1
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Silva-Dias L, Epstein IR, Dolnik M. Turing patterns on rotating spiral growing domains. Phys Chem Chem Phys 2024. [PMID: 39046428 DOI: 10.1039/d4cp01777c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
We investigate the emergence of Turing patterns in a system growing as a rotating spiral in two dimensions, utilizing the photosensitivity of the chlorine dioxide-iodine-malonic acid (CDIMA) reaction to control the growth process. We observe the formation of single and multiple (double and triple) stationary spiral patterns as well as transitional patterns. From numerical simulations of the Lengyel-Epstein model with an additional term to account for the effects of illumination on the reaction, we analyze the relationship between the final morphologies and the radial and angular growth velocities, identify conditions conducive to the formation of transitional structures, examine the importance of the size of the initial nucleation site in determining the spiral's multiplicity, and evaluate the stability and robustness of these Turing patterns. Our results indicate how inclusion of rotational degrees of freedom in the growth process may lead to the formation of a diverse new class of patterns in chemical and biological systems.
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Affiliation(s)
- Leonardo Silva-Dias
- Department of Chemistry, MS 015, Brandeis University, Waltham, MA 02454, USA.
- Department of Chemistry, Federal University of São Carlos, São Carlos, São Paulo, 13.565-905, Brazil
| | - Irving R Epstein
- Department of Chemistry, MS 015, Brandeis University, Waltham, MA 02454, USA.
| | - Milos Dolnik
- Department of Chemistry, MS 015, Brandeis University, Waltham, MA 02454, USA.
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2
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Ziegelbecker A, Sefc KM. Family resemblance in color-patch size is not affected by stress experience in a cichlid fish. Ecol Evol 2024; 14:e70009. [PMID: 39035042 PMCID: PMC11260441 DOI: 10.1002/ece3.70009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 06/14/2024] [Accepted: 07/01/2024] [Indexed: 07/23/2024] Open
Abstract
Animal body coloration is often linked to social dominance and mating success. This is because it can carry information on an animal's body condition and competitive ability by reflecting the genetic quality of individuals or by responding to their current or past living conditions. The present study investigates genetic and environmental effects on a conspicuous color pattern of the cichlid fish Tropheus sp. black "Ikola," in which the size of a carotenoid-based yellow area on the body co-varies with social dominance. To examine environmental plasticity of the color pattern, we tested for effects of early-life stress, induced by reduced feeding of juveniles prior to color pattern formation, as well as effects of a stress treatment administered to fully colored adult fish. None of the stress treatments affected the color pattern as quantified by the width of the yellow bar. However, offspring bar width was correlated to parental values in mid-parent-mid-offspring regression analyses, and animal models estimated significant additive genetic effects on bar width, indicating heritability of the trait. Depending on the random effects structure of the animal models (i.e., whether including or excluding maternal and brood effects), narrow-sense heritability estimates for bar width ranged between 0.2 and 0.8, with the strongest statistical support for the highest estimate. In each of the alternative models, a large proportion of the total variance in bar width was explained by the included random effects, suggesting that bar width is strongly determined by genetic factors or shared maternal and brood environments, with limited scope for environmental influences later in life.
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3
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Matas-Gil A, Endres RG. Unraveling biochemical spatial patterns: Machine learning approaches to the inverse problem of stationary Turing patterns. iScience 2024; 27:109822. [PMID: 38827409 PMCID: PMC11140185 DOI: 10.1016/j.isci.2024.109822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 03/14/2024] [Accepted: 04/24/2024] [Indexed: 06/04/2024] Open
Abstract
The diffusion-driven Turing instability is a potential mechanism for spatial pattern formation in numerous biological and chemical systems. However, engineering these patterns and demonstrating that they are produced by this mechanism is challenging. To address this, we aim to solve the inverse problem in artificial and experimental Turing patterns. This task is challenging since patterns are often corrupted by noise and slight changes in initial conditions can lead to different patterns. We used both least squares to explore the problem and physics-informed neural networks to build a noise-robust method. We elucidate the functionality of our network in scenarios mimicking biological noise levels and showcase its application using an experimentally obtained chemical pattern. The findings reveal the significant promise of machine learning in steering the creation of synthetic patterns in bioengineering, thereby advancing our grasp of morphological intricacies within biological systems while acknowledging existing limitations.
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Affiliation(s)
- Antonio Matas-Gil
- Department of Life Sciences & Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, London SW7 2BU, UK
| | - Robert G. Endres
- Department of Life Sciences & Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, London SW7 2BU, UK
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4
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Tseng CC, Woolley TE, Jiang TX, Wu P, Maini PK, Widelitz RB, Chuong CM. Gap junctions in Turing-type periodic feather pattern formation. PLoS Biol 2024; 22:e3002636. [PMID: 38743770 PMCID: PMC11161087 DOI: 10.1371/journal.pbio.3002636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/07/2024] [Accepted: 04/22/2024] [Indexed: 05/16/2024] Open
Abstract
Periodic patterning requires coordinated cell-cell interactions at the tissue level. Turing showed, using mathematical modeling, how spatial patterns could arise from the reactions of a diffusive activator-inhibitor pair in an initially homogeneous 2D field. Most activators and inhibitors studied in biological systems are proteins, and the roles of cell-cell interaction, ions, bioelectricity, etc. are only now being identified. Gap junctions (GJs) mediate direct exchanges of ions or small molecules between cells, enabling rapid long-distance communications in a cell collective. They are therefore good candidates for propagating nonprotein-based patterning signals that may act according to the Turing principles. Here, we explore the possible roles of GJs in Turing-type patterning using feather pattern formation as a model. We found 7 of the 12 investigated GJ isoforms are highly dynamically expressed in the developing chicken skin. In ovo functional perturbations of the GJ isoform, connexin 30, by siRNA and the dominant-negative mutant applied before placode development led to disrupted primary feather bud formation. Interestingly, inhibition of gap junctional intercellular communication (GJIC) in the ex vivo skin explant culture allowed the sequential emergence of new feather buds at specific spatial locations relative to the existing primary buds. The results suggest that GJIC may facilitate the propagation of long-distance inhibitory signals. Thus, inhibition of GJs may stimulate Turing-type periodic feather pattern formation during chick skin development, and the removal of GJ activity would enable the emergence of new feather buds if the local environment were competent and the threshold to form buds was reached. We further propose Turing-based computational simulations that can predict the sequential appearance of these ectopic buds. Our models demonstrate how a Turing activator-inhibitor system can continue to generate patterns in the competent morphogenetic field when the level of intercellular communication at the tissue scale is modulated.
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Affiliation(s)
- Chun-Chih Tseng
- Department of Biochemistry and Molecular Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | | | - Ting-Xin Jiang
- Department of Pathology, University of Southern California, Los Angeles, California, United States of America
| | - Ping Wu
- Department of Pathology, University of Southern California, Los Angeles, California, United States of America
| | - Philip K. Maini
- Wolfson Centre for Mathematical Biology, Mathematical Institute, Andrew Wiles Building, University of Oxford, Radcliffe Observatory Quarter, Oxford, United Kingdom
| | - Randall B. Widelitz
- Department of Pathology, University of Southern California, Los Angeles, California, United States of America
| | - Cheng-Ming Chuong
- Department of Pathology, University of Southern California, Los Angeles, California, United States of America
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5
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Chen J, Wang H, Wu S, Zhang A, Qiu Z, Huang P, Qu JY, Xu J. col1a2+ fibroblasts/muscle progenitors finetune xanthophore countershading by differentially expressing csf1a/1b in embryonic zebrafish. SCIENCE ADVANCES 2024; 10:eadj9637. [PMID: 38578990 PMCID: PMC10997200 DOI: 10.1126/sciadv.adj9637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 02/29/2024] [Indexed: 04/07/2024]
Abstract
Animals evolve diverse pigment patterns to adapt to the natural environment. Countershading, characterized by a dark-colored dorsum and a light-colored ventrum, is one of the most prevalent pigment patterns observed in vertebrates. In this study, we reveal a mechanism regulating xanthophore countershading in zebrafish embryos. We found that csf1a and csf1b mutants altered xanthophore countershading differently: csf1a mutants lack ventral xanthophores, while csf1b mutants have reduced dorsal xanthophores. Further study revealed that csf1a is expressed throughout the trunk, whereas csf1b is expressed dorsally. Ectopic expression of csf1a or csf1b in neurons attracted xanthophores into the spinal cord. Blocking csf1 signaling by csf1ra mutants disrupts spinal cord distribution and normal xanthophores countershading. Single-cell RNA sequencing identified two col1a2+ populations: csf1ahighcsf1bhigh muscle progenitors and csf1ahighcsf1blow fibroblast progenitors. Ablation of col1a2+ fibroblast and muscle progenitors abolished xanthophore patterns. Our study suggests that fibroblast and muscle progenitors differentially express csf1a and csf1b to modulate xanthophore patterning, providing insights into the mechanism of countershading.
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Affiliation(s)
- Jiahao Chen
- Department of Neurology, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou 510006, China
- Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, Guangzhou 510006, China
| | - Honggao Wang
- Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, Guangzhou 510006, China
| | - Shuting Wu
- Department of Neurobiology, Harvard Medical School, 220 Longwood Avenue, Boston, MA 02115, USA
| | - Ao Zhang
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, PRC
| | - Zhongkai Qiu
- Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, Guangzhou 510006, China
| | - Peng Huang
- Department of Biochemistry and Molecular Biology, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Jianan Y Qu
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Kowloon, China
| | - Jin Xu
- Department of Neurology, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou 510006, China
- Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, Guangzhou 510006, China
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6
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Sudderick ZR, Glover JD. Periodic pattern formation during embryonic development. Biochem Soc Trans 2024; 52:75-88. [PMID: 38288903 PMCID: PMC10903485 DOI: 10.1042/bst20230197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 12/21/2023] [Accepted: 01/08/2024] [Indexed: 02/29/2024]
Abstract
During embryonic development many organs and structures require the formation of series of repeating elements known as periodic patterns. Ranging from the digits of the limb to the feathers of the avian skin, the correct formation of these embryonic patterns is essential for the future form and function of these tissues. However, the mechanisms that produce these patterns are not fully understood due to the existence of several modes of pattern generation which often differ between organs and species. Here, we review the current state of the field and provide a perspective on future approaches to studying this fundamental process of embryonic development.
