Bird stem cell differentiation

We're going to pick up on cell differentiation from the chicken breast project. Our goal in this post is to explore how we can take a fertilized egg (embryonic egg cell), and transform it into skeletal muscle. A stretch goal is to do the same things for vascular cells, and motor neurons.

We'll go ahead and write what we know using SysML, so that we can reference it as we go.

part def Cell;
part def ChickenBreastCell :> Cell;
part def StemCell :> Cell;
part def <'ESC'> EmbryonicStemCell :> StemCell;
part def MesodermStemCell :> StemCell;
part def MesenchymalStemCell :> StemCell;
part def SkeletalMuscleCell :> Cell;
part def ChickenStemCell : StemCell;
part def BioReactor;
part SpecializedBioReactor : BioReactor {
	in salt, sugar, aminoacids, cells;
	out cells;
	action GrowCells;
}
action def CellDifferentiation {
	in undif_cell : StemCell;
	out dif_cell : Cell;
}
action GrowChicken{
	action MakeSkeletalMuscleFromEmbryonicStemCell {
		action MakeMesoderm : CellDifferentiation{
			:> undif_cell : EmbryonicStemCell;
			:> dif_cell : MesodermStemCell;
		}
		flow MakeMesoderm.dif_cell
			to MakeMesenchymal.undif_cell;
		action MakeMesenchymal : CellDifferentiation{
			:> undif_cell : MesodermStemCell;
			:> dif_cell : MesenchymalStemCell;
		}
		flow MakeMesenchymal.dif_cell
			to MakeSkeletalMuscle.undif_cell;
		action MakeSkeletalMuscle : CellDifferentiation{
			:> undif_cell : MesenchymalStemCell;
			:> dif_cell : SkeletalMuscleCell;
		}
	}
	action GrowChickenBreast {
		perform SpecializedBioReactor::GrowCells;
	}
}

We've already hit our first snag, bird (avionic) stem cell differentiation isn't well studied it seems. At least relative to the mammalian version. I found a paper that was published this year [1] that treats embryonic stem cell differentiation for bird species as something that is fairly novel. As a result the paper somewhat short of our three actions that we need to perform. Yet a paper, that doesn't seem peer reviewed, cites [1] that deals with mesenchyme cell differentiation [2]. We are two-thirds the way there, and have something analogous ([2]) that can help us doing conceptual problem solving for our final process.

And once I have a nice conceptual fit, and I need to jump into working on conceptual problems or try and design an experiment, I can move into simulation. There are two papers that look pretty neat [3] [4]. The first provides an outline of simulating of how stem cells differentiate. The second is more of a guide/outline of computational stem cell biology. It's kind of crazy that [3] was accepted almost nine years ago.

Today was a bit slower than I anticipated, but I think it is a good start to this leg of the project. Something I wouldn't mind doing at a later date is getting blob storage up and going, along with a plugin for images so I can post memes in the blog. I'm sure I could also add visuals/graphs as well. Besides that, the next time I open chicken cell differentiation stuff again I'm going to need to start reading journals it seems.

[1] Authors: Xi Chen, Zheng Guo, Xinyi Tong, Xizi Wang, Xugeng Liu, Hiroki Nagai, Ping Wu, Jiayi Lu, David Huss, Martin Tran, Carol Readhead, Christina Wu, Lin Cao, Yixin Huang, Zhaohan Zeng, Fan Feng, Nima Adhami, Sirjan Mor, Rusty Lansford, Cheng-Ming Chuong, Guojun Sheng, Carlos Lois & Qi-Long Ying. Title: Derivation of embryonic stem cells across avian species. Title of journal: Nature Biotechnology. Volume and issue number: None?. Date: 30 September 2025. Page number of article: Specified in []. DOI: https://doi.org/10.1038/s41587-025-02833-3. Owner of site: nature.com. Date of access: 24 December 2025.

[2] Authors: Katharine Goodwin, Michael A. Palmer, Bezia Lemma, and Celeste M. Nelson. Title: Origins of smooth muscle and evolutionary specializations of the pulmonary mesenchyme in the vertebrate lung. Title of journal: bioRxiv. Volume and issue number: None. Date: 13 July 2022. Page number of article: Specified in []. DOI: https://doi.org/10.1101/2022.07.13.499952 . Owner of site: biorRxiv.org. Date of access: 24 December 2025.

[3] Authors: Massimo Pisu , Alessandro Concas, Giacomo Cao. Title: A novel simulation model for stem cells differentiation. Title of journal: Journal of Biotechnology. Volume and issue date: 171-82. Date: March 12 2007. DOI: 10.1016/j.jbiotec.2007.02.028. Owner of site: PubMed. Date of access: 24 December 2025.

[4] Patrick Cahan, Davide Cacchiarelli, Sara-Jane Dunn, Martin Hemberg, Susana M. Chuva de Sousa Lopes, Samantha A. Morris, Owen J.L. Rackham, Antonio del Sol, and Christine A. Wells. Title: Computational Stem Cell Biology: Open Questions and Guiding Principles. Title of journal:. Volume and issue date: Volume 28, issue 1. Date: January 7 2021. DOI: https://doi.org/10.1016/j.stem.2020.12.012. Date of access: 24 December 2025.