Journal of Developmental Biology最新文献

{"title":"Transcription of <i>HOX</i> Genes Is Significantly Increased during Neuronal Differentiation of iPSCs Derived from Patients with Parkinson's Disease.","authors":"Viya B Fedoseyeva,&nbsp;Ekaterina V Novosadova,&nbsp;Valentina V Nenasheva,&nbsp;Lyudmila V Novosadova,&nbsp;Igor A Grivennikov,&nbsp;Vyacheslav Z Tarantul","doi":"10.3390/jdb11020023","DOIUrl":"https://doi.org/10.3390/jdb11020023","url":null,"abstract":"<p><p>Parkinson's disease (PD) is the most serious movement disorder, but the actual cause of this disease is still unknown. Induced pluripotent stem cell-derived neural cultures from PD patients carry the potential for experimental modeling of underlying molecular events. We analyzed the RNA-seq data of iPSC-derived neural precursor cells (NPCs) and terminally differentiated neurons (TDNs) from healthy donors (HD) and PD patients with mutations in <i>PARK2</i> published previously. The high level of transcription of <i>HOX</i> family protein-coding genes and lncRNA transcribed from the <i>HOX</i> clusters was revealed in the neural cultures from PD patients, while in HD NPCs and TDNs, the majority of these genes were not expressed or slightly transcribed. The results of this analysis were generally confirmed by qPCR. The <i>HOX</i> paralogs in the 3' clusters were activated more strongly than the genes of the 5' cluster. The abnormal activation of the <i>HOX</i> gene program upon neuronal differentiation in the cells of PD patients raises the possibility that the abnormal expression of these key regulators of neuronal development impacts PD pathology. Further research is needed to investigate this hypothesis.</p>","PeriodicalId":15563,"journal":{"name":"Journal of Developmental Biology","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2023-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10299083/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10078183","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Osteoderm Development during the Regeneration Process in <i>Eurylepis taeniolata</i> Blyth, 1854 (Scincidae, Sauria, Squamata).","authors":"Gennady O Cherepanov,&nbsp;Dmitry A Gordeev,&nbsp;Daniel A Melnikov,&nbsp;Natalia B Ananjeva","doi":"10.3390/jdb11020022","DOIUrl":"https://doi.org/10.3390/jdb11020022","url":null,"abstract":"<p><p>Osteoderms are bony structures that develop within the dermal layer of the skin in vertebrates and are very often found in different lizard families. Lizard osteoderms are diverse in topography, morphology, and microstructure. Of particular interest are the compound osteoderms of skinks, which are a complex of several bone elements known as osteodermites. We present new data on the development and regeneration of compound osteoderms based on the results of a histological and Computed Microtomography (micro-CT) study of a scincid lizard: <i>Eurylepis taeniolata</i>. The specimens studied are stored in the herpetological collections of the Saint-Petersburg State University and Zoological Institute of the Russian Academy of Sciences located in St. Petersburg, Russia. The topography of osteoderms in the integuments of the original tail area and its regenerated part was studied. A comparative histological description of the original and regenerated osteoderms of <i>Eurylepis taeniolata</i> is presented for the first time. The first description of the development of compound osteoderm microstructure in the process of caudal regeneration is also presented.</p>","PeriodicalId":15563,"journal":{"name":"Journal of Developmental Biology","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2023-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10299357/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10078184","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic and Epigenetic Regulation of <i>Drosophila</i> Oocyte Determination.","authors":"Brigite Cabrita,&nbsp;Rui Gonçalo Martinho","doi":"10.3390/jdb11020021","DOIUrl":"https://doi.org/10.3390/jdb11020021","url":null,"abstract":"<p><p>Primary oocyte determination occurs in many organisms within a germ line cyst, a multicellular structure composed of interconnected germ cells. However, the structure of the cyst is itself highly diverse, which raises intriguing questions about the benefits of this stereotypical multicellular environment for female gametogenesis. <i>Drosophila melanogaster</i> is a well-studied model for female gametogenesis, and numerous genes and pathways critical for the determination and differentiation of a viable female gamete have been identified. This review provides an up-to-date overview of <i>Drosophila</i> oocyte determination, with a particular emphasis on the mechanisms that regulate germ line gene expression.