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Developmental Biology: Computational and Experimental Approaches, 2nd Edition
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Developmental Biology: Computational and Experimental Approaches, 2nd Edition

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: 30 June 2025 | Viewed by 1280

Special Issue Editor

Dr. Mikhail P. Ponomarenko

E-Mail Website
Guest Editor
Institute of Cytology and Genetics, Novosibirsk State University, Novosibirsk, Russia
Interests: DNA sequence analysis; mutation; single-nucleotide polymorphism (SNP); quantitative sequence-activity relationships; DNA-protein affinity; TATA-binding protein binding site (TATA box); genome-wide prediction in silico; experimental verification; in vitro; in vivo; hereditary disease
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Developmental biology investigates ontogenesis, which is how a single cell eventually becomes a multicellular organism, with its particular shape, dimensions, structure, life cycle, and potential to produce the next generation. At the molecular level, the mechanisms associated with signal transduction, gene replication, translation, and regulation are basic to ontogenesis. This Special Issue, entitled “Developmental Biology: Computational and Experimental Approaches” includes 14 articles on human, animal, and plant gene expression during embryogenesis, prepuberty, and ageing under normal conditions and with mutations, exposure to stresses, infections, etc. These articles appeared in the International Journal of Molecular Sciences from 2022 to 2024. According to a recent finding by Zhimulev and colleagues, any eukaryotic genome has two distinct types of genetic organization within it, each with its specific replication timing, DNA replication origins, chromatin packaging levels, composition of regulatory proteins, and particulars of the genes—specificity, the organization of their promoters, and the lengths of their introns. The differences in these attributes differentiate the housekeeping genes from most of the rest, which are called "developmental". Can the genes' neighborhood give us a clue as to which is which? Find out with this Special Issue of Developmental Biology: Computational and Experimental Approaches, 2nd Edition.

Dr. Mikhail P. Ponomarenko
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.

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Keywords

  • animal
  • plant
  • fungus
  • biological organization hierarchy
  • evolutionary limitations

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Published Papers (4 papers)

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Research

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17 pages, 3638 KiB  
Article
New Cellular Interactions Due to the Radioprotective Effect of N-Acetylcysteine in a Model of Radiation-Induced Pancreatitis
by Grigory Demyashkin, Matvey Vadyukhin, Vladimir Shchekin, Tatyana Borovaya, Olga Zavialova, Dmitriy Belokopytov, Kirill Silakov, Petr Shegay and Andrei Kaprin
Int. J. Mol. Sci. 2025, 26(11), 5238; https://doi.org/10.3390/ijms26115238 - 29 May 2025
Viewed by 268
Abstract
Ionizing radiation at early stages leads to radiation-induced death of Langerhans islet cells and acinar cells, resulting in the development of acute/subacute pancreatitis. Conducting studies on radiation-induced changes in the pancreas following electron beam irradiation appears to be of great interest, and the [...] Read more.
Ionizing radiation at early stages leads to radiation-induced death of Langerhans islet cells and acinar cells, resulting in the development of acute/subacute pancreatitis. Conducting studies on radiation-induced changes in the pancreas following electron beam irradiation appears to be of great interest, and the evaluation of radioprotective agents for safeguarding normal tissues from radiation is equally important. The aim of this study was to preclinically investigate the antioxidant properties of N-Acetylcysteine in an animal model of radiation-induced pancreatitis over a three-month period. In this study, it was proven for the first time that even electrons can lead to characteristic signs of radiation-induced pancreatitis, the degree of which was assessed based on the levels of insulin, glucose, and amylase. Thus, conducting electron therapy also increases the risks of insulin resistance, as well as X-ray and gamma radiation. For the first time, a comprehensive analysis of biochemical, morphological, and immunohistochemical markers in the pancreas of a large cohort of electron-irradiated animals was conducted, including both acute and delayed effects of electron exposure. The crucial role of interleukins in shaping both the cellular and vascular components of the inflammatory response was identified. Additionally, the radioprotective properties of N-Acetylcysteine during electron irradiation of the pancreas were evaluated for the first time, and its effectiveness in reducing both acute and late complications of electron therapy was demonstrated. Thus, it can be concluded that N-Acetylcysteine is capable of effectively suppressing the inflammatory response in the pancreas. Full article
(This article belongs to the Special Issue Developmental Biology: Computational and Experimental Approaches, 2nd Edition)
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15 pages, 1247 KiB  
Article
Evolutionary Transcriptomics of Cancer Development
by Roman Ivanov, Dmitry Afonnikov, Yury Matushkin and Sergey Lashin
Int. J. Mol. Sci. 2025, 26(11), 5041; https://doi.org/10.3390/ijms26115041 - 23 May 2025
Viewed by 275
Abstract
Cancer progression is a complex, multi-stage development process characterized by dynamic changes at the molecular level. Understanding these changes may provide new insights into tumorigenesis and potential therapeutic targets. This study focuses on the evolutionary transcriptomics of cancer, specifically analyzing the Transcriptome Age [...] Read more.
Cancer progression is a complex, multi-stage development process characterized by dynamic changes at the molecular level. Understanding these changes may provide new insights into tumorigenesis and potential therapeutic targets. This study focuses on the evolutionary transcriptomics of cancer, specifically analyzing the Transcriptome Age Index (TAI) across different pathological stages. By examining various cancers at four distinct pathological stages, we identify a significant «hourglass» pattern in TAI indices of ductal carcinoma of the breast, bladder carcinoma, and liver carcinoma, suggesting a conserved evolutionary trajectory during tumor development. The results reveal that early and late stages of these cancers exhibit higher TAI values, indicative of more novel gene expression, while intermediate stages show a dip in TAI, reflecting a more ancient evolutionary origin of expressed genes. This «hourglass» pattern underscores the evolutionary constraints and innovations at play during tumor progression. Our findings contribute to the growing body of evidence that evolutionary principles are deeply embedded in cancer biology, offering new perspectives on the dynamics of gene expression in tumors. Full article
(This article belongs to the Special Issue Developmental Biology: Computational and Experimental Approaches, 2nd Edition)
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13 pages, 960 KiB  
Article
Impact of Chronic Fluoxetine Exposure on Oocyte Development and Reproductive Outcomes in a Mouse Model
by Maria D. Tkachenko, Nina M. Alyoshina, Yulia O. Nikishina, Veronika S. Frolova and Denis A. Nikishin
Int. J. Mol. Sci. 2025, 26(10), 4858; https://doi.org/10.3390/ijms26104858 - 19 May 2025
Viewed by 388
Abstract
Selective serotonin reuptake inhibitors (SSRIs), like fluoxetine, are increasingly used by women of a reproductive age, raising concerns about their impact on oocyte quality and early embryonic development. This study investigated the effects of chronic fluoxetine exposure on oocyte maturation, ovulation, and embryonic [...] Read more.
Selective serotonin reuptake inhibitors (SSRIs), like fluoxetine, are increasingly used by women of a reproductive age, raising concerns about their impact on oocyte quality and early embryonic development. This study investigated the effects of chronic fluoxetine exposure on oocyte maturation, ovulation, and embryonic development in a mouse model. Female mice were administered fluoxetine via drinking water, and their reproductive outcomes were compared to those of control mice. Oocyte quantity and quality were assessed following superovulation, including the analysis of spindle morphology, chromatin configuration, and maturation markers. In vitro maturation assays were conducted to evaluate the developmental competence of oocytes exposed to fluoxetine. Finally, the impact of fluoxetine on blastocyst formation, litter size, offspring growth, and ovarian reserve was examined. The results show that fluoxetine treatment reduced the number of ovulated oocytes but did not significantly affect oocyte quality or meiotic spindle formation. Fluoxetine exposure impaired cytoplasmic maturation at the germinal vesicle stage, resulting in a lower proportion of fully mature oocytes and reduced in vitro maturation efficiency. While blastocyst numbers were modestly reduced in fluoxetine-treated mice, litter size and offspring ovarian reserve were unaffected. Unexpectedly, offspring of fluoxetine-treated mothers exhibited increased body weight. These findings suggest that while fluoxetine may impair oocyte developmental competence through disruptions in cytoplasmic maturation, it does not severely compromise overall reproductive outcomes or offspring fertility. Full article
(This article belongs to the Special Issue Developmental Biology: Computational and Experimental Approaches, 2nd Edition)
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Review