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Affiliation(s)
- Zoe R. Sudderick
- The Roslin Institute & R(D)SVS, University of Edinburgh, Edinburgh, U.K
| | - James D. Glover
- The Roslin Institute & R(D)SVS, University of Edinburgh, Edinburgh, U.K
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7
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Borgqvist JG, Gerlee P, Lundholm C. Turing pattern formation on the sphere is robust to the removal of a hole. J Math Biol 2024; 88:23. [PMID: 38296874 PMCID: PMC10830788 DOI: 10.1007/s00285-023-02034-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 11/17/2023] [Accepted: 12/03/2023] [Indexed: 02/02/2024]
Abstract
The formation of buds on the cell membrane of budding yeast cells is thought to be driven by reactions and diffusion involving the protein Cdc42. These processes can be described by a coupled system of partial differential equations known as the Schnakenberg system. The Schnakenberg system is known to exhibit diffusion-driven pattern formation, thus providing a mechanism for bud formation. However, it is not known how the accumulation of bud scars on the cell membrane affect the ability of the Schnakenberg system to form patterns. We have approached this problem by modelling a bud scar on the cell membrane with a hole on the sphere. We have studied how the spectrum of the Laplace-Beltrami operator, which determines the resulting pattern, is affected by the size of the hole, and by numerically solving the Schnakenberg system on a sphere with a hole using the finite element method. Both theoretical predictions and numerical solutions show that pattern formation is robust to the introduction of a bud scar of considerable size, which lends credence to the hypothesis that bud formation is driven by diffusion-driven instability.
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Affiliation(s)
- Johannes G Borgqvist
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Andrew Wiles Building Radcliffe Observatory Quarter (550) Woodstock Road, Oxford, Oxfordshire, OX2 6GG, UK.
| | - Philip Gerlee
- Mathematical Sciences, University of Gothenburg, Chalmers tvärgata 3, 412 96, Gothenburg, Västra Götaland, Sweden
- Mathematical Sciences, Chalmers University of Technology, Chalmers tvärgata 3, 412 96, Gothenburg, Västra Götaland, Sweden
| | - Carl Lundholm
- Department of Mathematics and Mathematical Statistics, Umeå University, MIT Building, 3rd Floor Linneaus Väg, 907 36, Umeå, Västerbotten, Sweden
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8
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Aman AJ, Saunders LM, Carr AA, Srivatasan S, Eberhard C, Carrington B, Watkins-Chow D, Pavan WJ, Trapnell C, Parichy DM. Transcriptomic profiling of tissue environments critical for post-embryonic patterning and morphogenesis of zebrafish skin. eLife 2023; 12:RP86670. [PMID: 37695017 PMCID: PMC10495112 DOI: 10.7554/elife.86670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023] Open
Abstract
Pigment patterns and skin appendages are prominent features of vertebrate skin. In zebrafish, regularly patterned pigment stripes and an array of calcified scales form simultaneously in the skin during post-embryonic development. Understanding the mechanisms that regulate stripe patterning and scale morphogenesis may lead to the discovery of fundamental mechanisms that govern the development of animal form. To learn about cell types and signaling interactions that govern skin patterning and morphogenesis, we generated and analyzed single-cell transcriptomes of skin from wild-type fish as well as fish having genetic or transgenically induced defects in squamation or pigmentation. These data reveal a previously undescribed population of epidermal cells that express transcripts encoding enamel matrix proteins, suggest hormonal control of epithelial-mesenchymal signaling, clarify the signaling network that governs scale papillae development, and identify a critical role for the hypodermis in supporting pigment cell development. Additionally, these comprehensive single-cell transcriptomic data representing skin phenotypes of biomedical relevance should provide a useful resource for accelerating the discovery of mechanisms that govern skin development and homeostasis.
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Affiliation(s)
- Andrew J Aman
- Department of Biology, University of VirginiaCharlottesvilleUnited States
| | - Lauren M Saunders
- Department of Genome Sciences, University of WashingtonSeattleUnited States
| | - August A Carr
- Department of Biology, University of VirginiaCharlottesvilleUnited States
| | - Sanjay Srivatasan
- Department of Genome Sciences, University of WashingtonSeattleUnited States
| | - Colten Eberhard
- National Human Genome Research Institute, National Institutes of HealthBethesdaUnited States
| | - Blake Carrington
- National Human Genome Research Institute, National Institutes of HealthBethesdaUnited States
| | - Dawn Watkins-Chow
- National Human Genome Research Institute, National Institutes of HealthBethesdaUnited States
| | - William J Pavan
- National Human Genome Research Institute, National Institutes of HealthBethesdaUnited States
| | - Cole Trapnell
- Department of Genome Sciences, University of WashingtonSeattleUnited States
| | - David M Parichy
- Department of Biology, University of VirginiaCharlottesvilleUnited States
- Department of Cell Biology, University of VirginiaCharlottesvilleUnited States
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9
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Watanabe M. Fish-specific N-terminal domain sequence in Connexin 39.4 plays an important role in zebrafish stripe formation by regulating the opening and closing of gap junctions and hemichannels. Biochim Biophys Acta Gen Subj 2023; 1867:130342. [PMID: 36889448 DOI: 10.1016/j.bbagen.2023.130342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023]
Abstract
BACKGROUND Connexin 39.4 (Cx39.4) is involved in zebrafish (Danio rerio) skin patterning; when mutated, zebrafish exhibit a wavy stripe/labyrinth pattern instead of stripes. Cx39.4 is unique in that it has two additional serine/arginine (SR) residues, Ser2 and Arg3, at positions 2 and 3. Here, I investigated the role of these SR residues in Cx39.4 function. METHODS To examine the SR residues in Cx39.4, mutants of the SR residues were generated. Voltage-clamp recordings were performed using Xenopus oocytes to characterize the channel properties of the mutants. Transgenic zebrafish expressing each mutant were generated, and the effects of each mutation on fish skin patterning were evaluated. RESULTS The Cx39.4R3K mutant showed essentially the same properties as the wild-type (Cx39.4WT) in both electrophysiological analyses, leading to transgenic, complete phenotype rescue. Both the Cx39.4R3A mutant and deletion mutant of SR residues (Cx39.4delSR) showed a faster decay of gap junction activity and abnormal hemichannel activity, resulting in wide stripes and interstripes that indicate instability. Although the Cx39.4R3D mutant showed no channel activity in gap junctions or hemichannels, it caused unstable phenotypes in the transgene, namely a completely rescued phenotype in some individuals and loss of melanophores in others. CONCLUSIONS The SR residues in the NT domain of Cx39.4 are critical for the regulation of channel function, which appears to determine skin patterning. GENERAL SIGNIFICANCE These results elucidate the roles of the two SR residues unique to the NT domain of Cx39.4 in its channel function, which is important for zebrafish stripe pattern formation.
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Affiliation(s)
- Masakatsu Watanabe
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan.
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10
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Tseng CC, Woolley TE, Jiang TX, Wu P, Maini PK, Widelitz RB, Chuong CM. Gap junctions in Turing-type periodic feather pattern formation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.15.537019. [PMID: 37090608 PMCID: PMC10120740 DOI: 10.1101/2023.04.15.537019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Periodic patterning requires coordinated cell-cell interactions at the tissue level. Turing showed, using mathematical modeling, how spatial patterns could arise from the reactions of a diffusive activator-inhibitor pair in an initially homogenous two-dimensional field. Most activators and inhibitors studied in biological systems are proteins, and the roles of cell-cell interaction, ions, bioelectricity, etc. are only now being identified. Gap junctions (GJs) mediate direct exchanges of ions or small molecules between cells, enabling rapid long-distance communications in a cell collective. They are therefore good candidates for propagating non-protein-based patterning signals that may act according to the Turing principles. Here, we explore the possible roles of GJs in Turing-type patterning using feather pattern formation as a model. We found seven of the twelve investigated GJ isoforms are highly dynamically expressed in the developing chicken skin. In ovo functional perturbations of the GJ isoform, connexin 30, by siRNA and the dominant-negative mutant applied before placode development led to disrupted primary feather bud formation, including patches of smooth skin and buds of irregular sizes. Later, after the primary feather arrays were laid out, inhibition of gap junctional intercellular communication in the ex vivo skin explant culture allowed the emergence of new feather buds in temporal waves at specific spatial locations relative to the existing primary buds. The results suggest that gap junctional communication may facilitate the propagation of long-distance inhibitory signals. Thus, the removal of GJ activity would enable the emergence of new feather buds if the local environment is competent and the threshold to form buds is reached. We propose Turing-based computational simulations that can predict the appearance of these ectopic bud waves. Our models demonstrate how a Turing activator-inhibitor system can continue to generate patterns in the competent morphogenetic field when the level of intercellular communication at the tissue scale is modulated.
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Affiliation(s)
- Chun-Chih Tseng
- Department of Biochemistry and Molecular Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, U.S.A
- Current address: Department of Molecular Biology, Princeton University, Princeton, NJ 08540, U.S.A
| | - Thomas E. Woolley
- School of Mathematics, Cardiff University, Senghennydd Road, Cardiff, CF24 4AG, U.K
| | - Ting-Xin Jiang
- Department of Pathology, University of Southern California, Los Angeles, CA 90033, U.S.A
| | - Ping Wu
- Department of Pathology, University of Southern California, Los Angeles, CA 90033, U.S.A
| | - Philip K. Maini
- Wolfson Centre for Mathematical Biology, Mathematical Institute, Andrew Wiles Building, University of Oxford, Radcliffe Observatory Quarter, Woodstock Road, Oxford OX2 6GG, U.K
| | - Randall B. Widelitz
- Department of Pathology, University of Southern California, Los Angeles, CA 90033, U.S.A
| | - Cheng-Ming Chuong
- Department of Pathology, University of Southern California, Los Angeles, CA 90033, U.S.A
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11
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Abstract
The Turing model (or reaction-diffusion model), first published in 1952, is a mathematical model that can account for autonomy in the morphogenesis of organisms. Although initially controversial, the model has gradually gained wider acceptance among experimental embryologists due to the accumulation of experimental data to support it. More recently, this model and others based on it have been used not only to explain biological phenomena conceptually but also as working hypotheses for molecular-level experiments and as internal components of more-complex 3D models. In this Spotlight, I will provide a personal perspective from an experimental biologist on some of the recent developments of the Turing model.
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Affiliation(s)
- Shigeru Kondo
- Osaka University, Faculty of Frontia Bioscience, Osaka 565-0871, Japan
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12
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Eugenin E, Camporesi E, Peracchia C. Direct Cell-Cell Communication via Membrane Pores, Gap Junction Channels, and Tunneling Nanotubes: Medical Relevance of Mitochondrial Exchange. Int J Mol Sci 2022; 23:6133. [PMID: 35682809 PMCID: PMC9181466 DOI: 10.3390/ijms23116133] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/28/2022] [Accepted: 05/28/2022] [Indexed: 02/07/2023] Open
Abstract
The history of direct cell-cell communication has evolved in several small steps. First discovered in the 1930s in invertebrate nervous systems, it was thought at first to be an exception to the "cell theory", restricted to invertebrates. Surprisingly, however, in the 1950s, electrical cell-cell communication was also reported in vertebrates. Once more, it was thought to be an exception restricted to excitable cells. In contrast, in the mid-1960s, two startling publications proved that virtually all cells freely exchange small neutral and charged molecules. Soon after, cell-cell communication by gap junction channels was reported. While gap junctions are the major means of cell-cell communication, in the early 1980s, evidence surfaced that some cells might also communicate via membrane pores. Questions were raised about the possible artifactual nature of the pores. However, early in this century, we learned that communication via membrane pores exists and plays a major role in medicine, as the structures involved, "tunneling nanotubes", can rescue diseased cells by directly transferring healthy mitochondria into compromised cells and tissues. On the other hand, pathogens/cancer could also use these communication systems to amplify pathogenesis. Here, we describe the evolution of the discovery of these new communication systems and the potential therapeutic impact on several uncurable diseases.
