Development Growth & Differentiation最新文献

{"title":"A resource of single-cell gene expression profiles in a planarian Dugesia japonica","authors":"Makoto Kashima,&nbsp;Rei Komura,&nbsp;Yuki Sato,&nbsp;Chikara Hashimoto,&nbsp;Hiromi Hirata","doi":"10.1111/dgd.12893","DOIUrl":"10.1111/dgd.12893","url":null,"abstract":"<p>The freshwater planarian <i>Dugesia japonica</i> maintains an abundant heterogeneous cell population called neoblasts, which include adult pluripotent stem cells. Thus, it is an excellent model organism for stem cell and regeneration research. Recently, many single-cell RNA sequencing (scRNA-seq) databases of several model organisms, including other planarian species, have become publicly available; these are powerful and useful resources to search for gene expression in various tissues and cells. However, the only scRNA-seq dataset for <i>D. japonica</i> has been limited by the number of genes detected. Herein, we collected <i>D. japonica</i> cells, and conducted an scRNA-seq analysis. A novel, automatic, iterative cell clustering strategy produced a dataset of 3,404 cells, which could be classified into 63 cell types based on gene expression profiles. We introduced two examples for utilizing the scRNA-seq dataset in this study using <i>D. japonica</i>. First, the dataset provided results consistent with previous studies as well as novel functionally relevant insights, that is, the expression of <i>DjMTA</i> and <i>DjP2X-A</i> genes in neoblasts that give rise to differentiated cells. Second, we conducted an integrative analysis of the scRNA-seq dataset and time-course bulk RNA-seq of irradiated animals, demonstrating that the dataset can help interpret differentially expressed genes captured via bulk RNA-seq. Using the R package “Seurat” and GSE223927, researchers can easily access and utilize this dataset.</p>","PeriodicalId":50589,"journal":{"name":"Development Growth & Differentiation","volume":"66 1","pages":"43-55"},"PeriodicalIF":2.5,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41153587","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Generation of translucent Xenopus tropicalis through triple knockout of pigmentation genes","authors":"Keisuke Nakajima,&nbsp;Ichiro Tazawa,&nbsp;Nobuaki Furuno","doi":"10.1111/dgd.12891","DOIUrl":"10.1111/dgd.12891","url":null,"abstract":"Amphibians generally have three types of pigment cells, namely, melanophores (black and brown), xanthophores (yellow and red), and iridophores (iridescent). Single knockout of the tyr, slc2a7, and hps6 genes in Xenopus tropicalis results in the absence of melanophores, xanthophores, and iridophores, respectively. The generation of triple‐ knockout (3KO) X. tropicalis for these three genes could allow for observation of internal organs without sacrificing the animals, which would be transparent due to the absence of pigments. In this study, we generated 3KO X. tropicalis, which is one of the most widely used model amphibians, through crossing of a slc2a7 single‐knockout frog with a tyr and hps6 double‐knockout frog, followed by intercrossing of their offspring. The 3KO tadpoles had transparent bodies like the nop mutant and the frogs had translucent bodies. This translucency allowed us to observe the heart, lungs, stomach, liver, and digestive tract through the ventral body skin without surgery. After intravital staining, 3KO X. tropicalis showed much clearer fluorescent signals of mineralized tissues compared with the wild type. These 3KO X. tropicalis provide a useful mutant line for continuous observation of internal organs and fluorescent signals in the body. In particular, such 3KO frogs would revolutionize fluorescence monitoring in transgenic tadpoles and frogs expressing fluorescent proteins.","PeriodicalId":50589,"journal":{"name":"Development Growth & Differentiation","volume":"65 9","pages":"591-598"},"PeriodicalIF":2.5,"publicationDate":"2023-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41145234","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Studying zebrafish nervous system structure and function in health and disease with electron microscopy","authors":"Sebastian M. Markert","doi":"10.1111/dgd.12890","DOIUrl":"10.1111/dgd.12890","url":null,"abstract":"<p>Zebrafish (<i>Danio rerio</i>) is a well-established model for studying the nervous system. Findings in zebrafish often inform studies on human diseases of the nervous system and provide crucial insight into disease mechanisms. The functions of the nervous system often rely on communication between neurons. Signal transduction is achieved via release of signaling molecules in the form of neuropeptides or neurotransmitters at synapses. Snapshots of membrane dynamics of these processes are imaged by electron microscopy. Electron microscopy can reveal ultrastructure and thus synaptic processes. This is crucial both for mapping synaptic connections and for investigating synaptic functions. In addition, via volumetric electron microscopy, the overall architecture of the nervous system becomes accessible, where structure can inform function. Electron microscopy is thus of particular value for studying the nervous system. However, today a plethora of electron microscopy techniques and protocols exist. Which technique is most suitable highly depends on the research question and scope as well as on the type of tissue that is examined. This review gives an overview of the electron microcopy techniques used on the zebrafish nervous system. It aims to give researchers a guide on which techniques are suitable for their specific questions and capabilities as well as an overview of the capabilities of electron microscopy in neurobiological research in the zebrafish model.