Developmental Biology Research Research Articles

Editorial: Developmental biology and endocrine research for a successful pregnancy

Editorial: Developmental biology and endocrine research for a successful pregnancy

The System of Analysis for Mitosis and Meiosis

In cellular biology, mitosis and meiosis are essential processes that control cell division and genetic transmission. Numerous disciplines, including developmental biology, genetics, and cancer research, depend on an understanding of these processes. An innovative method for examining these processes is the Mitosis and Meiosis Analysis System (MMAS), which uses artificial intelligence (AI) methods for automated image analysis. An overview of MMAS, including its history, elements, and uses, is given in this paper. We go over how to accurately detect, classify, and quantify mitotic and meiotic events from microscopy images by integrating machine learning models, deep learning frameworks, and advanced image processing algorithms into MMAS. In addition, we discuss how MMAS is used in developmental biology, genetics, and cancer research, among other fields of cellular biology study. By automating image analysis and offering insightful information about cellular dynamics, MMAS is a potent tool that can speed up cellular biology research and deepen our understanding of basic biological processes.

The System of Analysis for Mitosis and Meiosis

In cellular biology, mitosis and meiosis are essential processes that control cell division and genetic transmission. Numerous disciplines, including developmental biology, genetics, and cancer research, depend on an understanding of these processes. An innovative method for examining these processes is the Mitosis and Meiosis Analysis System (MMAS), which uses artificial intelligence (AI) methods for automated image analysis. An overview of MMAS, including its history, elements, and uses, is given in this paper. We go over how to accurately detect, classify, and quantify mitotic and meiotic events from microscopy images by integrating machine learning models, deep learning frameworks, and advanced image processing algorithms into MMAS. In addition, we discuss how MMAS is used in developmental biology, genetics, and cancer research, among other fields of cellular biology study. By automating image analysis and offering insightful information about cellular dynamics, MMAS is a potent tool that can speed up cellular biology research and deepen our understanding of basic biological processes.

Identification, Expression and Evolutional Analysis of Two cyp19-like Genes in Amphioxus.

The mechanism of sex determination and differentiation in animals remains a central focus of reproductive and developmental biology research, and the regulation of sex differentiation in amphioxus remains poorly understood. Cytochrome P450 Family 19 Subfamily A member 1 (CYP19A1) is a crucial sex differentiation gene that catalyzes the conversion of androgens into estrogens. In this study, we identified two aromatase-like genes in amphioxus: cyp19-like1 and cyp19-like2. The cyp19-like1 is more primitive and may represent the ancestral form of cyp19 in zebrafish and other vertebrates, while the cyp19-like2 is likely the result of gene duplication within amphioxus. To gain further insights into the expression level of these two aromatase-like, we examined their expression in different tissues and during different stages of gonad development. While the expression level of the two genes differs in tissues, both are highly expressed in the gonad primordium and are primarily localized to microsomal membrane systems. However, as development proceeds, their expression level decreases significantly. This study enhances our understanding of sex differentiation mechanisms in amphioxus and provides valuable insights into the formation and evolution of sex determination mechanisms in vertebrates.

Revealing mitf functions and visualizing allografted tumor metastasis in colorless and immunodeficient Xenopus tropicalis

Transparent immunodeficient animal models not only enhance in vivo imaging investigations of visceral organ development but also facilitate in vivo tracking of transplanted tumor cells. However, at present, transparent and immunodeficient animal models are confined to zebrafish, presenting substantial challenges for real-time, in vivo imaging studies addressing specific biological inquiries. Here, we employed a mitf−/−/prkdc−/−/il2rg−/− triple-knockout strategy to establish a colorless and immunodeficient amphibian model of Xenopus tropicalis. By disrupting the mitf gene, we observed the loss of melanophores, xanthophores, and granular glands in Xenopus tropicalis. Through the endogenous mitf promoter to drive BRAFV600E expression, we confirmed mitf expression in melanophores, xanthophores and granular glands. Moreover, the reconstruction of the disrupted site effectively reinstated melanophores, xanthophores, and granular glands, further highlighting the crucial role of mitf as a regulator in their development. By crossing mitf−/− frogs with prkdc−/−/il2rg−/− frogs, we generated a mitf−/−/prkdc−/−/il2rg−/−Xenopus tropicalis line, providing a colorless and immunodeficient amphibian model. Utilizing this model, we successfully observed intravital metastases of allotransplanted xanthophoromas and migrations of allotransplanted melanomas. Overall, colorless and immunodeficient Xenopus tropicalis holds great promise as a valuable platform for tumorous and developmental biology research.

