Oxford, UK
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George UZ, Lubkin SR. Tissue geometry may govern lung branching mode selection. J Theor Biol 2018; 442:22-30. [PMID: 29330055 DOI: 10.1016/j.jtbi.2017.12.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 12/19/2017] [Accepted: 12/31/2017] [Indexed: 11/17/2022]
Abstract
Lung branching morphogenesis proceeds in three stereotyped modes (domain, planar, and orthogonal branching). Much is known about the molecular players, including growth factors such as fibroblast growth factor 10 but it is unknown how these signals could actuate the different branching patterns. With the aim of identifying mechanisms that may determine the different branching modes, we developed a computational model of the epithelial lung bud and its surrounding mesenchyme. We studied transport of morphogens and localization of morphogen flux at lobe surfaces and lobe edges. We find that a single simple mechanism is theoretically capable of directing an epithelial tubule to elongate, bend, flatten, or bifurcate, depending solely on geometric ratios of the tissues in the vicinity of a growing tubule tip. Furthermore, the same simple mechanism is capable of generating orthogonal or planar branching, depending only on the same geometric ratios.
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Affiliation(s)
- Uduak Z George
- College of Engineering, University of Georgia, Athens, GA 30602, USA.
| | - Sharon R Lubkin
- Department of Mathematics, North Carolina State University, Raleigh, NC 27695-8205, USA.
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Clément R, Mauroy B, Cornelissen AJM. Tissue growth pressure drives early blood flow in the chicken yolk sac. Dev Dyn 2017; 246:573-584. [PMID: 28474848 DOI: 10.1002/dvdy.24516] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 04/26/2017] [Accepted: 04/26/2017] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND Understanding how molecular and physical cues orchestrate vascular morphogenesis is a challenge for developmental biology. Only little attention has been paid to the impact of mechanical stress caused by tissue growth on early blood distribution. Here we study the peripheral accumulation of blood in the chicken embryonic yolk sac, which precedes sinus vein formation. RESULTS We report that blood accumulation starts before heart-induced blood circulation. We hypothesized that the driving force for the primitive blood flow is a growth-induced gradient of tissue pressure in the yolk sac mesoderm. Therefore, we studied embryos in which heart development was arrested after 2 days of incubation, and found that yolk sac growth and blood peripheral accumulation still occurred. This suggests that tissue growth is sufficient to initiate the flow and the formation of the sinus vein, whereas heart contractions are not required. We designed a simple mathematical model which makes explicit the growth-induced pressure gradient and the subsequent blood accumulation, and show that growth can indeed account for the observed blood accumulation. CONCLUSIONS This study shows that tissue growth pressure can drive early blood flow, and suggests that the mechanical environment, beyond hemodynamics, can contribute to vascular morphogenesis. Developmental Dynamics 246:573-584, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Raphaël Clément
- Laboratoire J.-A. Dieudonné, Université Côte d'Azur and CNRS UMR 7351, Parc Valrose, Nice, France.,Aix Marseille Univ, CNRS, IBDM, Marseille, France
| | - Benjamin Mauroy
- Laboratoire J.-A. Dieudonné, Université Côte d'Azur and CNRS UMR 7351, Parc Valrose, Nice, France
| | - Annemiek J M Cornelissen
- Laboratoire Matière et Systèmes Complexes (MSC), University Paris Diderot and CNRS UMR 7057, Paris, France
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Le Deunff E, Lecourt J, Malagoli P. Fine-tuning of root elongation by ethylene: a tool to study dynamic structure-function relationships between root architecture and nitrate absorption. ANNALS OF BOTANY 2016; 118:607-620. [PMID: 27411681 PMCID: PMC5055632 DOI: 10.1093/aob/mcw123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 02/26/2016] [Accepted: 05/12/2016] [Indexed: 05/08/2023]
Abstract
Background Recently developed genetic and pharmacological approaches have been used to explore NO3-/ethylene signalling interactions and how the modifications in root architecture by pharmacological modulation of ethylene biosynthesis affect nitrate uptake. Key Results Structure-function studies combined with recent approaches to chemical genomics highlight the non-specificity of commonly used inhibitors of ethylene biosynthesis such as AVG (l-aminoethoxyvinylglycine). Indeed, AVG inhibits aminotransferases such as ACC synthase (ACS) and tryptophan aminotransferase (TAA) involved in ethylene and auxin biosynthesis but also some aminotransferases implied in nitrogen (N) metabolism. In this framework, it can be assumed that the products of nitrate assimilation and hormones may interact through a hub in carbon (C) and N metabolism to drive the root morphogenetic programme (RMP). Although ethylene/auxin interactions play a major role in cell division and elongation in root meristems, shaping of the root system depends also on energetic considerations. Based on this finding, the analysis is extended to nutrient ion-hormone interactions assuming a fractal or constructal model for root development. Conclusion Therefore, the tight control of root structure-function in the RMP may explain why over-expressing nitrate transporter genes to decouple structure-function relationships and improve nitrogen use efficiency (NUE) has been unsuccessful.