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Affiliation(s)
- Eliseo Eugenin
- Department of Neuroscience, Cell Biology, and Anatomy, University of Texas Medical Branch (UTMB), 105 11th Street, Galveston, TX 77555, USA
| | - Enrico Camporesi
- Department of Surgery and TEAM Health Anesthesia, University of South Florida, 2 Tampa General Circle, Tampa, FL 33606, USA;
| | - Camillo Peracchia
- Department of Pharmacology and Physiology, School of Medicine and Dentistry, University Rochester, 601 Elmwood Avenue, Rochester, NY 14642, USA;
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13
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Wang C, Xu J, Kocher TD, Li M, Wang D. CRISPR knockouts of pmela and pmelb engineered a golden tilapia by regulating relative pigment cell abundance. J Hered 2022; 113:398-413. [PMID: 35385582 DOI: 10.1093/jhered/esac018] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/01/2022] [Indexed: 11/13/2022] Open
Abstract
Premelanosome protein (pmel) is a key gene for melanogenesis. Mutations in this gene are responsible for white plumage in chicken, but its role in pigmentation of fish remains to be demonstrated. In this study we found that most fishes have two pmel genes arising from the teleost-specific whole genome duplication. Both pmela and pmelb were expressed at high levels in the eyes and skin of Nile tilapia. We mutated both genes in tilapia using CRISPR/Cas9. Homozygous mutation of pmela resulted in yellowish body color with weak vertical bars and a hypo-pigmented retinal pigment epithelium (RPE) due to significantly reduced number and size of melanophores. In contrast, we observed an increased number and size of xanthophores in mutants compared to wild-type fish. Homozygous mutation of pmelb resulted in a similar, but milder phenotype than pmela-/- mutants. Double mutation of pmela and pmelb resulted in loss of additional melanophores compared to the pmela-/- mutants, and also an increase in the number and size of xanthophores, producing a golden body color. The RPE pigmentation of pmela-/-;pmelb-/- was similar to pmela-/- mutants, with much less pigmentation than pmelb-/- mutants and wild-type fish. Taken together, our results indicate that, while both pmel genes are important for the formation of body color in tilapia, pmela plays a more important role than pmelb. To our knowledge, this is the first report on mutation of pmelb or both pmela;pmelb in fish. Studies on these mutants suggest new strategies for breeding golden tilapia, and also provide a new model for studies of pmel function in vertebrates.
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Affiliation(s)
- Chenxu Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Jia Xu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Thomas D Kocher
- Department of Biology, University of Maryland College Park, Maryland, USA
| | - Minghui Li
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Deshou Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
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14
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Kondo S, Watanabe M, Miyazawa S. Studies of Turing pattern formation in zebrafish skin. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2021; 379:20200274. [PMID: 34743596 PMCID: PMC8580470 DOI: 10.1098/rsta.2020.0274] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/16/2021] [Indexed: 05/08/2023]
Abstract
Skin patterns are the first example of the existence of Turing patterns in living organisms. Extensive research on zebrafish, a model organism with stripes on its skin, has revealed the principles of pattern formation at the molecular and cellular levels. Surprisingly, although the networks of cell-cell interactions have been observed to satisfy the 'short-range activation and long-range inhibition' prerequisites for Turing pattern formation, numerous individual reactions were not envisioned based on the classical reaction-diffusion model. For example, in real skin, it is not an alteration in concentrations of chemicals, but autonomous migration and proliferation of pigment cells that establish patterns, and cell-cell interactions are mediated via direct contact through cell protrusions. Therefore, the classical reaction-diffusion mechanism cannot be used as it is for modelling skin pattern formation. Various studies are underway to adapt mathematical models to the experimental findings on research into skin patterns, and the purpose of this review is to organize and present them. These novel theoretical methods could be applied to autonomous pattern formation phenomena other than skin patterns. This article is part of the theme issue 'Recent progress and open frontiers in Turing's theory of morphogenesis'.
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Affiliation(s)
- Shigeru Kondo
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masakatsu Watanabe
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Seita Miyazawa
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
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15
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Konow C, Dolnik M, Epstein IR. Insights from chemical systems into Turing-type morphogenesis. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2021; 379:20200269. [PMID: 34743602 DOI: 10.1098/rsta.2020.0269] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
In 1952, Alan Turing proposed a theory showing how morphogenesis could occur from a simple two morphogen reaction-diffusion system [Turing, A. M. (1952) Phil. Trans. R. Soc. Lond. A 237, 37-72. (doi:10.1098/rstb.1952.0012)]. While the model is simple, it has found diverse applications in fields such as biology, ecology, behavioural science, mathematics and chemistry. Chemistry in particular has made significant contributions to the study of Turing-type morphogenesis, providing multiple reproducible experimental methods to both predict and study new behaviours and dynamics generated in reaction-diffusion systems. In this review, we highlight the historical role chemistry has played in the study of the Turing mechanism, summarize the numerous insights chemical systems have yielded into both the dynamics and the morphological behaviour of Turing patterns, and suggest future directions for chemical studies into Turing-type morphogenesis. This article is part of the theme issue 'Recent progress and open frontiers in Turing's theory of morphogenesis'.
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Affiliation(s)
- C Konow
- Department of Chemistry, Brandeis University, Waltham, MA 02453, USA
| | - M Dolnik
- Department of Chemistry, Brandeis University, Waltham, MA 02453, USA
| | - I R Epstein
- Department of Chemistry, Brandeis University, Waltham, MA 02453, USA
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16
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Morozov A. Towards creating a mechanistic predictive theory of self-organized vegetation patterns: Comment on "Belowground feedbacks as drivers of spatial self-organization and community assembly" by Inderjit, Callaway and Meron. Phys Life Rev 2021; 40:54-56. [PMID: 34838506 DOI: 10.1016/j.plrev.2021.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 11/09/2021] [Indexed: 11/29/2022]
Affiliation(s)
- Andrew Morozov
- Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia; School of Computing and Mathematical Sciences, University of Leicester, UK.
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17
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McCluskey BM, Liang Y, Lewis VM, Patterson LB, Parichy DM. Pigment pattern morphospace of Danio fishes: evolutionary diversification and mutational effects. Biol Open 2021; 10:271991. [PMID: 34463758 PMCID: PMC8487636 DOI: 10.1242/bio.058814] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 08/13/2021] [Indexed: 11/29/2022] Open
Abstract
Molecular and cellular mechanisms underlying variation in adult form remain largely unknown. Adult pigment patterns of fishes in the genus Danio, which includes zebrafish, Danio rerio, consist of horizontal stripes, vertical bars, spots and uniform patterns, and provide an outstanding opportunity to identify causes of species level variation in a neural crest derived trait. Understanding pigment pattern variation requires quantitative approaches to assess phenotypes, yet such methods have been mostly lacking for pigment patterns. We introduce metrics derived from information theory that describe patterns and pattern variation in Danio fishes. We find that these metrics used singly and in multivariate combinations are suitable for distinguishing general pattern types, and can reveal even subtle phenotypic differences attributable to mutations. Our study provides new tools for analyzing pigment pattern in Danio and potentially other groups, and sets the stage for future analyses of pattern morphospace and its mechanistic underpinnings. Summary: A multidimensional morphospace for pigment patterns yields quantitative insights into the evolution and genetics of diverse pigment patterns across zebrafish and related species.
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Affiliation(s)
| | - Yipeng Liang
- Department of Biology, University of Virginia, Charlottesville, USA
| | - Victor M Lewis
- Department of Biology, University of Virginia, Charlottesville, USA
| | | | - David M Parichy
- Department of Biology, University of Virginia, Charlottesville, USA.,Biology Department, Rhode Island College, Providence, USA.,Department of Cell Biology, University of Virginia, Charlottesville, USA
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18
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Kaelin CB, McGowan KA, Barsh GS. Developmental genetics of color pattern establishment in cats. Nat Commun 2021; 12:5127. [PMID: 34493721 PMCID: PMC8423757 DOI: 10.1038/s41467-021-25348-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 07/22/2021] [Indexed: 11/09/2022] Open
Abstract
Intricate color patterns are a defining aspect of morphological diversity in the Felidae. We applied morphological and single-cell gene expression analysis to fetal skin of domestic cats to identify when, where, and how, during fetal development, felid color patterns are established. Early in development, we identify stripe-like alterations in epidermal thickness preceded by a gene expression pre-pattern. The secreted Wnt inhibitor encoded by Dickkopf 4 plays a central role in this process, and is mutated in cats with the Ticked pattern type. Our results bring molecular understanding to how the leopard got its spots, suggest that similar mechanisms underlie periodic color pattern and periodic hair follicle spacing, and identify targets for diverse pattern variation in other mammals.
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Affiliation(s)
- Christopher B Kaelin
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Kelly A McGowan
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Gregory S Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
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19
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Eom DS, Patterson LB, Bostic RR, Parichy DM. Immunoglobulin superfamily receptor Junctional adhesion molecule 3 (Jam3) requirement for melanophore survival and patterning during formation of zebrafish stripes. Dev Biol 2021; 476:314-327. [PMID: 33933422 PMCID: PMC10069301 DOI: 10.1016/j.ydbio.2021.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/03/2021] [Accepted: 04/22/2021] [Indexed: 12/14/2022]
Abstract
Adhesive interactions are essential for tissue patterning and morphogenesis yet difficult to study owing to functional redundancies across genes and gene families. A useful system in which to dissect roles for cell adhesion and adhesion-dependent signaling is the pattern formed by pigment cells in skin of adult zebrafish, in which stripes represent the arrangement of neural crest derived melanophores, cells homologous to melanocytes. In a forward genetic screen for adult pattern defects, we isolated the pissarro (psr) mutant, having a variegated phenotype of spots, as well as defects in adult fin and lens. We show that psr corresponds to junctional adhesion protein 3b (jam3b) encoding a zebrafish orthologue of the two immunoglobulin-like domain receptor JAM3 (JAM-C), known for roles in adhesion and signaling in other developing tissues, and for promoting metastatic behavior of human and murine melanoma cells. We found that zebrafish jam3b is expressed post-embryonically in a variety of cells including melanophores, and that jam3b mutants have defects in melanophore survival. Jam3b supported aggregation of cells in vitro and was required autonomously by melanophores for an adherent phenotype in vivo. Genetic analyses further indicated both overlapping and non-overlapping functions with the related receptor, Immunoglobulin superfamily 11 (Igsf11) and Kit receptor tyrosine kinase. These findings suggest a model for Jam3b function in zebrafish melanophores and hint at the complexity of adhesive interactions underlying pattern formation.