Mesenchyme instructs growth while epithelium directs branching in the mouse mammary gland.

The mammary gland is a unique organ that undergoes dynamic alterations throughout a female's reproductive life, making it an ideal model for developmental, stem cell and cancer biology research. Mammary gland development begins in utero and proceeds via a quiescent bud stage before the initial outgrowth and subsequent branching morphogenesis. How mammary epithelial cells transit from quiescence to an actively proliferating and branching tissue during embryogenesis and, importantly, how the branch pattern is determined remain largely unknown. Here, we provide evidence indicating that epithelial cell proliferation and onset of branching are independent processes, yet partially coordinated by the Eda signaling pathway. Through heterotypic and heterochronic epithelial-mesenchymal recombination experiments between mouse mammary and salivary gland tissues and ex vivo live imaging, we demonstrate that unlike previously concluded, the mode of branching is an intrinsic property of the mammary epithelium whereas the pace of growth and the density of ductal tree are determined by the mesenchyme. Transcriptomic profiling and ex vivo and in vivo functional studies in mice disclose that mesenchymal Wnt/ß-catenin signaling, and in particular IGF-1 downstream of it critically regulate mammary gland growth. These results underscore the general need to carefully deconstruct the different developmental processes producing branched organs.

Role and ethics of cynomolgus monkey (Macaca fascicularis) blastoids in primate developmental biology research.

This review on cynomolgus monkey (Macaca fascicularis) blastoids discusses a breakthrough in modeling early non-human primate embryogenesis, offering insights into embryonic development and implantation processes. It acknowledges ethical challenges and animal welfare considerations in developmental biology, suggests potential applications in human reproductive medicine, and highlights the need for ongoing ethical and technical refinement.

Facilitating long-term cell examinations and time-lapse recordings in cell biology research with CO2 mini-incubators

In recent years, microscopy has revolutionized the study of dynamic living cells. However, performing long-term live cell imaging requires stable environmental conditions such as temperature, pH, and humidity. While standard incubators have traditionally provided these conditions, other solutions, like stagetop incubators are available. To further enhance the accessibility of stable cell culture environments for live cell imaging, we developed a portable CO2 cell culture mini-incubator that can be easily adapted to any x–y inverted microscope stage, enabling long-term live cell imaging. This mini-incubator provides and maintains stable environmental conditions and supports cell viability comparable to standard incubators. Moreover, it allows for parallel experiments in the same environment, saving both time and resources. To demonstrate its functionality, different cell lines (VERO and MDA-MB-231) were cultured and evaluated using various assays, including crystal violet staining, MTT, and flow cytometry tests to assess cell adhesion, viability, and apoptosis, respectively. Time-lapse imaging was performed over an 85-h period with MDA-MB-231 cells cultured in the mini-incubator. The results indicate that this device is a viable solution for long-term imaging and can be applied in developmental biology, cell biology, and cancer biology research where long-term time-lapse recording is required.

Generation of canine induced pluripotent stem cells under feeder-free conditions using Sendai virus vector encoding six canine reprogramming factors

Although it is in its early stages, canine induced pluripotent stem cells (ciPSCs) hold great potential for innovative translational research in regenerative medicine, developmental biology, drug screening, and disease modeling. However, almost all ciPSCs were generated from fibroblasts, and available canine cell sources for reprogramming are still limited. Furthermore, no report is available to generate ciPSCs under feeder-free conditions because of their low reprogramming efficiency. Here, we reanalyzed canine pluripotency-associated genes and designed canine LIN28A, NANOG, OCT3/4, SOX2, KLF4, and C-MYC encoding Sendai virus vector, called 159cf. and 162cf. We demonstrated that not only canine fibroblasts but also canine urine-derived cells, which can be isolated using a noninvasive and straightforward method, were successfully reprogrammed with or without feeder cells. ciPSCs existed in undifferentiated states, differentiating into the three germ layers invitro and invivo. We successfully generated ciPSCs under feeder-free conditions, which can promote studies in veterinary and consequently human regenerative medicines.

