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Roshal DS, Fedorenko KK, Martin M, Baghdiguian S, Rochal SB. Topological balance of cell distributions in plane monolayers. J Phys Condens Matter 2024; 36:265101. [PMID: 38537291 DOI: 10.1088/1361-648x/ad387a] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 03/27/2024] [Indexed: 04/06/2024]
Abstract
Most of normal proliferative epithelia of plants and metazoans are topologically invariant and characterized by similar cell distributions according to the number of cell neighbors (DCNs). Here we study peculiarities of these distributions and explain why the DCN obtained from the location of intercellular boundaries and that based on the Voronoi tessellation with nodes located on cell nuclei may differ from each other. As we demonstrate, special microdomains where four or more intercellular boundaries converge are topologically charged. Using this fact, we deduce a new equation describing the topological balance of the DCNs. The developed theory is applied for a series of microphotographs of non-tumoral epithelial cells of the human cervix (HCerEpiC) to improve the image processing near the edges of microphotographs and reveal the topological invariance of the examined monolayers. Special contact microdomains may be present in epithelia of various natures, however, considering the well-known vertex model of epithelium, we show that such contacts are absent in the usual solid-like state of the model and appear only in the liquid-like cancer state. Also, we discuss a possible biological role of special contacts in context of proliferative epithelium dynamics and tissue morphogenesis.
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Affiliation(s)
- Daria S Roshal
- Faculty of Physics, Southern Federal University, Zorge 5, Rostov-on-Don 344090, Russia
| | - Kirill K Fedorenko
- Faculty of Physics, Southern Federal University, Zorge 5, Rostov-on-Don 344090, Russia
| | - Marianne Martin
- VBIC, INSERM U1047, University of Montpellier, Montpellier 34095, France
| | - Stephen Baghdiguian
- Institut des Sciences de l'Evolution-Montpellier, Université de Montpellier, CNRS, Ecole Pratique des Hautes Etudes, Institut de Recherche pour le Développement, Montpellier 34095, France
| | - Sergei B Rochal
- Faculty of Physics, Southern Federal University, Zorge 5, Rostov-on-Don 344090, Russia
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2
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Barsimantov Mandel J, Solorio L, Tepole AB. Geometry of adipocyte packing in subcutaneous tissue contributes to nonlinear tissue properties captured through a Gaussian process surrogate model. Soft Matter 2024. [PMID: 38477130 DOI: 10.1039/d3sm01661g] [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] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
Subcutaneous tissue mechanical response is governed by the geometry and mechanical properties at the microscale and drives physiological and clinical processes such as drug delivery. Even though adipocyte packing is known to change with age, disease, and from one individual to another, the link between the geometry of the packing and the overall mechanical response of adipose tissue remains poorly understood. Here we create 1200 periodic representative volume elements (RVEs) that sample the possible space of Laguerre packings describing adipose tissue. RVE mechanics are modeled under tri-axial loading. Equilibrium configuration of RVEs is solved by minimizing an energetic potential that includes volume change contributions from adipocyte expansion, and area change contributions from collagen foam stretching. The resulting mechanical response across all RVE samples is interpolated with the aid of a Gaussian process (GP), revealing how the microscale geometry dictates the overall RVE mechanics. For example, increase in adipocyte size and increase in sphericity lead to adipose tissue softening. We showcase the use of the homogenized model in finite element simulations of drug injection by implementing a Blatz-Ko model, informed by the GP, as a custom material in the popular open-source package FEBio. These simulations show how microscale geometry can lead to vastly different injection dynamics even if the constituent parameters are held constant, highlighting the importance of characterizing individual's adipose tissue structure in the development of personalized therapies.
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Affiliation(s)
| | - Luis Solorio
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, USA
| | - Adrian Buganza Tepole
- School of Mechanical Engineering, Purdue University, 205 Gates Rd, West Lafayette, USA.
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, USA
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3
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Andrés-San Román JA, Gordillo-Vázquez C, Franco-Barranco D, Morato L, Fernández-Espartero CH, Baonza G, Tagua A, Vicente-Munuera P, Palacios AM, Gavilán MP, Martín-Belmonte F, Annese V, Gómez-Gálvez P, Arganda-Carreras I, Escudero LM. CartoCell, a high-content pipeline for 3D image analysis, unveils cell morphology patterns in epithelia. Cell Rep Methods 2023; 3:100597. [PMID: 37751739 PMCID: PMC10626192 DOI: 10.1016/j.crmeth.2023.100597] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 07/19/2023] [Accepted: 08/31/2023] [Indexed: 09/28/2023]
Abstract
Decades of research have not yet fully explained the mechanisms of epithelial self-organization and 3D packing. Single-cell analysis of large 3D epithelial libraries is crucial for understanding the assembly and function of whole tissues. Combining 3D epithelial imaging with advanced deep-learning segmentation methods is essential for enabling this high-content analysis. We introduce CartoCell, a deep-learning-based pipeline that uses small datasets to generate accurate labels for hundreds of whole 3D epithelial cysts. Our method detects the realistic morphology of epithelial cells and their contacts in the 3D structure of the tissue. CartoCell enables the quantification of geometric and packing features at the cellular level. Our single-cell cartography approach then maps the distribution of these features on 2D plots and 3D surface maps, revealing cell morphology patterns in epithelial cysts. Additionally, we show that CartoCell can be adapted to other types of epithelial tissues.
