Journal of experimental zoology. Part B, Molecular and developmental evolution最新文献

{"title":"Transcriptional background effects on a tumor driver gene in different pigment cell types of medaka","authors":"Shahad Abdulsahib,&nbsp;William Boswell,&nbsp;Mikki Boswell,&nbsp;Markita Savage,&nbsp;Manfred Schartl,&nbsp;Yuan Lu","doi":"10.1002/jez.b.23224","DOIUrl":"10.1002/jez.b.23224","url":null,"abstract":"<p>The <i>Xiphophorus</i> melanoma receptor kinase gene, <i>xmrk</i>, is a bona fide oncogene driving melanocyte tumorigenesis of <i>Xiphophorus</i> fish. When ectopically expressed in medaka, it not only induces development of several pigment cell tumor types in different strains of medaka but also induces different tumor types within the same animal, suggesting its oncogenic activity has a transcriptomic background effect. Although the central pathways that <i>xmrk</i> utilizes to lead to melanomagenesis are well documented, genes and genetic pathways that modulate the oncogenic effect and alter the course of disease have not been studied so far. To understand how the genetic networks between different histocytes of <i>xmrk-</i>driven tumors are composed, we isolated two types of tumors, melanoma and xanthoerythrophoroma, from the same <i>xmrk</i> transgenic medaka individuals, established the transcriptional profiles of both <i>xmrk-</i>driven tumors, and compared (1) genes that are co-expressed with <i>xmrk</i> in both tumor types, and (2) differentially expressed genes and their associated molecular functions, between the two tumor types. Transcriptomic comparisons between the two tumor types show melanoma and xanthoerythrophoroma are characterized by transcriptional features representing varied functions, indicating distinct molecular interactions between the driving oncogene and the cell-type-specific transcriptomes. Melanoma tumors exhibit gene signatures that are relevant to proliferation and invasion, while xanthoerythrophoroma tumors are characterized by expression profiles related to metabolism and DNA repair. We conclude the transcriptomic backgrounds, exemplified by cell-type-specific genes that are downstream of <i>xmrk</i> effected signaling pathways, contribute the potential to change the course of tumor development and may affect overall tumor outcomes.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":"342 3","pages":"252-259"},"PeriodicalIF":2.2,"publicationDate":"2023-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jez.b.23224","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50158087","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Suppressors of cGAS-STING are downregulated during fin-limb regeneration and aging in aquatic vertebrates","authors":"Sabateeshan Mathavarajah,&nbsp;Andrew W. Thompson,&nbsp;Matthew R. Stoyek,&nbsp;T. Alexander Quinn,&nbsp;Stéphane Roy,&nbsp;Ingo Braasch,&nbsp;Graham Dellaire","doi":"10.1002/jez.b.23227","DOIUrl":"10.1002/jez.b.23227","url":null,"abstract":"<p>During the early stages of limb and fin regeneration in aquatic vertebrates (i.e., fishes and amphibians), blastema undergo transcriptional rewiring of innate immune signaling pathways to promote immune cell recruitment. In mammals, a fundamental component of innate immune signaling is the cytosolic DNA sensing pathway, cGAS-STING. However, to what extent the cGAS-STING pathway influences regeneration in aquatic anamniotes is unknown. In jawed vertebrates, negative regulation of cGAS-STING activity is accomplished by suppressors of cytosolic DNA such as Trex1, Pml, and PML-like exon 9 (Plex9) exonucleases. Here, we examine the expression of these suppressors of cGAS-STING, as well as inflammatory genes and cGAS activity during caudal fin and limb regeneration using the spotted gar (<i>Lepisosteus oculatus</i>) and axolotl (<i>Ambystoma mexicanum</i>) model species, and during age-related senescence in zebrafish (<i>Danio rerio</i>). In the regenerative blastema of wounded gar and axolotl, we observe increased inflammatory gene expression, including interferon genes and interleukins 6 and 8. We also observed a decrease in axolotl <i>Trex1</i> and gar <i>pml</i> expression during the early phases of wound healing which correlates with a dramatic increase in cGAS activity. In contrast, the <i>plex9.1</i> gene does not change in expression during wound healing in gar. However, we observed decreased expression of <i>plex9.1</i> in the senescing cardiac tissue of aged zebrafish, where 2′3′-cGAMP levels are elevated. Finally, we demonstrate a similar pattern of <i>Trex1</i>, <i>pml</i>, and <i>plex9.1</i> gene regulation across species in response to exogenous 2′3′-cGAMP. Thus, during the early stages of limb-fin regeneration, Pml, Trex1, and Plex9.1 exonucleases are downregulated, presumably to allow an evolutionarily ancient cGAS-STING activity to promote inflammation and the recruitment of immune cells.