T. Destanque, J. Le Luyer, V. Quillien, M. Sham Koua, P. Auffrey, C.-L. Ky
Early development stages in marine bivalve are critical periods where larvae transition from pelagic free-life to sessile mature individuals. The successive metamorphosis requires the expression of key genes, the functions of which might be under high selective pressure, hence understanding larval development represents key knowledge for both fundamental and applied research. Phenotypic larvae development is well known, but the underlying molecular mechanisms such as associated gene expression dynamic and molecular cross-talks remains poorly described for several nonmodel species, such as P. margaritifera. We designed a whole transcriptome RNA-sequencing analysis to describe such gene expression dynamics following four larval developmental stages: d-shape, Veliger, Umbo and Eye-spot. Larval gene expression and annotated functions drastically diverge. Metabolic function (gene expression related to lipid, amino acid and carbohydrate use) is highly upregulated in the first development stages, with increasing demand from d-shape to umbo. Morphogenesis and larval transition are partly ordered by Thyroid hormones and Wnt signaling. While larvae shells show some similar characteristic to adult shells, the cause of initialization of biomineralization differ from the one found in adults. The present study provides a global overview of Pinctada margaritifera larval stages transitioning through gene expression dynamics, molecular mechanisms and ontogeny of biomineralization, immune system, and sensory perception processes.
海洋双壳类动物的早期发育阶段是幼虫从浮游自由生活过渡到无梗成熟个体的关键时期。连续的变态过程需要关键基因的表达,而这些基因的功能可能受到很大的选择压力,因此了解幼虫的发育是基础研究和应用研究的关键知识。幼虫发育的表型已广为人知,但其潜在的分子机制,如相关基因的表达动态和分子交叉关系,对一些非模式物种(如玛格丽特)的描述仍然很少。我们设计了一项全转录组 RNA 序列分析,以描述 d 形、Veliger、Umbo 和 Eye-spot 四个幼虫发育阶段的基因表达动态。幼虫的基因表达与注释的功能大相径庭。代谢功能(与脂质、氨基酸和碳水化合物的使用有关的基因表达)在最初的发育阶段高度上调,从d形到umbo的需求不断增加。甲状腺激素和 Wnt 信号在一定程度上决定了形态发生和幼虫过渡。虽然幼虫的外壳显示出与成虫外壳相似的特征,但生物矿化初始化的原因却与成虫不同。本研究通过生物矿化、免疫系统和感官知觉过程的基因表达动态、分子机制和本体发育,全面概述了鲎幼虫阶段的过渡。
{"title":"Substantial gene expression shifts during larval transitions in the pearl oyster Pinctada margaritifera","authors":"T. Destanque, J. Le Luyer, V. Quillien, M. Sham Koua, P. Auffrey, C.-L. Ky","doi":"10.1002/jez.b.23243","DOIUrl":"10.1002/jez.b.23243","url":null,"abstract":"<p>Early development stages in marine bivalve are critical periods where larvae transition from pelagic free-life to sessile mature individuals. The successive metamorphosis requires the expression of key genes, the functions of which might be under high selective pressure, hence understanding larval development represents key knowledge for both fundamental and applied research. Phenotypic larvae development is well known, but the underlying molecular mechanisms such as associated gene expression dynamic and molecular cross-talks remains poorly described for several nonmodel species, such as <i>P. margaritifera</i>. We designed a whole transcriptome RNA-sequencing analysis to describe such gene expression dynamics following four larval developmental stages: \u0000<span>d</span>-shape, Veliger, Umbo and Eye-spot. Larval gene expression and annotated functions drastically diverge. Metabolic function (gene expression related to lipid, amino acid and carbohydrate use) is highly upregulated in the first development stages, with increasing demand from \u0000<span>d</span>-shape to umbo. Morphogenesis and larval transition are partly ordered by Thyroid hormones and Wnt signaling. While larvae shells show some similar characteristic to adult shells, the cause of initialization of biomineralization differ from the one found in adults. The present study provides a global overview of <i>Pinctada margaritifera</i> larval stages <i>transitioning</i> through gene expression dynamics, molecular mechanisms and ontogeny of biomineralization, immune system, and sensory perception processes.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":"342 2","pages":"76-84"},"PeriodicalIF":2.2,"publicationDate":"2024-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jez.b.23243","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139691997","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}