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Affiliation(s)
- Jesús A Andrés-San Román
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41013 Seville, Spain
| | - Carmen Gordillo-Vázquez
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41013 Seville, Spain
| | - Daniel Franco-Barranco
- Department of Computer Science and Artificial Intelligence, University of the Basque Country (UPV/EHU), 20018 San Sebastian, Spain; Donostia International Physics Center (DIPC), 20018 San Sebastian, Spain
| | - Laura Morato
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41013 Seville, Spain
| | - Cecilia H Fernández-Espartero
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41013 Seville, Spain
| | - Gabriel Baonza
- Program of Tissue and Organ Homeostasis, Centro de Biología Molecular Severo Ochoa, CSIC-UAM and Ramón & Cajal Health Research Institute (IRYCIS), Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain
| | - Antonio Tagua
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41013 Seville, Spain
| | | | - Ana M Palacios
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41013 Seville, Spain
| | - María P Gavilán
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), JA/CSIC/Universidad de Sevilla/Universidad Pablo de Olavide and Departamento de Citología e Histología Normal y Patológica, Facultad de Medicina, Universidad de Sevilla, 41009 Seville, Spain
| | - Fernando Martín-Belmonte
- Program of Tissue and Organ Homeostasis, Centro de Biología Molecular Severo Ochoa, CSIC-UAM and Ramón & Cajal Health Research Institute (IRYCIS), Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain
| | - Valentina Annese
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41013 Seville, Spain
| | - Pedro Gómez-Gálvez
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41013 Seville, Spain; MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Trumpington, Cambridge CB2 0QH, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK.
| | - Ignacio Arganda-Carreras
- Department of Computer Science and Artificial Intelligence, University of the Basque Country (UPV/EHU), 20018 San Sebastian, Spain; Donostia International Physics Center (DIPC), 20018 San Sebastian, Spain; Ikerbasque, Basque Foundation for Science, 48009 Bilbao, Spain; Biofisika Institute, 48940 Leioa, Spain.
| | - Luis M Escudero
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41013 Seville, Spain; Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), 28029 Madrid, Spain.
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4
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Abstract
Background: Reelin has fundamental functions in the developing and mature brain. Its absence gives rise to the Reeler phenotype in mice, the first described cerebellar mutation. In homozygous mutants missing the Reelin gene ( reln -/-), neurons are incapable of correctly positioning themselves in layered brain areas such as the cerebral and cerebellar cortices. We here demonstrate that by employing ex vivo cultured cerebellar slices one can reduce the number of animals and use a non-recovery procedure to analyze the effects of Reelin on the migration of Purkinje neurons (PNs). Methods: We generated mouse hybrids (L7-GFP relnF1/) with green fluorescent protein (GFP)-tagged PNs, directly visible under fluorescence microscopy. We then cultured the slices obtained from mice with different reln genotypes and demonstrated that when the slices from reln -/- mutants were co-cultured with those from reln +/- mice, the Reelin produced by the latter induced migration of the PNs to partially rescue the normal layered cortical histology. We have confirmed this observation with Voronoi tessellation to analyze PN dispersion. Results: In images of the co-cultured slices from reln -/- mice, Voronoi polygons were larger than in single-cultured slices of the same genetic background but smaller than those generated from slices of reln +/- animals. The mean roundness factor, area disorder, and roundness factor homogeneity were different when slices from reln -/- mice were cultivated singularly or co-cultivated, supporting mathematically the transition from the clustered organization of the PNs in the absence of Reelin to a layered structure when the protein is supplied ex vivo. Conclusions: Neurobiologists are the primary target users of this 3Rs approach. They should adopt it for the possibility to study and manipulate ex vivo the activity of a brain-secreted or genetically engineered protein (scientific perspective), the potential reduction (up to 20%) of the animals used, and the total avoidance of severe surgery (3Rs perspective).
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Affiliation(s)
- Adalberto Merighi
- Department of Veterinary Sciences, University of Turin, Grugliasco, 10095, Italy
| | - Laura Lossi
- Department of Veterinary Sciences, University of Turin, Grugliasco, 10095, Italy
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5
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Merighi A, Lossi L. Co-cultures of cerebellar slices from mice with different reelin genetic backgrounds as a model to study cortical lamination. F1000Res 2023; 11:1183. [PMID: 37881513 PMCID: PMC10594056 DOI: 10.12688/f1000research.126787.2] [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] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/07/2023] [Indexed: 10/27/2023] Open
Abstract
Background: Reelin has fundamental functions in the developing and mature brain. Its absence gives rise to the Reeler phenotype in mice, the first described cerebellar mutation. In homozygous mutants missing the Reelin gene ( reln -/-), neurons are incapable of correctly positioning themselves in layered brain areas such as the cerebral and cerebellar cortices. We here demonstrate that by employing ex vivo cultured cerebellar slices one can reduce the number of animals and use a non-recovery procedure to analyze the effects of Reelin on the migration of Purkinje neurons (PNs). Methods: We generated mouse hybrids (L7-GFP relnF1/) with green fluorescent protein (GFP)-tagged PNs, directly visible under fluorescence microscopy. We then cultured the slices obtained from mice with different reln genotypes and demonstrated that when the slices from reln -/- mutants were co-cultured with those from reln +/- mice, the Reelin produced by the latter induced migration of the PNs to partially rescue the normal layered cortical histology. We have confirmed this observation with Voronoi tessellation to analyze PN dispersion. Results: In images of the co-cultured slices from reln -/- mice, Voronoi polygons were larger than in single-cultured slices of the same genetic background but smaller than those generated from slices of reln +/- animals. The mean roundness factor, area disorder, and roundness factor homogeneity were different when slices from reln -/- mice were cultivated singularly or co-cultivated, supporting mathematically the transition from the clustered organization of the PNs in the absence of Reelin to a layered structure when the protein is supplied ex vivo. Conclusions: Neurobiologists are the primary target users of this 3Rs approach. They should adopt it for the possibility to study and manipulate ex vivo the activity of a brain-secreted or genetically engineered protein (scientific perspective), the potential reduction (up to 20%) of the animals used, and the total avoidance of severe surgery (3Rs perspective).