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":"342 3","pages":"241-251"},"PeriodicalIF":2.2,"publicationDate":"2023-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jez.b.23227","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50158086","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Using Xenopus to discover new candidate genes involved in BOR and other congenital hearing loss syndromes","authors":"Scott J. Neal,&nbsp;Anindita Rajasekaran,&nbsp;Nisveta Jusić,&nbsp;Louis Taylor,&nbsp;Mai Read,&nbsp;Dominique Alfandari,&nbsp;Francesca Pignoni,&nbsp;Sally A. Moody","doi":"10.1002/jez.b.23222","DOIUrl":"10.1002/jez.b.23222","url":null,"abstract":"<p>Hearing in infants is essential for brain development, acquisition of verbal language skills, and development of social interactions. Therefore, it is important to diagnose hearing loss soon after birth so that interventions can be provided as early as possible. Most newborns in the United States are screened for hearing deficits and commercially available next-generation sequencing hearing loss panels often can identify the causative gene, which may also identify congenital defects in other organs. One of the most prevalent autosomal dominant congenital hearing loss syndromes is branchio-oto-renal syndrome (BOR), which also presents with defects in craniofacial structures and the kidney. Currently, mutations in three genes, <i>SIX1, SIX5</i>, and <i>EYA1</i>, are known to be causative in about half of the BOR patients that have been tested. To uncover new candidate genes that could be added to congenital hearing loss genetic screens, we have combined the power of <i>Drosophila</i> mutants and protein biochemical assays with the embryological advantages of <i>Xenopus</i>, a key aquatic animal model with a high level of genomic similarity to human, to identify potential Six1 transcriptional targets and interacting proteins that play a role during otic development. We review our transcriptomic, yeast 2-hybrid, and proteomic approaches that have revealed a large number of new candidates. We also discuss how we have begun to identify how Six1 and co-factors interact to direct developmental events necessary for normal otic development.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":"342 3","pages":"212-240"},"PeriodicalIF":2.2,"publicationDate":"2023-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jez.b.23222","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41202828","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The paradise fish, an advanced animal model for behavioral genetics and evolutionary developmental biology","authors":"Nóra Szabó,&nbsp;Erika Fodor,&nbsp;Zoltán Varga,&nbsp;Anita Tarján-Rácz,&nbsp;Kata Szabó,&nbsp;Ádám Miklósi,&nbsp;Máté Varga","doi":"10.1002/jez.b.23223","DOIUrl":"10.1002/jez.b.23223","url":null,"abstract":"<p>Paradise fish (<i>Macropodus opercularis</i>) is an air-breathing freshwater fish species with a signature labyrinth organ capable of extracting oxygen from the air that helps these fish to survive in hypoxic environments. The appearance of this evolutionary innovation in anabantoids resulted in a rewired circulatory system, but also in the emergence of species-specific behaviors, such as territorial display, courtship and parental care in the case of the paradise fish. Early zoologists were intrigued by the structure and function of the labyrinth apparatus and a series of detailed descriptive histological studies at the beginning of the 20th century revealed the ontogenesis and function of this specialized system. A few decades later, these fish became the subject of numerous ethological studies, and detailed ethograms of their behavior were constructed. These latter studies also demonstrated a strong genetic component underlying their behavior, but due to lack of adequate molecular tools, the fine genetic dissection of the behavior was not possible at the time. The technological breakthroughs that transformed developmental biology and behavioral genetics in the past decades, however, give us now a unique opportunity to revisit these old questions. Building on the classic descriptive studies, the new methodologies will allow us to follow the development of the labyrinth apparatus at a cellular resolution, reveal the genes involved in this process and also the genetic architecture behind the complex behaviors that we can observe in this species.