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Affiliation(s)
- Dae Seok Eom
- Department of Biology, University of Virginia, Charlottesville, VA, USA.
| | | | - Raegan R Bostic
- Department of Biology, University of Virginia, Charlottesville, VA, USA; Department of Cell Biology, University of Virginia, Charlottesville, VA, USA
| | - David M Parichy
- Department of Biology, University of Virginia, Charlottesville, VA, USA; Department of Cell Biology, University of Virginia, Charlottesville, VA, USA.
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20
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Abstract
Morphogenesis is one of the most remarkable examples of biological pattern formation. Despite substantial progress in the field, we still do not understand the organizational principles responsible for the robust convergence of the morphogenesis process across scales to form viable organisms under variable conditions. Achieving large-scale coordination requires feedback between mechanical and biochemical processes, spanning all levels of organization and relating the emerging patterns with the mechanisms driving their formation. In this review, we highlight the role of mechanics in the patterning process, emphasizing the active and synergistic manner in which mechanical processes participate in developmental patterning rather than merely following a program set by biochemical signals. We discuss the value of applying a coarse-grained approach toward understanding this complex interplay, which considers the large-scale dynamics and feedback as well as complementing the reductionist approach focused on molecular detail. A central challenge in this approach is identifying relevant coarse-grained variables and developing effective theories that can serve as a basis for an integrated framework for understanding this remarkable pattern-formation process. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Yonit Maroudas-Sacks
- Department of Physics, Technion-Israel Institute of Technology, Haifa 32000, Israel;
| | - Kinneret Keren
- Department of Physics, Technion-Israel Institute of Technology, Haifa 32000, Israel; .,Network Biology Research Laboratories and The Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa 32000, Israel
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21
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Trends and variation in vertebrate patterns as outcomes of self-organization. Curr Opin Genet Dev 2021; 69:147-153. [PMID: 34058514 DOI: 10.1016/j.gde.2021.05.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/29/2021] [Accepted: 05/03/2021] [Indexed: 11/22/2022]
Abstract
In extant vertebrates, natural motifs such as coat markings, spongy bone structures, neuronal arborescence or collective swarms correspond to diverse pattern types, from fractals to periodic stripes or tessellations, and so on. In this subphylum, evolution produced an apparent paradox: a given pattern may vary tremendously in its extent, periodicity or regularity, but follows general geometrical trends and is produced with meticulous precision. In this review, we discuss the role of self-organization, a patterning strategy in which spontaneous order arises through local interactions without gradient formation, in shaping both natural pattern differences and common themes. Mathematical models evidenced a wide high adaptability of self-organizing dynamics, long-advocating for their contribution to natural pattern diversity. Recent empirical and theoretical approaches taking into account network topologies and natural variation also replaced outcomes of self-organization in more constrained biological contexts, shedding light on mechanisms ensuring pattern fidelity.
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22
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Wang C, Lu B, Li T, Liang G, Xu M, Liu X, Tao W, Zhou L, Kocher TD, Wang D. Nile Tilapia: A Model for Studying Teleost Color Patterns. J Hered 2021; 112:469-484. [PMID: 34027978 DOI: 10.1093/jhered/esab018] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 04/08/2021] [Indexed: 11/12/2022] Open
Abstract
The diverse color patterns of cichlid fishes play an important role in mate choice and speciation. Here we develop the Nile tilapia (Oreochromis niloticus) as a model system for studying the developmental genetics of cichlid color patterns. We identified 4 types of pigment cells: melanophores, xanthophores, iridophores and erythrophores, and characterized their first appearance in wild-type fish. We mutated 25 genes involved in melanogenesis, pteridine metabolism, and the carotenoid absorption and cleavage pathways. Among the 25 mutated genes, 13 genes had a phenotype in both the F0 and F2 generations. None of F1 heterozygotes had phenotype. By comparing the color pattern of our mutants with that of red tilapia (Oreochromis spp), a natural mutant produced during hybridization of tilapia species, we found that the pigmentation of the body and eye is controlled by different genes. Previously studied genes like mitf, kita/kitlga, pmel, tyrb, hps4, gch2, csf1ra, pax7b, and bco2b were proved to be of great significance for color patterning in tilapia. Our results suggested that tilapia, a fish with 4 types of pigment cells and a vertically barred wild-type color pattern, together with various natural and artificially induced color gene mutants, can serve as an excellent model system for study color patterning in vertebrates.
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Affiliation(s)
- Chenxu Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Baoyue Lu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Tao Li
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Guangyuan Liang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Mengmeng Xu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Xingyong Liu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Wenjing Tao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Linyan Zhou
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Thomas D Kocher
- the Department of Biology, University of Maryland, College Park, MD
| | - Deshou Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
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23
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Influence of survival, promotion, and growth on pattern formation in zebrafish skin. Sci Rep 2021; 11:9864. [PMID: 33972585 PMCID: PMC8110552 DOI: 10.1038/s41598-021-89116-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/14/2021] [Indexed: 11/24/2022] Open
Abstract
The coloring of zebrafish skin is often used as a model system to study biological pattern formation. However, the small number and lack of movement of chromatophores defies traditional Turing-type pattern generating mechanisms. Recent models invoke discrete short-range competition and long-range promotion between different pigment cells as an alternative to a reaction-diffusion scheme. In this work, we propose a lattice-based “Survival model,” which is inspired by recent experimental findings on the nature of long-range chromatophore interactions. The Survival model produces stationary patterns with diffuse stripes and undergoes a Turing instability. We also examine the effect that domain growth, ubiquitous in biological systems, has on the patterns in both the Survival model and an earlier “Promotion” model. In both cases, domain growth alone is capable of orienting Turing patterns above a threshold wavelength and can reorient the stripes in ablated cells, though the wavelength for which the patterns orient is much larger for the Survival model. While the Survival model is a simplified representation of the multifaceted interactions between pigment cells, it reveals complex organizational behavior and may help to guide future studies.
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24
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Galipot P, Damerval C, Jabbour F. The seven ways eukaryotes produce repeated colour motifs on external tissues. Biol Rev Camb Philos Soc 2021; 96:1676-1693. [PMID: 33955646 DOI: 10.1111/brv.12720] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/29/2021] [Accepted: 03/31/2021] [Indexed: 02/03/2023]
Abstract
The external tissues of numerous eukaryote species show repeated colour patterns, usually characterized by units that are present at least twice on the body. These dotted, striped or more complex phenotypes carry out crucial biological functions, such as partner recognition, aposematism or camouflage. Very diverse mechanisms explaining the formation of repeated colour patterns in eukaryotes have been identified and described, and it is timely to review this field from an evolutionary and developmental biology perspective. We propose a novel classification consisting of seven families of primary mechanisms: Turing(-like), cellular automaton, multi-induction, physical cracking, random, neuromuscular and printing. In addition, we report six pattern modifiers, acting synergistically with these primary mechanisms to enhance the spectrum of repeated colour patterns. We discuss the limitations of our classification in light of currently unexplored extant diversity. As repeated colour patterns require both the production of a repetitive structure and colouration, we also discuss the nature of the links between these two processes. A more complete understanding of the formation of repeated colour patterns in eukaryotes will require (i) a deeper exploration of biological diversity, tackling the issue of pattern elaboration during the development of non-model taxa, and (ii) exploring some of the most promising ways to discover new families of mechanisms. Good starting points include evaluating the role of mechanisms known to produce non-repeated colour patterns and that of mechanisms responsible for repeated spatial patterns lacking colouration.
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Affiliation(s)
- Pierre Galipot
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP39, Paris, 75005, France.,Génétique Quantitative et Evolution-Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Gif-sur-Yvette, 91190, France
| | - Catherine Damerval
- Génétique Quantitative et Evolution-Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Gif-sur-Yvette, 91190, France
| | - Florian Jabbour
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP39, Paris, 75005, France
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25
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A complex genetic architecture in zebrafish relatives Danio quagga and D. kyathit underlies development of stripes and spots. PLoS Genet 2021; 17:e1009364. [PMID: 33901178 PMCID: PMC8102007 DOI: 10.1371/journal.pgen.1009364] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 05/06/2021] [Accepted: 04/08/2021] [Indexed: 02/07/2023] Open
Abstract
Vertebrate pigmentation is a fundamentally important, multifaceted phenotype. Zebrafish, Danio rerio, has been a valuable model for understanding genetics and development of pigment pattern formation due to its genetic and experimental tractability, advantages that are shared across several Danio species having a striking array of pigment patterns. Here, we use the sister species D. quagga and D. kyathit, with stripes and spots, respectively, to understand how natural genetic variation impacts phenotypes at cellular and organismal levels. We first show that D. quagga and D. kyathit phenotypes resemble those of wild-type D. rerio and several single locus mutants of D. rerio, respectively, in a morphospace defined by pattern variation along dorsoventral and anteroposterior axes. We then identify differences in patterning at the cellular level between D. quagga and D. kyathit by repeated daily imaging during pattern development and quantitative comparisons of adult phenotypes, revealing that patterns are similar initially but diverge ontogenetically. To assess the genetic architecture of these differences, we employ reduced-representation sequencing of second-generation hybrids. Despite the similarity of D. quagga to D. rerio, and D. kyathit to some D. rerio mutants, our analyses reveal a complex genetic basis for differences between D. quagga and D. kyathit, with several quantitative trait loci contributing to variation in overall pattern and cellular phenotypes, epistatic interactions between loci, and abundant segregating variation within species. Our findings provide a window into the evolutionary genetics of pattern-forming mechanisms in Danio and highlight the complexity of differences that can arise even between sister species. Further studies of natural genetic diversity underlying pattern variation in D. quagga and D. kyathit should provide insights complementary to those from zebrafish mutant phenotypes and more distant species comparisons. Pigment patterns of fishes are diverse and function in a wide range of behaviors. Common pattern themes include stripes and spots, exemplified by the closely related minnows Danio quagga and D. kyathit, respectively. We show that these patterns arise late in development owing to alterations in the development and arrangements of pigment cells. In the closely related model organism zebrafish (D. rerio) single genes can switch the pattern from stripes to spots. Yet, we show that pattern differences between D. quagga and D. kyathit have a more complex genetic basis, depending on multiple genes and interactions between these genes. Our findings illustrate the importance of characterizing naturally occurring genetic variants, in addition to laboratory induced mutations, for a more complete understanding of pigment pattern development and evolution.