Embryos of Ilyanassa obsoleta (from Massachusetts and Florida) and Phrontis vibex (from Florida) were exposed to temperatures from 33 to 37°C. In both species, very young embryos are especially sensitive to thermal stress. Brief early heat shock did not disturb spiral cleavage geometry but led to variable, typically severe defects in larval morphogenesis and tissue differentiation. In Ilyanassa but not P. vibex, early heat shock resulted in immediate slowing or arrest of interphase progression during early cleavage. This reversible arrest was correlated with improved prognosis for larval development and (in Massachusetts snails, at least) depended on parental acclimation to warm temperature (~25.5°C). Embryos from Massachusetts snails housed at lower temperature (16°C) exhibited cytokinesis failure when briefly incubated at 33°C during early cleavage, and tissue differentiation failure during incubation at 33°C begun at later stages. This preliminary study reveals a case in which stress-conditioned parents may endow embryos with protection against potentially lethal thermal stress during the most vulnerable stages of life.
{"title":"Acclimation of intertidally reproducing sea-snails protects embryos from lethal effects of transient hyperthermia","authors":"Morgan Q. Goulding","doi":"10.1002/jez.b.23240","DOIUrl":"10.1002/jez.b.23240","url":null,"abstract":"<p>Embryos of <i>Ilyanassa obsoleta</i> (from Massachusetts and Florida) and <i>Phrontis vibex</i> (from Florida) were exposed to temperatures from 33 to 37°C. In both species, very young embryos are especially sensitive to thermal stress. Brief early heat shock did not disturb spiral cleavage geometry but led to variable, typically severe defects in larval morphogenesis and tissue differentiation. In <i>Ilyanassa</i> but not <i>P. vibex</i>, early heat shock resulted in immediate slowing or arrest of interphase progression during early cleavage. This reversible arrest was correlated with improved prognosis for larval development and (in Massachusetts snails, at least) depended on parental acclimation to warm temperature (~25.5°C). Embryos from Massachusetts snails housed at lower temperature (16°C) exhibited cytokinesis failure when briefly incubated at 33°C during early cleavage, and tissue differentiation failure during incubation at 33°C begun at later stages. This preliminary study reveals a case in which stress-conditioned parents may endow embryos with protection against potentially lethal thermal stress during the most vulnerable stages of life.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":"342 2","pages":"101-105"},"PeriodicalIF":2.2,"publicationDate":"2024-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139642275","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}
Extreme environmental conditions have profound impacts on shaping the evolutionary trajectory of organisms. Exposure to these conditions elicits stress responses, that can trigger phenotypic changes in novel directions. The Mexican Tetra, Astyanax mexicanus, is an excellent model for understanding evolutionary mechanisms in response to extreme or new environments. This fish species consists of two morphs; the classical surface-dwelling fish and the blind cave-dwellers that inhabit dark and biodiversity-reduced ecosystems. In this review, we explore the specific stressors present in cave environments and examine the diverse adaptive strategies employed by cave populations to not only survive but thrive as successful colonizers. By analyzing the evolutionary responses of A. mexicanus, we gain valuable insights into the genetic, physiological, and behavioral adaptations that enable organisms to flourish under challenging environmental conditions.