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Affiliation(s)
- Adalberto Merighi
- Department of Veterinary Sciences, University of Turin, Grugliasco, 10095, Italy
| | - Laura Lossi
- Department of Veterinary Sciences, University of Turin, Grugliasco, 10095, Italy
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6
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Ronteix G, Aristov A, Bonnet V, Sart S, Sobel J, Esposito E, Baroud CN. Griottes: a generalist tool for network generation from segmented tissue images. BMC Biol 2022; 20:178. [PMID: 35953853 PMCID: PMC9367069 DOI: 10.1186/s12915-022-01376-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 07/15/2022] [Indexed: 11/10/2022] Open
Abstract
Background Microscopy techniques and image segmentation algorithms have improved dramatically this decade, leading to an ever increasing amount of biological images and a greater reliance on imaging to investigate biological questions. This has created a need for methods to extract the relevant information on the behaviors of cells and their interactions, while reducing the amount of computing power required to organize this information. Results This task can be performed by using a network representation in which the cells and their properties are encoded in the nodes, while the neighborhood interactions are encoded by the links. Here, we introduce Griottes, an open-source tool to build the “network twin” of 2D and 3D tissues from segmented microscopy images. We show how the library can provide a wide range of biologically relevant metrics on individual cells and their neighborhoods, with the objective of providing multi-scale biological insights. The library’s capacities are demonstrated on different image and data types. Conclusions This library is provided as an open-source tool that can be integrated into common image analysis workflows to increase their capacities.
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Affiliation(s)
- Gustave Ronteix
- Institut Pasteur, Université Paris Cité, Physical microfluidics and Bioengineering, Paris, F-75015, France.,LadHyX, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, 91120, France
| | - Andrey Aristov
- Institut Pasteur, Université Paris Cité, Physical microfluidics and Bioengineering, Paris, F-75015, France
| | - Valentin Bonnet
- Institut Pasteur, Université Paris Cité, Physical microfluidics and Bioengineering, Paris, F-75015, France.,LadHyX, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, 91120, France
| | - Sebastien Sart
- Institut Pasteur, Université Paris Cité, Physical microfluidics and Bioengineering, Paris, F-75015, France
| | - Jeremie Sobel
- Institut Pasteur, Université Paris Cité, Physical microfluidics and Bioengineering, Paris, F-75015, France
| | - Elric Esposito
- UTechS PBI, Institut Pasteur, 25-28 Rue du Dr Roux, Paris, 75015, France
| | - Charles N Baroud
- Institut Pasteur, Université Paris Cité, Physical microfluidics and Bioengineering, Paris, F-75015, France. .,LadHyX, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, 91120, France.
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7
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Guan G, Zhao Z, Tang C. Delineating mechanisms and design principles of Caenorhabditis elegans embryogenesis using in toto high-resolution imaging data and computational modeling. Comput Struct Biotechnol J 2022; 20:5500-5515. [PMID: 36284714 PMCID: PMC9562942 DOI: 10.1016/j.csbj.2022.08.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 11/19/2022] Open
Abstract
The nematode (roundworm) Caenorhabditis elegans is one of the most popular animal models for the study of developmental biology, as its invariant development and transparent body enable in toto cellular-resolution fluorescence microscopy imaging of developmental processes at 1-min intervals. This has led to the development of various computational tools for the systematic and automated analysis of imaging data to delineate the molecular and cellular processes throughout the embryogenesis of C. elegans, such as those associated with cell lineage, cell migration, cell morphology, and gene activity. In this review, we first introduce C. elegans embryogenesis and the development of techniques for tracking cell lineage and reconstructing cell morphology during this process. We then contrast the developmental modes of C. elegans and the customized technologies used for studying them with the ones of other animal models, highlighting its advantage for studying embryogenesis with exceptional spatial and temporal resolution. This is followed by an examination of the physical models that have been devised—based on accurate determinations of developmental processes afforded by analyses of imaging data—to interpret the early embryonic development of C. elegans from subcellular to intercellular levels of multiple cells, which focus on two key processes: cell polarization and morphogenesis. We subsequently discuss how quantitative data-based theoretical modeling has improved our understanding of the mechanisms of C. elegans embryogenesis. We conclude by summarizing the challenges associated with the acquisition of C. elegans embryogenesis data, the construction of algorithms to analyze them, and the theoretical interpretation.
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8
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Saraswathibhatla A, Zhang J, Notbohm J. Coordination of contractile tension and cell area changes in an epithelial cell monolayer. Phys Rev E 2022; 105:024404. [PMID: 35291100 DOI: 10.1103/physreve.105.024404] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
During tissue development and repair, cells contract and expand in coordination with their neighbors, giving rise to tissue deformations that occur on length scales far larger than that of a single cell. The biophysical mechanisms by which the contractile forces of each cell cause deformations on multicellular length scales are not fully clear. To investigate this question, we began with the principle of force equilibrium, which dictates a balance of tensile forces between neighboring cells. Based on this principle, we hypothesized that coordinated changes in cell area result from tension transmitted across the cell layer. To test this hypothesis, spatial correlations of both contractile tension and the divergence of cell velocities were measured as readouts of coordinated contractility and collective area changes, respectively. Experiments were designed to alter the spatial correlation of contractile tension using three different methods, including disrupting cell-cell adhesions, modulating the alignment of actomyosin stress fibers between neighboring cells, and changing the size of the cell monolayer. In all experiments, the spatial correlations of both tension and divergence increased or decreased together, in agreement with our hypothesis. To relate our findings to the intracellular mechanism connecting changes in cell area to contractile tension, we disrupted activation of extracellular signal-regulated kinase (ERK), which is known to mediate the intracellular relationship between cell area and contraction. Consistent with prior knowledge, a temporal cross-correlation between cell area and tension revealed that ERK was responsible for a proportional relationship between cell area and contraction. Inhibition of ERK activation reduced the spatial correlations of the divergence of cell velocity but not of tension. Together, our findings suggest that coordination of cell contraction and expansion requires transfer of cell tension over space and ERK-mediated coordination between cell area and contraction in time.