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20 pages, 1602 KiB  
Review
Insights on SNPs of Human Activation-Induced Cytidine Deaminase AID
by Ekaterina A. Koveshnikova and Aleksandra A. Kuznetsova
Int. J. Mol. Sci. 2025, 26(13), 6107; https://doi.org/10.3390/ijms26136107 (registering DOI) - 25 Jun 2025
Abstract
DNA-deaminase AID plays a pivotal role in adaptive immunity, antibody diversification and epigenetic regulation. AID catalyzes cytidine deamination in immunoglobulin genes, facilitating somatic hypermutation (SHM), class-switch recombination (CSR) and gene conversion (GC). However, the dysregulation of AID activity can lead to oncogenic mutations [...] Read more.
DNA-deaminase AID plays a pivotal role in adaptive immunity, antibody diversification and epigenetic regulation. AID catalyzes cytidine deamination in immunoglobulin genes, facilitating somatic hypermutation (SHM), class-switch recombination (CSR) and gene conversion (GC). However, the dysregulation of AID activity can lead to oncogenic mutations and immune disorders such as hyper-IgM syndrome type 2 (HIGM2). At present the number of studies investigating the role of AID polymorphic variants in the promotion of pathology is low. The current review examines the structural and functional aspects of AID, focusing on the impact of amino acid substitutions—both natural polymorphisms and artificial mutations—on its catalytic activity, substrate binding and interactions with regulatory proteins. Additionally, a bioinformatic analysis of single-nucleotide polymorphisms of AID deposited in the dbSNP database was performed. SNPs leading to amino acid substitutions in the primary protein structure were analyzed. The bioinformatic analysis of SNPs in the AID gene predicts that among 208 SNPs causing amino acid substitutions in the primary protein structure, 62 substitutions may have significant negative impact on the functioning of AID. The integration of computational predictions with experimental data underscores the importance of AID regulation in maintaining immune homeostasis and highlights potential markers for immune-related pathologies. This comprehensive analysis provides insights into the molecular mechanisms of AID dysfunction and its implications for disease. Full article
(This article belongs to the Special Issue Developmental Biology: Computational and Experimental Approaches, 2nd Edition)
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