{"title":"Unraveling stress resilience: Insights from adaptations to extreme environments by Astyanax mexicanus cavefish","authors":"Ansa E. Cobham, Nicolas Rohner","doi":"10.1002/jez.b.23238","DOIUrl":"10.1002/jez.b.23238","url":null,"abstract":"<p>Extreme environmental conditions have profound impacts on shaping the evolutionary trajectory of organisms. Exposure to these conditions elicits stress responses, that can trigger phenotypic changes in novel directions. The Mexican Tetra, <i>Astyanax mexicanus</i>, is an excellent model for understanding evolutionary mechanisms in response to extreme or new environments. This fish species consists of two morphs; the classical surface-dwelling fish and the blind cave-dwellers that inhabit dark and biodiversity-reduced ecosystems. In this review, we explore the specific stressors present in cave environments and examine the diverse adaptive strategies employed by cave populations to not only survive but thrive as successful colonizers. By analyzing the evolutionary responses of <i>A. mexicanus</i>, we gain valuable insights into the genetic, physiological, and behavioral adaptations that enable organisms to flourish under challenging environmental conditions.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":"342 3","pages":"178-188"},"PeriodicalIF":2.2,"publicationDate":"2024-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jez.b.23238","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139512550","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":"B. Duygu Özpolat","doi":"10.1002/jez.b.23239","DOIUrl":"10.1002/jez.b.23239","url":null,"abstract":"","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":"342 2","pages":"63-64"},"PeriodicalIF":2.2,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139491563","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}
In vitro assays are crucial tools for gaining detailed insights into various biological processes, including metabolism. Cave morphs of the river-dwelling fish species, Astyanax mexicanus, have adapted their metabolism allowing them to thrive in the biodiversity-deprived and nutrient-limited environment of caves. Liver-derived cells from the cave and river morphs of A. mexicanus have proven to be excellent in vitro resources to better understand the unique metabolism of these fish. However, the current 2D cultures have not fully captured the complex metabolic profile of the Astyanax liver. It is known that 3D culturing can modulate the transcriptomic state of cells when compared to its 2D monolayer culture. Therefore, to broaden the possibilities of the in vitro system by modeling a wider gamut of metabolic pathways, we cultured the liver-derived Astyanax cells of both surface and cavefish into 3D spheroids. We successfully established 3D cultures at various cell seeding densities for several weeks and characterized the resultant transcriptomic and metabolic variations. We found that the 3D cultured Astyanax cells exhibit an altered transcriptomic profile and consequently represent a wider range of metabolic pathways, including cell cycle changes and antioxidant activities, associated with liver functioning as compared to its monolayer culture. Enzymatic assay measuring antioxidants in 2D culture and 3D spheroids also revealed enhanced antioxidative capacity of 3D cultured spheroids, in line with the differential gene expression data. Additionally, the spheroids also exhibited surface and cave-specific metabolic signatures, making it a suitable system for evolutionary studies associated with cave adaptation. Notably, cavefish derived spheroids enriched for genes responding to xenobiotic stimulus, while the ones from surface enriched for immune response, both of which resonated with known physiologically adaptations associated with each morph. Taken together, the liver-derived spheroids prove to be a promising in vitro model for widening our understanding of metabolism in A. mexicanus and of vertebrates in general.