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Affiliation(s)
| | - Jun Zhang
- Department of Engineering Physics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Biophysics Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Jacob Notbohm
- Department of Engineering Physics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Biophysics Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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9
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McKinley ET, Shao J, Ellis ST, Heiser CN, Roland JT, Macedonia MC, Vega PN, Shin S, Coffey RJ, Lau KS. MIRIAM: A machine and deep learning single-cell segmentation and quantification pipeline for multi-dimensional tissue images. Cytometry A 2022; 101:521-528. [PMID: 35084791 PMCID: PMC9167255 DOI: 10.1002/cyto.a.24541] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [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: 09/20/2021] [Revised: 12/16/2021] [Accepted: 01/17/2022] [Indexed: 11/25/2022]
Abstract
Increasingly, highly multiplexed tissue imaging methods are used to profile protein expression at the single‐cell level. However, a critical limitation is the lack of robust cell segmentation tools for tissue sections. We present Multiplexed Image Resegmentation of Internal Aberrant Membranes (MIRIAM) that combines (a) a pipeline for cell segmentation and quantification that incorporates machine learning‐based pixel classification to define cellular compartments, (b) a novel method for extending incomplete cell membranes, and (c) a deep learning‐based cell shape descriptor. Using human colonic adenomas as an example, we show that MIRIAM is superior to widely utilized segmentation methods and provides a pipeline that is broadly applicable to different imaging platforms and tissue types.
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Affiliation(s)
- Eliot T McKinley
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Justin Shao
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Samuel T Ellis
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Cody N Heiser
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA.,Program in Chemical & Physical Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Joseph T Roland
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mary C Macedonia
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Paige N Vega
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Susie Shin
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Robert J Coffey
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA.,Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ken S Lau
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.,Program in Chemical & Physical Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.,Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
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10
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Shahpari MS, Namavar MRN, Kamali Dolatabadi LKD, Aligholi HA, Emamghoreishi ME. Morphological changes in the substantia nigra pars reticulata of the mice during kindling. Neurosci Lett 2021; 764:136278. [PMID: 34600041 DOI: 10.1016/j.neulet.2021.136278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 09/27/2021] [Accepted: 09/27/2021] [Indexed: 11/21/2022]
Abstract
Substantia nigra pars reticulata (SNpr) has been implicated in modulation, propagation and cessation of seizures. This study aimed to determine whether structural changes occur in SNpr during kindling. Male mice were randomly divided into four groups including early and late-phase kindled groups and their time-matched controls. Kindling was induced by every other day administration of a subconvulsive dose of PTZ (40 mg/kg, i.p.). The first occurrence of seizure behaviors was used to categorize the early and late phases of kindling. There was no significant difference in the volume of SNpr between the early- and late-phase kindled groups. The diameter of SNpr was significantly increased in the early phase group and decreased in the late phase group as compared to their matched controls (p < 0.05). Reduced neural cells and increased dead cell numbers were observed in the SNpr of the late-phase group in comparison to its control group (p < 0.05). These findings suggest that SNpr is a sensitive and vulnerable structure involving seizure propagation in the processes of epileptogenesis.
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11
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Melo HPM, Maia FR, Nunes AS, Reis RL, Oliveira JM, Araújo NAM. Combining experiments and in silico modeling to infer the role of adhesion and proliferation on the collective dynamics of cells. Sci Rep 2021; 11:19894. [PMID: 34615941 DOI: 10.1038/s41598-021-99390-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 09/23/2021] [Indexed: 02/06/2023] Open
Abstract
The collective dynamics of cells on surfaces and interfaces poses technological and theoretical challenges in the study of morphogenesis, tissue engineering, and cancer. Different mechanisms are at play, including, cell–cell adhesion, cell motility, and proliferation. However, the relative importance of each one is elusive. Here, experiments with a culture of glioblastoma multiforme cells on a substrate are combined with in silico modeling to infer the rate of each mechanism. By parametrizing these rates, the time-dependence of the spatial correlation observed experimentally is reproduced. The obtained results suggest a reduction in cell–cell adhesion with the density of cells. The reason for such reduction and possible implications for the collective dynamics of cancer cells are discussed.
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12
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Heger L, Lühr JJ, Amon L, Smith AS, Eissing N, Dudziak D. Six-Color Confocal Immunofluorescence Microscopy with 4-Laser Lines. Methods Mol Biol 2021; 2350:21-30. [PMID: 34331276 DOI: 10.1007/978-1-0716-1593-5_2] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
Confocal immunofluorescence microscopy is an advanced imaging technique routinely applied in the laboratory and clinics. Histological analyses are performed from tissue material. In general, a single fluorochrome per laser is employed, limiting simultaneous analysis to four antigens in one staining with a conventional 4-laser line microscope. Here, we describe a protocol for combining fluorochromes with the same excitation but different emission properties that allows for the analysis of six different antigens in confocal immunofluorescence microscopy with a conventional 4-laser line microscope. The proposed multiplexed method permits the identification and characterization of complex cell populations in rare tissue material.