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Parichy DM. Evolution of pigment cells and patterns: recent insights from teleost fishes. Curr Opin Genet Dev 2021; 69:88-96. [PMID: 33743392 DOI: 10.1016/j.gde.2021.02.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/04/2021] [Accepted: 02/09/2021] [Indexed: 01/08/2023]
Abstract
Skin pigment patterns of vertebrates are stunningly diverse, and nowhere more so than in teleost fishes. Several species, including relatives of zebrafish, recently evolved cichlid fishes of East Africa, clownfishes, deep sea fishes, and others are providing insights into pigment pattern evolution. This overview describes recent advances in understanding periodic patterns, like stripes and spots, the loss of patterns, and the role of cell-type diversification in generating pigmentation phenotypes. Advances in this area are being facilitated by the application of modern methods of gene editing, genomics, computational analysis, and other approaches to non-traditional model organisms having interesting pigmentary phenotypes. Several topics worthy of future attention are outlined as well.
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Affiliation(s)
- David M Parichy
- Department of Biology, Department of Cell Biology, University of Virginia, Charlottesville, VA 22903, United States.
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27
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Usui Y, Watanabe M. Role of the Connexin C-terminus in skin pattern formation of Zebrafish. BBA ADVANCES 2021; 1:100006. [PMID: 37082017 PMCID: PMC10074918 DOI: 10.1016/j.bbadva.2021.100006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Background Zebrafish display a striped skin pattern on their body; two types of connexins, namely, Connexin39.4 (Cx39.4) and Connexin41.8 (Cx41.8), are involved in stripe pattern formation. Herein, we investigated the role of the C-terminal (CT) domains of Cx39.4 and Cx41.8 in vivo and in vitro. Methods To investigate the role of CT domains in vivo, we established transgenic zebrafish lines expressing the CT-domain-modified connexin series in pigmented cells and observed skin patterns in fish. To investigate the role of the CT domains in vitro, we expressed the CT-domain modified connexin series in Neuro-2a (N2a) cells and calculated the plaque formation frequency. Results The overexpression of Cx39.4 lacking a CT domain produced skin patterns similar to that produced by full-length Cx39.4 in the cx39.4 -/- mutant and in cx39.4 and cx41.8 double-knockout mutant zebrafish. Fluorescence-protein-fused CT-domain-modified Cx39.4 formed gap junction plaques between N2a cells. The overexpression of CT-truncated Cx41.8 rescued the mutant phenotype in the cx41.8 -/- mutant but did not function in the double knockout zebrafish. Fluorescence-protein-fused CT-truncated Cx41.8 hardly formed plaques between N2a cells without Cx39.4 but formed gap junction plaques when co-expressed with Cx39.4. Conclusions The CT domain of Cx39.4 is not required for protein function, at least in the pigment cells of zebrafish. However, the need for the CT domain of Cx41.8 depends on Cx39.4 expression. General significance These results provide evidence for the interactions between Cx39.4 and Cx41.8 in pigment cells of zebrafish and suggest that at least one connexin must have a CT domain.
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28
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Effective nonlocal kernels on reaction-diffusion networks. J Theor Biol 2020; 509:110496. [PMID: 33007272 DOI: 10.1016/j.jtbi.2020.110496] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 07/30/2020] [Accepted: 09/14/2020] [Indexed: 02/07/2023]
Abstract
A new method to derive an essential integral kernel from any given reaction-diffusion network is proposed. Any network describing metabolites or signals with arbitrary many factors can be reduced to a single or a simpler system of integro-differential equations called "effective equation" including the reduced integral kernel (called "effective kernel") in the convolution type. As one typical example, the Mexican hat shaped kernel is theoretically derived from two component activator-inhibitor systems. It is also shown that a three component system with quite different appearance from activator-inhibitor systems is reduced to an effective equation with the Mexican hat shaped kernel. It means that the two different systems have essentially the same effective equations and that they exhibit essentially the same spatial and temporal patterns. Thus, we can identify two different systems with the understanding in unified concept through the reduced effective kernels. Other two applications of this method are also given: Applications to pigment patterns on skins (two factors network with long range interaction) and waves of differentiation (called proneural waves) in visual systems on brains (four factors network with long range interaction). In the applications, we observe the reproduction of the same spatial and temporal patterns as those appearing in pre-existing models through the numerical simulations of the effective equations.
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29
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A continuation method for spatially discretized models with nonlocal interactions conserving size and shape of cells and lattices. J Math Biol 2020; 81:981-1028. [PMID: 32959067 PMCID: PMC7560951 DOI: 10.1007/s00285-020-01534-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 07/15/2020] [Indexed: 11/18/2022]
Abstract
In this paper, we introduce a continuation method for the spatially discretized models, while conserving the size and shape of the cells and lattices. This proposed method is realized using the shift operators and nonlocal operators of convolution types. Through this method and using the shift operator, the nonlinear spatially discretized model on the uniform and nonuniform lattices can be systematically converted into a spatially continuous model; this renders both models point-wisely equivalent. Moreover, by the convolution with suitable kernels, we mollify the shift operator and approximate the spatially discretized models using the nonlocal evolution equations, rendering suitable for the application in both experimental and mathematical analyses. We also demonstrate that this approximation is supported by the singular limit analysis, and that the information of the lattice and cells is expressed in the shift and nonlocal operators. The continuous models designed using our method can successfully replicate the patterns corresponding to those of the original spatially discretized models obtained from the numerical simulations. Furthermore, from the observations of the isotropy of the Delta–Notch signaling system in a developing real fly brain, we propose a radially symmetric kernel for averaging the cell shape using our continuation method. We also apply our method for cell division and proliferation to spatially discretized models of the differentiation wave and describe the discrete models on the sphere surface. Finally, we demonstrate an application of our method in the linear stability analysis of the planar cell polarity model.
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Owen JP, Kelsh RN, Yates CA. A quantitative modelling approach to zebrafish pigment pattern formation. eLife 2020; 9:52998. [PMID: 32716296 PMCID: PMC7384860 DOI: 10.7554/elife.52998] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 06/21/2020] [Indexed: 12/14/2022] Open
Abstract
Pattern formation is a key aspect of development. Adult zebrafish exhibit a striking striped pattern generated through the self-organisation of three different chromatophores. Numerous investigations have revealed a multitude of individual cell-cell interactions important for this self-organisation, but it has remained unclear whether these known biological rules were sufficient to explain pattern formation. To test this, we present an individual-based mathematical model incorporating all the important cell-types and known interactions. The model qualitatively and quantitatively reproduces wild type and mutant pigment pattern development. We use it to resolve a number of outstanding biological uncertainties, including the roles of domain growth and the initial iridophore stripe, and to generate hypotheses about the functions of leopard. We conclude that our rule-set is sufficient to recapitulate wild-type and mutant patterns. Our work now leads the way for further in silico exploration of the developmental and evolutionary implications of this pigment patterning system.
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Affiliation(s)
- Jennifer P Owen
- Department of Biology and Biochemistry and Department of Mathematical Sciences, University of Bath, Claverton Down, Bath, United Kingdom
| | - Robert N Kelsh
- Department of Biology and Biochemistry and Department of Mathematical Sciences, University of Bath, Claverton Down, Bath, United Kingdom
| | - Christian A Yates
- Department of Biology and Biochemistry and Department of Mathematical Sciences, University of Bath, Claverton Down, Bath, United Kingdom
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31
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Inaba M, Chuong CM. Avian Pigment Pattern Formation: Developmental Control of Macro- (Across the Body) and Micro- (Within a Feather) Level of Pigment Patterns. Front Cell Dev Biol 2020; 8:620. [PMID: 32754601 PMCID: PMC7365947 DOI: 10.3389/fcell.2020.00620] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 06/22/2020] [Indexed: 12/13/2022] Open
Abstract
Animal color patterns are of interest to many fields, such as developmental biology, evolutionary biology, ethology, mathematical biology, bio-mimetics, etc. The skin provides easy access to experimentation and analysis enabling the developmental pigment patterning process to be analyzed at the cellular and molecular level. Studies in animals with distinct pigment patterns (such as zebrafish, horse, feline, etc.) have revealed some genetic information underlying color pattern formation. Yet, how the complex pigment patterns in diverse avian species are established remains an open question. Here we summarize recent progress. Avian plumage shows color patterns occurring at different spatial levels. The two main levels are macro- (across the body) and micro- (within a feather) pigment patterns. At the cellular level, colors are mainly produced by melanocytes generating eumelanin (black) and pheomelanin (yellow, orange). These melanin-based patterns are regulated by melanocyte migration, differentiation, cell death, and/or interaction with neighboring skin cells. In addition, non-melanin chemical pigments and structural colors add more colors to the available palette in different cell types or skin regions. We discuss classic and recent tissue transplantation experiments that explore the avian pigment patterning process and some potential molecular mechanisms. We find color patterns can be controlled autonomously by melanocytes but also non-autonomously by dermal cells. Complex plumage color patterns are generated by the combination of these multi-scale patterning mechanisms. These interactions can be further modulated by environmental factors such as sex hormones, which generate striking sexual dimorphic colors in avian integuments and can also be influenced by seasons and aging.
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Affiliation(s)
- Masafumi Inaba
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Cheng-Ming Chuong
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
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32
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Volkening A, Abbott MR, Chandra N, Dubois B, Lim F, Sexton D, Sandstede B. Modeling Stripe Formation on Growing Zebrafish Tailfins. Bull Math Biol 2020; 82:56. [PMID: 32356149 DOI: 10.1007/s11538-020-00731-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 04/03/2020] [Indexed: 12/26/2022]
Abstract
As zebrafish develop, black and gold stripes form across their skin due to the interactions of brightly colored pigment cells. These characteristic patterns emerge on the growing fish body, as well as on the anal and caudal fins. While wild-type stripes form parallel to a horizontal marker on the body, patterns on the tailfin gradually extend distally outward. Interestingly, several mutations lead to altered body patterns without affecting fin stripes. Through an exploratory modeling approach, our goal is to help better understand these differences between body and fin patterns. By adapting a prior agent-based model of cell interactions on the fish body, we present an in silico study of stripe development on tailfins. Our main result is a demonstration that two cell types can produce stripes on the caudal fin. We highlight several ways that bone rays, growth, and the body-fin interface may be involved in patterning, and we raise questions for future work related to pattern robustness.
