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Substantial gene expression shifts during larval transitions in the pearl oyster Pinctada margaritifera 珍珠贝幼虫过渡期基因表达的重大转变
IF 2.2 3区 生物学 Q3 DEVELOPMENTAL BIOLOGY Pub Date : 2024-02-06 DOI: 10.1002/jez.b.23243
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。
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引用次数: 0
Acclimation of intertidally reproducing sea-snails protects embryos from lethal effects of transient hyperthermia 对潮间带繁殖的海螺进行驯化可保护胚胎免受瞬时高热的致命影响。
IF 2.2 3区 生物学 Q3 DEVELOPMENTAL BIOLOGY Pub Date : 2024-01-30 DOI: 10.1002/jez.b.23240
Morgan Q. Goulding

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.

将 Ilyanassa obsoleta(产于马萨诸塞州和佛罗里达州)和 Phrontis vibex(产于佛罗里达州)的胚胎暴露在 33 至 37°C 的温度下。在这两个物种中,非常幼小的胚胎对热应力特别敏感。短暂的早期热休克不会干扰螺旋裂解的几何形状,但会导致幼体形态发生和组织分化出现各种典型的严重缺陷。在 Ilyanassa 而非 P. vibex 中,早期热休克会导致早期分裂过程中的相间进展立即减慢或停止。这种可逆的停滞与幼体发育预后的改善有关,而且(至少在马萨诸塞州的蜗牛中)取决于亲本对温暖温度(约 25.5°C)的适应。在较低温度(16°C)下饲养的马萨诸塞州蜗牛的胚胎在早期分裂过程中,在 33°C下短暂孵化会出现细胞分裂失败,而在后期阶段,在 33°C下孵化会出现组织分化失败。这项初步研究揭示了一种情况,即在胚胎最脆弱的生命阶段,应激调节亲本可能赋予胚胎保护,使其免受可能致命的热应激。
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引用次数: 0
Unraveling stress resilience: Insights from adaptations to extreme environments by Astyanax mexicanus cavefish 揭示压力恢复能力:从墨西哥洞穴鱼对极端环境的适应中获得启示。
IF 2.2 3区 生物学 Q3 DEVELOPMENTAL BIOLOGY Pub Date : 2024-01-21 DOI: 10.1002/jez.b.23238
Ansa E. Cobham, Nicolas Rohner

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.

极端环境条件对生物进化轨迹的形成有着深远的影响。暴露在这些条件下会引起应激反应,从而引发新方向的表型变化。墨西哥四大家鱼(Astyanax mexicanus)是了解生物应对极端或新环境的进化机制的绝佳模型。该鱼种由两种形态组成:一种是传统的表面栖息鱼类,另一种是栖息在黑暗和生物多样性减少的生态系统中的盲洞栖息鱼类。在这篇综述中,我们探讨了洞穴环境中存在的特定压力因素,并研究了洞穴种群作为成功的殖民者为生存和发展所采取的各种适应策略。通过分析墨西哥蛙的进化反应,我们对使生物在具有挑战性的环境条件下繁衍生息的遗传、生理和行为适应性有了宝贵的认识。
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引用次数: 0
In the Spotlight—Early Career Researcher 聚焦--早期职业研究人员。
IF 2.2 3区 生物学 Q3 DEVELOPMENTAL BIOLOGY Pub Date : 2024-01-18 DOI: 10.1002/jez.b.23239
B. Duygu Özpolat
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引用次数: 0
3D spheroid culturing of Astyanax mexicanus liver-derived cell lines recapitulates distinct transcriptomic and metabolic states of in vivo tissue environment 三维球形培养墨西哥黄羊肝脏衍生细胞系可再现体内组织环境的不同转录组学和代谢状态。
IF 2.2 3区 生物学 Q3 DEVELOPMENTAL BIOLOGY Pub Date : 2024-01-08 DOI: 10.1002/jez.b.23236
Tathagata Biswas, Naresh Rajendran, Huzaifa Hassan, Hua Li, Chongbei Zhao, Nicolas Rohner

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.