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":"342 3","pages":"189-199"},"PeriodicalIF":2.2,"publicationDate":"2023-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jez.b.23223","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41202827","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Close to complete conservation of the brachyceran opsin repertoire in the stalk-eyed fly Teleopsis dalmanni","authors":"Markus Friedrich","doi":"10.1002/jez.b.23220","DOIUrl":"10.1002/jez.b.23220","url":null,"abstract":"<p>Due to the unique morphology of their adult visual system, stalk-eyed flies represent an important model of exaggerated trait evolution through sexual selection. Early physiological measurements indicated wavelength sensitivity peaks in the ultraviolet (360 nm), blue (450), blue-green (490 nm), and red (&gt;550 nm) ranges in the compound eye retina of the stalk-eyed fly <i>Teleopsis dalmanni</i>, consistent with the trichromatic color and broad range motion detection vision system of brachyceran Diptera. A previous study of dipteran opsin gene diversification, however, detected only homologs of members of the long wavelength range sensitive opsin subfamilies <i>Rh2</i> and <i>Rh6</i> in <i>T. dalmanni</i>. Here, I report findings from analyzing the most recent <i>T. dalmanni</i> genome assembly, which revealed the conservation of most brachyceran opsin homologs except for the UV wavelength range-sensitive homolog Rh4. These results and other examples highlight the caution that needs to be applied to gene loss conclusions.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":"340 7","pages":"469-473"},"PeriodicalIF":2.2,"publicationDate":"2023-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41182735","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development and circuitry of the tunicate larval Motor Ganglion, a putative hindbrain/spinal cord homolog","authors":"Katarzyna M. Piekarz,&nbsp;Alberto Stolfi","doi":"10.1002/jez.b.23221","DOIUrl":"10.1002/jez.b.23221","url":null,"abstract":"<p>The Motor Ganglion (MG) is a small collection of neurons that control the swimming movements of the tunicate tadpole larva. Situated at the base of the tail, molecular and functional comparisons suggest that may be a homolog of the spinal cord and/or hindbrain (“rhombospinal” region) of vertebrates. Here we review the most current knowledge of the development, connectivity, functions, and unique identities of the neurons that comprise the MG, drawn mostly from studies in <i>Ciona</i> spp. The simple cell lineages, minimal cellular composition, and comprehensively mapped “connectome” of the <i>Ciona</i> MG all make this an excellent model for studying the development and physiology of motor control in aquatic larvae.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":"342 3","pages":"200-211"},"PeriodicalIF":2.2,"publicationDate":"2023-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10524493","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assessment of various standard fish diets on gut microbiome of platyfish Xiphophorus maculatus","authors":"Erika Soria,&nbsp;Crystal Russo,&nbsp;Camila Carlos-Shanley,&nbsp;Merritt Drewery,&nbsp;Will Boswell,&nbsp;Markita Savage,&nbsp;Lindsey Sanchez,&nbsp;Carolyn Chang,&nbsp;Zoltan M. Varga,&nbsp;Michael L. Kent,&nbsp;Thomas J. Sharpton,&nbsp;Yuan Lu","doi":"10.1002/jez.b.23218","DOIUrl":"10.1002/jez.b.23218","url":null,"abstract":"<p>Diet is an external factor that affects the physiological baseline of research animals. It can shape gut microbiome, which can impact the host. As a result, dietary variation can challenge experimental reproducibility and data integration across studies when not appropriately considered. To control for diet-induced variation, reference diets have been developed for common biomedical models. However, such reference diets have not yet been developed for nontraditional model organisms, such as <i>Xiphophorus</i> species. In this study, we compared two diets designed for zebrafish, a commercial zebrafish diet (Gemma and GEM), and a proposed zebrafish reference diet developed by the Watts laboratory at the University of Alabama at Birmingham (WAT) to the <i>Xiphophorus</i> Genetic Stock Center custom diet (CON) to evaluate the influence of diet on the <i>Xiphophorus</i> gut microbiome. <i>Xiphophorus maculatus</i> were fed the three diets from 2 to 6 months of age. Feces were collected and the gut microbiome was assessed using 16S rRNA sequencing every month. We observed substantial diet-driven variation in the gut microbiome. Our results indicate that diets developed specifically for zebrafish can affect the gut microbiome composition and may not be optimal for <i>Xiphophorus</i>.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":"342 3","pages":"271-277"},"PeriodicalIF":2.2,"publicationDate":"2023-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10962282/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10062580","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In the Spotlight—Established Researcher","authors":"Günter P. Wagner","doi":"10.1002/jez.b.23219","DOIUrl":"10.1002/jez.b.23219","url":null,"abstract":"","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":"340 8","pages":"484-485"},"PeriodicalIF":2.2,"publicationDate":"2023-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10009254","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic tools for the study of the mangrove killifish, Kryptolebias marmoratus, an emerging vertebrate model for phenotypic plasticity","authors":"Cheng-Yu Li,&nbsp;Helena Boldt,&nbsp;Emily Parent,&nbsp;Jax Ficklin,&nbsp;Althea James,&nbsp;Troy J. Anlage,&nbsp;Lena M. Boyer,&nbsp;Brianna R. Pierce,&nbsp;Kellee R. Siegfried,&nbsp;Matthew P. Harris,&nbsp;Eric S. Haag","doi":"10.1002/jez.b.23216","DOIUrl":"10.1002/jez.b.23216","url":null,"abstract":"<p><i>Kryptolebias marmoratus</i> (Kmar), a teleost fish of the order Cyprinodontiformes, has a suite of unique phenotypes and behaviors not observed in other fishes. Many of these phenotypes are discrete and highly plastic—varying over time within an individual, and in some cases reversible. Kmar and its interfertile sister species, <i>K. hermaphroditus</i>, are the only known self-fertile vertebrates. This unusual sexual mode has the potential to provide unique insights into the regulation of vertebrate sexual development, and also lends itself to genetics. Kmar is easily adapted to the lab and requires little maintenance. However, its internal fertilization and small clutch size limits its experimental use. To support Kmar as a genetic model, we compared alternative husbandry techniques to maximize recovery of early cleavage-stage embryos. We find that frequent egg collection enhances yield, and that protease treatment promotes the greatest hatching success. We completed a forward mutagenesis screen and recovered several mutant lines that serve as important tools for genetics in this model. Several will serve as useful viable recessive markers for marking crosses. Importantly, the mutant <i>kissylips</i> lays embryos at twice the rate of wild-type. Combining frequent egg collection with the <i>kissylips</i> mutant background allows for a substantial enhancement of early embryo yield. These improvements were sufficient to allow experimental analysis of early development and the successful mono- and bi-allelic targeted knockout of an endogenous <i>tyrosinase</i> gene with CRISPR/Cas9 nucleases. Collectively, these tools will facilitate modern developmental genetics in this fascinating fish, leading to future insights into the regulation of plasticity.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":"342 3","pages":"164-177"},"PeriodicalIF":2.2,"publicationDate":"2023-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jez.b.23216","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9957433","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In the Spotlight—Early career researcher","authors":"Patricia Schneider","doi":"10.1002/jez.b.23217","DOIUrl":"10.1002/jez.b.23217","url":null,"abstract":"","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":"342 3","pages":"119-120"},"PeriodicalIF":2.2,"publicationDate":"2023-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10319307","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}