</p>","PeriodicalId":15563,"journal":{"name":"Journal of Developmental Biology","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2023-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10299578/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10077660","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Attenuation of Dopaminergic Neurodegeneration in a <i>C. elegans</i> Parkinson's Model through Regulation of Xanthine Dehydrogenase (XDH-1) Expression by the RNA Editase, ADR-2.","authors":"Lindsey A Starr,&nbsp;Luke E McKay,&nbsp;Kylie N Peter,&nbsp;Lena M Seyfarth,&nbsp;Laura A Berkowitz,&nbsp;Kim A Caldwell,&nbsp;Guy A Caldwell","doi":"10.3390/jdb11020020","DOIUrl":"https://doi.org/10.3390/jdb11020020","url":null,"abstract":"<p><p>Differential RNA editing by adenosine deaminases that act on RNA (ADARs) has been implicated in several neurological disorders, including Parkinson's disease (PD). Here, we report results of a RNAi screen of genes differentially regulated in <i>adr-2</i> mutants, normally encoding the only catalytically active ADAR in <i>Caenorhabditis elegans</i>, ADR-2. Subsequent analysis of candidate genes that alter the misfolding of human α-synuclein (α-syn) and dopaminergic neurodegeneration, two PD pathologies, reveal that reduced expression of <i>xdh-1</i>, the ortholog of human xanthine dehydrogenase (XDH), is protective against α-synuclein-induced dopaminergic neurodegeneration. Further, RNAi experiments show that WHT-2, the worm ortholog of the human ABCG2 transporter and a predicted interactor of XDH-1, is the rate-limiting factor in the ADR-2, XDH-1, WHT-2 system for dopaminergic neuroprotection. In silico structural modeling of WHT-2 indicates that the editing of one nucleotide in the <i>wht-2</i> mRNA leads to the substitution of threonine with alanine at residue 124 in the WHT-2 protein, changing hydrogen bonds in this region. Thus, we propose a model where <i>wht-2</i> is edited by ADR-2, which promotes optimal export of uric acid, a known substrate of WHT-2 and a product of XDH-1 activity. In the absence of editing, uric acid export is limited, provoking a reduction in <i>xdh-1</i> transcription to limit uric acid production and maintain cellular homeostasis. As a result, elevation of uric acid is protective against dopaminergic neuronal cell death. In turn, increased levels of uric acid are associated with a decrease in ROS production. Further, downregulation of <i>xdh-1</i> is protective against PD pathologies because decreased levels of XDH-1 correlate to a concomitant reduction in xanthine oxidase (XO), the form of the protein whose by-product is superoxide anion. These data indicate that modifying specific targets of RNA editing may represent a promising therapeutic strategy for PD.</p>","PeriodicalId":15563,"journal":{"name":"Journal of Developmental Biology","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2023-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10204437/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9516138","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Presence of Two <i>MyoD</i> Genes in a Subset of Acanthopterygii Fish Is Associated with a Polyserine Insert in MyoD1.","authors":"Lewis J White,&nbsp;Alexander J Russell,&nbsp;Alastair R Pizzey,&nbsp;Kanchon K Dasmahapatra,&nbsp;Mary E Pownall","doi":"10.3390/jdb11020019","DOIUrl":"https://doi.org/10.3390/jdb11020019","url":null,"abstract":"<p><p>The <i>MyoD</i> gene was duplicated during the teleost whole genome duplication and, while a second <i>MyoD</i> gene (<i>MyoD2</i>) was subsequently lost from the genomes of some lineages (including zebrafish), many fish lineages (including <i>Alcolapia</i> species) have retained both <i>MyoD</i> paralogues. Here we reveal the expression patterns of the two <i>MyoD</i> genes in <i>Oreochromis</i> (<i>Alcolapia) alcalica</i> using in situ hybridisation. We report our analysis of MyoD1 and MyoD2 protein sequences from 54 teleost species, and show that <i>O. alcalica</i>, along with some other teleosts, include a polyserine repeat between the amino terminal transactivation domains (TAD) and the cysteine-histidine rich region (H/C) in MyoD1. The evolutionary history of <i>MyoD1</i> and <i>MyoD2</i> is compared to the presence of this polyserine region using phylogenetics, and its functional relevance is tested using overexpression in a heterologous system to investigate subcellular localisation, stability, and activity of MyoD proteins that include and do not include the polyserine region.