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Untangling the relationship between developmental and evolutionary integration 解开发展与进化整合之间的关系
IF 7.3 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2023-08-01 DOI: 10.1016/j.semcdb.2022.05.026
Kory M. Evans, Thaddaeus J. Buser, Olivier Larouche, Matthew A. Kolmann

Patterns of integration and modularity among organismal traits are prevalent across the tree of life, and at multiple scales of biological organization. Over the past several decades, researchers have studied these patterns at the developmental, and evolutionary levels. While their work has identified the potential drivers of these patterns at different scales, there appears to be a lack of consensus on the relationship between developmental and evolutionary integration. Here, we review and summarize key studies and build a framework to describe the conceptual relationship between these patterns across organismal scales and illustrate how, and why some of these studies may have yielded seemingly conflicting outcomes. We find that among studies that analyze patterns of integration and modularity using morphological data, the lack of consensus may stem in part from the difficulty of fully disentangling the developmental and functional causes of integration. Nonetheless, in some empirical systems, patterns of evolutionary modularity have been found to coincide with expectations based on developmental processes, suggesting that in some circumstances, developmental modularity may translate to evolutionary modularity. We also advance an extension to Hallgrímsson et al.’s palimpsest model to describe how patterns of trait modularity may shift across different evolutionary scales. Finally, we also propose some directions for future research which will hopefully be useful for investigators interested in these issues.

生物体特征之间的整合和模块化模式在整个生命树和生物组织的多个尺度上普遍存在。在过去的几十年里,研究人员从发展和进化的层面研究了这些模式。虽然他们的工作已经在不同的尺度上确定了这些模式的潜在驱动因素,但对于发展和进化整合之间的关系似乎缺乏共识。在这里,我们回顾和总结了关键研究,并建立了一个框架来描述这些模式之间的概念关系,并说明其中一些研究可能产生了看似矛盾的结果。我们发现,在使用形态学数据分析整合和模块化模式的研究中,缺乏共识可能部分源于难以完全解开整合的发育和功能原因。尽管如此,在一些经验系统中,已经发现进化模块化的模式与基于发展过程的期望一致,这表明在某些情况下,发展模块化可能转化为进化模块化。我们还对Hallgrímsson等人的重写模型进行了扩展,以描述特征模块化模式如何在不同的进化尺度上发生变化。最后,我们还提出了一些未来研究的方向,希望对对这些问题感兴趣的研究人员有用。
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引用次数: 3
Structuralism and Adaptationism: Friends? Or foes? 结构主义与适应主义:朋友?还是敌人?
IF 7.3 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2023-08-01 DOI: 10.1016/j.semcdb.2022.02.022
Rachael L. Brown

Historically, the empirical study of phenotypic diversification has fallen into two rough camps; (1) "structuralist approaches" focusing on developmental constraint, bias, and innovation (with evo-devo at the core); and (2) "adaptationist approaches" focusing on adaptation, and natural selection. Whilst debates, such as that surrounding the proposed "Extended" Evolutionary Synthesis, often juxtapose these two positions, this review focuses on the grey space in between. Specifically, here I present a novel analysis of structuralism which enables us to take a more nuanced look at the motivations behind the structuralist and adaptationist positions. This makes clear how the two approaches can conflict, and points of potential commensurability. The review clarifies (a) the value of the evo-devo approach to phenotypic diversity, but also (b) how it properly relates to other predominant approaches to the same issues in evolutionary biology more broadly.

从历史上看,表型多样化的实证研究大致分为两个阵营;(1) “结构主义方法”关注发展约束、偏见和创新(以evo-devo为核心);(2)侧重于适应和自然选择的“适应主义方法”。虽然围绕拟议的“扩展”进化综合的辩论经常将这两种立场并置,但本综述侧重于两者之间的灰色空间。具体来说,我在这里对结构主义进行了一次新颖的分析,使我们能够更细致地看待结构主义和适应主义立场背后的动机。这清楚地表明了这两种方法是如何冲突的,以及潜在的可公度点。这篇综述澄清了(a)进化-进化方法对表型多样性的价值,但也澄清了(b)它如何与进化生物学中更广泛的其他主要方法正确相关。
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引用次数: 4
Reframing research on evolutionary novelty and co-option: Character identity mechanisms versus deep homology 进化新颖性与合作选择的重构研究:角色同一性机制与深度同源性
IF 7.3 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2023-08-01 DOI: 10.1016/j.semcdb.2022.03.030
James DiFrisco , Günter P. Wagner , Alan C. Love

A central topic in research at the intersection of development and evolution is the origin of novel traits. Despite progress on understanding how developmental mechanisms underlie patterns of diversity in the history of life, the problem of novelty continues to challenge researchers. Here we argue that research on evolutionary novelty and the closely associated phenomenon of co-option can be reframed fruitfully by: (1) specifying a conceptual model of mechanisms that underwrite character identity, (2) providing a richer and more empirically precise notion of co-option that goes beyond common appeals to “deep homology”, and (3) attending to the nature of experimental interventions that can determine whether and how the co-option of identity mechanisms can help to explain novel character origins. This reframing has the potential to channel future investigation to make substantive progress on the problem of evolutionary novelty. To illustrate this potential, we apply our reframing to two case studies: treehopper helmets and beetle horns.