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Affiliation(s)
- A Volkening
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL, USA.
| | - M R Abbott
- Mathematics, Statistics, and Computer Science, Macalester College, St. Paul, MN, USA
| | - N Chandra
- Division of Applied Mathematics, Brown University, Providence, RI, USA
| | - B Dubois
- Division of Applied Mathematics, Brown University, Providence, RI, USA
| | - F Lim
- Division of Applied Mathematics, Brown University, Providence, RI, USA
| | - D Sexton
- Department of Mathematics, University of Idaho, Moscow, ID, USA
| | - B Sandstede
- Division of Applied Mathematics, Brown University, Providence, RI, USA
- Data Science Initiative, Brown University, Providence, RI, USA
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33
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Koshikawa S. Evolution of wing pigmentation in Drosophila: Diversity, physiological regulation, and cis-regulatory evolution. Dev Growth Differ 2020; 62:269-278. [PMID: 32171022 PMCID: PMC7384037 DOI: 10.1111/dgd.12661] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/04/2020] [Accepted: 03/04/2020] [Indexed: 12/20/2022]
Abstract
Fruit flies (Drosophila and its close relatives, or “drosophilids”) are a group that includes an important model organism, Drosophila melanogaster, and also very diverse species distributed worldwide. Many of these species have black or brown pigmentation patterns on their wings, and have been used as material for evo‐devo research. Pigmentation patterns are thought to have evolved rapidly compared with body plans or body shapes; hence they are advantageous model systems for studying evolutionary gains of traits and parallel evolution. Various groups of drosophilids, including genus Idiomyia (Hawaiian Drosophila), have a variety of pigmentations, ranging from simple black pigmentations around crossveins to a single antero‐distal spot and a more complex mottled pattern. Pigmentation patterns are sometimes obviously used for sexual displays; however, in some cases they may have other functions. The process of wing formation in Drosophila, the general mechanism of pigmentation formation, and the transport of substances necessary for pigmentation, including melanin precursors, through wing veins are summarized here. Lastly, the evolution of the expression of genes regulating pigmentation patterns, the role of cis‐regulatory regions, and the conditions required for the evolutionary emergence of pigmentation patterns are discussed. Future prospects for research on the evolution of wing pigmentation pattern formation in drosophilids are presented, particularly from the point of view of how they compare with other studies of the evolution of new traits.
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Affiliation(s)
- Shigeyuki Koshikawa
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Japan.,Graduate School of Environmental Science, Hokkaido University, Sapporo, Japan
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34
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Abstract
Self-organized pattern behavior is ubiquitous throughout nature, from fish schooling to collective cell dynamics during organism development. Qualitatively these patterns display impressive consistency, yet variability inevitably exists within pattern-forming systems on both microscopic and macroscopic scales. Quantifying variability and measuring pattern features can inform the underlying agent interactions and allow for predictive analyses. Nevertheless, current methods for analyzing patterns that arise from collective behavior capture only macroscopic features or rely on either manual inspection or smoothing algorithms that lose the underlying agent-based nature of the data. Here we introduce methods based on topological data analysis and interpretable machine learning for quantifying both agent-level features and global pattern attributes on a large scale. Because the zebrafish is a model organism for skin pattern formation, we focus specifically on analyzing its skin patterns as a means of illustrating our approach. Using a recent agent-based model, we simulate thousands of wild-type and mutant zebrafish patterns and apply our methodology to better understand pattern variability in zebrafish. Our methodology is able to quantify the differential impact of stochasticity in cell interactions on wild-type and mutant patterns, and we use our methods to predict stripe and spot statistics as a function of varying cellular communication. Our work provides an approach to automatically quantifying biological patterns and analyzing agent-based dynamics so that we can now answer critical questions in pattern formation at a much larger scale.
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Affiliation(s)
- Melissa R McGuirl
- Division of Applied Mathematics, Brown University, Providence, RI 02912;
| | - Alexandria Volkening
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208
| | - Björn Sandstede
- Division of Applied Mathematics, Brown University, Providence, RI 02912
- Data Science Initiative, Brown University, Providence, RI 02912
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35
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Slater FC, Bauer WM, Renier CM, Pastor J, Liang JO, Welsh CA. Mathematical Analysis of Melanocyte Patterns on Danio rerio. Zebrafish 2020; 17:59-72. [DOI: 10.1089/zeb.2018.1699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Affiliation(s)
| | - William M. Bauer
- Science Department, Cloquet Senior High School, Cloquet, Minnesota
| | - Colleen M. Renier
- Essentia Institute of Rural Health, Essentia Health, Duluth, Minnesota
| | - John Pastor
- Department of Biology, University of Minnesota Duluth, Duluth, Minnesota
| | - Jennifer O. Liang
- Department of Biology, University of Minnesota Duluth, Duluth, Minnesota
| | - Cynthia A. Welsh
- Science Department, Cloquet Senior High School, Cloquet, Minnesota
- Department of Science Research, Cloquet Senior High School, Cloquet, Minnesota
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36
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Schweisguth F, Corson F. Self-Organization in Pattern Formation. Dev Cell 2020; 49:659-677. [PMID: 31163171 DOI: 10.1016/j.devcel.2019.05.019] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 02/16/2019] [Accepted: 05/07/2019] [Indexed: 12/19/2022]
Abstract
Self-organization is pervasive in development, from symmetry breaking in the early embryo to tissue patterning and morphogenesis. For a few model systems, the underlying molecular and cellular processes are now sufficiently characterized that mathematical models can be confronted with experiments, to explore the dynamics of pattern formation. Here, we review selected systems, ranging from cyanobacteria to mammals, where different forms of cell-cell communication, acting alone or together with positional cues, drive the patterning of cell fates, highlighting the insights that even very simple models can provide as well as the challenges on the path to a predictive understanding of development.
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Affiliation(s)
- François Schweisguth
- Institut Pasteur, Department of Developmental and Stem Cell Biology F-75015 Paris, France; CNRS, UMR 3738 F-75015 Paris, France.
| | - Francis Corson
- Laboratoire de Physique de l'Ecole Normale Supérieure, CNRS, Sorbonne Université, Université Paris Diderot 75005 Paris, France.
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37
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Patterson LB, Parichy DM. Zebrafish Pigment Pattern Formation: Insights into the Development and Evolution of Adult Form. Annu Rev Genet 2019; 53:505-530. [DOI: 10.1146/annurev-genet-112618-043741] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Vertebrate pigment patterns are diverse and fascinating adult traits that allow animals to recognize conspecifics, attract mates, and avoid predators. Pigment patterns in fish are among the most amenable traits for studying the cellular basis of adult form, as the cells that produce diverse patterns are readily visible in the skin during development. The genetic basis of pigment pattern development has been most studied in the zebrafish, Danio rerio. Zebrafish adults have alternating dark and light horizontal stripes, resulting from the precise arrangement of three main classes of pigment cells: black melanophores, yellow xanthophores, and iridescent iridophores. The coordination of adult pigment cell lineage specification and differentiation with specific cellular interactions and morphogenetic behaviors is necessary for stripe development. Besides providing a nice example of pattern formation responsible for an adult trait of zebrafish, stripe-forming mechanisms also provide a conceptual framework for posing testable hypotheses about pattern diversification more broadly. Here, we summarize what is known about lineages and molecular interactions required for pattern formation in zebrafish, we review some of what is known about pattern diversification in Danio, and we speculate on how patterns in more distant teleosts may have evolved to produce a stunningly diverse array of patterns in nature.
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Affiliation(s)
| | - David M. Parichy
- Department of Biology and Department of Cell Biology, University of Virginia, Charlottesville, Virginia 22903, USA
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38
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Smith S, Grima R. Spatial Stochastic Intracellular Kinetics: A Review of Modelling Approaches. Bull Math Biol 2019; 81:2960-3009. [PMID: 29785521 PMCID: PMC6677717 DOI: 10.1007/s11538-018-0443-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Accepted: 05/03/2018] [Indexed: 01/22/2023]
Abstract
Models of chemical kinetics that incorporate both stochasticity and diffusion are an increasingly common tool for studying biology. The variety of competing models is vast, but two stand out by virtue of their popularity: the reaction-diffusion master equation and Brownian dynamics. In this review, we critically address a number of open questions surrounding these models: How can they be justified physically? How do they relate to each other? How do they fit into the wider landscape of chemical models, ranging from the rate equations to molecular dynamics? This review assumes no prior knowledge of modelling chemical kinetics and should be accessible to a wide range of readers.
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Affiliation(s)
- Stephen Smith
- School of Biological Sciences, University of Edinburgh, Mayfield Road, Edinburgh, EH9 3JR, Scotland, UK
| | - Ramon Grima
- School of Biological Sciences, University of Edinburgh, Mayfield Road, Edinburgh, EH9 3JR, Scotland, UK.
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39
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Irion U, Nüsslein-Volhard C. The identification of genes involved in the evolution of color patterns in fish. Curr Opin Genet Dev 2019; 57:31-38. [PMID: 31421397 PMCID: PMC6838669 DOI: 10.1016/j.gde.2019.07.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/19/2019] [Accepted: 07/03/2019] [Indexed: 12/14/2022]
Abstract
The genetic basis of morphological variation, both within and between species, provides a major topic in evolutionary biology. Teleost fish produce most elaborate color patterns, and among the more than 20000 species a number have been chosen for more detailed analyses because they are suitable to study particular aspects of color pattern evolution. In several fish species, color variants and pattern variants have been collected, transcriptome analyses have been carried out, and the recent advent of gene editing tools, such as CRISPR/Cas9, has allowed the production of mutants. Covering mostly the literature from the last three years, we discuss the cellular basis of coloration and the identification of loci involved in color pattern differences between sister species in cichlids and Danio species, in which cis-regulatory changes seem to prevail.
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Affiliation(s)
- Uwe Irion
- Max-Planck-Institute for Developmental Biology, Tübingen, Germany
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40
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Smith S, Dalchau N. Model reduction enables Turing instability analysis of large reaction-diffusion models. J R Soc Interface 2019. [PMID: 29540540 PMCID: PMC5908523 DOI: 10.1098/rsif.2017.0805] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Synthesizing a genetic network which generates stable Turing patterns is one of the great challenges of synthetic biology, but a significant obstacle is the disconnect between the mathematical theory and the biological reality. Current mathematical understanding of patterning is typically restricted to systems of two or three chemical species, for which equations are tractable. However, when models seek to combine descriptions of intercellular signal diffusion and intracellular biochemistry, plausible genetic networks can consist of dozens of interacting species. In this paper, we suggest a method for reducing large biochemical systems that relies on removing the non-diffusible species, leaving only the diffusibles in the model. Such model reduction enables analysis to be conducted on a smaller number of differential equations. We provide conditions to guarantee that the full system forms patterns if the reduced system does, and vice versa. We confirm our technique with three examples: the Brusselator, an example proposed by Turing, and a biochemically plausible patterning system consisting of 17 species. These examples show that our method significantly simplifies the study of pattern formation in large systems where several species can be considered immobile.
