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A journey through translational control 通过平移控制的旅程。
IF 7.3 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2023-09-01 DOI: 10.1016/j.semcdb.2023.08.003
Huili Guo
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引用次数: 0
Plasma membrane repair empowers the necrotic survivors as innate immune modulators 质膜修复使坏死幸存者成为先天免疫调节剂
IF 7.3 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2023-08-28 DOI: 10.1016/j.semcdb.2023.08.001
Shiqi Xu , Tyler J. Yang , Suhong Xu , Yi-Nan Gong

The plasma membrane is crucial to the survival of animal cells, and damage to it can be lethal, often resulting in necrosis. However, cells possess multiple mechanisms for repairing the membrane, which allows them to maintain their integrity to some extent, and sometimes even survive. Interestingly, cells that survive a near-necrosis experience can recognize sub-lethal membrane damage and use it as a signal to secrete chemokines and cytokines, which activate the immune response. This review will present evidence of necrotic cell survival in both in vitro and in vivo systems, including in C. elegans, mouse models, and humans. We will also summarize the various membrane repair mechanisms cells use to maintain membrane integrity. Finally, we will propose a mathematical model to illustrate how near-death experiences can transform dying cells into innate immune modulators for their microenvironment. By utilizing their membrane repair activity, the biological effects of cell death can extend beyond the mere elimination of the cells.

质膜对动物细胞的存活至关重要,对质膜的破坏可能是致命的,通常会导致细胞坏死。然而,细胞具有多种修复膜的机制,这使得它们在一定程度上保持完整性,有时甚至存活。有趣的是,在接近坏死的情况下存活下来的细胞可以识别亚致死膜损伤,并将其作为分泌趋化因子和细胞因子的信号,从而激活免疫反应。这篇综述将提供坏死细胞在体外和体内系统中存活的证据,包括秀丽隐杆线虫、小鼠模型和人类。我们还将总结细胞用于维持膜完整性的各种膜修复机制。最后,我们将提出一个数学模型来说明濒死体验如何将濒死细胞转化为其微环境的先天免疫调节剂。通过利用它们的膜修复活性,细胞死亡的生物学效应可以超越细胞的纯粹消除。
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引用次数: 2
Selective induction of programmed cell death using synthetic biology tools 利用合成生物学工具选择性诱导程序性细胞死亡
IF 7.3 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2023-08-17 DOI: 10.1016/j.semcdb.2023.07.012
Kateryna Shkarina , Petr Broz

Regulated cell death (RCD) controls the removal of dispensable, infected or malignant cells, and is thus essential for development, homeostasis and immunity of multicellular organisms. Over the last years different forms of RCD have been described (among them apoptosis, necroptosis, pyroptosis and ferroptosis), and the cellular signaling pathways that control their induction and execution have been characterized at the molecular level. It has also become apparent that different forms of RCD differ in their capacity to elicit inflammation or an immune response, and that RCD pathways show a remarkable plasticity. Biochemical and genetic studies revealed that inhibition of a given pathway often results in the activation of back-up cell death mechanisms, highlighting close interconnectivity based on shared signaling components and the assembly of multivalent signaling platforms that can initiate different forms of RCD. Due to this interconnectivity and the pleiotropic effects of ‘classical’ cell death inducers, it is challenging to study RCD pathways in isolation. This has led to the development of tools based on synthetic biology that allow the targeted induction of RCD using chemogenetic or optogenetic methods. Here we discuss recent advances in the development of such toolset, highlighting their advantages and limitations, and their application for the study of RCD in cells and animals.

调节细胞死亡(RCD)控制可有可无、感染或恶性细胞的清除,因此对多细胞生物的发育、体内平衡和免疫至关重要。在过去的几年里,人们描述了不同形式的RCD(其中包括细胞凋亡、坏死坏死、焦亡和铁亡),并在分子水平上表征了控制其诱导和执行的细胞信号通路。很明显,不同形式的RCD在引发炎症或免疫反应的能力上是不同的,并且RCD途径表现出显著的可塑性。生化和遗传学研究表明,抑制特定途径通常会导致备用细胞死亡机制的激活,强调基于共享信号组件和多价信号平台组装的密切互联性,可以启动不同形式的RCD。由于这种相互联系和“经典”细胞死亡诱导剂的多效性,孤立地研究RCD途径具有挑战性。这导致了基于合成生物学的工具的发展,这些工具允许使用化学遗传学或光遗传学方法靶向诱导RCD。在此,我们讨论了这些工具集的最新进展,重点介绍了它们的优点和局限性,以及它们在细胞和动物RCD研究中的应用。
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引用次数: 1
C. elegans as a model for health and disease 秀丽隐杆线虫作为健康和疾病的典范。
IF 7.3 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2023-08-09 DOI: 10.1016/j.semcdb.2023.07.006
Steven Zuryn
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引用次数: 0
Vagal sensory pathway for the gut-brain communication 迷走神经感觉通路的肠脑通讯
IF 7.3 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2023-08-08 DOI: 10.1016/j.semcdb.2023.07.009
Yiyun Cao , Rui Li , Ling Bai

