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J. Dev. Biol., Volume 13, Issue 3 (September 2025) – 10 articles

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15 pages, 5043 KiB  
Article
Drosophila COMPASS Complex Subunits Set1 and Ash2 Are Required for Oocyte Determination and Maintenance of the Synaptonemal Complex
by Brigite Cabrita, Mary Enyioko and Rui Gonçalo Martinho
J. Dev. Biol. 2025, 13(3), 30; https://doi.org/10.3390/jdb13030030 - 19 Aug 2025
Viewed by 178
Abstract
Female gametogenesis is orchestrated by dynamic epigenetic modifications. In mammals, SETDB1, a histone H3K9 methyltransferase, is required for proper meiotic progression and early embryonic development. In Drosophila, the ortholog of SETDB1 plays a critical role in germ cell differentiation, transposon silencing, and [...] Read more.
Female gametogenesis is orchestrated by dynamic epigenetic modifications. In mammals, SETDB1, a histone H3K9 methyltransferase, is required for proper meiotic progression and early embryonic development. In Drosophila, the ortholog of SETDB1 plays a critical role in germ cell differentiation, transposon silencing, and the transcriptional repression of specific germline genes during oocyte fate determination. Moreover, Polycomb group (PcG) proteins in both mammals and Drosophila are essential for primary oocyte viability and meiosis, functioning through the silencing of early prophase I genes during later stages of prophase. While the repressive roles of epigenetic regulators in both Drosophila and mammalian oogenesis are well characterized, the functions of epigenetic activators remain less defined. Gene expression is controlled by the opposing activities of PcG and Trithorax group (TrxG) proteins, with the latter constituting a diverse family of chromatin remodelling factors that include H3K4 methyltransferases. In Drosophila, SET domain containing 1 (Set1)—the ortholog of mammalian SETD1A/B—acts as the primary regulator of global H3K4me2/3 levels. Set1 is critical for germline stem cell (GSC) self-renewal, functioning through both cell-autonomous and non-cell-autonomous mechanisms, with its depletion in the germline resulting in a progressive loss of GSC. More recently, Set1 has been implicated in germline cyst differentiation, although the mechanisms underlying this role remain poorly understood due to the complexity of the observed phenotypes. To investigate this, we analyzed ovaries from recently eclosed females in which Set1 and its highly conserved COMPASS partner, absent, small, or homeotic discs 2 (Ash2), were depleted—thus minimizing the confounding effects from GSC loss. We observed striking defects in both oocyte determination and Synaptonemal Complex (SC) integrity in one- to two-day-old females, within otherwise normal egg chambers. Interestingly, while defects in oocyte fate and oocyte–chromatin architecture were partially recovered in older egg chambers, SC integrity remained compromised. These findings suggest a critical window for SC assembly during germline cyst differentiation, after which this assembly cannot occur. Full article
(This article belongs to the Special Issue Feature Papers in Journal of Developmental Biology 2025)
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14 pages, 3175 KiB  
Article
GLP-1-Mediated Pregnancy and Neonatal Complications in Mice
by Rajalakshmi Ramamoorthy, Arianna K. Carden, Hussain Hussain, Brian Z. Druyan, Ping Ping Chen, Rima Hajjar, Carmen Fernandez, Nila Elumalai, Amirah B. Rashed, Karen Young, Anna Rosa Speciale, Emily M. West, Staci Marbin, Bradley Safro, Ian J. Bishop, Arumugam R. Jayakumar, Luis Sanchez-Ramos and Michael J. Paidas
J. Dev. Biol. 2025, 13(3), 29; https://doi.org/10.3390/jdb13030029 - 15 Aug 2025
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Abstract
Glucagon-like peptide 1 (GLP-1), a hormone derived from the proglucagon gene, regulates various physiological processes; however, its impact on pregnancy outcomes remains poorly understood. Assessing the effects of GLP-1 on neonates is vital as GLP-1 is increasingly administered during pregnancy. This study evaluates [...] Read more.