{"title":"3D spheroid culturing of Astyanax mexicanus liver-derived cell lines recapitulates distinct transcriptomic and metabolic states of in vivo tissue environment","authors":"Tathagata Biswas, Naresh Rajendran, Huzaifa Hassan, Hua Li, Chongbei Zhao, Nicolas Rohner","doi":"10.1002/jez.b.23236","DOIUrl":"10.1002/jez.b.23236","url":null,"abstract":"<p>In vitro assays are crucial tools for gaining detailed insights into various biological processes, including metabolism. Cave morphs of the river-dwelling fish species, <i>Astyanax mexicanus</i>, have adapted their metabolism allowing them to thrive in the biodiversity-deprived and nutrient-limited environment of caves. Liver-derived cells from the cave and river morphs of <i>A. mexicanus</i> have proven to be excellent in vitro resources to better understand the unique metabolism of these fish. However, the current 2D cultures have not fully captured the complex metabolic profile of the <i>Astyanax</i> liver. It is known that 3D culturing can modulate the transcriptomic state of cells when compared to its 2D monolayer culture. Therefore, to broaden the possibilities of the in vitro system by modeling a wider gamut of metabolic pathways, we cultured the liver-derived <i>Astyanax</i> cells of both surface and cavefish into 3D spheroids. We successfully established 3D cultures at various cell seeding densities for several weeks and characterized the resultant transcriptomic and metabolic variations. We found that the 3D cultured <i>Astyanax</i> cells exhibit an altered transcriptomic profile and consequently represent a wider range of metabolic pathways, including cell cycle changes and antioxidant activities, associated with liver functioning as compared to its monolayer culture. Enzymatic assay measuring antioxidants in 2D culture and 3D spheroids also revealed enhanced antioxidative capacity of 3D cultured spheroids, in line with the differential gene expression data. Additionally, the spheroids also exhibited surface and cave-specific metabolic signatures, making it a suitable system for evolutionary studies associated with cave adaptation. Notably, cavefish derived spheroids enriched for genes responding to xenobiotic stimulus, while the ones from surface enriched for immune response, both of which resonated with known physiologically adaptations associated with each morph. Taken together, the liver-derived spheroids prove to be a promising in vitro model for widening our understanding of metabolism in <i>A. mexicanus</i> and of vertebrates in general.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":"342 3","pages":"301-312"},"PeriodicalIF":2.2,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jez.b.23236","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139403055","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}
Yue Liu, Jack C. Koch, Lucía Arregui, Allyssa Oune, Sarah Bodenstein, Maria T. Gutierrez-Wing, Terrence R. Tiersch
Development of reliable germplasm repositories is critical for preservation of genetic resources of aquatic species, which are widely utilized to support biomedical innovation by providing a foundational source for naturally occurring variation and development of new variants through genetic manipulations. A significant barrier in repository development is the lack of cryopreservation capability and reproducibility across the research community, posing great risks of losing advances developed from billions of dollars of research investment. The emergence of open scientific hardware has fueled a new movement across biomedical research communities. With the increasing accessibility of consumer-level fabrication technologies, such as three-dimensional printers, open hardware devices can be custom designed, and design files distributed to community members for enhancing rigor, reproducibility, and standardization. The overall goal of this review is to explore pathways to create open-hardware ecosystems among the communities using aquatic model resources for biomedical research. To gain feedback and insights from community members, an interactive workshop focusing on open-hardware applications in germplasm repository development was held at the 2022 Aquatic Models for Human Disease Conference, Woods Hole, Massachusetts. This work integrates conceptual strategies with practical insights derived from workshop interactions using examples of germplasm repository development. These insights can be generalized for establishment of open-hardware ecosystems for a broad biomedical research community. The specific objectives were to: (1) introduce an open-hardware ecosystem concept to support biomedical research; (2) explore pathways toward open-hardware ecosystems through four major areas, and (3) identify opportunities and future directions.