</p>","PeriodicalId":15563,"journal":{"name":"Journal of Developmental Biology","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2023-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10204381/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9508967","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reproductive-Toxicity-Related Endpoints in <i>C. elegans</i> Are Consistent with Reduced Concern for Dimethylarsinic Acid Exposure Relative to Inorganic Arsenic.","authors":"Jessica A Camacho, Bonnie Welch, Robert L Sprando, Piper R Hunt","doi":"10.3390/jdb11020018","DOIUrl":"10.3390/jdb11020018","url":null,"abstract":"<p><p>Exposures to arsenic and mercury are known to pose significant threats to human health; however, the effects specific to organic vs. inorganic forms are not fully understood. <i>Caenorhabditis elegans'</i> (<i>C. elegans</i>) transparent cuticle, along with the conservation of key genetic pathways regulating developmental and reproductive toxicology (DART)-related processes such as germ stem cell renewal and differentiation, meiosis, and embryonic tissue differentiation and growth, support this model's potential to address the need for quicker and more dependable testing methods for DART hazard identification. Organic and inorganic forms of mercury and arsenic had different effects on reproductive-related endpoints in <i>C. elegans</i>, with methylmercury (meHgCl) having effects at lower concentrations than mercury chloride (HgCl₂), and sodium arsenite (NaAsO₂) having effects at lower concentrations than dimethylarsinic acid (DMA). Progeny to adult ratio changes and germline apoptosis were seen at concentrations that also affected gravid adult gross morphology. For both forms of arsenic tested, germline histone regulation was altered at concentrations below those that affected progeny/adult ratios, while concentrations for these two endpoints were similar for the mercury compounds. These <i>C. elegans</i> findings are consistent with corresponding mammalian data, where available, suggesting that small animal model test systems may help to fill critical data gaps by contributing to weight of evidence assessments.</p>","PeriodicalId":15563,"journal":{"name":"Journal of Developmental Biology","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2023-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10204422/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9508968","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Selecting Normalizers for MicroRNA RT-qPCR Expression Analysis in Murine Preimplantation Embryos and the Associated Conditioned Culture Media.","authors":"David C Hawke,&nbsp;Andrew J Watson,&nbsp;Dean H Betts","doi":"10.3390/jdb11020017","DOIUrl":"https://doi.org/10.3390/jdb11020017","url":null,"abstract":"<p><p>Normalizing RT-qPCR miRNA datasets that encompass numerous preimplantation embryo stages requires the identification of miRNAs that may be used as stable reference genes. A need has also arisen for the normalization of the accompanying conditioned culture media as extracellular miRNAs may serve as biomarkers of embryo developmental competence. Here, we evaluate the stability of six commonly used miRNA normalization candidates, as well as small nuclear U6, using five different means of evaluation (BestKeeper, NormFinder, geNorm, the comparative Delta Ct method and RefFinder comprehensive analysis) to assess their stability throughout murine preimplantation embryo development from the oocyte to the late blastocyst stages, both in whole embryos and the associated conditioned culture media. In descending order of effectiveness, miR-16, miR-191 and miR-106 were identified as the most stable individual reference miRNAs for developing whole CD1 murine preimplantation embryos, while miR-16, miR-106 and miR-103 were ideal for the conditioned culture media. Notably, the widely used U6 reference was among the least appropriate for normalizing both whole embryo and conditioned media miRNA datasets. Incorporating multiple reference miRNAs into the normalization basis via a geometric mean was deemed beneficial, and combinations of each set of stable miRNAs are further recommended, pending validation on a per experiment basis.</p>","PeriodicalId":15563,"journal":{"name":"Journal of Developmental Biology","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2023-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10123758/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9389214","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparison of Pronase versus Manual Dechorionation of Zebrafish Embryos for Small Molecule Treatments.","authors":"Eva H Hasegawa,&nbsp;Gist H Farr,&nbsp;Lisa Maves","doi":"10.3390/jdb11020016","DOIUrl":"10.3390/jdb11020016","url":null,"abstract":"<p><p>Zebrafish are a powerful animal model for small molecule screening. Small molecule treatments of zebrafish embryos usually require that the chorion, an acellular envelope enclosing the embryo, is removed in order for chemical compounds to access the embryo from the bath medium. For large-scale studies requiring hundreds of embryos, manual dechorionation, using forceps, can be a time-consuming and limiting process. Pronase is a non-specific protease that is widely used as an enzymatic alternative for dechorionating zebrafish embryos. However, whether pronase treatments alter the effects of subsequent small molecule treatments has not been addressed. Here, we provide a detailed protocol for large-scale pronase