The communication between the gut and brain is crucial for regulating various essential physiological functions, such as energy balance, fluid homeostasis, immune response, and emotion. The vagal sensory pathway plays an indispensable role in connecting the gut to the brain. Recently, our knowledge of the vagal gut-brain axis has significantly advanced through molecular genetic studies, revealing a diverse range of vagal sensory cell types with distinct peripheral innervations, response profiles, and physiological functions. Here, we review the current understanding of how vagal sensory neurons contribute to gut-brain communication. First, we highlight recent transcriptomic and genetic approaches that have characterized different vagal sensory cell types. Then, we focus on discussing how different subtypes encode numerous gut-derived signals and how their activities are translated into physiological and behavioral regulations. The emerging insights into the diverse cell types and functional properties of vagal sensory neurons have paved the way for exciting future directions, which may provide valuable insights into potential therapeutic targets for disorders involving gut-brain communication.

肠道和大脑之间的交流对于调节各种基本生理功能至关重要,如能量平衡、体液平衡、免疫反应和情绪。迷走神经感觉通路在连接肠道和大脑方面起着不可或缺的作用。最近,通过分子遗传学研究,我们对迷走肠-脑轴的认识有了显著的进展,揭示了迷走神经感觉细胞类型的多样性,它们具有不同的外周神经支配、反应谱和生理功能。在这里,我们回顾了目前对迷走神经感觉神经元如何促进肠-脑通讯的理解。首先,我们强调了最近的转录组学和遗传学方法,这些方法表征了不同的迷走神经感觉细胞类型。然后,我们重点讨论了不同亚型如何编码大量肠道衍生信号,以及它们的活动如何转化为生理和行为调节。对迷走神经感觉神经元的不同细胞类型和功能特性的新见解为令人兴奋的未来方向铺平了道路,这可能为肠-脑通讯疾病的潜在治疗靶点提供有价值的见解。
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引用次数: 0
The Calvin-Benson-Bassham cycle in C4 and Crassulacean acid metabolism species C4和天冬酸代谢物种的Calvin-Benson-Bassham循环
IF 7.3 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2023-08-04 DOI: 10.1016/j.semcdb.2023.07.013
Martha Ludwig , James Hartwell , Christine A. Raines , Andrew J. Simkin

The Calvin-Benson-Bassham (CBB) cycle is the ancestral CO2 assimilation pathway and is found in all photosynthetic organisms. Biochemical extensions to the CBB cycle have evolved that allow the resulting pathways to act as CO2 concentrating mechanisms, either spatially in the case of C4 photosynthesis or temporally in the case of Crassulacean acid metabolism (CAM). While the biochemical steps in the C4 and CAM pathways are known, questions remain on their integration and regulation with CBB cycle activity. The application of omic and transgenic technologies is providing a more complete understanding of the biochemistry of C4 and CAM species and will also provide insight into the CBB cycle in these plants. As the global population increases, new solutions are required to increase crop yields and meet demands for food and other bioproducts. Previous work in C3 species has shown that increasing carbon assimilation through genetic manipulation of the CBB cycle can increase biomass and yield. There may also be options to improve photosynthesis in species using C4 photosynthesis and CAM through manipulation of the CBB cycle in these plants. This is an underexplored strategy and requires more basic knowledge of CBB cycle operation in these species to enable approaches for increased productivity.