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Affiliation(s)
- Lukas Heger
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Jennifer J Lühr
- Department of Physics, Nano-Optics, Sandoghdar Division, Max Planck Institute for the Science of Light, Erlangen, Germany
| | - Lukas Amon
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Ana-Sunčana Smith
- Physics Underlying Life Sciences Group, Institute for Theoretical Physics, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany.,Group for Computational Life Sciences, Division of Physical Chemistry, Institute Ruąer Bošković, Zagreb, Croatia
| | - Nathalie Eissing
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Diana Dudziak
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany. .,Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany. .,Comprehensive Cancer Center Erlangen-European Metropolitan Area of Nuremberg (CCC ER-EMN), Erlangen, Germany. .,Medical Immunology Campus Erlangen, Erlangen, Germany.
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13
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Holcomb MC, Gao GJJ, Servati M, Schneider D, McNeely PK, Thomas JH, Blawzdziewicz J. Mechanical feedback and robustness of apical constrictions in Drosophila embryo ventral furrow formation. PLoS Comput Biol 2021; 17:e1009173. [PMID: 34228708 PMCID: PMC8284804 DOI: 10.1371/journal.pcbi.1009173] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 08/21/2020] [Revised: 07/16/2021] [Accepted: 06/10/2021] [Indexed: 11/19/2022] Open
Abstract
Formation of the ventral furrow in the Drosophila embryo relies on the apical constriction of cells in the ventral region to produce bending forces that drive tissue invagination. In our recent paper we observed that apical constrictions during the initial phase of ventral furrow formation produce elongated patterns of cellular constriction chains prior to invagination and argued that these are indicative of tensile stress feedback. Here, we quantitatively analyze the constriction patterns preceding ventral furrow formation and find that they are consistent with the predictions of our active-granular-fluid model of a monolayer of mechanically coupled stress-sensitive constricting particles. Our model shows that tensile feedback causes constriction chains to develop along underlying precursor tensile stress chains that gradually strengthen with subsequent cellular constrictions. As seen in both our model and available optogenetic experiments, this mechanism allows constriction chains to penetrate or circumvent zones of reduced cell contractility, thus increasing the robustness of ventral furrow formation to spatial variation of cell contractility by rescuing cellular constrictions in the disrupted regions.
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Affiliation(s)
- Michael C. Holcomb
- Department of Physics and Astronomy, Texas Tech University, Lubbock, Texas, United States of America
| | - Guo-Jie Jason Gao
- Department of Mathematical and Systems Engineering, Shizuoka University, Hamamatsu, Japan
| | - Mahsa Servati
- Department of Physics and Astronomy, Texas Tech University, Lubbock, Texas, United States of America
| | - Dylan Schneider
- Department of Mechanical Engineering, Texas Tech University, Lubbock, Texas, United States of America
| | - Presley K. McNeely
- Department of Physics and Astronomy, Texas Tech University, Lubbock, Texas, United States of America
| | - Jeffrey H. Thomas
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Jerzy Blawzdziewicz
- Department of Physics and Astronomy, Texas Tech University, Lubbock, Texas, United States of America
- Department of Mechanical Engineering, Texas Tech University, Lubbock, Texas, United States of America
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14
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Lau C, Kalantari B, Batts KP, Ferrell LD, Nyberg SL, Graham RP, Moreira RK. The Voronoi theory of the normal liver lobular architecture and its applicability in hepatic zonation. Sci Rep 2021; 11:9343. [PMID: 33927276 PMCID: PMC8085188 DOI: 10.1038/s41598-021-88699-2] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 04/12/2021] [Indexed: 11/24/2022] Open
Abstract
The precise characterization of the lobular architecture of the liver has been subject of investigation since the earliest historical publications, but an accurate model to describe the hepatic lobular microanatomy is yet to be proposed. Our aim was to evaluate whether Voronoi diagrams can be used to describe the classic liver lobular architecture. We examined the histology of normal porcine and human livers and analyzed the geometric relationships of various microanatomic structures utilizing digital tools. The Voronoi diagram model described the organization of the hepatic classic lobules with overall accuracy nearly 90% based on known histologic landmarks. We have also designed a Voronoi-based algorithm of hepatic zonation, which also showed an overall zonal accuracy of nearly 90%. Therefore, we have presented evidence that Voronoi diagrams represent the basis of the two-dimensional organization of the normal liver and that this concept may have wide applicability in liver pathology and research.
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Affiliation(s)
- C Lau
- Department of Computer Science, Rutgers University, Brunswick, NJ, USA
| | - B Kalantari
- Department of Computer Science, Rutgers University, Brunswick, NJ, USA
| | | | - L D Ferrell
- Department of Pathology, University of California, San Francisco, CA, USA
| | - S L Nyberg
- Division of Transplantation Surgery, Department of Surgery, Mayo Clinic, Rochester, MN, USA
| | - R P Graham
- Department of Pathology and Laboratory Medicine, Mayo Clinic, Rochester, MN, USA
| | - Roger K Moreira
- Department of Pathology and Laboratory Medicine, Mayo Clinic, Rochester, MN, USA.
