Journal of Developmental Biology最新文献

{"title":"Regionalized Protein Localization Domains in the Zebrafish Hair Cell Kinocilium.","authors":"Timothy Erickson,&nbsp;William Paul Biggers,&nbsp;Kevin Williams,&nbsp;Shyanne E Butland,&nbsp;Alexandra Venuto","doi":"10.3390/jdb11020028","DOIUrl":"https://doi.org/10.3390/jdb11020028","url":null,"abstract":"<p><p>Sensory hair cells are the receptors for auditory, vestibular, and lateral line sensory organs in vertebrates. These cells are distinguished by \"hair\"-like projections from their apical surface collectively known as the hair bundle. Along with the staircase arrangement of the actin-filled stereocilia, the hair bundle features a single, non-motile, true cilium called the kinocilium. The kinocilium plays an important role in bundle development and the mechanics of sensory detection. To understand more about kinocilial development and structure, we performed a transcriptomic analysis of zebrafish hair cells to identify cilia-associated genes that have yet to be characterized in hair cells. In this study, we focused on three such genes-<i>ankef1a</i>, <i>odf3l2a</i>, and <i>saxo2</i>-because human or mouse orthologs are either associated with sensorineural hearing loss or are located near uncharacterized deafness loci. We made transgenic fish that express fluorescently tagged versions of their proteins, demonstrating their localization to the kinocilia of zebrafish hair cells. Furthermore, we found that Ankef1a, Odf3l2a, and Saxo2 exhibit distinct localization patterns along the length of the kinocilium and within the cell body. Lastly, we have reported a novel overexpression phenotype of Saxo2. Overall, these results suggest that the hair cell kinocilium in zebrafish is regionalized along its proximal-distal axis and set the groundwork to understand more about the roles of these kinocilial proteins in hair cells.</p>","PeriodicalId":15563,"journal":{"name":"Journal of Developmental Biology","volume":"11 2","pages":""},"PeriodicalIF":2.7,"publicationDate":"2023-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10299642/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9722380","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 Lost and Found: Unraveling the Functions of Orphan Genes.","authors":"Ali Zeeshan Fakhar,&nbsp;Jinbao Liu,&nbsp;Karolina M Pajerowska-Mukhtar,&nbsp;M Shahid Mukhtar","doi":"10.3390/jdb11020027","DOIUrl":"10.3390/jdb11020027","url":null,"abstract":"<p><p>Orphan Genes (OGs) are a mysterious class of genes that have recently gained significant attention. Despite lacking a clear evolutionary history, they are found in nearly all living organisms, from bacteria to humans, and they play important roles in diverse biological processes. The discovery of OGs was first made through comparative genomics followed by the identification of unique genes across different species. OGs tend to be more prevalent in species with larger genomes, such as plants and animals, and their evolutionary origins remain unclear but potentially arise from gene duplication, horizontal gene transfer (HGT), or de novo origination. Although their precise function is not well understood, OGs have been implicated in crucial biological processes such as development, metabolism, and stress responses. To better understand their significance, researchers are using a variety of approaches, including transcriptomics, functional genomics, and molecular biology. This review offers a comprehensive overview of the current knowledge of OGs in all domains of life, highlighting the possible role of dark transcriptomics in their evolution. More research is needed to fully comprehend the role of OGs in biology and their impact on various biological processes.</p>","PeriodicalId":15563,"journal":{"name":"Journal of Developmental Biology","volume":"11 2","pages":""},"PeriodicalIF":2.7,"publicationDate":"2023-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10299390/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9717109","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":"An Emerging Animal Model for Querying the Role of Whole Genome Duplication in Development, Evolution, and Disease.","authors":"Mara Schvarzstein, Fatema Alam, Muhammad Toure, Judith L Yanowitz","doi":"10.3390/jdb11020026","DOIUrl":"10.3390/jdb11020026","url":null,"abstract":"<p><p>Whole genome duplication (WGD) or polyploidization can occur at the cellular, tissue, and organismal levels. At the cellular level, tetraploidization has been proposed as a driver of aneuploidy and genome instability and correlates strongly with cancer progression, metastasis, and the development of drug resistance. WGD is also a key developmental strategy for regulating cell size, metabolism, and cellular function. In specific tissues, WGD is involved in normal development (e.g., organogenesis), tissue homeostasis, wound healing, and regeneration. At the organismal level, WGD propels evolutionary processes such as adaptation, speciation, and crop domestication. An essential strategy to further our understanding of the mechanisms promoting WGD and its effects is to compare isogenic strains that differ only in their ploidy. <i>Caenorhabditis elegans</i> (<i>C. elegans</i>) is emerging as an animal model for these comparisons, in part because relatively stable and fertile tetraploid strains can be produced rapidly from nearly any diploid strain. Here, we review the use of Caenorhabditis polyploids as tools to understand important developmental processes (e.g., sex determination, dosage compensation, and allometric relationships) and cellular processes (e.g., cell cycle regulation and chromosome dynamics during meiosis). We also discuss how the unique characteristics of the <i>C. elegans</i> WGD model will enable significant advances in our understanding of the mechanisms of polyploidization and its role in development and disease.