{"title":"Exploring pathways toward open-hardware ecosystems to safeguard genetic resources for biomedical research communities using aquatic model species","authors":"Yue Liu, Jack C. Koch, Lucía Arregui, Allyssa Oune, Sarah Bodenstein, Maria T. Gutierrez-Wing, Terrence R. Tiersch","doi":"10.1002/jez.b.23234","DOIUrl":"10.1002/jez.b.23234","url":null,"abstract":"<p>Development of reliable germplasm repositories is critical for preservation of genetic resources of aquatic species, which are widely utilized to support biomedical innovation by providing a foundational source for naturally occurring variation and development of new variants through genetic manipulations. A significant barrier in repository development is the lack of cryopreservation capability and reproducibility across the research community, posing great risks of losing advances developed from billions of dollars of research investment. The emergence of open scientific hardware has fueled a new movement across biomedical research communities. With the increasing accessibility of consumer-level fabrication technologies, such as three-dimensional printers, open hardware devices can be custom designed, and design files distributed to community members for enhancing rigor, reproducibility, and standardization. The overall goal of this review is to explore pathways to create open-hardware ecosystems among the communities using aquatic model resources for biomedical research. To gain feedback and insights from community members, an interactive workshop focusing on open-hardware applications in germplasm repository development was held at the 2022 Aquatic Models for Human Disease Conference, Woods Hole, Massachusetts. This work integrates conceptual strategies with practical insights derived from workshop interactions using examples of germplasm repository development. These insights can be generalized for establishment of open-hardware ecosystems for a broad biomedical research community. The specific objectives were to: (1) introduce an open-hardware ecosystem concept to support biomedical research; (2) explore pathways toward open-hardware ecosystems through four major areas, and (3) identify opportunities and future directions.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":"342 3","pages":"278-290"},"PeriodicalIF":2.2,"publicationDate":"2024-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139377744","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":"In the spotlight-Established researcher.","authors":"Eduardo E Zattara","doi":"10.1002/jez.b.23237","DOIUrl":"https://doi.org/10.1002/jez.b.23237","url":null,"abstract":"","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139097981","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}
Romel S. Sánchez, María A Lazarte, Virginia S. L. Abdala, Sara S. Sánchez
In anurans, the vertebral column diverges widely from that of other tetrapods; yet the molecular mechanisms underlying its morphogenesis remain largely unexplored. In this study, we investigate the role of the homeologous uncx.L and uncx.S genes in the vertebral column morphogenesis of the allotetraploid frog Xenopus laevis. We initiated our study by cloning the uncx orthologous genes in the anuran Xenopus and determining their spatial expression patterns using in situ hybridization. Additionally, we employed gain-of-function and loss-of-function approaches through dexamethasone-inducible uncx constructs and antisense morpholino oligonucleotides, respectively. Comparative analysis of the messenger RNA sequences of homeologous uncx genes revealed that the uncx.L variant lacks the eh1-like repressor domain. Our spatial expression analysis indicated that in the presomitic mesoderm and somites, the transcripts of uncx.L and uncx.S are located in overlapping domains. Alterations in the function of uncx genes significantly impact the development and differentiation of the sclerotome and myotome, resulting in axial skeleton malformations. Our findings suggest a scenario where the homeologous genes uncx.L and uncx.S exhibit antagonistic functions during somitogenesis. Specifically, uncx.S appears to be crucial for sclerotome development and differentiation, while uncx.L primarily influences myotome development. Postallotetraploidization, the uncx.L gene in X. laevis evolved to lose its eh1-like repressor domain, transforming into a “native dominant negative” variant that potentially competes with uncx.S for the same target genes. Finally, the histological analysis revealed that uncx.S expression is necessary for the correct formation of pedicles and neural arch of the vertebrae, and uncx.L is required for trunk muscle development.