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Affiliation(s)
- Erwan Le Deunff
- Université de Caen Basse-Normandie, UMR Écophysiologie Végétale & Agronomie, Nutritions NCS, F-14032 Caen, France
- INRA, UMR 950, Écophysiologie Végétale & Agronomie, Nutritions NCS, F-14032 Caen, France
| | - Julien Lecourt
- East Malling Research, New Road, East Malling ME19 6BJ, Kent, UK
| | - Philippe Malagoli
- Université Blaise Pascal-INRA, 24, avenue des Landais, BP 80 006, F-63177 Aubière, France
- INRA, UMR 547 PIAF, Bâtiment Biologie Végétale Recherche, BP 80 006, F-63177 Aubière, France
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Borek B, Hasty J, Tsimring L. Turing Patterning Using Gene Circuits with Gas-Induced Degradation of Quorum Sensing Molecules. PLoS One 2016; 11:e0153679. [PMID: 27148743 PMCID: PMC4858293 DOI: 10.1371/journal.pone.0153679] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 04/01/2016] [Indexed: 01/30/2023] Open
Abstract
The Turing instability was proposed more than six decades ago as a mechanism leading to spatial patterning, but it has yet to be exploited in a synthetic biology setting. Here we characterize the Turing instability in a specific gene circuit that can be implemented in vitro or in populations of clonal cells producing short-range activator N-Acyl homoserine lactone (AHL) and long-range inhibitor hydrogen peroxide (H2O2) gas. Slowing the production rate of the AHL-degrading enzyme, AiiA, generates stable fixed states, limit cycle oscillations and Turing patterns. Further tuning of signaling parameters determines local robustness and controls the range of unstable wavenumbers in the patterning regime. These findings provide a roadmap for optimizing spatial patterns of gene expression based on familiar quorum and gas sensitive E. coli promoters. The circuit design and predictions may be useful for (re)programming spatial dynamics in synthetic and natural gene expression systems.
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Affiliation(s)
- Bartłomiej Borek
- BioCircuits Institute, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92037-0328, United States of America
- San Diego Center for Systems Biology, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92037-0375, United States of America
| | - Jeff Hasty
- BioCircuits Institute, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92037-0328, United States of America
- San Diego Center for Systems Biology, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92037-0375, United States of America
- Department of Bioengineering, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92037-0412, United States of America
- Molecular Biology Section, Division of Biological Sciences, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92037-0116, United States of America
| | - Lev Tsimring
- BioCircuits Institute, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92037-0328, United States of America
- San Diego Center for Systems Biology, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92037-0375, United States of America
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Guo Y, Sun M, Garfinkel A, Zhao X. Mechanisms of side branching and tip splitting in a model of branching morphogenesis. PLoS One 2014; 9:e102718. [PMID: 25050616 PMCID: PMC4106868 DOI: 10.1371/journal.pone.0102718] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 06/24/2014] [Indexed: 11/29/2022] Open
Abstract
Recent experimental work in lung morphogenesis has described an elegant pattern of branching phenomena. Two primary forms of branching have been identified: side branching and tip splitting. In our previous study of lung branching morphogenesis, we used a 4 variable partial differential equation (PDE), due to Meinhardt, as our mathematical model to describe the reaction and diffusion of morphogens creating those branched patterns. By altering key parameters in the model, we were able to reproduce all the branching styles and the switch between branching modes. Here, we attempt to explain the branching phenomena described above, as growing out of two fundamental instabilities, one in the longitudinal (growth) direction and the other in the transverse direction. We begin by decoupling the original branching process into two semi-independent sub-processes, 1) a classic activator/inhibitor system along the growing stalk, and 2) the spatial growth of the stalk. We then reduced the full branching model into an activator/inhibitor model that embeds growth of the stalk as a controllable parameter, to explore the mechanisms that determine different branching patterns. We found that, in this model, 1) side branching results from a pattern-formation instability of the activator/inhibitor subsystem in the longitudinal direction. This instability is far from equilibrium, requiring a large inhomogeneity in the initial conditions. It successively creates periodic activator peaks along the growing stalk, each of which later on migrates out and forms a side branch; 2) tip splitting is due to a Turing-style instability along the transversal direction, that creates the spatial splitting of the activator peak into 2 simultaneously-formed peaks at the growing tip, the occurrence of which requires the widening of the growing stalk. Tip splitting is abolished when transversal stalk widening is prevented; 3) when both instabilities are satisfied, tip bifurcation occurs together with side branching.
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Affiliation(s)
- Yina Guo
- Institute of Robotics and Automatic Information Systems, Nankai University, Tianjin, China
| | - Mingzhu Sun
- Institute of Robotics and Automatic Information Systems, Nankai University, Tianjin, China
- State Key Laboratory of Robotics, Shenyang, China
| | - Alan Garfinkel
- Department of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail: (XZ); (AG)
| | - Xin Zhao
- Institute of Robotics and Automatic Information Systems, Nankai University, Tianjin, China
- Tianjin Key Laboratory of Intelligent Robotics, Tianjin, China
- * E-mail: (XZ); (AG)
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