Immunohistochemical characterisation of the adult Nothobranchius furzeri intestine.

Nothobranchius furzeri is emerging as an exciting vertebrate organism in the field of biomedicine, developmental biology and ecotoxicology research. Its short generation time, compressed lifespan and accelerated ageing make it a versatile model for longitudinal studies with high traceability. Although in recent years the use of this model has increased enormously, there is still little information on the anatomy, morphology and histology of its main organs. In this paper, we present a description of the digestive system of N. furzeri, with emphasis on the intestine. We note that the general architecture of the intestinal tissue is shared with other vertebrates, and includes a folding mucosa, an outer muscle layer and a myenteric plexus. By immunohistochemical analysis, we reveal that the mucosa harbours the same type of epithelial cells observed in mammals, including enterocytes, goblet cells and enteroendocrine cells, and that the myenteric neurons express neurotransmitters common to other species, such as serotonin, substance P and tyrosine hydroxylase. In addition, we detect the presence of a proliferative compartment at the base of the intestinal folds. The description of the normal intestinal morphology provided here constitutes a baseline information to contrast with tissue alterations in future lines of research assessing pathologies, ageing-related diseases or damage caused by toxic agents.

Prediction and Analysis of Transcription Factor Binding Sites: Practical Examples and Case Studies Using R Programming.

Transcription factors (TFs) bind to specific regions of DNA known as transcription factor binding sites (TFBSs) and modulate gene expression by interacting with the transcriptional machinery. TFBSs are typically located upstream of target genes, within a few thousand base pairs of the transcription start site. The binding of TFs to TFBSs influences the recruitment of the transcriptional machinery, thereby regulating gene transcription in a precise and specific manner. This chapter provides practical examples and case studies demonstrating the extraction of upstream gene regions from the genome, identification of TFBSs using PWMEnrich R/Bioconductor package, interpretation of results, and preparation of publication-ready figures and tables. The EOMES promoter is used as a case study for single DNA sequence analysis, revealing potential regulation by the LHX9-FOXP1 complex during embryonic development. Additionally, an example is presented on how to investigate TFBSs in the upstream regions of a group of genes, using a case study of differentially expressed genes in response to human parainfluenza virus type 1 (HPIV1) infection and interferon-beta. Key regulators identified in this context include the STAT1:STAT2 heterodimer and interferon regulatory factor family proteins. The presented protocol is designed to be accessible to individuals with basic computer literacy. Understanding the interactions between TFs and TFBSs provides insights into the complex transcriptional regulatory networks that govern gene expression, with broad implications for several fields such as developmental biology, immunology, and disease research.

An interview with Aimee Jaramillo-Lambert.

Aimee Jaramillo-Lambert is currently an Assistant Professor at the University of Delaware. Aimee was awarded the Society for Developmental Biology 2023 Elizabeth D. Hay New Investigator Award in recognition of her outstanding research in developmental biology during the early stages of her independent career. We caught up with Aimee over a video call to talk about her research into sexual reproduction in Caenorhabditis elegans, the importance of mentorship, and what drives her work in diversity, equity and inclusion.

Striped Expression of Leucine-Rich Repeat Proteins Coordinates Cell Intercalation and Compartment Boundary Formation in the Early Drosophila Embryo.