在发展和进化的交叉研究中,一个中心话题是新特征的起源。尽管在理解生命史上多样性模式的发展机制方面取得了进展,但新颖性问题仍然对研究人员构成挑战。在这里,我们认为,对进化新颖性和密切相关的共同选择现象的研究可以通过以下方式进行富有成效的重新定义:(1)指定一个支持性格认同的机制的概念模型,(2)提供一个更丰富、更具经验精确的共同选择概念,超越了对“深度同源性”的普遍诉求,以及(3)关注实验干预的性质,这些干预可以确定身份机制的共同选择是否以及如何有助于解释新角色的起源。这种重新构建有可能引导未来的研究在进化新颖性问题上取得实质性进展。为了说明这一潜力,我们将我们的重新定义应用于两个案例研究:树蛙头盔和甲虫角。
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引用次数: 12
Deep conservation and co-option of programmed cell death facilitates evolution of alternative phenotypes at multiple biological levels 程序性细胞死亡的深度保护和共选择促进了多种生物学水平上的替代表型的进化
IF 7.3 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2023-08-01 DOI: 10.1016/j.semcdb.2022.05.024
Lisa Hanna, Ehab Abouheif

Alternative phenotypes, such as polyphenisms and sexual dimorphisms, are widespread in nature and appear at all levels of biological organization, from genes and cells to morphology and behavior. Yet, our understanding of the mechanisms through which alternative phenotypes develop and how they evolve remains understudied. In this review, we explore the association between alternative phenotypes and programmed cell death, a mechanism responsible for the elimination of superfluous cells during development. We discuss the ancient origins and deep conservation of programmed cell death (its function, forms and underlying core regulatory gene networks), and propose that it was co-opted repeatedly to generate alternative phenotypes at the level of cells, tissues, organs, external morphology, and even individuals. We review several examples from across the tree of life to explore the conditions under which programmed cell death is likely to facilitate the evolution of alternative phenotypes.

替代表型,如多基因和性二型,在自然界中广泛存在,并出现在生物组织的各个层面,从基因和细胞到形态和行为。然而,我们对替代表型发展的机制以及它们如何进化的理解仍然不足。在这篇综述中,我们探讨了替代表型与程序性细胞死亡之间的关系,程序性细胞死是一种负责在发育过程中消除多余细胞的机制。我们讨论了程序性细胞死亡的古老起源和深层保守性(其功能、形式和潜在的核心调控基因网络),并提出它被反复选择,以在细胞、组织、器官、外部形态甚至个体层面产生替代表型。我们回顾了生命树上的几个例子,以探索程序性细胞死亡可能促进替代表型进化的条件。
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引用次数: 3
Balance between the cell viability and death in 3D 在3D中细胞存活和死亡之间的平衡
IF 7.3 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2023-07-30 DOI: 10.1016/j.semcdb.2022.09.005
Angela C. Debruyne , Irina A. Okkelman , Ruslan I. Dmitriev

Cell death is a phenomenon, frequently perceived as an absolute event for cell, tissue and the organ. However, the rising popularity and complexity of such 3D multicellular ‘tissue building blocks’ as heterocellular spheroids, organoids, and ‘assembloids’ prompts to revise the definition and quantification of cell viability and death. It raises several questions on the overall viability of all the cells within 3D volume and on choosing the appropriate, continuous, and non-destructive viability assay enabling for a single-cell analysis. In this review, we look at cell viability and cell death modalities with attention to the intrinsic features of such 3D models as spheroids, organoids, and bioprints. Furthermore, we look at emerging and promising methodologies, which can help define and understand the balance between cell viability and death in dynamic and complex 3D environments. We conclude that the recent innovations in biofabrication, biosensor probe development, and fluorescence microscopy can help answer these questions.