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15
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Rundo L, Tangherloni A, Tyson DR, Betta R, Militello C, Spolaor S, Nobile MS, Besozzi D, Lubbock ALR, Quaranta V, Mauri G, Lopez CF, Cazzaniga P. ACDC: Automated Cell Detection and Counting for Time-Lapse Fluorescence Microscopy. Appl Sci (Basel) 2020; 10:6187. [PMID: 34306736 DOI: 10.3390/app10186187] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Advances in microscopy imaging technologies have enabled the visualization of live-cell dynamic processes using time-lapse microscopy imaging. However, modern methods exhibit several limitations related to the training phases and to time constraints, hindering their application in the laboratory practice. In this work, we present a novel method, named Automated Cell Detection and Counting (ACDC), designed for activity detection of fluorescent labeled cell nuclei in time-lapse microscopy. ACDC overcomes the limitations of the literature methods, by first applying bilateral filtering on the original image to smooth the input cell images while preserving edge sharpness, and then by exploiting the watershed transform and morphological filtering. Moreover, ACDC represents a feasible solution for the laboratory practice, as it can leverage multi-core architectures in computer clusters to efficiently handle large-scale imaging datasets. Indeed, our Parent-Workers implementation of ACDC allows to obtain up to a 3.7× speed-up compared to the sequential counterpart. ACDC was tested on two distinct cell imaging datasets to assess its accuracy and effectiveness on images with different characteristics. We achieved an accurate cell-count and nuclei segmentation without relying on large-scale annotated datasets, a result confirmed by the average Dice Similarity Coefficients of 76.84 and 88.64 and the Pearson coefficients of 0.99 and 0.96, calculated against the manual cell counting, on the two tested datasets.
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16
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Zheng Y, Li YW, Ciamarra MP. Hyperuniformity and density fluctuations at a rigidity transition in a model of biological tissues. Soft Matter 2020; 16:5942-5950. [PMID: 32542303 DOI: 10.1039/d0sm00776e] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The suppression of density fluctuations at different length scales is the hallmark of hyperuniformity. Here, we explore the presence of this hidden order in a manybody interacting model of biological tissue, known to exhibit a transition, or sharp crossover, from a solid to a fluid like phase. We show that the density fluctuations in the rigid phase are only suppressed up to a finite lengthscale. This length scale monotonically increases and grows rapidly as we approach the fluid phase reminiscent to divergent behavior at a critical point, such that the system is effectively hyperuniform in the fluid phase. Furthermore, complementary behavior of the structure factor across the critical point also indicates that hyperuniformity found in the fluid phase is stealthy.
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Affiliation(s)
- Yuanjian Zheng
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore.
| | - Yan-Wei Li
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore.
| | - Massimo Pica Ciamarra
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore. and MajuLab, CNRS-UCA-SU-NUS-NTU International Joint Research Unit, Singapore and CNR-SPIN, Dipartimento di Scienze Fisiche, Università di Napoli Federico II, I-80126, Napoli, Italy
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17
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Leedale JA, Kyffin JA, Harding AL, Colley HE, Murdoch C, Sharma P, Williams DP, Webb SD, Bearon RN. Multiscale modelling of drug transport and metabolism in liver spheroids. Interface Focus 2020; 10:20190041. [PMID: 32194929 PMCID: PMC7061947 DOI: 10.1098/rsfs.2019.0041] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/13/2019] [Indexed: 12/22/2022] Open
Abstract
In early preclinical drug development, potential candidates are tested in the laboratory using isolated cells. These in vitro experiments traditionally involve cells cultured in a two-dimensional monolayer environment. However, cells cultured in three-dimensional spheroid systems have been shown to more closely resemble the functionality and morphology of cells in vivo. While the increasing usage of hepatic spheroid cultures allows for more relevant experimentation in a more realistic biological environment, the underlying physical processes of drug transport, uptake and metabolism contributing to the spatial distribution of drugs in these spheroids remain poorly understood. The development of a multiscale mathematical modelling framework describing the spatio-temporal dynamics of drugs in multicellular environments enables mechanistic insight into the behaviour of these systems. Here, our analysis of cell membrane permeation and porosity throughout the spheroid reveals the impact of these properties on drug penetration, with maximal disparity between zonal metabolism rates occurring for drugs of intermediate lipophilicity. Our research shows how mathematical models can be used to simulate the activity and transport of drugs in hepatic spheroids and in principle any organoid, with the ultimate aim of better informing experimentalists on how to regulate dosing and culture conditions to more effectively optimize drug delivery.
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Affiliation(s)
- Joseph A Leedale
- EPSRC Liverpool Centre for Mathematics in Healthcare, Department of Mathematical Sciences, University of Liverpool, Liverpool L69 7ZL, UK
| | - Jonathan A Kyffin
- Department of Applied Mathematics, Liverpool John Moores University, Liverpool L3 3AF, UK
| | - Amy L Harding
- School of Clinical Dentistry, University of Sheffield, Claremont Crescent, Sheffield S10 2TA, UK
| | - Helen E Colley
- School of Clinical Dentistry, University of Sheffield, Claremont Crescent, Sheffield S10 2TA, UK
| | - Craig Murdoch
- School of Clinical Dentistry, University of Sheffield, Claremont Crescent, Sheffield S10 2TA, UK
| | - Parveen Sharma
- MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool L69 3GE, UK
| | - Dominic P Williams
- AstraZeneca, IMED Biotech Unit, Drug Safety and Metabolism, Cambridge Science Park, Cambridge CB4 0FZ, UK
| | - Steven D Webb
- EPSRC Liverpool Centre for Mathematics in Healthcare, Department of Mathematical Sciences, University of Liverpool, Liverpool L69 7ZL, UK.,Department of Applied Mathematics, Liverpool John Moores University, Liverpool L3 3AF, UK
| | - Rachel N Bearon
- EPSRC Liverpool Centre for Mathematics in Healthcare, Department of Mathematical Sciences, University of Liverpool, Liverpool L69 7ZL, UK
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18
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Abstract
Active glassy matter has recently emerged as a novel class of non-equilibrium soft matter, combining energy-driven, active particle movement with dense and disordered glass-like behavior. Here we review the state-of-the-art in this field from an experimental, numerical, and theoretical perspective. We consider both non-living and living active glassy systems, and discuss how several hallmarks of glassy dynamics (dynamical slowdown, fragility, dynamical heterogeneity, violation of the Stokes-Einstein relation, and aging) are manifested in such materials. We start by reviewing the recent experimental evidence in this area of research, followed by an overview of the main numerical simulation studies and physical theories of active glassy matter. We conclude by outlining several open questions and possible directions for future work.