Planar polarity is a commonly observed phenomenon in which proteins display a consistent asymmetry in their subcellular localization or activity across the plane of a tissue. During animal development, planar polarity is a fundamental mechanism for coordinating the behaviors of groups of cells to achieve anisotropic tissue remodeling, growth, and organization. Therefore, a primary focus of developmental biology research has been to understand the molecular mechanisms underlying planar polarity in a variety of systems to identify conserved principles of tissue organization. In the early Drosophila embryo, the germband neuroectoderm epithelium rapidly doubles in length along the anterior-posterior axis through a process known as convergent extension (CE); it also becomes subdivided into tandem tissue compartments through the formation of compartment boundaries (CBs). Both processes are dependent on the planar polarity of proteins involved in cellular tension and adhesion. The enrichment of actomyosin-based tension and adherens junction-based adhesion at specific cell-cell contacts is required for coordinated cell intercalation, which drives CE, and the creation of highly stable cell-cell contacts at CBs. Recent studies have revealed a system for rapid cellular polarization triggered by the expression of leucine-rich-repeat (LRR) cell-surface proteins in striped patterns. In particular, the non-uniform expression of Toll-2, Toll-6, Toll-8, and Tartan generates local cellular asymmetries that allow cells to distinguish between cell-cell contacts oriented parallel or perpendicular to the anterior-posterior axis. In this review, we discuss (1) the biomechanical underpinnings of CE and CB formation, (2) how the initial symmetry-breaking events of anterior-posterior patterning culminate in planar polarity, and (3) recent advances in understanding the molecular mechanisms downstream of LRR receptors that lead to planar polarized tension and junctional adhesion.

An interview with Hernan Garcia.

Hernan Garcia is a Principal Investigator and Associate Professor of Genetics, Genomics and Development and Physics at the University of California, Berkley (USA). His research aims to understand, predict and control developmental programs. In 2022, Hernan was awarded the Elizabeth D. Hay New Investigator award by the Society for Developmental Biology (SDB) recognizing his outstanding research in developmental biology. We spoke to Hernan to learn more about his education, career path and approach to running a lab.

The constitutively active pSMAD2/3 relatively improves the proliferation of chicken primordial germ cells

AbstractIn many multicellular organisms, mature gametes originate from primordial germ cells (PGCs). Improvements in the culture of PGCs are important not only for developmental biology research, but also for preserving endangered species, and for genome editing and transgenic animal technologies. SMAD2/3 appear to be powerful regulators of gene expression; however, their potential positive impact on the regulation of PGC proliferation has not been taken into consideration. Here, the effect of TGF‐β signaling as the upstream activator of SMAD2/3 transcription factors was evaluated on chicken PGCs' proliferation. For this, chicken PGCs at stages 26−28 Hamburger−Hamilton were obtained from the embryonic gonadal regions and cultured on different feeders or feeder‐free substrates. The results showed that TGF‐β signaling agonists (IDE1 and Activin‐A) improved PGC proliferation to some extent while treatment with SB431542, the antagonist of TGF‐β, disrupted PGCs' proliferation. However, the transfection of PGCs with constitutively active SMAD2/3 (SMAD2/3CA) resulted in improved PGC proliferation for more than 5 weeks. The results confirmed the interactions between overexpressed SMAD2/3CA and pluripotency‐associated genes NANOG, OCT4, and SOX2. According to the results, the application of SMAD2/3CA could represent a step toward achieving an efficient expansion of avian PGCs.

Lifting the cloche: Jeroen Bakkers interviews Didier Stainier.

Didier Stainier is Director of the Department of Developmental Genetics at the Max Planck Institute for Heart and Lung Research in Bad Nauheim, Germany. He became acquainted with the zebrafish model as a PhD student in Walter Gilbert's lab at Harvard, which motivated him to champion the use of this powerful model organism to study heart development as a postdoctoral fellow with Mark Fishman at Massachusetts General Hospital. Although his scientific focus has expanded significantly since then, zebrafish modelling and heart development and regeneration remain key topics in his research. The developmental biology and zebrafish modelling communities have embraced him as an inspiring mentor and advocate for basic research. Jeroen Bakkers is a group leader at the Hubrecht Institute for Developmental Biology and Stem Cell Research and Professor of Molecular Cardiogenetics at the University Medical Center Utrecht, The Netherlands. Jeroen did hid PhD with Herman Spaink at Leiden University, The Netherlands. A short visit to Massachusetts Institute of Technology during his doctoral training introduced him to the zebrafish model, which he applied to his PhD project. Zebrafish development remained the focus of his career, including during his postdoctoral training in the lab of Matthias Hammerschmidt at the Max Planck Institute of Immunology and Epigenetics in Freiburg and in his own lab at the Hubrecht Institute, where his group uses this powerful model organism to investigate cardiac development, disease and regeneration. Jeroen and Didier met up at a recent conference to talk about their shared interest in cardiac regeneration, a zebrafish mutant with a curious name and Didier's commitment to mentorship.