Calvin Benson Bassham(CBB)循环是祖先的CO2同化途径,在所有光合生物中都有发现。CBB循环的生物化学扩展已经进化,允许产生的途径作为CO2浓缩机制,无论是在C4光合作用的空间上,还是在景天莲酸代谢(CAM)的时间上。虽然C4和CAM途径中的生化步骤是已知的,但它们与CBB循环活性的整合和调节仍存在问题。omic和转基因技术的应用为C4和CAM物种的生物化学提供了更完整的理解,也将为这些植物的CBB循环提供见解。随着全球人口的增加,需要新的解决方案来提高作物产量,满足对粮食和其他生物产品的需求。先前对C3物种的研究表明,通过CBB循环的遗传操作来增加碳同化可以增加生物量和产量。还可以通过操纵这些植物的CBB循环,使用C4光合作用和CAM来改善物种的光合作用。这是一个未充分探索的战略,需要对这些物种的CBB循环操作有更多的基本知识,以实现提高生产力的方法。
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引用次数: 1
Patterns of selection across gene regulatory networks 跨基因调控网络的选择模式
IF 7.3 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2023-08-01 DOI: 10.1016/j.semcdb.2022.03.029
Jeanne M.C. McDonald, Robert D. Reed

Gene regulatory networks (GRNs) are the core engine of organismal development. If we would like to understand the origin and diversification of phenotypes, it is necessary to consider the structure of GRNs in order to reconstruct the links between genetic mutations and phenotypic change. Much of the progress in evolutionary developmental biology, however, has occurred without a nuanced consideration of the evolution of functional relationships between genes, especially in the context of their broader network interactions. Characterizing and comparing GRNs across traits and species in a more detailed way will allow us to determine how network position influences what genes drive adaptive evolution. In this perspective paper, we consider the architecture of developmental GRNs and how positive selection strength may vary across a GRN. We then propose several testable models for these patterns of selection and experimental approaches to test these models.

基因调控网络是生物体发育的核心引擎。如果我们想了解表型的起源和多样化,就有必要考虑GRNs的结构,以重建遗传突变和表型变化之间的联系。然而,进化发育生物学的大部分进展都没有对基因之间功能关系的进化进行细致的考虑,尤其是在它们更广泛的网络相互作用的背景下。以更详细的方式描述和比较不同特征和物种的GRN,将使我们能够确定网络位置如何影响哪些基因驱动适应性进化。在这篇前瞻性论文中,我们考虑了发展性GRN的架构,以及正选择强度在GRN中的变化。然后,我们为这些选择模式提出了几个可测试的模型,并提出了测试这些模型的实验方法。
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引用次数: 6
Neural crest cells as a source of microevolutionary variation 神经嵴细胞作为微进化变异的来源
IF 7.3 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2023-08-01 DOI: 10.1016/j.semcdb.2022.06.001
A. Allyson Brandon, Daniela Almeida, Kara E. Powder

Vertebrates have some of the most complex and diverse features in animals, from varied craniofacial morphologies to colorful pigmentation patterns and elaborate social behaviors. All of these traits have their developmental origins in a multipotent embryonic lineage of neural crest cells. This “fourth germ layer” is a vertebrate innovation and the source of a wide range of adult cell types. While others have discussed the role of neural crest cells in human disease and animal domestication, less is known about their role in contributing to adaptive changes in wild populations. Here, we review how variation in the development of neural crest cells and their derivatives generates considerable phenotypic diversity in nature. We focus on the broad span of traits under natural and sexual selection whose variation may originate in the neural crest, with emphasis on behavioral factors such as intraspecies communication that are often overlooked. In all, we encourage the integration of evolutionary ecology with developmental biology and molecular genetics to gain a more complete understanding of the role of this single cell type in trait covariation, evolutionary trajectories, and vertebrate diversity.

脊椎动物具有动物中最复杂和最多样的特征,从不同的颅面形态到丰富多彩的色素沉着模式和复杂的社会行为。所有这些特征都起源于神经嵴细胞的多能胚胎谱系。这种“第四胚层”是脊椎动物的创新,也是多种成年细胞类型的来源。虽然其他人已经讨论了神经嵴细胞在人类疾病和动物驯化中的作用,但对它们在野生种群适应性变化中的作用知之甚少。在这里,我们回顾了神经嵴细胞及其衍生物的发育变化如何在自然界中产生相当大的表型多样性。我们关注自然选择和性别选择下的广泛特征,这些特征的变异可能起源于神经嵴,重点关注经常被忽视的行为因素,如种内交流。总之,我们鼓励将进化生态学与发育生物学和分子遗传学相结合,以更全面地了解这种单细胞类型在性状协变、进化轨迹和脊椎动物多样性中的作用。
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引用次数: 8
Development and regeneration of the vagus nerve 迷走神经的发育和再生
IF 7.3 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2023-08-01 DOI: 10.1016/j.semcdb.2023.07.008
Adam J. Isabella , Cecilia B. Moens

