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EyeVolve, a modular PYTHON based model for simulating developmental eye type diversification

Vision is among the oldest and arguably most important sensory modalities for animals to interact with their external environment. Although many different eye types exist within the animal kingdom, mounting evidence indicates that the genetic networks required for visual system formation and functio...

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Autores principales: Lavin, Ryan, Rathore, Shubham, Bauer, Brian, Disalvo, Joe, Mosley, Nick, Shearer, Evan, Elia, Zachary, Cook, Tiffany A., Buschbeck, Elke K.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9459020/
https://www.ncbi.nlm.nih.gov/pubmed/36092740
http://dx.doi.org/10.3389/fcell.2022.964746
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author Lavin, Ryan
Rathore, Shubham
Bauer, Brian
Disalvo, Joe
Mosley, Nick
Shearer, Evan
Elia, Zachary
Cook, Tiffany A.
Buschbeck, Elke K.
author_facet Lavin, Ryan
Rathore, Shubham
Bauer, Brian
Disalvo, Joe
Mosley, Nick
Shearer, Evan
Elia, Zachary
Cook, Tiffany A.
Buschbeck, Elke K.
author_sort Lavin, Ryan
collection PubMed
description Vision is among the oldest and arguably most important sensory modalities for animals to interact with their external environment. Although many different eye types exist within the animal kingdom, mounting evidence indicates that the genetic networks required for visual system formation and function are relatively well conserved between species. This raises the question as to how common developmental programs are modified in functionally different eye types. Here, we approached this issue through EyeVolve, an open-source PYTHON-based model that recapitulates eye development based on developmental principles originally identified in Drosophila melanogaster. Proof-of-principle experiments showed that this program’s animated timeline successfully simulates early eye tissue expansion, neurogenesis, and pigment cell formation, sequentially transitioning from a disorganized pool of progenitor cells to a highly organized lattice of photoreceptor clusters wrapped with support cells. Further, tweaking just five parameters (precursor pool size, founder cell distance and placement from edge, photoreceptor subtype number, and cell death decisions) predicted a multitude of visual system layouts, reminiscent of the varied eye types found in larval and adult arthropods. This suggests that there are universal underlying mechanisms that can explain much of the existing arthropod eye diversity. Thus, EyeVolve sheds light on common principles of eye development and provides a new computational system for generating specific testable predictions about how development gives rise to diverse visual systems from a commonly specified neuroepithelial ground plan.
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spelling pubmed-94590202022-09-10 EyeVolve, a modular PYTHON based model for simulating developmental eye type diversification Lavin, Ryan Rathore, Shubham Bauer, Brian Disalvo, Joe Mosley, Nick Shearer, Evan Elia, Zachary Cook, Tiffany A. Buschbeck, Elke K. Front Cell Dev Biol Cell and Developmental Biology Vision is among the oldest and arguably most important sensory modalities for animals to interact with their external environment. Although many different eye types exist within the animal kingdom, mounting evidence indicates that the genetic networks required for visual system formation and function are relatively well conserved between species. This raises the question as to how common developmental programs are modified in functionally different eye types. Here, we approached this issue through EyeVolve, an open-source PYTHON-based model that recapitulates eye development based on developmental principles originally identified in Drosophila melanogaster. Proof-of-principle experiments showed that this program’s animated timeline successfully simulates early eye tissue expansion, neurogenesis, and pigment cell formation, sequentially transitioning from a disorganized pool of progenitor cells to a highly organized lattice of photoreceptor clusters wrapped with support cells. Further, tweaking just five parameters (precursor pool size, founder cell distance and placement from edge, photoreceptor subtype number, and cell death decisions) predicted a multitude of visual system layouts, reminiscent of the varied eye types found in larval and adult arthropods. This suggests that there are universal underlying mechanisms that can explain much of the existing arthropod eye diversity. Thus, EyeVolve sheds light on common principles of eye development and provides a new computational system for generating specific testable predictions about how development gives rise to diverse visual systems from a commonly specified neuroepithelial ground plan. Frontiers Media S.A. 2022-08-26 /pmc/articles/PMC9459020/ /pubmed/36092740 http://dx.doi.org/10.3389/fcell.2022.964746 Text en Copyright © 2022 Lavin, Rathore, Bauer, Disalvo, Mosley, Shearer, Elia, Cook and Buschbeck. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Cell and Developmental Biology
Lavin, Ryan
Rathore, Shubham
Bauer, Brian
Disalvo, Joe
Mosley, Nick
Shearer, Evan
Elia, Zachary
Cook, Tiffany A.
Buschbeck, Elke K.
EyeVolve, a modular PYTHON based model for simulating developmental eye type diversification
title EyeVolve, a modular PYTHON based model for simulating developmental eye type diversification
title_full EyeVolve, a modular PYTHON based model for simulating developmental eye type diversification
title_fullStr EyeVolve, a modular PYTHON based model for simulating developmental eye type diversification
title_full_unstemmed EyeVolve, a modular PYTHON based model for simulating developmental eye type diversification
title_short EyeVolve, a modular PYTHON based model for simulating developmental eye type diversification
title_sort eyevolve, a modular python based model for simulating developmental eye type diversification
topic Cell and Developmental Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9459020/
https://www.ncbi.nlm.nih.gov/pubmed/36092740
http://dx.doi.org/10.3389/fcell.2022.964746
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