细胞死亡是一种现象,通常被视为细胞、组织和器官的绝对事件。然而,异细胞球体、类器官和“组装体”等3D多细胞“组织构建块”的日益流行和复杂性促使人们修改了细胞活力和死亡的定义和量化。它提出了关于3D体积内所有细胞的总体生存能力以及选择合适的、连续的和无损的生存能力测定以进行单细胞分析的几个问题。在这篇综述中,我们关注细胞活力和细胞死亡模式,并关注球体、类器官和生物打印等3D模型的内在特征。此外,我们着眼于新兴和有前景的方法,这些方法可以帮助定义和理解动态和复杂3D环境中细胞活力和死亡之间的平衡。我们的结论是,最近在生物制造、生物传感器探针开发和荧光显微镜方面的创新可以帮助回答这些问题。
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引用次数: 2
Strategic use of organoids and organs-on-chip as biomimetic tools 策略性地使用类器官和芯片器官作为仿生工具
IF 7.3 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2023-07-30 DOI: 10.1016/j.semcdb.2022.09.010
Anderson K. Santos , Sérgio Scalzo , Raysa T.V. de Souza , Pedro H.G. Santana , Bruno L. Marques , Lucas F. Oliveira , Daniel M. Filho , Alexandre Hiroaki Kihara , Helton da Costa Santiago , Ricardo C. Parreira , Alexander Birbrair , Henning Ulrich , Rodrigo R. Resende

Organoid development and organ-on-a-chip are technologies based on differentiating stem cells, forming 3D multicellular structures resembling organs and tissues in vivo. Hence, both can be strategically used for disease modeling, drug screening, and host-pathogen studies. In this context, this review highlights the significant advancements in the area, providing technical approaches to organoids and organ-on-a-chip that best imitate in vivo physiology.

类器官发育和芯片上的器官是基于分化干细胞的技术,在体内形成类似器官和组织的3D多细胞结构。因此,两者都可以战略性地用于疾病建模、药物筛选和宿主病原体研究。在这方面,这篇综述强调了该领域的重大进展,为类器官和芯片上的器官提供了最能模仿体内生理学的技术方法。
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引用次数: 4
The impact of antidepressants on human neurodevelopment: Brain organoids as experimental tools 抗抑郁药对人类神经发育的影响:脑类器官作为实验工具
IF 7.3 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2023-07-30 DOI: 10.1016/j.semcdb.2022.09.007
Luciana Simões Rafagnin Marinho , Gabrielly Maria Denadai Chiarantin , Juliane Midori Ikebara , Débora Sterzeck Cardoso , Théo Henrique de Lima-Vasconcellos , Guilherme Shigueto Vilar Higa , Mariana Sacrini Ayres Ferraz , Roberto De Pasquale , Silvia Honda Takada , Fabio Papes , Alysson R. Muotri , Alexandre Hiroaki Kihara

The use of antidepressants during pregnancy benefits the mother's well-being, but the effects of such substances on neurodevelopment remain poorly understood. Moreover, the consequences of early exposure to antidepressants may not be immediately apparent at birth. In utero exposure to selective serotonin reuptake inhibitors (SSRIs) has been related to developmental abnormalities, including a reduced white matter volume. Several reports have observed an increased incidence of autism spectrum disorder (ASD) and attention deficit hyperactivity disorder (ADHD) after prenatal exposure to SSRIs such as sertraline, the most widely prescribed SSRI. The advent of human-induced pluripotent stem cell (hiPSC) methods and assays now offers appropriate tools to test the consequences of such compounds for neurodevelopment in vitro. In particular, hiPSCs can be used to generate cerebral organoids – self-organized structures that recapitulate the morphology and complex physiology of the developing human brain, overcoming the limitations found in 2D cell culture and experimental animal models for testing drug efficacy and side effects. For example, single-cell RNA sequencing (scRNA-seq) and electrophysiological measurements on organoids can be used to evaluate the impact of antidepressants on the transcriptome and neuronal activity signatures in developing neurons. While the analysis of large-scale transcriptomic data depends on dimensionality reduction methods, electrophysiological recordings rely on temporal data series to discriminate statistical characteristics of neuronal activity, allowing for the rigorous analysis of the effects of antidepressants and other molecules that affect the developing nervous system, especially when applied in combination with relevant human cellular models such as brain organoids.