Practical pursuit in stem cell biology: Innovation, translation, and incomplete theorization

This paper aims to contribute to the study of practical pursuit-worthiness in science by engaging with a case in therapeutic stem cell biology. Induced pluripotent stem cell (iPSC) research emerged from research in developmental biology and the molecular biology of cell fate conversion. It took on practical significance when proposed as an alternative to therapeutic stem cell research that used human embryonic stem cells. The supposed ability of iPSC research to tackle ethical and regulatory constraints on research at the beginning of the twentieth century was a central part of the heuristic assessment of iPSC. However, the development and transfer of knowledge from experimental and theoretical biology to preclinical pursuit conflicted with the framing of biomedical innovation in public policy. The framing of innovation operated as part of the heuristic assessment of the pursuit-worthiness of iPSCs in the United States and was characterized by attempts to underdetermine conflicting ethical and socio-economic values – to seek innovations that are “incompletely theorized” in the sense that they purportedly allow stakeholders to refrain from engagement with the divisive values that created impediments to research in stem cell biology. When conflict arose with the epistemic standards in preclinical pursuit required to ensure the safety and efficacy of biomedical innovations, it resulted in the critical appraisal of the values used to rationalize policies for the distribution of federal resources for biomedical research. The case demonstrates how non-epistemic values impinge on standards of assessment in translational science, how background assumptions about innovation can drive practical pursuit, and how conflicting values and goals in research creates an important context for the appraisal of emerging science, technology and policy.

Facile methods for reusing laboratory plastic in developmental biology experiments

Plastic pollution negatively affects ecosystems and human health globally, with single-use plastic representing the majority of marine litter in some areas. Life science laboratories prefer pristine conditions for experimental reliability and therefore make use of factory standardized single-use plastic products. This contributes to overall plastic waste in the United States and globally. Here, we investigate the potential of reusing plastic culture dishes and subsequently propose methods to mitigate single-use plastic waste in developmental biology research laboratories. We tested the efficacy of bleach and ethyl alcohol in sterilizing used dishes. We then tested the feasibility of washing and reusing plastic to culture Xenopus laevis embryos subjected to various manipulations. Cleaning and reusing laboratory plastic did not affect the development or survival of X. laevis, indicating that these cleaning methods do not adversely affect experimental outcome and can be used to sterilize plastic before reuse or recycling. Lastly, we performed a survey of various life science laboratories to estimate both waste reduction and savings associated with recycling single-use plastics. Standardization of these procedures would allow research laboratories to benefit economically while practicing environmentally conscious consumption.

Fritz Müller: 200 years of a pioneer evolutionist

Abstract Fritz Müller is known for explaining the evolutionary consequences of what is now called Müllerian mimicry, but his scientific contributions encompass a wide range of organisms and both ecological and evolutionary processes. His originality is seen in aspects as different as the discovery of the mutualistic nature of ant–fungus symbiosis, pioneering research in evolutionary developmental biology and the first mathematical treatment in a Darwinian framework. From his intimate knowledge of the natural history of Brazil and original observations of morphology and development, Müller provided evidence supporting natural selection. From the 20th century onwards, however, his scientific legacy has been re-examined only for single topics. To celebrate the bicentenary of his birth in 2022, this article briefly discusses his importance for current ecological and evolutionary knowledge.

Past, Present, and Future of Direct Cell Reprogramming.

Budding off from the broader developmental biology and stem cell research fields, cellular reprogramming is now established as a prominent discipline in its own right. Direct cell reprogramming is defined as the cell fate conversion of a somatic cell toward another identity without a pluripotent intermediate state. In addition to the opportunity for mechanistic dissection of lineage commitment in human cells, the field offer the promise of diverse applications such as for disease modeling, cell replacement therapy, regenerative medicine, and immunotherapy that have recently spurred innovation and out of the box thinking to unleash the potential of cellular plasticity.