dechorionation of zebrafish embryos. We tested whether pronase treatment can influence the efficacy of drug treatments in zebrafish embryos. We used a zebrafish model for Duchenne muscular dystrophy (DMD) to investigate whether the efficacies of trichostatin-A (TSA) or salermide + oxamflatin, small molecule inhibitors known to ameliorate the zebrafish <i>dmd</i> muscle degeneration phenotype, are significantly altered when embryos are treated with pronase versus manual dechorionation. We also tested the effects of pronase on the ability of the anthracycline cancer drug doxorubicin to induce cardiotoxicity in zebrafish embryos. When comparing pronase- versus forceps-dechorionated embryos used in these small molecule treatments, we found no appreciable effects of pronase on animal survival or on the effects of the small molecules. The significant difference that was detected was a small improvement in the ability of salermide + oxamflatin to ameliorate the <i>dmd</i> phenotype in pronase-treated embryos when compared with manual dechorionation. Our study supports the use of pronase treatment as a dechorionation method for zebrafish drug screening experiments.</p>","PeriodicalId":15563,"journal":{"name":"Journal of Developmental Biology","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2023-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10123619/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9382422","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Refined Single Cell Landscape of Haematopoiesis in the Mouse Foetal Liver.","authors":"Elena Ceccacci, Emanuela Villa, Fabio Santoro, Saverio Minucci, Christiana Ruhrberg, Alessandro Fantin","doi":"10.3390/jdb11020015","DOIUrl":"10.3390/jdb11020015","url":null,"abstract":"<p><p>During prenatal life, the foetal liver is colonised by several waves of haematopoietic progenitors to act as the main haematopoietic organ. Single cell (sc) RNA-seq has been used to identify foetal liver cell types via their transcriptomic signature and to compare gene expression patterns as haematopoietic development proceeds. To obtain a refined single cell landscape of haematopoiesis in the foetal liver, we have generated a scRNA-seq dataset from a whole mouse E12.5 liver that includes a larger number of cells than prior datasets at this stage and was obtained without cell type preselection to include all liver cell populations. We combined mining of this dataset with that of previously published datasets at other developmental stages to follow transcriptional dynamics as well as the cell cycle state of developing haematopoietic lineages. Our findings corroborate several prior reports on the timing of liver colonisation by haematopoietic progenitors and the emergence of differentiated lineages and provide further molecular characterisation of each cell population. Extending these findings, we demonstrate the existence of a foetal intermediate haemoglobin profile in the mouse, similar to that previously identified in humans, and a previously unidentified population of primitive erythroid cells in the foetal liver.</p>","PeriodicalId":15563,"journal":{"name":"Journal of Developmental Biology","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2023-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10123705/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9382417","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Principles of Zebrafish Nephron Segment Development.","authors":"Thanh Khoa Nguyen,&nbsp;Madeline Petrikas,&nbsp;Brooke E Chambers,&nbsp;Rebecca A Wingert","doi":"10.3390/jdb11010014","DOIUrl":"https://doi.org/10.3390/jdb11010014","url":null,"abstract":"<p><p>Nephrons are the functional units which comprise the kidney. Each nephron contains a number of physiologically unique populations of specialized epithelial cells that are organized into discrete domains known as segments. The principles of nephron segment development have been the subject of many studies in recent years. Understanding the mechanisms of nephrogenesis has enormous potential to expand our knowledge about the basis of congenital anomalies of the kidney and urinary tract (CAKUT), and to contribute to ongoing regenerative medicine efforts aimed at identifying renal repair mechanisms and generating replacement kidney tissue. The study of the zebrafish embryonic kidney, or pronephros, provides many opportunities to identify the genes and signaling pathways that control nephron segment development. Here, we describe recent advances of nephron segment patterning and differentiation in the zebrafish, with a focus on distal segment formation.</p>","PeriodicalId":15563,"journal":{"name":"Journal of Developmental Biology","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2023-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10052950/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9580879","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}