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Affiliation(s)
- Stephen Smith
- Biological Computation group, Microsoft Research, Cambridge CB1 2FB, UK.,School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, UK
| | - Neil Dalchau
- Biological Computation group, Microsoft Research, Cambridge CB1 2FB, UK
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41
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Saunders LM, Mishra AK, Aman AJ, Lewis VM, Toomey MB, Packer JS, Qiu X, McFaline-Figueroa JL, Corbo JC, Trapnell C, Parichy DM. Thyroid hormone regulates distinct paths to maturation in pigment cell lineages. eLife 2019; 8:e45181. [PMID: 31140974 PMCID: PMC6588384 DOI: 10.7554/elife.45181] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 05/24/2019] [Indexed: 12/11/2022] Open
Abstract
Thyroid hormone (TH) regulates diverse developmental events and can drive disparate cellular outcomes. In zebrafish, TH has opposite effects on neural crest derived pigment cells of the adult stripe pattern, limiting melanophore population expansion, yet increasing yellow/orange xanthophore numbers. To learn how TH elicits seemingly opposite responses in cells having a common embryological origin, we analyzed individual transcriptomes from thousands of neural crest-derived cells, reconstructed developmental trajectories, identified pigment cell-lineage specific responses to TH, and assessed roles for TH receptors. We show that TH promotes maturation of both cell types but in distinct ways. In melanophores, TH drives terminal differentiation, limiting final cell numbers. In xanthophores, TH promotes accumulation of orange carotenoids, making the cells visible. TH receptors act primarily to repress these programs when TH is limiting. Our findings show how a single endocrine factor integrates very different cellular activities during the generation of adult form.
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Affiliation(s)
- Lauren M Saunders
- Department of Genome SciencesUniversity of WashingtonSeattleUnited States
- Department of BiologyUniversity of VirginiaCharlottesvilleUnited States
- Department of Cell BiologyUniversity of VirginiaCharlottesvilleUnited States
| | - Abhishek K Mishra
- Department of BiologyUniversity of VirginiaCharlottesvilleUnited States
- Department of Cell BiologyUniversity of VirginiaCharlottesvilleUnited States
| | - Andrew J Aman
- Department of BiologyUniversity of VirginiaCharlottesvilleUnited States
- Department of Cell BiologyUniversity of VirginiaCharlottesvilleUnited States
| | - Victor M Lewis
- Department of Genome SciencesUniversity of WashingtonSeattleUnited States
- Department of BiologyUniversity of VirginiaCharlottesvilleUnited States
- Department of Cell BiologyUniversity of VirginiaCharlottesvilleUnited States
| | - Matthew B Toomey
- Department of Pathology and ImmunologyWashington University School of MedicineSt. LouisUnited States
| | - Jonathan S Packer
- Department of Genome SciencesUniversity of WashingtonSeattleUnited States
| | - Xiaojie Qiu
- Department of Genome SciencesUniversity of WashingtonSeattleUnited States
| | | | - Joseph C Corbo
- Department of Pathology and ImmunologyWashington University School of MedicineSt. LouisUnited States
| | - Cole Trapnell
- Department of Genome SciencesUniversity of WashingtonSeattleUnited States
| | - David M Parichy
- Department of BiologyUniversity of VirginiaCharlottesvilleUnited States
- Department of Cell BiologyUniversity of VirginiaCharlottesvilleUnited States
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42
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Carrillo JA, Murakawa H, Sato M, Togashi H, Trush O. A population dynamics model of cell-cell adhesion incorporating population pressure and density saturation. J Theor Biol 2019; 474:14-24. [PMID: 31059713 DOI: 10.1016/j.jtbi.2019.04.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 04/03/2019] [Accepted: 04/29/2019] [Indexed: 12/25/2022]
Abstract
We discuss several continuum cell-cell adhesion models based on the underlying microscopic assumptions. We propose an improvement on these models leading to sharp fronts and intermingling invasion fronts between different cell type populations. The model is based on basic principles of localized repulsion and nonlocal attraction due to adhesion forces at the microscopic level. The new model is able to capture both qualitatively and quantitatively experiments by Katsunuma et al. (2016). We also review some of the applications of these models in other areas of tissue growth in developmental biology. We finally explore the resulting qualitative behavior due to cell-cell repulsion.
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Affiliation(s)
- Jose A Carrillo
- Department of Mathematics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.
| | - Hideki Murakawa
- Department of Applied Mathematics and Informatics, Ryukoku University, Seta Otsu 520-2194, Japan.
| | - Makoto Sato
- Laboratory of Developmental Neurobiology, Graduate School of Medical Sciences, Mathematical Neuroscience Unit, Institute for Frontier Science Initiative, Kanazawa University, 13-1 Takaramachi, Kanazawa, Ishikawa 920-8640, Japan.
| | - Hideru Togashi
- Division of Molecular and Cellular Biology, Department of Biochemistry and Molecular Biology, Kobe University Graduate School of Medicine, 7-5-1, Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan.
| | - Olena Trush
- Laboratory of Developmental Neurobiology, Graduate School of Medical Sciences, Kanazawa University, 13-1 Takaramachi, Kanazawa, Ishikawa 920-8640, Japan.
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43
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Kiskowski M, Glimm T, Moreno N, Gamble T, Chiari Y. Isolating and quantifying the role of developmental noise in generating phenotypic variation. PLoS Comput Biol 2019; 15:e1006943. [PMID: 31009449 PMCID: PMC6497311 DOI: 10.1371/journal.pcbi.1006943] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 05/02/2019] [Accepted: 03/11/2019] [Indexed: 02/07/2023] Open
Abstract
Genotypic variation, environmental variation, and their interaction may produce variation in the developmental process and cause phenotypic differences among individuals. Developmental noise, which arises during development from stochasticity in cellular and molecular processes when genotype and environment are fixed, also contributes to phenotypic variation. While evolutionary biology has long focused on teasing apart the relative contribution of genes and environment to phenotypic variation, our understanding of the role of developmental noise has lagged due to technical difficulties in directly measuring the contribution of developmental noise. The influence of developmental noise is likely underestimated in studies of phenotypic variation due to intrinsic mechanisms within organisms that stabilize phenotypes and decrease variation. Since we are just beginning to appreciate the extent to which phenotypic variation due to stochasticity is potentially adaptive, the contribution of developmental noise to phenotypic variation must be separated and measured to fully understand its role in evolution. Here, we show that variation in the component of the developmental process corresponding to environmental and genetic factors (here treated together as a unit called the LALI-type) versus the contribution of developmental noise, can be distinguished for leopard gecko (Eublepharis macularius) head color patterns using mathematical simulations that model the role of random variation (corresponding to developmental noise) in patterning. Specifically, we modified the parameters of simulations corresponding to variation in the LALI-type to generate the full range of phenotypic variation in color pattern seen on the heads of eight leopard geckos. We observed that over the range of these parameters, variation in color pattern due to LALI-type variation exceeds that due to developmental noise in the studied gecko cohort. However, the effect of developmental noise on patterning is also substantial. Our approach addresses one of the major goals of evolutionary biology: to quantify the role of stochasticity in shaping phenotypic variation.
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Affiliation(s)
- Maria Kiskowski
- University of South Alabama, Department of Mathematics and Statistics, Mobile, AL, United States of America
- * E-mail:
| | - Tilmann Glimm
- Western Washington University, Department of Mathematics, Bellingham, WA, United States of America
| | - Nickolas Moreno
- University of South Alabama, Department of Biology, Mobile, AL, United States of America
| | - Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, WI, United States of America
- Bell Museum of Natural History, University of Minnesota, St. Paul, MN, United States of America
- Milwaukee Public Museum, Milwaukee, WI, United States of America
| | - Ylenia Chiari
- University of South Alabama, Department of Biology, Mobile, AL, United States of America
- George Mason University, Department of Biology, Science & Technology Campus, Manassas, VA, United States of America
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44
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Inaba M, Jiang TX, Liang YC, Tsai S, Lai YC, Widelitz RB, Chuong CM. Instructive role of melanocytes during pigment pattern formation of the avian skin. Proc Natl Acad Sci U S A 2019; 116:6884-6890. [PMID: 30886106 PMCID: PMC6452743 DOI: 10.1073/pnas.1816107116] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Animal skin pigment patterns are excellent models to study the mechanism of biological self-organization. Theoretical approaches developed mathematical models of pigment patterning and molecular genetics have brought progress; however, the responsible cellular mechanism is not fully understood. One long unsolved controversy is whether the patterning information is autonomously determined by melanocytes or nonautonomously determined from the environment. Here, we transplanted purified melanocytes and demonstrated that melanocytes could form periodic pigment patterns cell autonomously. Results of heterospecific transplantation among quail strains are consistent with this finding. Further, we observe that developing melanocytes directly connect with each other via filopodia to form a network in culture and in vivo. This melanocyte network is reminiscent of zebrafish pigment cell networks, where connexin is implicated in stripe formation via genetic studies. Indeed, we found connexin40 (cx40) present on developing melanocytes in birds. Stripe patterns can form in quail skin explant cultures. Several calcium channel modulators can enhance or suppress pigmentation globally, but a gap junction inhibitor can change stripe patterning. Most interestingly, in ovo, misexpression of dominant negative cx40 expands the black region, while overexpression of cx40 expands the yellow region. Subsequently, melanocytes instruct adjacent dermal cells to express agouti signaling protein (ASIP), the regulatory factor for pigment switching, which promotes pheomelanin production. Thus, we demonstrate Japanese quail melanocytes have an autonomous periodic patterning role during body pigment stripe formation. We also show dermal agouti stripes and how the coupling of melanocytes with dermal cells may confer stable and distinct pigment stripe patterns.
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Affiliation(s)
- Masafumi Inaba
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
| | - Ting-Xin Jiang
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
| | - Ya-Chen Liang
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
- Integrative Stem Cell Center, China Medical University Hospital, China Medical University, 40447 Taichung, Taiwan
| | - Stephanie Tsai
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
- Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90089
- Graduate School of Clinical Dentistry, National Taiwan University, 100 Taipei, Taiwan
| | - Yung-Chih Lai
- Integrative Stem Cell Center, China Medical University Hospital, China Medical University, 40447 Taichung, Taiwan
| | - Randall Bruce Widelitz
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
| | - Cheng Ming Chuong
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033;
- Integrative Stem Cell Center, China Medical University Hospital, China Medical University, 40447 Taichung, Taiwan
- Center for the Integrative and Evolutionary Galliformes Genomics, National Chung Hsing University, 40227 Taichung, Taiwan
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45
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Iwata M, Otaki JM. Insights into eyespot color-pattern formation mechanisms from color gradients, boundary scales, and rudimentary eyespots in butterfly wings. JOURNAL OF INSECT PHYSIOLOGY 2019; 114:68-82. [PMID: 30797779 DOI: 10.1016/j.jinsphys.2019.02.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 02/20/2019] [Accepted: 02/20/2019] [Indexed: 06/09/2023]
Abstract
Butterfly eyespot color patterns are traditionally explained by the gradient model, where positional information is stably provided by a morphogen gradient from a single organizer and its output is a set of non-graded (or graded) colors based on pre-determined threshold levels. An alternative model is the induction model, in which the outer black ring and the inner black core disk of an eyespot are specified by graded signals from the primary and secondary organizers that also involve lateral induction. To examine the feasibility of these models, we analyzed eyespot color gradients, boundary scales, and rudimentary eyespots in various nymphalid butterflies. Most parts of eyespots showed color gradients with gradual or fluctuating changes with sharp boundaries in many species, but some species had eyespots that were composed of a constant color within a given part. Thus, a plausible model should be flexible enough to incorporate this diversity. Some boundary scales appeared to have two kinds of pigments, and others had "misplaced" colors, suggesting an overlapping of two signals and a difficulty in assuming sharp threshold boundaries. Rudimentary eyespots of three Junonia species revealed that the outer black ring is likely determined first and the inner yellow or red ring is laterally induced. This outside-to-inside determination together with the lateral induction may favor the induction model, in which dynamic signal interactions play a major role. The implications of these results for the ploidy hypothesis and color-pattern rules are discussed.