Glucagon-like peptide 1 (GLP-1), a hormone derived from the proglucagon gene, regulates various physiological processes; however, its impact on pregnancy outcomes remains poorly understood. Assessing the effects of GLP-1 on neonates is vital as GLP-1 is increasingly administered during pregnancy. This study evaluates the effect of GLP-1 exposure on maternal complications and neonatal defects in mice. Pregnant female A/J mice received subcutaneous injections of recombinant GLP-1 (rGLP-1; 1000 nmol/kg) on embryonic day 1 (EP, early pregnancy) or day 15 (E15, late pregnancy). Maternal and neonatal body weights, morphology, and mortality were recorded, and mRNA sequencing was conducted to analyze gene expression in neonatal tissues. Maternal body weight decreased following rGLP-1 exposure, and pups born to both the early and late exposure groups experienced significant weight loss. Pups in the late exposure group exhibited uniform skin detachment and a dramatically higher mortality rate than those born to the early exposure group. Further, RT-PCR analysis confirms the significantly increased expression of selected genes in the skin and associated pathogenesis. RNA sequencing of pups’ skin, brain, lung, and liver tissues from the late exposure group showed altered gene expression. Since maternal weight loss, increased neonatal mortality, and altered gene expression have been observed, GLP-1 receptor agonists (GLP-1RAs) should be avoided during pregnancy. Full article
(This article belongs to the Special Issue Embryonic Development and Regenerative Medicine)
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12 pages, 545 KiB  
Review
The Congenital Malformation of the Interatrial Septum—A Review of Its Development and Embryology with Clinical Implications
by Rui Caetano Oliveira, Paula Martins and Maria de Fátima Martins
J. Dev. Biol. 2025, 13(3), 28; https://doi.org/10.3390/jdb13030028 - 5 Aug 2025
Viewed by 369
Abstract
The development process of the heart and cardiovascular system is fundamental in human development and highly regulated by genetic factors. This process needs to be highly regulated to prevent malformations. Nevertheless, some heart defects may be identified, especially with modern imaging methodology. Atrial [...] Read more.
The development process of the heart and cardiovascular system is fundamental in human development and highly regulated by genetic factors. This process needs to be highly regulated to prevent malformations. Nevertheless, some heart defects may be identified, especially with modern imaging methodology. Atrial septal defects (ASDs) are particularly common. Understanding the mechanisms involved in ASD formation is fundamental for developing new treatment strategies. In this article, we explore cardiac development and embryology, with a focus on atrial septal defects and their clinical implications. Full article
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12 pages, 2254 KiB  
Article
Evolution of the Jawed Vertebrate (Gnathostomata) Stomach Through Gene Repertoire Loss: Findings from Agastric Species
by Jackson Dann and Frank Grützner
J. Dev. Biol. 2025, 13(3), 27; https://doi.org/10.3390/jdb13030027 - 5 Aug 2025
Viewed by 364
Abstract
The stomach has been a highly conserved organ throughout vertebrate evolution; however, there are now over 20 lineages composed of monotremes, lungfish and teleost fish displaying a secondary loss of stomach function and morphology. This “agastric phenotype” has evolved convergently and is typified [...] Read more.
The stomach has been a highly conserved organ throughout vertebrate evolution; however, there are now over 20 lineages composed of monotremes, lungfish and teleost fish displaying a secondary loss of stomach function and morphology. This “agastric phenotype” has evolved convergently and is typified by a loss of gastric glands and gastric acid secretion and a near-to-complete loss of storage capacity of the stomach. All agastric species have lost the genes for gastric enzymes (Pga and Pgc) and proton pump subunits (Atp4a and Atp4b), and gastrin (Gast) has been lost in monotremes. As a key gastric hormone, the conservation of gastrin has not yet been investigated in the lungfish or agastric teleosts, and it is unclear how the loss of gastrin affects the evolution and selection of the native receptor (Cckbr), gastrin-releasing peptide (Grp) and gastrin-releasing peptide receptor (Grpr) in vertebrates. Furthermore, there are still many genes implicated in gastric development and function which have yet to be associated with the agastric phenotype. We analysed the evolution, selection and conservation of the gastrin pathway and a novel gastric gene repertoire (Gkn1, Gkn2, Tff1, Tff2, Vsig1 and Anxa10) to determine the correlation with the agastric phenotype. We found that the loss of gastrin or its associated genes does not correlate with the agastric phenotype, and their conservation is due to multiple pleiotropic roles throughout vertebrate evolution. We found a loss of the gastric gene repertoire in the agastric phenotype, except in the echidna, which retained several genes (Gkn1, Tff2 and Vsig1). Our findings suggest that the gastrin physiological pathway evolved differently in pleiotropic roles throughout vertebrate evolution and support the convergent evolution of the agastric phenotype through shared independent gene-loss events. Full article
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18 pages, 3973 KiB  
Article
Identification and Characterization of Static Craniofacial Defects in Pre-Metamorphic Xenopus laevis Tadpoles
by Emilie Jones, Jay Miguel Fonticella and Kelly A. McLaughlin
J. Dev. Biol. 2025, 13(3), 26; https://doi.org/10.3390/jdb13030026 - 25 Jul 2025
Viewed by 436
Abstract
Craniofacial development is a complex, highly conserved process involving multiple tissue types and molecular pathways, with perturbations resulting in congenital defects that often require invasive surgical interventions to correct. Remarkably, some species, such as Xenopus laevis, can correct some craniofacial abnormalities during [...] Read more.