</p>","PeriodicalId":50589,"journal":{"name":"Development Growth & Differentiation","volume":"65 9","pages":"502-516"},"PeriodicalIF":2.5,"publicationDate":"2023-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/dgd.12890","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41177348","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Retraction statement: Lgr5 positive stem cells sorted from small intestines of diabetic mice differentiate into higher proportion of absorptive cells and Paneth cells in vitro","authors":"","doi":"10.1111/dgd.12885","DOIUrl":"10.1111/dgd.12885","url":null,"abstract":"<p>Xian-Yang Zhong, Tao Yu, Wa Zhong, Jie-Yao Li, Zhong-Sheng Xia, Yu-Hong Yuan, Zhong Yu, Qi-Kui Chen. Lgr5 positive stem cells sorted from small intestines of diabetic mice differentiate into higher proportion of absorptive cells and Paneth cells in vitro. Development, Growth &amp; Differentiation 2015, 57 (6), pp. 453–465 (https://onlinelibrary.wiley.com/doi/10.1111/dgd.12226).</p><p>The above article, published online on 30 June 2015 in Wiley Online Library (wileyonlinelibrary.com), has been retracted by agreement between the journal's Editor in Chief Naoto Ueno and John Wiley and Sons Australia, Ltd. following concerns raised by a third party about figures within the article. During the journal's investigation into the concerns raised, the authors were not able to gather comprehensive original data for the relevant figures several years after publication. Accordingly, the editors consider that the results in the published article are unreliable and do not sufficiently support the conclusions. The co-authors were not available to confirm the retraction.</p>","PeriodicalId":50589,"journal":{"name":"Development Growth & Differentiation","volume":"65 8","pages":"498"},"PeriodicalIF":2.5,"publicationDate":"2023-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/dgd.12885","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10205427","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Can we model autism using zebrafish?","authors":"Philip Washbourne","doi":"10.1111/dgd.12888","DOIUrl":"10.1111/dgd.12888","url":null,"abstract":"<p>Autism spectrum disorder (ASD) is one of the most common, heritable neuropsychiatric disorders in the world, affecting almost 1% of the population. The core symptoms used to diagnose ASD are decreased social interaction and increased repetitive behaviors. Despite the large number of affected individuals, the precise mechanisms that cause this disorder remain unclear. The identification of genes and environmental factors associated with ASD allows the study of the underlying mechanisms in animal models. Although ASD presents as a human disorder, based on recent advances in understanding their brain anatomy, physiology, behavior, and evolutionary conservation of neuronal cell types, I propose that zebrafish may provide novel insights into the etiology.</p>","PeriodicalId":50589,"journal":{"name":"Development Growth & Differentiation","volume":"65 8","pages":"453-458"},"PeriodicalIF":2.5,"publicationDate":"2023-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10262457","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Invention sharing is the mother of developmental biology (part 4)","authors":"Hajime Ogino,&nbsp;Yasuhiro Kamei,&nbsp;Toshinori Hayashi,&nbsp;Joe Sakamoto,&nbsp;Makoto Suzuki,&nbsp;Takeshi Igawa,&nbsp;Mariko Kondo,&nbsp;Masanori Taira","doi":"10.1111/dgd.12883","DOIUrl":"10.1111/dgd.12883","url":null,"abstract":"Part 4 of this special issue releases four methods, two protocols, and two technical notes. Suzuki et al. (2022) developed a method for studying how cells communicate with each other using semaphorin and plexin proteins in a worm model. The method utilizes the infrared laser-evoked gene operator (IR-LEGO) system to activate genes in specific cells and observe the resulting influences on the worm vulva formation. Using this method, the authors demonstrated that the direction and level of semaphorin and plexin signaling are crucial for regulating cell behavior. Seki et al. (2023) developed a method for optogenetic behavior analysis in medaka (Oryzias latipes). Using the CRISPR/Cas9 knock-in method, the authors generated a transgenic medaka line expressing an optogenetic channel, Chloromonas oogama channelrhodopsin (CoChR), in the nervous system. The potential of this receptor to regulate the motor