</p>","PeriodicalId":15563,"journal":{"name":"Journal of Developmental Biology","volume":"11 2","pages":""},"PeriodicalIF":2.7,"publicationDate":"2023-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10299280/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9717103","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":"Evo Devo of the Vertebrates Integument.","authors":"Danielle Dhouailly","doi":"10.3390/jdb11020025","DOIUrl":"https://doi.org/10.3390/jdb11020025","url":null,"abstract":"All living jawed vertebrates possess teeth or did so ancestrally. Integumental surface also includes the cornea. Conversely, no other anatomical feature differentiates the clades so readily as skin appendages do, multicellular glands in amphibians, hair follicle/gland complexes in mammals, feathers in birds, and the different types of scales. Tooth-like scales are characteristic of chondrichthyans, while mineralized dermal scales are characteristic of bony fishes. Corneous epidermal scales might have appeared twice, in squamates, and on feet in avian lineages, but posteriorly to feathers. In contrast to the other skin appendages, the origin of multicellular glands of amphibians has never been addressed. In the seventies, pioneering dermal–epidermal recombination between chick, mouse and lizard embryos showed that: (1) the clade type of the appendage is determined by the epidermis; (2) their morphogenesis requires two groups of dermal messages, first for primordia formation, second for appendage final architecture; (3) the early messages were conserved during amniotes evolution. Molecular biology studies that have identified the involved pathways, extending those data to teeth and dermal scales, suggest that the different vertebrate skin appendages evolved in parallel from a shared placode/dermal cells unit, present in a common toothed ancestor, c.a. 420 mya.","PeriodicalId":15563,"journal":{"name":"Journal of Developmental Biology","volume":"11 2","pages":""},"PeriodicalIF":2.7,"publicationDate":"2023-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10299021/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9773856","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":"Jak2 and Jaw Muscles Are Required for Buccopharyngeal Membrane Perforation during Mouth Development.","authors":"Amanda J G Dickinson","doi":"10.3390/jdb11020024","DOIUrl":"https://doi.org/10.3390/jdb11020024","url":null,"abstract":"<p><p>The mouth is a central feature of our face, without which we could not eat, breathe, or communicate. A critical and early event in mouth formation is the creation of a \"hole\" which connects the digestive system and the external environment. This hole, which has also been called the primary or embryonic mouth in vertebrates, is initially covered by a 1-2 cell layer thick structure called the buccopharyngeal membrane. When the buccopharyngeal membrane does not rupture, it impairs early mouth functions and may also lead to further craniofacial malformations. Using a chemical screen in an animal model (<i>Xenopus laevis</i>) and genetic data from humans, we determined that Janus kinase 2 (Jak2) has a role in buccopharyngeal membrane rupture. We have determined that decreased Jak2 function, using antisense morpholinos or a pharmacological antagonist, caused a persistent buccopharyngeal membrane as well as the loss of jaw muscles. Surprisingly, we observed that the jaw muscle compartments were connected to the oral epithelium that is continuous with the buccopharyngeal membrane. Severing such connections resulted in buccopharyngeal membrane buckling and persistence. We also noted puncta accumulation of F-actin, an indicator of tension, in the buccopharyngeal membrane during perforation. Taken together, the data has led us to a hypothesis that muscles are required to exert tension across the buccopharyngeal membrane, and such tension is necessary for its perforation.</p>","PeriodicalId":15563,"journal":{"name":"Journal of Developmental Biology","volume":"11 2","pages":""},"PeriodicalIF":2.7,"publicationDate":"2023-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10298892/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10078182","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":"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":"11 2","pages":""},"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":"11 2","pages":""},"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":"11 2","pages":""},"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":"11 2","pages":""},"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":"11 2","pages":""},"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}