Craniofacial development is a complex, highly conserved process involving multiple tissue types and molecular pathways, with perturbations resulting in congenital defects that often require invasive surgical interventions to correct. Remarkably, some species, such as Xenopus laevis, can correct some craniofacial abnormalities during pre-metamorphic stages through thyroid hormone-independent mechanisms. However, the full scope of factors mediating remodeling initiation and coordination remain unclear. This study explores the differential remodeling responses of craniofacial defects by comparing the effects of two pharmacological agents, thioridazine-hydrochloride (thio) and ivermectin (IVM), on craniofacial morphology in X. laevis. Thio-exposure reliably induces a craniofacial defect that can remodel in pre-metamorphic animals, while IVM induces a permanent, non-correcting phenotype. We examined developmental changes from feeding stages to hindlimb bud stages and mapped the effects of each agent on the patterning of craniofacial tissue types including: cartilage, muscle, and nerves. Our findings reveal that thio-induced craniofacial defects exhibit significant consistent remodeling, particularly in muscle, with gene expression analysis revealing upregulation of key remodeling genes, matrix metalloproteinases 1 and 13, as well as their regulator, prolactin.2. In contrast, IVM-induced defects show no significant remodeling, highlighting the importance of specific molecular and cellular factors in pre-metamorphic craniofacial correction. Additionally, unique neuronal profiles suggest a previously underappreciated role for the nervous system in tissue remodeling. This study provides novel insights into the molecular and cellular mechanisms underlying craniofacial defect remodeling and lays the groundwork for future investigations into tissue repair in vertebrates. Full article
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15 pages, 4716 KiB  
Article
Deletion of Ptpmt1 by αMHC-Cre in Mice Results in Left Ventricular Non-Compaction
by Lei Huang, Maowu Cao, Xiangbin Zhu, Na Li, Can Huang, Kunfu Ouyang and Ze'e Chen
J. Dev. Biol. 2025, 13(3), 25; https://doi.org/10.3390/jdb13030025 - 18 Jul 2025
Viewed by 462
Abstract
Background: Left ventricular non-compaction cardiomyopathy (LVNC) is a congenital heart disease characterized by abnormal prenatal development of the left ventricle that has an aberrantly thick trabecular layer and a thinner compacted myocardial layer. However, the underlying molecular mechanisms of LVNC regulated by mitochondrial [...] Read more.