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Affiliation(s)
- Masaki Iwata
- The BCPH Unit of Molecular Physiology, Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Senbaru, Nishihara, Okinawa 903-0213, Japan; Department of International Agricultural Development, Faculty of International Agriculture and Food Studies, Tokyo University of Agriculture, Sakuragaoka, Setagaya, Tokyo 156-8502, Japan
| | - Joji M Otaki
- The BCPH Unit of Molecular Physiology, Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Senbaru, Nishihara, Okinawa 903-0213, Japan.
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46
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Guy Preis S, Chayet H, Katz A, Yashunsky V, Kaner A, Ullman S, Braslavsky I. Labyrinth ice pattern formation induced by near-infrared irradiation. SCIENCE ADVANCES 2019; 5:eaav1598. [PMID: 30944855 PMCID: PMC6440752 DOI: 10.1126/sciadv.aav1598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 02/13/2019] [Indexed: 06/09/2023]
Abstract
Patterns are broad phenomena that relate to biology, chemistry, and physics. The dendritic growth of crystals is the most well-known ice pattern formation process. Tyndall figures are water-melting patterns that occur when ice absorbs light and becomes superheated. Here, we report a previously undescribed ice and water pattern formation process induced by near-infrared irradiation that heats one phase more than the other in a two-phase system. The pattern formed during the irradiation of ice crystals tens of micrometers thick in solution near equilibrium. Dynamic holes and a microchannel labyrinth then formed in specific regions and were characterized by a typical distance between melted points. We concluded that the differential absorption of water and ice was the driving force for the pattern formation. Heating ice by laser absorption might be useful in applications such as the cryopreservation of biological samples.
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Affiliation(s)
- Shlomit Guy Preis
- Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Haim Chayet
- Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Adam Katz
- Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Victor Yashunsky
- Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Avigail Kaner
- Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Shimon Ullman
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Ido Braslavsky
- Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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47
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Salis P, Lorin T, Lewis V, Rey C, Marcionetti A, Escande ML, Roux N, Besseau L, Salamin N, Sémon M, Parichy D, Volff JN, Laudet V. Developmental and comparative transcriptomic identification of iridophore contribution to white barring in clownfish. Pigment Cell Melanoma Res 2019; 32:391-402. [PMID: 30633441 DOI: 10.1111/pcmr.12766] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 12/11/2018] [Accepted: 12/26/2018] [Indexed: 12/18/2022]
Abstract
Actinopterygian fishes harbor at least eight distinct pigment cell types, leading to a fascinating diversity of colors. Among this diversity, the cellular origin of the white color appears to be linked to several pigment cell types such as iridophores or leucophores. We used the clownfish Amphiprion ocellaris, which has a color pattern consisting of white bars over a darker body, to characterize the pigment cells that underlie the white hue. We observe by electron microscopy that cells in white bars are similar to iridophores. In addition, the transcriptomic signature of clownfish white bars exhibits similarities with that of zebrafish iridophores. We further show by pharmacological treatments that these cells are necessary for the white color. Among the top differentially expressed genes in white skin, we identified several genes (fhl2a, fhl2b, saiyan, gpnmb, and apoD1a) and show that three of them are expressed in iridophores. Finally, we show by CRISPR/Cas9 mutagenesis that these genes are critical for iridophore development in zebrafish. Our analyses provide clues to the genomic underpinning of color diversity and allow identification of new iridophore genes in fish.
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Affiliation(s)
- Pauline Salis
- Observatoire Océanologique de Banyuls-sur-Mer, UMR CNRS 7232 BIOM, Sorbonne Université, Banyuls-sur-Mer, France
| | - Thibault Lorin
- IGFL, ENS de Lyon, UMR 5242 CNRS, Université Claude Bernard Lyon I, Lyon Cedex 07, France
| | - Victor Lewis
- Department of Biology, University of Washington, Seattle, Washington.,Department of Biology, Department of Cell Biology, University of Virginia, Charlottesville, Virginia
| | - Carine Rey
- ENS de Lyon, CNRS UMR 5239, INSERM U1210, LBMC, Université Claude Bernard, Lyon, France.,LBBE, CNRS, Université Lyon 1, Villeurbanne, France
| | - Anna Marcionetti
- Department of Computational Biology, Biophore, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marie-Line Escande
- Observatoire Océanologique de Banyuls-sur-Mer, UMR CNRS 7232 BIOM, Sorbonne Université, Banyuls-sur-Mer, France
| | - Natacha Roux
- Observatoire Océanologique de Banyuls-sur-Mer, UMR CNRS 7232 BIOM, Sorbonne Université, Banyuls-sur-Mer, France
| | - Laurence Besseau
- Observatoire Océanologique de Banyuls-sur-Mer, UMR CNRS 7232 BIOM, Sorbonne Université, Banyuls-sur-Mer, France
| | - Nicolas Salamin
- Department of Computational Biology, Biophore, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marie Sémon
- ENS de Lyon, CNRS UMR 5239, INSERM U1210, LBMC, Université Claude Bernard, Lyon, France
| | - David Parichy
- Department of Biology, Department of Cell Biology, University of Virginia, Charlottesville, Virginia
| | - Jean-Nicolas Volff
- IGFL, ENS de Lyon, UMR 5242 CNRS, Université Claude Bernard Lyon I, Lyon Cedex 07, France
| | - Vincent Laudet
- Observatoire Océanologique de Banyuls-sur-Mer, UMR CNRS 7232 BIOM, Sorbonne Université, Banyuls-sur-Mer, France
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48
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Usui Y, Aramaki T, Kondo S, Watanabe M. The minimal gap-junction network among melanophores and xanthophores required for stripe-pattern formation in zebrafish. Development 2019; 146:dev.181065. [DOI: 10.1242/dev.181065] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 10/24/2019] [Indexed: 12/16/2022]
Abstract
Connexin39.4 (Cx39.4) and Connexin41.8 (Cx41.8), two gap-junction proteins expressed in both melanophores and xanthophores, are critical for the intercellular communication among pigment cells that is necessary for generating the stripe pigment pattern of zebrafish. We previously characterized the gap-junction properties of Cx39.4 and Cx41.8, but how these proteins contribute to stripe formation remains unclear; this is because distinct types of connexins potentially form heteromeric gap junctions, which precludes accurate elucidation of individual connexin functions in vivo. Here, by arranging Cx39.4 and Cx41.8 expression in pigment cells, we identified the simplest gap-junction network required for stripe generation: Cx39.4 expression in melanophores is required but expression in xanthophores is not necessary for stripe patterning, whereas Cx41.8 expression in xanthophores is sufficient for the patterning, and Cx41.8 expression in melanophores might stabilize the stripes. Moreover, patch-clamp recordings revealed that Cx39.4 gap junctions exhibit spermidine-dependent rectification property. Our results suggest that Cx39.4 facilitates the critical cell-cell interactions between melanophores and xanthophores that mediate a unidirectional activation-signal transfer from xanthophores to melanophores, which is essential for melanophore survival.
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Affiliation(s)
- Yuu Usui
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Toshihiro Aramaki
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shigeru Kondo
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
- CREST, Japan Science and Technology Agency, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masakatsu Watanabe
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
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49
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Affiliation(s)
- Hugo F Gante
- Department of Biology, The Center for Genomic Advocacy (TCGA), College of Arts and Sciences, Indiana State University, Terre Haute, IN 47809, USA.
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50
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Salis P, Roux N, Soulat O, Lecchini D, Laudet V, Frédérich B. Ontogenetic and phylogenetic simplification during white stripe evolution in clownfishes. BMC Biol 2018; 16:90. [PMID: 30180844 PMCID: PMC6123960 DOI: 10.1186/s12915-018-0559-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 08/02/2018] [Indexed: 12/11/2022] Open
Abstract
Background Biologists have long been fascinated by the striking diversity of complex color patterns in tropical reef fishes. However, the origins and evolution of this diversity are still poorly understood. Disentangling the evolution of simple color patterns offers the opportunity to dissect both ultimate and proximate causes underlying color diversity. Results Here, we study clownfishes, a tribe of 30 species within the Pomacentridae that displays a relatively simple color pattern made of zero to three vertical white stripes on a dark body background. Mapping the number of white stripes on the evolutionary tree of clownfishes reveals that their color pattern diversification results from successive caudal to rostral losses of stripes. Moreover, we demonstrate that stripes always appear with a rostral to caudal stereotyped sequence during larval to juvenile transition. Drug treatments (TAE 684) during this period leads to a dose-dependent loss of stripes, demonstrating that white stripes are made of iridophores and that these cells initiate the stripe formation. Surprisingly, juveniles of several species (e.g., Amphiprion frenatus) have supplementary stripes when compared to their respective adults. These stripes disappear caudo-rostrally during the juvenile phase leading to the definitive color pattern. Remarkably, the reduction of stripe number over ontogeny matches the sequences of stripe losses during evolution, showing that color pattern diversification among clownfish lineages results from changes in developmental processes. Finally, we reveal that the diversity of striped patterns plays a key role for species recognition. Conclusions Overall, our findings illustrate how developmental, ecological, and social processes have shaped the diversification of color patterns during the radiation of an emblematic coral reef fish lineage. Electronic supplementary material The online version of this article (10.1186/s12915-018-0559-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pauline Salis
- Observatoire Océanologique de Banyuls-sur-Mer, UMR CNRS 7232 BIOM, Sorbonne Université Paris, 1, Avenue Pierre Fabre, 66650, Banyuls-sur-Mer, France
| | - Natacha Roux
- Observatoire Océanologique de Banyuls-sur-Mer, UMR CNRS 7232 BIOM, Sorbonne Université Paris, 1, Avenue Pierre Fabre, 66650, Banyuls-sur-Mer, France
| | - Olivier Soulat
- Aquarium de Canet-en-Roussillon, 2 Boulevard de la Jetée, 66140, Canet-en-Roussillon, France
| | - David Lecchini
- EPHE-UPVD-CNRS, USR3278 CRIOBE, PSL Research University, BP 1013, 98729, Papetoai, Moorea, French Polynesia
| | - Vincent Laudet
- Observatoire Océanologique de Banyuls-sur-Mer, UMR CNRS 7232 BIOM, Sorbonne Université Paris, 1, Avenue Pierre Fabre, 66650, Banyuls-sur-Mer, France.
| | - Bruno Frédérich
- Laboratory of Functional and Evolutionary Morphology, FOCUS, University of Liège, Liège, Belgium
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