activity of the fish such as body bending, turning movements, and pectoral fin locomotion was evaluated by stimulating with different intensities, durations, or wavelengths of light. Ishii et al. (2023) developed an X-ray micro-computed tomography (microCT) method to observe the soft tissues of Xenopus tadpoles in three dimensions. Using this method, the authors revealed a transient ventricular contraction in the early stages of telencephalon regeneration. This method could potentially be applied to the analysis of other amphibian and fish larvae, facilitating comparative morphological studies of postembryonic development in vertebrates. Hasan et al. (2023) developed a method for preparing primary cell cultures from the limb tissue of an Iberian ribbed newt (Pleurodeles waltl). The Iberian ribbed newt is emerging as a model animal in the limelight, especially in regeneration studies. The limb tissues are cut into small pieces and seeded as “explants” in culture dishes coated with fibronectin and gelatin. The cells spread out from the explants can be cryopreserved with a proliferation capacity comparable to freshly prepared cells. Yoshimatsu et al. (2022) provided a step-by-step protocol for deriving transgene-free-induced pluripotent stem cells from the fibroblasts of multiple mammalian species, including human, mouse, marmoset, dog, pig, ferret, and Syrian hamster, a unique model of hibernation. The reprogramming factors are expressed by episomal transfection of DNA vectors. The episomal transfection may be followed by transfection of the mRNAs encoding these factors to increase the induction efficiency further. This protocol is expected to accelerate stem cell biology and regenerative medicine. Ikuta et al. (2023) provided a standard protocol for cardiac regeneration experiments in Iberian ribbed newts. This protocol describes tissue-amputation and cryo-injury techniques to inflict cardiac injuries for investigating subsequent regeneration processes. Both techniques are simple, require no special equipment, and can be applied to other newt and salamande","PeriodicalId":50589,"journal":{"name":"Development Growth & Differentiation","volume":"65 6","pages":"286-287"},"PeriodicalIF":2.5,"publicationDate":"2023-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10115356","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"How do maternal androgens and estrogens affect sex determination in reptiles with temperature-dependent sex?","authors":"Florencia E. Valli,&nbsp;Melina S. Simoncini,&nbsp;Marcela A. González,&nbsp;Carlos I. Piña","doi":"10.1111/dgd.12887","DOIUrl":"10.1111/dgd.12887","url":null,"abstract":"<p>Temperature sex determination (TSD) in reptiles has been studied to elucidate the mechanisms by which temperature is transformed into a biological signal that determines the sex of the embryo. Temperature is thought to trigger signals that alter gene expression and hormone metabolism, which will determine the development of female or male gonads. In this review, we focus on collecting and discussing important and recent information on the role of maternal steroid hormones in sex determination in oviparous reptiles such as crocodiles, turtles, and lizards that possess TSD. In particular, we focus on maternal androgens and estrogens deposited in the egg yolk and their metabolites that could also influence the sex of offspring. Finally, we suggest guidelines for future research to help clarify the link between maternal steroid hormones and offspring sex.</p>","PeriodicalId":50589,"journal":{"name":"Development Growth & Differentiation","volume":"65 9","pages":"565-576"},"PeriodicalIF":2.5,"publicationDate":"2023-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10212260","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Establishment of a new method to isolate viable x-ray-sensitive cells from planarian by fluorescence-activated cell sorting","authors":"Miyuki Ishida,&nbsp;Yoshihito Kuroki,&nbsp;Kiyokazu Agata","doi":"10.1111/dgd.12886","DOIUrl":"10.1111/dgd.12886","url":null,"abstract":"<p>Planarians show outstanding regenerative ability due to the proliferation of neoblasts. Hence the method to isolate planarian neoblasts is important to understand the regeneration process. In our previous study, we reported a method to isolate planarian neoblasts of <i>Dugesia japonica</i> using fluorescence-activated cell sorting (FACS). However, we have not yet succeeded in cultivating these cells even under in vivo conditions after transplantation into x-ray-irradiated planarians. This suggests that dissociated cells might enter apoptotic or necrotic states in the process of fluorescent dye staining and sorting. Here, we developed a new method to isolate viable neoblasts, which can proliferate in the x-ray-irradiated planarians. First, the toxicity of various fluorescence dyes was investigated. All nuclear fluorescent dyes such as Hoechst 33342, DRAQ5, and DyeCycle, showed, more or less, toxicity to mammalian culture cells. In contrast, cytoplasmic fluorescent dye for live cells, calcein AM, was less toxic on these cells. Next, we stained the dissociated planarian cells with only calcein AM, and then collected the x-ray-sensitive fraction. Although the purity of neoblasts was slightly lower than that of the original staining method (ca. 97% → ca. 89%), the sorted cells could actively proliferate when they were injected into x-ray-irradiated planarians. This simple staining and sorting method will provide new opportunities to isolate viable neoblasts and understand regenerating processes.