Background: Left ventricular non-compaction cardiomyopathy (LVNC) is a congenital heart disease characterized by abnormal prenatal development of the left ventricle that has an aberrantly thick trabecular layer and a thinner compacted myocardial layer. However, the underlying molecular mechanisms of LVNC regulated by mitochondrial phosphatase genes remain largely unresolved. Methods: We generated a mouse model with cardiac-specific deletion (CKO) of Ptpmt1, a type of mitochondrial phosphatase gene, using the αMHC-Cre, and investigated the effects of cardiac-specific Ptpmt1 deficiency on cardiac development. Morphological, histological, and immunofluorescent analyses were conducted in Ptpmt1 CKO and littermate controls. A transcriptional atlas was identified by RNA sequencing (RNA-seq) analysis. Results: We found that CKO mice were born at the Mendelian ratio with normal body weights. However, most of the CKO mice died within 24 h after birth, developing spontaneous ventricular tachycardia. Morphological and histological analysis further revealed that newborn CKO mice developed an LVNC phenotype, evidenced by a thicker trabecular layer and a thinner myocardium layer, when compared with the littermate control. We then examined the embryonic hearts and found that such an LVNC phenotype could also be observed in CKO hearts at E15.5 but not at E13.5. We also performed the EdU incorporation assay and demonstrated that cardiac cell proliferation in both myocardium and trabecular layers was significantly reduced in CKO hearts at E15.5, which is also consistent with the dysregulation of genes associated with heart development and cardiomyocyte proliferation in CKO hearts at the same stage, as revealed by both the transcriptome analysis and the quantitative real-time PCR. Deletion of Ptpmt1 in mouse cardiomyocytes also induced an increase in phosphorylated eIF2α and ATF4 levels, indicating a mitochondrial stress response in CKO hearts. Conclusions: Our results demonstrated that Ptpmt1 may play an essential role in regulating left ventricular compaction during mouse heart development. Full article
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20 pages, 3164 KiB  
Review
Is Hydra Axis Definition a Fluctuation-Based Process Picking Up External Cues?
by Mikhail A. Zhukovsky, Si-Eun Sung and Albrecht Ott
J. Dev. Biol. 2025, 13(3), 24; https://doi.org/10.3390/jdb13030024 - 17 Jul 2025
Viewed by 602
Abstract
Axis definition plays a key role in the establishment of animal body plans, both in normal development and regeneration. The cnidarian Hydra can re-establish its simple body plan when regenerating from a random cell aggregate or a sufficiently small tissue fragment. At the [...] Read more.
Axis definition plays a key role in the establishment of animal body plans, both in normal development and regeneration. The cnidarian Hydra can re-establish its simple body plan when regenerating from a random cell aggregate or a sufficiently small tissue fragment. At the beginning of regeneration, a hollow cellular spheroid forms, which then undergoes symmetry breaking and de novo body axis definition. In the past, we have published related work in a physics journal, which is difficult to read for scientists from other disciplines. Here, we review our work for readers not so familiar with this type of approach at a level that requires very little knowledge in mathematics. At the same time, we present a few aspects of Hydra biology that we believe to be linked to our work. These biological aspects may be of interest to physicists or members of related disciplines to better understand our approach. The proposed theoretical model is based on fluctuations of gene expression that are triggered by mechanical signaling, leading to increasingly large groups of cells acting in sync. With a single free parameter, the model quantitatively reproduces the experimentally observed expression pattern of the gene ks1, a marker for ‘head forming potential’. We observed that Hydra positions its axis as a function of a weak temperature gradient, but in a non-intuitive way. Supposing that a large fluctuation including ks1 expression is locked to define the head position, the model reproduces this behavior as well—without further changes. We explain why we believe that the proposed fluctuation-based symmetry breaking process agrees well with recent experimental findings where actin filament organization or anisotropic mechanical stimulation act as axis-positioning events. The model suggests that the Hydra spheroid exhibits huge sensitivity to external perturbations that will eventually position the axis. Full article
(This article belongs to the Special Issue Feature Papers in Journal of Developmental Biology 2025)
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14 pages, 1891 KiB  
Article
HP1-Mediated Silencing of the Doublesex1 Gene for Female Determination in the Crustacean Daphnia magna
by Junya Leim, Nikko Adhitama, Quang Dang Nong, Pijar Religia, Yasuhiko Kato and Hajime Watanabe
J. Dev. Biol. 2025, 13(3), 23; https://doi.org/10.3390/jdb13030023 - 3 Jul 2025
Viewed by 2384
Abstract
The crustacean Daphnia magna produces genetically identical females and males by parthenogenesis. Males are produced in response to environmental cues including crowding and lack of food. For male development, the DM-domain containing transcription factor Doublesex1 (DSX1) is expressed spatiotemporally in male-specific traits and [...] Read more.
