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Biomedicines
Special Issues
Theoretical Approaches to Developmental Biology
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Theoretical Approaches to Developmental Biology

A special issue of Biomedicines (ISSN 2227-9059). This special issue belongs to the section "Molecular and Translational Medicine".

Deadline for manuscript submissions: closed (30 June 2022) | Viewed by 4931

Special Issue Editor

Dr. David G. Miguez

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Guest Editor
Systems Biology Lab, Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid, Madrid, Spain
Interests: systems biology; developmental biology; biophysics

Special Issue Information

Dear Colleagues,

The field of Developmental Biology is currently undergoing several simultaneous revolutions, due to important advances in microscopy techniques, in organoid research, and the arisal of new animal models. From a theoretical perspective, Developmental Biology is also experiencing an interesting transformation, with many of the most groundbreaking experimental contributions now supported and complemented by mathematical models and equations.

This Special Issue of Biomedicines focuses on recent advances in the field of Developmental Biology that benefit from theoretical and/or computational tools to understand the underlying principles that govern the pattern formation, the morphogenesis, the regulation of stem cell differentiation, and the dynamics of key events during the formation of tissues and organs in the embryo. The ultimate goal is to stimulate interdisciplinary research by closing the gap between experimentalists and theoreticians working in the field of Developmental Biology, and to foster collaborations that will strongly benefit both communities and that will improve our understanding of developmental systems.

Potential topics include but are not limited to:

  • Basic research focusing on morphogenes and signaling pathways in development;
  • Basic research focused on computational models of signaling pathways that are supported or complemented by experimental data;
  • Basic research focused on theoretical approaches to understanding stem cell differentiation based on experimental data;
  • Basic research focusing on interdisciplinary approaches to studying biological pattern formation;
  • Basic research focusing on new computational tools applied to the study of organogenesis;
  • Review articles focusing on nonlinear dynamics and feedback regulation in development.

Dr. David G. Miguez
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biomedicines is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • signaling pathways
  • morphogenes
  • patterns
  • reaction–diffusion
  • modelling
  • branching processes
  • neurogenesis
  • stem cells
  • organoids
  • systems
  • simulations
  • tissue formation
  • forces

Published Papers (2 papers)

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Research

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21 pages, 4449 KiB  
Article
Pattern of Repetitive Element Transcription Segregate Cell Lineages during the Embryogenesis of Sea Urchin Strongylocentrotus purpuratus
by Nick Panyushev, Larisa Okorokova, Lavrentii Danilov and Leonid Adonin
Biomedicines 2021, 9(11), 1736; https://doi.org/10.3390/biomedicines9111736 - 21 Nov 2021
Cited by 3 | Viewed by 2461
Abstract
Repetitive elements (REs) occupy a significant part of eukaryotic genomes and are shown to play diverse roles in genome regulation. During embryogenesis of the sea urchin, a large number of REs are expressed, but the role of these elements in the regulation of [...] Read more.
Repetitive elements (REs) occupy a significant part of eukaryotic genomes and are shown to play diverse roles in genome regulation. During embryogenesis of the sea urchin, a large number of REs are expressed, but the role of these elements in the regulation of biological processes remains unknown. The aim of this study was to identify the RE expression at different stages of embryogenesis. REs occupied 44% of genomic DNA of Strongylocentrotus purpuratus. The most prevalent among these elements were the unknown elements—in total, they contributed 78.5% of REs (35% in total genome occupancy). It was revealed that the transcription pattern of genes and REs changes significantly during gastrulation. Using the de novo transcriptome assembly, we showed that the expression of RE is independent of its copy number in the genome. We also identified copies that are expressed. Only active RE copies were used for mapping and quantification of RE expression in the single-cell RNA sequencing data. REs expression was observed in all cell lineages and they were detected as population markers. Moreover, the primary mesenchyme cell (PMC) line had the greatest diversity of REs among the markers. Our data suggest a role for RE in the organization of developmental domains during the sea urchin embryogenesis at the single-cell resolution level. Full article
(This article belongs to the Special Issue Theoretical Approaches to Developmental Biology)
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Review

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15 pages, 40317 KiB  
Review
Quantitative Approaches to Study Retinal Neurogenesis
by Diego Pérez-Dones, Mario Ledesma-Terrón and David G. Míguez
Biomedicines 2021, 9(9), 1222; https://doi.org/10.3390/biomedicines9091222 - 14 Sep 2021
Viewed by 1725
Abstract
The study of the development of the vertebrate retina can be addressed from several perspectives: from a purely qualitative to a more quantitative approach that takes into account its spatio-temporal features, its three-dimensional structure and also the regulation and properties at the systems [...] Read more.
The study of the development of the vertebrate retina can be addressed from several perspectives: from a purely qualitative to a more quantitative approach that takes into account its spatio-temporal features, its three-dimensional structure and also the regulation and properties at the systems level. Here, we review the ongoing transition toward a full four-dimensional characterization of the developing vertebrate retina, focusing on the challenges at the experimental, image acquisition, image processing and quantification. Using the developing zebrafish retina, we illustrate how quantitative data extracted from these type of highly dense, three-dimensional tissues depend strongly on the image quality, image processing and algorithms used to segment and quantify. Therefore, we propose that the scientific community that focuses on developmental systems could strongly benefit from a more detailed disclosure of the tools and pipelines used to process and analyze images from biological samples. Full article
(This article belongs to the Special Issue Theoretical Approaches to Developmental Biology)
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