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Affiliation(s)
- Liesbeth M C Janssen
- Theory of Polymers and Soft Matter, Department of Applied Physics, Eindhoven University of Technology, PO Box 513, 5600MB Eindhoven, The Netherlands
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19
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Peercy BE, Starz-Gaiano M. Clustered cell migration: Modeling the model system of Drosophila border cells. Semin Cell Dev Biol 2019; 100:167-176. [PMID: 31837934 DOI: 10.1016/j.semcdb.2019.11.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 07/01/2019] [Revised: 11/11/2019] [Accepted: 11/15/2019] [Indexed: 01/19/2023]
Abstract
In diverse developmental contexts, certain cells must migrate to fulfill their roles. Many questions remain unanswered about the genetic and physical properties that govern cell migration. While the simplest case of a single cell moving alone has been well-studied, additional complexities arise in considering how cohorts of cells move together. Significant differences exist between models of collectively migrating cells. We explore the experimental model of migratory border cell clusters in Drosophila melanogaster egg chambers, which are amenable to direct observation and precise genetic manipulations. This system involves two special characteristics that are worthy of attention: border cell clusters contain a limited number of both migratory and non-migratory cells that require coordination, and they navigate through a heterogeneous three-dimensional microenvironment. First, we review how clusters of motile border cells are specified and guided in their migration by chemical signals and the physical impact of adjacent tissue interactions. In the second part, we examine questions around the 3D structure of the motile cluster and surrounding microenvironment in understanding the limits to cluster size and speed of movement through the egg chamber. Mathematical models have identified sufficient gene regulatory networks for specification, the key forces that capture emergent behaviors observed in vivo, the minimal regulatory topologies for signaling, and the distribution of key signaling cues that direct cell behaviors. This interdisciplinary approach to studying border cells is likely to reveal governing principles that apply to different types of cell migration events.
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Affiliation(s)
- Bradford E Peercy
- Department of Mathematics and Statistics, UMBC, Baltimore, MD 21250, United States.
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20
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Lovrić J, Kaliman S, Barfuss W, Schröder-Turk GE, Smith AS. Geometric effects in random assemblies of ellipses. Soft Matter 2019; 15:8566-8577. [PMID: 31637393 DOI: 10.1039/c9sm01067j] [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] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Assemblies of anisotropic particles commonly appear in studies of active many-body systems. However, in two dimensions, the geometric ramifications of the finite density of such objects are not entirely understood. To fully characterize these effects, we perform an in-depth study of random assemblies generated by a slow compression of frictionless elliptical particles. The obtained configurations are then analysed using the Set Voronoi tessellation, which takes the particle shape into account. Not only do we analyse most scalar and vectorial morphological measures, which are commonly discussed in the literature or which have recently been addressed in experiments, but we also systematically explore the correlations between them. While in a limited range of parameters similarities with findings in 3D assemblies could be identified, important differences are found when a broad range of aspect ratios and packing fractions are considered. The data discussed in this study should thus provide a unique reference set such that geometric effects and differences from random assemblies could be clearly identified in more complex systems, including ones with soft and active particles that are typically found in biological systems.
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Affiliation(s)
- Jakov Lovrić
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
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21
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Klatt MA, Lovrić J, Chen D, Kapfer SC, Schaller FM, Schönhöfer PWA, Gardiner BS, Smith AS, Schröder-Turk GE, Torquato S. Universal hidden order in amorphous cellular geometries. Nat Commun 2019; 10:811. [PMID: 30778054 PMCID: PMC6379405 DOI: 10.1038/s41467-019-08360-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [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: 06/27/2018] [Accepted: 01/03/2019] [Indexed: 12/04/2022] Open
Abstract
Partitioning space into cells with certain extreme geometrical properties is a central problem in many fields of science and technology. Here we investigate the Quantizer problem, defined as the optimisation of the moment of inertia of Voronoi cells, i.e., similarly-sized ‘sphere-like’ polyhedra that tile space are preferred. We employ Lloyd’s centroidal Voronoi diagram algorithm to solve this problem and find that it converges to disordered states associated with deep local minima. These states are universal in the sense that their structure factors are characterised by a complete independence of a wide class of initial conditions they evolved from. They moreover exhibit an anomalous suppression of long-wavelength density fluctuations and quickly become effectively hyperuniform. Our findings warrant the search for novel amorphous hyperuniform phases and cellular materials with unique physical properties. Disordered hyperuniformity implies a hidden order on length scales that can be found in various amorphous materials. Klatt et al. analyse the evolution of random point patterns using Llyod’s algorithm and show that they converge to an effectively hyperuniform state regardless of the initial conditions.