The crustacean Daphnia magna produces genetically identical females and males by parthenogenesis. Males are produced in response to environmental cues including crowding and lack of food. For male development, the DM-domain containing transcription factor Doublesex1 (DSX1) is expressed spatiotemporally in male-specific traits and orchestrates male trait formation in both somatic and gonadal tissues. However, it remains unknown how the dsx1 gene is silenced in females to avoid male trait development. Heterochromatin Protein 1 (HP1) plays a crucial role in epigenetic gene silencing during developmental processes. Here we report the identification of four HP1 orthologs in D. magna. None of these orthologs exhibited sexually dimorphic expression, and among them, HP1-1 was most abundantly expressed during embryogenesis. The knock-down of HP1-1 in female embryos led to the derepression of dsx1 in the male-specific traits, resulting in the development of male characteristics, such as the elongation of the first antennae. These results suggest that HP1-1 silences dsx1 for female development while environmental cues unlock this silencing to induce male production. We infer the HP1-dependent formation of a sex-specific chromatin structure on the dsx1 locus is a key process in the environmental sex determination of D. magna. Full article
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25 pages, 5014 KiB  
Article
Investigating Psychopharmaceutical Effects on Early Vertebrate Development Using a Zebrafish Model System
by Nathan Zimmerman, Aaron Marta, Carly Baker, Zeljka Korade, Károly Mirnics and Annemarie Shibata
J. Dev. Biol. 2025, 13(3), 22; https://doi.org/10.3390/jdb13030022 - 27 Jun 2025
Viewed by 564
Abstract
Cholesterol homeostasis is necessary for normal vertebrate development. The disruption of cholesterol homeostasis can cause abnormal body and nervous system development and lead to dysfunctional behavior and increased mortality. Commonly prescribed psychopharmaceuticals can alter cholesterol synthesis and may disrupt early vertebrate development. A [...] Read more.
Cholesterol homeostasis is necessary for normal vertebrate development. The disruption of cholesterol homeostasis can cause abnormal body and nervous system development and lead to dysfunctional behavior and increased mortality. Commonly prescribed psychopharmaceuticals can alter cholesterol synthesis and may disrupt early vertebrate development. A high-throughput vertebrate zebrafish model system was used to test the hypothesis that exposure to psychopharmaceutical medications alters cholesterol biosynthesis and disrupts gene transcription, early whole-body and brain development, and nervous system function, resulting in abnormal behavior. Exposure to cariprazine, aripiprazole, trazodone, and AY9944 increased 7-dehydrocholesterol levels compared to vehicle-treated zebrafish. Significant differences in disease-associated gene expression, brain structure, and functional behaviors were observed in psychopharmaceutical and AY9944-treated zebrafish compared to controls. These data reveal that the high-throughput zebrafish model system can discern psychopharmaceutical effects on cholesterol synthesis, gene transcription, and key features of early vertebrate development that influences behavior. Full article
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14 pages, 1562 KiB  
Article
Drosophila Males Differentially Express Small Proteins Regulating Stem Cell Division Frequency in Response to Mating
by Manashree S. Malpe, Leon F. McSwain, Heath M. Aston, Karl A. Kudyba, Chun Ng, Megan P. Wright and Cordula Schulz
J. Dev. Biol. 2025, 13(3), 21; https://doi.org/10.3390/jdb13030021 - 23 Jun 2025
Viewed by 567
Abstract
The germline stem cells (GSCs) in the male gonad of Drosophila can increase their division frequency in response to a demand for more sperm caused by repeated mating. However, the molecules and mechanisms regulating and mediating this response have yet to be fully [...] Read more.
The germline stem cells (GSCs) in the male gonad of Drosophila can increase their division frequency in response to a demand for more sperm caused by repeated mating. However, the molecules and mechanisms regulating and mediating this response have yet to be fully explored. Here, we present the results of a transcriptome analysis comparing expression from the testis tips from non-mated and mated males. An overlapping set of 18 differentially expressed genes (DEGs) from two independent wild-type (wt) strains revealed that the majority of the DEGs encode secreted proteins, which suggests roles for them in cell–cell interactions. Consistent with a role for secretion in regulating GSC divisions, knocking down Signal Recognition Particle (SRP) components within the germline cells using RNA Interference (RNAi), prevented the increase in GSC division frequency in response to mating. The major class of DEGs encodes polypeptides below the size of 250 amino acids, also known as small proteins. Upon reducing germline expression of small proteins, males no longer increased GSC division frequency after repeated mating. We hypothesize that mating induces cellular interactions via small proteins to ensure continued GSC divisions for the production of sperm. Full article
(This article belongs to the Special Issue Drosophila in Developmental Biology—Past, Present and Future)
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