体外试验是详细了解包括新陈代谢在内的各种生物过程的重要工具。河栖鱼类墨西哥蓑鲉(Astyanax mexicanus)的洞穴形态适应了它们的新陈代谢,使它们能够在生物多样性匮乏、营养有限的洞穴环境中茁壮成长。事实证明,来自洞穴和河流形态的墨西哥蓑鲉肝脏衍生细胞是更好地了解这些鱼类独特新陈代谢的绝佳体外资源。然而,目前的二维培养并未完全捕捉到Astyanax肝脏复杂的新陈代谢特征。众所周知,与二维单层培养相比,三维培养可以改变细胞的转录组状态。因此,为了通过模拟更广泛的代谢途径来拓宽体外系统的可能性,我们将体表和洞穴鱼的肝脏衍生 Astyanax 细胞培养成三维球形。我们以不同的细胞播种密度成功建立了三维培养物,并对由此产生的转录组和代谢变化进行了表征。我们发现,与单层培养的Astyanax细胞相比,三维培养的Astyanax细胞表现出改变的转录组特征,因此代表了更广泛的代谢途径,包括细胞周期变化和抗氧化活性,这些都与肝脏功能有关。测量二维培养和三维球体中抗氧化剂的酶学测定也显示,三维培养球体的抗氧化能力更强,这与差异基因表达数据一致。此外,球体还表现出表面和洞穴特异性代谢特征,使其成为与洞穴适应性相关的进化研究的合适系统。值得注意的是,洞穴鱼衍生的球形体富集了响应异生物刺激的基因,而来自体表的球形体富集了免疫反应基因,这两种基因都与每种形态的已知生理适应相关。综上所述,肝脏衍生球形体被证明是一种很有前途的体外模型,可拓宽我们对墨西哥蛙和一般脊椎动物新陈代谢的了解。
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引用次数: 0
Exploring pathways toward open-hardware ecosystems to safeguard genetic resources for biomedical research communities using aquatic model species 利用水生模式物种探索开放式硬件生态系统的路径,以保护生物医学研究界的遗传资源。
IF 2.2 3区 生物学 Q3 DEVELOPMENTAL BIOLOGY Pub Date : 2024-01-07 DOI: 10.1002/jez.b.23234
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.

开发可靠的种质资源库对于保存水生物种的遗传资源至关重要,这些资源被广泛用于支持生物医学创新,为自然发生的变异和通过遗传操作开发新变种提供了基础来源。资源库开发的一个重大障碍是缺乏低温保存能力和整个研究界的可重复性,这带来了失去数十亿美元研究投资所取得的进展的巨大风险。开放式科学硬件的出现推动了生物医学研究界的一场新运动。随着三维打印机等消费级制造技术的日益普及,开放式硬件设备可以进行定制设计,并将设计文件分发给社区成员,以提高严谨性、可重复性和标准化。本综述的总体目标是探索在使用水产模型资源进行生物医学研究的社区中创建开放硬件生态系统的途径。为了获得社区成员的反馈和见解,在马萨诸塞州伍兹霍尔举行的 2022 年人类疾病水生模型会议上,举办了一次互动研讨会,重点讨论种质资源库开发中的开放式硬件应用。这项工作利用种质资源库开发实例,将概念性战略与研讨会互动中获得的实际见解相结合。这些见解可用于为广大生物医学研究界建立开放式硬件生态系统。具体目标是(1) 引入支持生物医学研究的开放式硬件生态系统概念;(2) 通过四个主要领域探索建立开放式硬件生态系统的途径;(3) 确定机遇和未来方向。
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引用次数: 0
In the spotlight-Established researcher. 聚光灯下--资深研究员。
IF 2.2 3区 生物学 Q3 DEVELOPMENTAL BIOLOGY Pub Date : 2024-01-04 DOI: 10.1002/jez.b.23237
Eduardo E Zattara
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引用次数: 0
Antagonistic regulation of homeologous uncx.L and uncx.S genes orchestrates myotome and sclerotome differentiation in the evolutionarily divergent vertebral column of Xenopus laevis 同源的uncx.L和uncx.S基因的拮抗调控协调了在进化过程中发生分化的爪蟾脊椎中肌节和硬节的分化。
IF 2.2 3区 生物学 Q3 DEVELOPMENTAL BIOLOGY Pub Date : 2023-12-28 DOI: 10.1002/jez.b.23235
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.

