IVEN: A quantitative tool to describe 3D cell position and neighbourhood reveals architectural changes in FGF4-treated preimplantation embryos.

Architectural changes at the cellular and organism level are integral and necessary to successful development and growth. During mammalian preimplantation development, cells reduce in size and the architecture of the embryo changes significantly. Such changes must be coordinated correctly to ensure...

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Autores principales:	Jessica E Forsyth, Ali H Al-Anbaki, Roberto de la Fuente, Nikkinder Modare, Diego Perez-Cortes, Isabel Rivera, Rowena Seaton Kelly, Simon Cotter, Berenika Plusa
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/e0f5a5b746b64ad780975bfb580a5756
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spelling	oai:doaj.org-article:e0f5a5b746b64ad780975bfb580a57562021-12-02T19:54:21ZIVEN: A quantitative tool to describe 3D cell position and neighbourhood reveals architectural changes in FGF4-treated preimplantation embryos.1544-91731545-788510.1371/journal.pbio.3001345https://doaj.org/article/e0f5a5b746b64ad780975bfb580a57562021-07-01T00:00:00Zhttps://doi.org/10.1371/journal.pbio.3001345https://doaj.org/toc/1544-9173https://doaj.org/toc/1545-7885Architectural changes at the cellular and organism level are integral and necessary to successful development and growth. During mammalian preimplantation development, cells reduce in size and the architecture of the embryo changes significantly. Such changes must be coordinated correctly to ensure continued development of the embryo and, ultimately, a successful pregnancy. However, the nature of such transformations is poorly defined during mammalian preimplantation development. In order to quantitatively describe changes in cell environment and organism architecture, we designed Internal Versus External Neighbourhood (IVEN). IVEN is a user-interactive, open-source pipeline that classifies cells into different populations based on their position and quantifies the number of neighbours of every cell within a dataset in a 3D environment. Through IVEN-driven analyses, we show how transformations in cell environment, defined here as changes in cell neighbourhood, are related to changes in embryo geometry and major developmental events during preimplantation mammalian development. Moreover, we demonstrate that modulation of the FGF pathway alters spatial relations of inner cells and neighbourhood distributions, leading to overall changes in embryo architecture. In conjunction with IVEN-driven analyses, we uncover differences in the dynamic of cell size changes over the preimplantation period and determine that cells within the mammalian embryo initiate growth phase only at the time of implantation.Jessica E ForsythAli H Al-AnbakiRoberto de la FuenteNikkinder ModareDiego Perez-CortesIsabel RiveraRowena Seaton KellySimon CotterBerenika PlusaPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Biology, Vol 19, Iss 7, p e3001345 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Jessica E Forsyth Ali H Al-Anbaki Roberto de la Fuente Nikkinder Modare Diego Perez-Cortes Isabel Rivera Rowena Seaton Kelly Simon Cotter Berenika Plusa IVEN: A quantitative tool to describe 3D cell position and neighbourhood reveals architectural changes in FGF4-treated preimplantation embryos.
description	Architectural changes at the cellular and organism level are integral and necessary to successful development and growth. During mammalian preimplantation development, cells reduce in size and the architecture of the embryo changes significantly. Such changes must be coordinated correctly to ensure continued development of the embryo and, ultimately, a successful pregnancy. However, the nature of such transformations is poorly defined during mammalian preimplantation development. In order to quantitatively describe changes in cell environment and organism architecture, we designed Internal Versus External Neighbourhood (IVEN). IVEN is a user-interactive, open-source pipeline that classifies cells into different populations based on their position and quantifies the number of neighbours of every cell within a dataset in a 3D environment. Through IVEN-driven analyses, we show how transformations in cell environment, defined here as changes in cell neighbourhood, are related to changes in embryo geometry and major developmental events during preimplantation mammalian development. Moreover, we demonstrate that modulation of the FGF pathway alters spatial relations of inner cells and neighbourhood distributions, leading to overall changes in embryo architecture. In conjunction with IVEN-driven analyses, we uncover differences in the dynamic of cell size changes over the preimplantation period and determine that cells within the mammalian embryo initiate growth phase only at the time of implantation.
format	article
author	Jessica E Forsyth Ali H Al-Anbaki Roberto de la Fuente Nikkinder Modare Diego Perez-Cortes Isabel Rivera Rowena Seaton Kelly Simon Cotter Berenika Plusa
author_facet	Jessica E Forsyth Ali H Al-Anbaki Roberto de la Fuente Nikkinder Modare Diego Perez-Cortes Isabel Rivera Rowena Seaton Kelly Simon Cotter Berenika Plusa
author_sort	Jessica E Forsyth
title	IVEN: A quantitative tool to describe 3D cell position and neighbourhood reveals architectural changes in FGF4-treated preimplantation embryos.
title_short	IVEN: A quantitative tool to describe 3D cell position and neighbourhood reveals architectural changes in FGF4-treated preimplantation embryos.
title_full	IVEN: A quantitative tool to describe 3D cell position and neighbourhood reveals architectural changes in FGF4-treated preimplantation embryos.
title_fullStr	IVEN: A quantitative tool to describe 3D cell position and neighbourhood reveals architectural changes in FGF4-treated preimplantation embryos.
title_full_unstemmed	IVEN: A quantitative tool to describe 3D cell position and neighbourhood reveals architectural changes in FGF4-treated preimplantation embryos.
title_sort	iven: a quantitative tool to describe 3d cell position and neighbourhood reveals architectural changes in fgf4-treated preimplantation embryos.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/e0f5a5b746b64ad780975bfb580a5756
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IVEN: A quantitative tool to describe 3D cell position and neighbourhood reveals architectural changes in FGF4-treated preimplantation embryos.

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