在怀孕期间使用抗抑郁药有利于母亲的健康,但这些物质对神经发育的影响仍知之甚少。此外,早期接触抗抑郁药的后果可能在出生时并不明显。子宫内暴露于选择性血清素再摄取抑制剂(SSRIs)与发育异常有关,包括白质体积减少。一些报告观察到,在产前接触最广泛使用的SSRI,如舍曲林后,自闭症谱系障碍(ASD)和注意力缺陷多动障碍(ADHD)的发病率增加。人类诱导多能干细胞(hiPSC)方法和测定的出现现在提供了合适的工具来测试这些化合物对体外神经发育的影响。特别是,hiPSCs可用于生成大脑类器官,这是一种自组织结构,概括了发育中的人脑的形态和复杂生理,克服了2D细胞培养和实验动物模型中用于测试药物疗效和副作用的局限性。例如,单细胞RNA测序(scRNA-seq)和类器官的电生理测量可用于评估抗抑郁药对发育中神经元的转录组和神经元活动特征的影响。虽然大规模转录组数据的分析依赖于降维方法,但电生理记录依赖于时间数据序列来区分神经元活动的统计特征,从而能够严格分析抗抑郁药和其他影响发育中神经系统的分子的影响,尤其是当与相关的人类细胞模型如脑类器官结合应用时。
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引用次数: 4
Deconstructing organs: From decellularized organs, and stem cells niche to constructed organoids and engineering new organs 解构器官:从脱细胞器官、干细胞龛到构建类器官和工程新器官
IF 7.3 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2023-07-30 DOI: 10.1016/j.semcdb.2022.12.003
Rodrigo R. Resende
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引用次数: 0
Application of stem cells in engineered vascular graft and vascularized organs 干细胞在工程血管移植及血管化器官中的应用
IF 7.3 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2023-07-30 DOI: 10.1016/j.semcdb.2022.10.003
Shanlan Zhao , Qiao Zhang , Min Liu , Jiahui Du , Tingting Wang , Yanzhao Li , Wen Zeng

Recent studies report that stem cell therapies have been applied successfully to patients, This has increased anticipations that this regeneration strategy could be a potential method to treat a wide range of intractable diseases some day. Stem cells offer new prospects for the treatment of incurable diseases and for tissue regeneration and repairation because of their unique biological properties. Angiogenesis a key process in tissue regeneration and repairation. Vascularization of organs is one of the main challenges hindering the clinical application of engineered tissues. Efficient production of engineered vascular grafts and vascularized organs is of critical importance for regenerative medicine. In this review, we focus on the types of stem cells that are widely used in tissue engineering and regeneration, as well as their application of these stem cells in the construction of tissue-engineered vascular grafts and vascularization of tissue-engineered organs.

最近的研究报告称,干细胞疗法已成功应用于患者,这增加了人们对这种再生策略有朝一日可能成为治疗各种棘手疾病的潜在方法的预期。干细胞由于其独特的生物学特性,为治疗不治之症以及组织再生和修复提供了新的前景。血管生成是组织再生和修复的关键过程。器官血管化是阻碍工程组织临床应用的主要挑战之一。高效生产工程化血管移植物和血管化器官对再生医学至关重要。在这篇综述中,我们重点介绍了在组织工程和再生中广泛使用的干细胞类型,以及这些干细胞在组织工程血管移植物构建和组织工程器官血管化中的应用。
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引用次数: 3
Organoids as a novel tool in modelling infectious diseases 类器官作为传染病建模的新工具
IF 7.3 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2023-07-30 DOI: 10.1016/j.semcdb.2022.09.003
Lucas Felipe de Oliveira , Daniel Mendes Filho , Bruno Lemes Marques , Giovana Figueiredo Maciel , Ricardo Cambraia Parreira , José Rodrigues do Carmo Neto , Priscilla Elias Ferreira Da Silva , Rhanoica Oliveira Guerra , Marcos Vinicius da Silva , Helton da Costa Santiago , Alexander Birbrair , Alexandre H. Kihara , Valdo José Dias da Silva , Talita Glaser , Rodrigo R. Resende , Henning Ulrich

Infectious diseases worldwide affect human health and have important societal impacts. A better understanding of infectious diseases is urgently needed. In vitro and in vivo infection models have brought notable contributions to the current knowledge of these diseases. Organoids are multicellular culture systems resembling tissue architecture and function, recapitulating many characteristics of human disease and elucidating mechanisms of host–infectious agent interactions in the respiratory and gastrointestinal systems, the central nervous system and the skin. Here, we discuss the applicability of the organoid technology for modeling pathogenesis, host response and features, which can be explored for the development of preventive and therapeutic treatments.

世界各地的传染病影响着人类健康,并具有重要的社会影响。迫切需要更好地了解传染病。体外和体内感染模型为目前对这些疾病的了解做出了显著贡献。类器官是一种类似组织结构和功能的多细胞培养系统,概括了人类疾病的许多特征,并阐明了呼吸和胃肠系统、中枢神经系统和皮肤中宿主-传染源相互作用的机制。在这里,我们讨论了类器官技术在建模发病机制、宿主反应和特征方面的适用性,这些技术可用于开发预防和治疗方法。
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引用次数: 1
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