有尾目动物的椎柱与其他四足动物的椎柱差异很大,但其形态发生的分子机制在很大程度上仍未被探索。本研究探讨了同源的uncx.L和uncx.S基因在异源四倍体蛙类椎柱形态发生中的作用。我们首先克隆了无尾目章鱼的uncx同源基因,并利用原位杂交技术确定了它们的空间表达模式。此外,我们还分别通过地塞米松诱导的uncx构建体和反义吗啉寡核苷酸采用了功能增益和功能缺失的方法。同源uncx基因信使核糖核酸序列的比较分析表明,uncx.L变体缺乏类似eh1的抑制结构域。我们的空间表达分析表明,在前绒毛中胚层和体节中,uncx.L和uncx.S的转录本位于重叠的区域。uncx基因功能的改变极大地影响了硬骨和肌骨的发育和分化,导致中轴骨骼畸形。我们的研究结果表明,同源基因uncx.L和uncx.S在体细胞发生过程中表现出拮抗功能。具体来说,uncx.S似乎对硬骨体的发育和分化至关重要,而uncx.L则主要影响肌骨体的发育。X.laevis的uncx.L基因在异位四倍体化后失去了类似于eh1的抑制结构域,变成了一种 "原生显性阴性 "变体,有可能与uncx.S竞争相同的靶基因。最后,组织学分析表明,uncx.S的表达是椎骨脊柱和神经弓正确形成的必要条件,而uncx.L则是躯干肌肉发育的必要条件。
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引用次数: 0
Skeletal Class III phenotype: Link between animal models and human genetics: A scoping review 骨骼 III 级表型:动物模型与人类遗传学之间的联系:范围综述
IF 2.2 3区 生物学 Q3 DEVELOPMENTAL BIOLOGY Pub Date : 2023-12-18 DOI: 10.1002/jez.b.23230
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.

本研究旨在从动物研究中找出证据,研究导致骨骼三级(SCIII)错颌畸形表型的上下颌骨差异的遗传变异。按照 JBI 的《证据综合手册》和用于范围界定综述的 PRISMA 扩展标准,我们提出了一个参与者、概念和背景问题,并在 PubMed、Scopus、WOS、Scielo、Open Gray 和 Mednar 数据库中进行了系统检索。在已确定的 779 项研究中,有 13 项符合筛选标准,并纳入了数据提取。SCIII错颌畸形表型在Danio rerio、Dicentrarchus labrax和Equus africanus asinus模型中被描述为下颌前突;在Felis silvestris catus、Canis familiaris、Salmo trutta和Mus musculus模型中被描述为上颌缺损。已确定的遗传变异突显了 BMP 和 TGF-β 信号传导的重要性。它们的调节途径和遗传相互作用将它们与细胞骨调节事件联系起来,特别是出生后颅骨滑膜的骨化调节。总之,在动物模型中发现了 20 个与骨骼 SCIII 畸形表型相关的遗传变异。它们之间的相互作用和调控途径证实了这些变体在骨骼生长、分化事件和出生后颅骨突触骨化调控中的作用。
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引用次数: 0
Semi-automated, high-content imaging of drug transporter knockout sea urchin (Lytechinus pictus) embryos 药物转运体基因敲除海胆(Lytechinus pictus)胚胎的半自动高含量成像
IF 2.2 3区 生物学 Q3 DEVELOPMENTAL BIOLOGY Pub Date : 2023-12-12 DOI: 10.1002/jez.b.23231
Evan Tjeerdema, Yoon Lee, Rachel Metry, Amro Hamdoun

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.

海胆的一个显著特征是它们的繁殖力极强。海胆产生数百万个透明的、同步发育的胚胎,非常适合进行时空发育分析。这一生物学特性已被有效地用于生化变化的集合测量。然而,它在成像研究中未得到充分利用,其中使用单胚胎测量。在这里,我们提出了一个例子,说明如何使用稳定的遗传学和高含量成像,以及基于机器学习的图像分析,在基于成像的药物筛选中利用海胆的繁殖能力和同步性。在我们最近创建的海胆ABCB1基因敲除系的基础上,我们开发了一种高通量测定方法来探测这种药物转运体在胚胎中的作用。我们使用高含量成像来比较纯合子敲除和野生型胚胎中典型底物和转运体抑制剂的积累和毒性,包括荧光分子和抗有丝分裂癌症药物。为了测量由此产生的图像数据的反应,我们使用了一个嵌套的卷积神经网络,该网络根据荧光或细胞分裂快速分类胚胎。该方法鉴定海胆胚胎的准确率为99.8%,鉴定双细胞和异常胚胎的准确率分别为96.3%和89.1%。结果表明,ABCB1基因敲除胚胎转运蛋白底物钙黄蛋白积累速度比野生型快3.09倍。同样,基因敲除对有丝分裂毒素长春花碱和紫杉醇的敏感性分别是前者的4.71倍和3.07倍。本研究为海胆胚胎的大规模药理筛选铺平了道路。
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