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Affiliation(s)
- Michael A Klatt
- Institute of Stochastics, Karlsruhe Institute of Technology (KIT), Englerstr. 2, 76131, Karlsruhe, Germany.,Department of Physics, Princeton University, Princeton, NJ, 08544, USA
| | - Jakov Lovrić
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička 54, 10 000 Zagreb, Croatia.,School of Engineering and Information Technology, Murdoch University, 90 South St, Murdoch, WA, 6150, Australia.,PULS Group, Department of Physics and Interdisciplinary Center for Nanostructured Films, Friedrich-Alexander-Universität Erlangen-Nürnberg, Cauerstraße 3, 91058 Erlangen, Germany
| | - Duyu Chen
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Sebastian C Kapfer
- Institut für Theoretische Physik I, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 7, 91058, Erlangen, Germany
| | - Fabian M Schaller
- Institute of Stochastics, Karlsruhe Institute of Technology (KIT), Englerstr. 2, 76131, Karlsruhe, Germany.,Institut für Theoretische Physik I, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 7, 91058, Erlangen, Germany
| | - Philipp W A Schönhöfer
- School of Engineering and Information Technology, Murdoch University, 90 South St, Murdoch, WA, 6150, Australia.,Institut für Theoretische Physik I, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 7, 91058, Erlangen, Germany
| | - Bruce S Gardiner
- School of Engineering and Information Technology, Murdoch University, 90 South St, Murdoch, WA, 6150, Australia.,School of Computer Science and Software Engineering, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Ana-Sunčana Smith
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička 54, 10 000 Zagreb, Croatia.,PULS Group, Department of Physics and Interdisciplinary Center for Nanostructured Films, Friedrich-Alexander-Universität Erlangen-Nürnberg, Cauerstraße 3, 91058 Erlangen, Germany
| | - Gerd E Schröder-Turk
- School of Engineering and Information Technology, Murdoch University, 90 South St, Murdoch, WA, 6150, Australia.,Institut für Theoretische Physik I, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 7, 91058, Erlangen, Germany.,Department of Applied Mathematics, Research School of Physical Sciences and Engineering, The Australian National University, Canberra, ACT, 0200, Australia
| | - Salvatore Torquato
- Department of Chemistry, Department of Physics, Princeton Institute for the Science and Technology of Materials, and Program in Applied and Computational Mathematics, Princeton University, Princeton, NJ, 08544, USA.
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22
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Abstract
Although cell shape can reflect the mechanical and biochemical properties of the cell and its environment, quantification of 3D cell shapes within 3D tissues remains difficult, typically requiring digital reconstruction from a stack of 2D images. We investigate a simple alternative technique to extract information about the 3D shapes of cells in a tissue; this technique connects the ensemble of 3D shapes in the tissue with the distribution of 2D shapes observed in independent 2D slices. Using cell vertex model geometries, we find that the distribution of 2D shapes allows clear determination of the mean value of a 3D shape index. We analyze the errors that may arise in practice in the estimation of the mean 3D shape index from 2D imagery and find that typically only a few dozen cells in 2D imagery are required to reduce uncertainty below 2%. Even though we developed the method for isotropic animal tissues, we demonstrate it on an anisotropic plant tissue. This framework could also be naturally extended to estimate additional 3D geometric features and quantify their uncertainty in other materials.
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Affiliation(s)
- Tristan A. Sharp
- Dept. of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA, United States of America
- * E-mail:
| | - Matthias Merkel
- Physics Department, Syracuse University, Syracuse, NY, United States of America
| | - M. Lisa Manning
- Physics Department, Syracuse University, Syracuse, NY, United States of America
- Syracuse Biomaterials Institute, Syracuse, NY, United States of America
| | - Andrea J. Liu
- Dept. of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA, United States of America
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23
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Abstract
Single molecular species can self-assemble into Frank-Kasper (FK) phases, finite approximants of dodecagonal quasicrystals, defying intuitive notions that thermodynamic ground states are maximally symmetric. FK phases are speculated to emerge as the minimal-distortional packings of space-filling spherical domains, but a precise measure of this distortion and how it affects assembly thermodynamics remains ambiguous. We use two complementary approaches to demonstrate that the principles driving FK lattice formation in diblock copolymers emerge directly from the strong-stretching theory of spherical domains, in which a minimal interblock area competes with a minimal stretching of space-filling chains. The relative stability of FK lattices is studied first using a diblock foam model with unconstrained particle volumes and shapes, which correctly predicts not only the equilibrium σ lattice but also the unequal volumes of the equilibrium domains. We then provide a molecular interpretation for these results via self-consistent field theory, illuminating how molecular stiffness increases the sensitivity of the intradomain chain configurations and the asymmetry of local domain packing. These findings shed light on the role of volume exchange on the formation of distinct FK phases in copolymers and suggest a paradigm for formation of FK phases in soft matter systems in which unequal domain volumes are selected by the thermodynamic competition between distinct measures of shape asymmetry.
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Affiliation(s)
- Abhiram Reddy
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA 01003
| | - Michael B Buckley
- Department of Physics, University of Massachusetts, Amherst, MA 01003
| | - Akash Arora
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455
| | - Frank S Bates
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455
| | - Kevin D Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455
| | - Gregory M Grason
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA 01003;
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24
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Abstract
Vertex models are a popular approach to simulating the mechanical and dynamical properties of dense biological tissues, describing the tissue as a network of polygons. Recently a class of two-dimensional vertex models was shown to exhibit a disordered rigidity transition controlled by the preferred cellular geometry, which was subsequently echoed by experimental findings. An attractive variant of these models uses a Voronoi tessellation to describe the cells, which reduces the number of degrees of freedom as compared the original vertex model. The Voronoi model was also endowed with a non-equilibrium model of cellular motility, leading to rich, glassy behavior. This glassy behavior was suggested to be inextricably linked to an underlying jamming transition. We test this conjecture, exploring the low-effective-temperature limit of the 2D Voronoi model by studying cell trajectories from detailed dynamical simulations in combination with rigidity measurements of energy-minimized disordered cell configurations. We find that the zero-temperature limit of this model has no unjamming transition. We show that this absence of an unjamming transition is intimately linked to the marginality of the model, i.e. the fact that the constraints imposed on cell areas and perimeters precisely balance the number of degrees of freedom in the model. Our work suggests that constraint counting arguments are useful to understand rigidity in a broad class of models of dense biological tissues.
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Affiliation(s)
- Daniel M Sussman
- Department of Physics, Syracuse University, Physics Building, Syracuse, New York 13210, USA.
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