The vagus nerve, with its myriad constituent axon branches and innervation targets, has long been a model of anatomical complexity in the nervous system. The branched architecture of the vagus nerve is now appreciated to be highly organized around the topographic and/or molecular identities of the neurons that innervate each target tissue. However, we are only just beginning to understand the developmental mechanisms by which heterogeneous vagus neuron identity is specified, patterned, and used to guide the axons of particular neurons to particular targets. Here, we summarize our current understanding of the complex topographic and molecular organization of the vagus nerve, the developmental basis of neuron specification and patterned axon guidance that supports this organization, and the regenerative mechanisms that promote, or inhibit, the restoration of vagus nerve organization after nerve damage. Finally, we highlight key unanswered questions in these areas and discuss potential strategies to address these questions.

迷走神经具有无数组成轴突分支和神经支配目标,长期以来一直是神经系统解剖复杂性的模型。迷走神经的分支结构现在被认为是高度组织的,围绕着支配每个目标组织的神经元的地形和/或分子特征。然而,我们才刚刚开始了解异质迷走神经神经元身份被指定、定型并用于引导特定神经元轴突到达特定目标的发育机制。在这里,我们总结了我们目前对迷走神经复杂的地形和分子组织的理解,支持这种组织的神经元规范和模式轴突引导的发育基础,以及促进或抑制神经损伤后迷走神经组织恢复的再生机制。最后,我们强调了这些领域中未解决的关键问题,并讨论了解决这些问题的潜在策略。
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引用次数: 1
Clade-specific genes and the evolutionary origin of novelty; new tools in the toolkit 分支特异性基因和新颖性的进化起源;工具箱中的新工具
IF 7.3 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2023-08-01 DOI: 10.1016/j.semcdb.2022.05.025
Longjun Wu, J. David Lambert

Clade-specific (a.k.a. lineage-specific) genes are very common and found at all taxonomic levels and in all clades examined. They can arise by duplication of previously existing genes, which can involve partial truncations or combinations with other protein domains or regulatory sequences. They can also evolve de novo from non-coding sequences, leading to potentially truly novel protein domains. Finally, since clade-specific genes are generally defined by lack of sequence homology with other proteins, they can also arise by sequence evolution that is rapid enough that previous sequence homology can no longer be detected. In such cases, where the rapid evolution is followed by constraint, we consider them to be ontologically non-novel but likely novel at a functional level. In general, clade-specific genes have received less attention from biologists but there are increasing numbers of fascinating examples of their roles in important traits. Here we review some selected recent examples, and argue that attention to clade-specific genes is an important corrective to the focus on the conserved developmental regulatory toolkit that has been the habit of evo-devo as a field. Finally, we discuss questions that arise about the evolution of clade-specific genes, and how these might be addressed by future studies. We highlight the hypothesis that clade-specific genes are more likely to be involved in synapomorphies that arose in the stem group where they appeared, compared to other genes.

分支特异性(又称谱系特异性)基因非常常见,在所有分类水平和所有检查的分支中都能发现。它们可以通过复制先前存在的基因而产生,这可能涉及部分截短或与其他蛋白质结构域或调控序列的组合。它们还可以从非编码序列从头进化,从而产生潜在的真正新颖的蛋白质结构域。最后,由于分支特异性基因通常是由与其他蛋白质缺乏序列同源性来定义的,它们也可能是由足够快的序列进化引起的,从而无法再检测到以前的序列同源性。在这种情况下,快速进化之后是约束,我们认为它们在本体论上是不新颖的,但在功能层面上可能是新颖的。一般来说,分支特异性基因很少受到生物学家的关注,但越来越多的令人着迷的例子表明它们在重要性状中的作用。在这里,我们回顾了一些最近选择的例子,并认为对分支特异性基因的关注是对保守发育调控工具包的重要纠正,而保守发育调控工具箱一直是进化论领域的习惯。最后,我们讨论了关于分支特异性基因进化的问题,以及未来的研究如何解决这些问题。我们强调了这样一种假设,即与其他基因相比,分支特异性基因更有可能参与在其出现的茎群中出现的突触形态。
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引用次数: 4
期刊
Seminars in cell & developmental biology
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