{"title":"Antagonistic regulation of homeologous uncx.L and uncx.S genes orchestrates myotome and sclerotome differentiation in the evolutionarily divergent vertebral column of Xenopus laevis","authors":"Romel S. Sánchez, María A Lazarte, Virginia S. L. Abdala, Sara S. Sánchez","doi":"10.1002/jez.b.23235","DOIUrl":"10.1002/jez.b.23235","url":null,"abstract":"<p>In anurans, the vertebral column diverges widely from that of other tetrapods; yet the molecular mechanisms underlying its morphogenesis remain largely unexplored. In this study, we investigate the role of the homeologous <i>uncx.L</i> and <i>uncx.S</i> genes in the vertebral column morphogenesis of the allotetraploid frog <i>Xenopus laevis</i>. We initiated our study by cloning the <i>uncx</i> orthologous genes in the anuran <i>Xenopus</i> and determining their spatial expression patterns using <i>in situ</i> hybridization. Additionally, we employed gain-of-function and loss-of-function approaches through dexamethasone-inducible <i>uncx</i> constructs and antisense morpholino oligonucleotides, respectively. Comparative analysis of the messenger RNA sequences of homeologous <i>uncx</i> genes revealed that the <i>uncx.L</i> variant lacks the eh1-like repressor domain. Our spatial expression analysis indicated that in the presomitic mesoderm and somites, the transcripts of <i>uncx.L</i> and <i>uncx.S</i> are located in overlapping domains. Alterations in the function of <i>uncx</i> genes significantly impact the development and differentiation of the sclerotome and myotome, resulting in axial skeleton malformations. Our findings suggest a scenario where the homeologous genes <i>uncx.L</i> and <i>uncx.S</i> exhibit antagonistic functions during somitogenesis. Specifically, <i>uncx.S</i> appears to be crucial for sclerotome development and differentiation, while <i>uncx.L</i> primarily influences myotome development. Postallotetraploidization, the <i>uncx.L</i> gene in <i>X. laevis</i> evolved to lose its eh1-like repressor domain, transforming into a “native dominant negative” variant that potentially competes with <i>uncx.S</i> for the same target genes. Finally, the histological analysis revealed that <i>uncx.S</i> expression is necessary for the correct formation of pedicles and neural arch of the vertebrae, and <i>uncx.L</i> is required for trunk muscle development.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":"342 4","pages":"350-367"},"PeriodicalIF":2.2,"publicationDate":"2023-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139058402","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}
Alexandra Dehesa-Santos, Maria Cristina Faria-Teixeira, Alejandro Iglesias-Linares
This study aimed to identify evidence from animal studies examining genetic variants underlying maxillomandibular discrepancies resulting in a skeletal Class III (SCIII) malocclusion phenotype. Following the Manual for Evidence Synthesis of the JBI and the PRISMA extension for scoping reviews, a participant, concept, context question was formulated and systematic searches were executed in the PubMed, Scopus, WOS, Scielo, Open Gray, and Mednar databases. Of the 779 identified studies, 13 met the selection criteria and were included in the data extraction. The SCIII malocclusion phenotype was described as mandibular prognathism in the Danio rerio, Dicentrarchus labrax, and Equus africanus asinus models; and as maxillary deficiency in the Felis silvestris catus, Canis familiaris, Salmo trutta, and Mus musculus models. The identified genetic variants highlight the significance of BMP and TGF-β signaling. Their regulatory pathways and genetic interactions link them to cellular bone regulation events, particularly ossification regulation of postnatal cranial synchondroses. In conclusion, twenty genetic variants associated with the skeletal SCIII malocclusion phenotype were identified in animal models. Their interactions and regulatory pathways corroborate the role of these variants in bone growth, differentiation events, and ossification regulation of postnatal cranial synchondroses.