</p>","PeriodicalId":50589,"journal":{"name":"Development Growth & Differentiation","volume":"65 9","pages":"577-590"},"PeriodicalIF":2.5,"publicationDate":"2023-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/dgd.12886","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10147740","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phenotype–genotype relationships in Xenopus sox9 crispants provide insights into campomelic dysplasia and vertebrate jaw evolution","authors":"Nusrat Hossain,&nbsp;Takeshi Igawa,&nbsp;Makoto Suzuki,&nbsp;Ichiro Tazawa,&nbsp;Yuta Nakao,&nbsp;Toshinori Hayashi,&nbsp;Nanoka Suzuki,&nbsp;Hajime Ogino","doi":"10.1111/dgd.12884","DOIUrl":"10.1111/dgd.12884","url":null,"abstract":"<p>Since CRISPR-based genome editing technology works effectively in the diploid frog <i>Xenopus tropicalis</i>, a growing number of studies have successfully modeled human genetic diseases in this species. However, most of their targets were limited to non-syndromic diseases that exhibit abnormalities in a small fraction of tissues or organs in the body. This is likely because of the complexity of interpreting the phenotypic variations resulting from somatic mosaic mutations generated in the founder animals (crispants). In this study, we attempted to model the syndromic disease campomelic dysplasia (CD) by generating <i>sox9</i> crispants in <i>X. tropicalis</i>. The resulting crispants failed to form neural crest cells at neurula stages and exhibited various combinations of jaw, gill, ear, heart, and gut defects at tadpole stages, recapitulating part of the syndromic phenotype of CD patients. Genotyping of the crispants with a variety of allelic series of mutations suggested that the heart and gut defects depend primarily on frame-shift mutations expected to be null, whereas the jaw, gill, and ear defects could be induced not only by such mutations but also by in-frame deletion mutations expected to delete part of the jawed vertebrate-specific domain from the encoded Sox9 protein. These results demonstrate that <i>Xenopus</i> crispants are useful for investigating the phenotype–genotype relationships behind syndromic diseases and examining the tissue-specific role of each functional domain within a single protein, providing novel insights into vertebrate jaw evolution.</p>","PeriodicalId":50589,"journal":{"name":"Development Growth & Differentiation","volume":"65 8","pages":"481-497"},"PeriodicalIF":2.5,"publicationDate":"2023-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10066894","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomic evidence for Brachyury expression in the caudal tip region of adult Ptychodera flava (Hemichordata)","authors":"Asuka Arimoto,&nbsp;Koki Nishitsuji,&nbsp;Kanako Hisata,&nbsp;Noriyuki Satoh,&nbsp;Kuni Tagawa","doi":"10.1111/dgd.12882","DOIUrl":"10.1111/dgd.12882","url":null,"abstract":"<p>Most metazoans have a single copy of the T-box transcription factor gene <i>Brachyury</i>. This gene is expressed in cells of the blastopore of late blastulae and the archenteron invagination region of gastrulae. It appears to be crucial for gastrulation and mesoderm differentiation of embryos. Although this expression pattern is shared by most deuterostomes, <i>Brachyury</i> expression has not been reported in adult stages. Here we show that <i>Brachyury</i> of an indirect developer, the hemichordate acorn worm <i>Ptychodera flava</i>, is expressed not only in embryonic cells, but also in cells of the caudal tip (anus) region of adults. This spatially restricted expression, shown by whole-mount in situ hybridization, was confirmed by Iso-Seq RNA sequencing and single-cell RNA-seq (scRNA-seq) analysis. Iso-Seq analysis showed that gene expression occurs only in the caudal region of adults, but not in anterior regions, including the stomochord. scRNA-seq analysis showed a cluster that contained <i>Brachyury</i>-expressing cells comprising epidermis- and mesoderm-related cells, but which is unlikely to be associated with the nervous system or muscle. Although further investigation is required to examine the roles of <i>Brachyury</i> in adults, this study provides important clues for extending studies on <i>Brachyury</i> expression involved in development of the most posterior region of deuterostomes.</p>","PeriodicalId":50589,"journal":{"name":"Development Growth & Differentiation","volume":"65 8","pages":"470-480"},"PeriodicalIF":2.5,"publicationDate":"2023-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10114685","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}