{"title":"Skeletal Class III phenotype: Link between animal models and human genetics: A scoping review","authors":"Alexandra Dehesa-Santos, Maria Cristina Faria-Teixeira, Alejandro Iglesias-Linares","doi":"10.1002/jez.b.23230","DOIUrl":"10.1002/jez.b.23230","url":null,"abstract":"<p>This study aimed to identify evidence from animal studies examining genetic variants underlying maxillomandibular discrepancies resulting in a skeletal Class III (SCIII) malocclusion phenotype. Following the Manual for Evidence Synthesis of the JBI and the PRISMA extension for scoping reviews, a participant, concept, context question was formulated and systematic searches were executed in the PubMed, Scopus, WOS, Scielo, Open Gray, and Mednar databases. Of the 779 identified studies, 13 met the selection criteria and were included in the data extraction. The SCIII malocclusion phenotype was described as mandibular prognathism in <i>the Danio rerio</i>, <i>Dicentrarchus labrax</i>, and <i>Equus africanus asinus</i> models; and as maxillary deficiency in <i>the Felis silvestris catus</i>, <i>Canis familiaris</i>, <i>Salmo trutta</i>, and <i>Mus musculus</i> models. The identified genetic variants highlight the significance of BMP and TGF-β signaling. Their regulatory pathways and genetic interactions link them to cellular bone regulation events, particularly ossification regulation of postnatal cranial synchondroses. In conclusion, twenty genetic variants associated with the skeletal SCIII malocclusion phenotype were identified in animal models. Their interactions and regulatory pathways corroborate the role of these variants in bone growth, differentiation events, and ossification regulation of postnatal cranial synchondroses.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":"342 1","pages":"21-44"},"PeriodicalIF":2.2,"publicationDate":"2023-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jez.b.23230","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138716101","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}
A defining feature of sea urchins is their extreme fecundity. Urchins produce millions of transparent, synchronously developing embryos, ideal for spatial and temporal analysis of development. This biological feature has been effectively utilized for ensemble measurement of biochemical changes. However, it has been underutilized in imaging studies, where single embryo measurements are used. Here we present an example of how stable genetics and high content imaging, along with machine learning-based image analysis, can be used to exploit the fecundity and synchrony of sea urchins in imaging-based drug screens. Building upon our recently created sea urchin ABCB1 knockout line, we developed a high-throughput assay to probe the role of this drug transporter in embryos. We used high content imaging to compare accumulation and toxicity of canonical substrates and inhibitors of the transporter, including fluorescent molecules and antimitotic cancer drugs, in homozygous knockout and wildtype embryos. To measure responses from the resulting image data, we used a nested convolutional neural network, which rapidly classified embryos according to fluorescence or cell division. This approach identified sea urchin embryos with 99.8% accuracy and determined two-cell and aberrant embryos with 96.3% and 89.1% accuracy, respectively. The results revealed that ABCB1 knockout embryos accumulated the transporter substrate calcein 3.09 times faster than wildtypes. Similarly, knockouts were 4.71 and 3.07 times more sensitive to the mitotic poisons vinblastine and taxol. This study paves the way for large scale pharmacological screens in the sea urchin embryo.
{"title":"Semi-automated, high-content imaging of drug transporter knockout sea urchin (Lytechinus pictus) embryos","authors":"Evan Tjeerdema, Yoon Lee, Rachel Metry, Amro Hamdoun","doi":"10.1002/jez.b.23231","DOIUrl":"10.1002/jez.b.23231","url":null,"abstract":"<p>A defining feature of sea urchins is their extreme fecundity. Urchins produce millions of transparent, synchronously developing embryos, ideal for spatial and temporal analysis of development. This biological feature has been effectively utilized for ensemble measurement of biochemical changes. However, it has been underutilized in imaging studies, where single embryo measurements are used. Here we present an example of how stable genetics and high content imaging, along with machine learning-based image analysis, can be used to exploit the fecundity and synchrony of sea urchins in imaging-based drug screens. Building upon our recently created sea urchin ABCB1 knockout line, we developed a high-throughput assay to probe the role of this drug transporter in embryos. We used high content imaging to compare accumulation and toxicity of canonical substrates and inhibitors of the transporter, including fluorescent molecules and antimitotic cancer drugs, in homozygous knockout and wildtype embryos. To measure responses from the resulting image data, we used a nested convolutional neural network, which rapidly classified embryos according to fluorescence or cell division. This approach identified sea urchin embryos with 99.8% accuracy and determined two-cell and aberrant embryos with 96.3% and 89.1% accuracy, respectively. The results revealed that ABCB1 knockout embryos accumulated the transporter substrate calcein 3.09 times faster than wildtypes. Similarly, knockouts were 4.71 and 3.07 times more sensitive to the mitotic poisons vinblastine and taxol. This study paves the way for large scale pharmacological screens in the sea urchin embryo.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":"342 3","pages":"313-329"},"PeriodicalIF":2.2,"publicationDate":"2023-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jez.b.23231","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138628735","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}