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Mechanisms Underlying the Formation and Evolution of Vertebrate Color Patterns. 脊椎动物颜色模式形成和进化的机制。
IF 8.7 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2023-11-27 Epub Date: 2023-07-24 DOI: 10.1146/annurev-genet-031423-120918
Claudius F Kratochwil, Ricardo Mallarino

Vertebrates exhibit a wide range of color patterns, which play critical roles in mediating intra- and interspecific communication. Because of their diversity and visual accessibility, color patterns offer a unique and fascinating window into the processes underlying biological organization. In this review, we focus on describing many of the general principles governing the formation and evolution of color patterns in different vertebrate groups. We characterize the types of patterns, review the molecular and developmental mechanisms by which they originate, and discuss their role in constraining or facilitating evolutionary change. Lastly, we outline outstanding questions in the field and discuss different approaches that can be used to address them. Overall, we provide a unifying conceptual framework among vertebrate systems that may guide research into naturally evolved mechanisms underlying color pattern formation and evolution.

脊椎动物表现出广泛的颜色模式,在介导种内和种间交流中发挥着关键作用。由于其多样性和视觉可及性,颜色图案为了解生物组织的基本过程提供了一个独特而迷人的窗口。在这篇综述中,我们重点描述了控制不同脊椎动物群体颜色模式形成和进化的许多一般原则。我们描述了模式的类型,回顾了它们起源的分子和发育机制,并讨论了它们在限制或促进进化变化中的作用。最后,我们概述了该领域悬而未决的问题,并讨论了可用于解决这些问题的不同方法。总的来说,我们在脊椎动物系统中提供了一个统一的概念框架,可以指导对颜色模式形成和进化的自然进化机制的研究。《遗传学年度评论》第57卷预计最终在线出版日期为2023年11月。请参阅http://www.annualreviews.org/page/journal/pubdates用于修订估算。
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引用次数: 0
Microglial Transcriptional Signatures in the Central Nervous System: Toward A Future of Unraveling Their Function in Health and Disease. 中枢神经系统的小胶质细胞转录特征:走向揭示其在健康和疾病中的功能的未来。
IF 11.1 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2023-11-27 Epub Date: 2023-06-29 DOI: 10.1146/annurev-genet-022223-093643
Haley A Vecchiarelli, Marie-Ève Tremblay

Microglia, the resident immune cells of the central nervous system (CNS), are primarily derived from the embryonic yolk sac and make their way to the CNS during early development. They play key physiological and immunological roles across the life span, throughout health, injury, and disease. Recent transcriptomic studies have identified gene transcript signatures expressed by microglia that may provide the foundation for unprecedented insights into their functions. Microglial gene expression signatures can help distinguish them from macrophage cell types to a reasonable degree of certainty, depending on the context. Microglial expression patterns further suggest a heterogeneous population comprised of many states that vary according to the spatiotemporal context. Microglial diversity is most pronounced during development, when extensive CNS remodeling takes place, and following disease or injury. A next step of importance for the field will be to identify the functional roles performed by these various microglial states, with the perspective of targeting them therapeutically.

小胶质细胞是中枢神经系统(CNS)的常驻免疫细胞,主要来源于胚胎卵黄囊,并在发育早期进入中枢神经系统。它们在整个生命周期、健康、受伤和疾病中发挥着关键的生理和免疫作用。最近的转录组学研究已经确定了小胶质细胞表达的基因转录特征,这可能为前所未有的了解其功能提供基础。小胶质细胞基因表达特征可以帮助它们从巨噬细胞类型中区分出来,这在一定程度上取决于环境。小胶质细胞表达模式进一步表明,一个由许多状态组成的异质群体根据时空背景而变化。小胶质细胞的多样性在发育过程中最为明显,此时发生了广泛的中枢神经系统重塑,以及在疾病或损伤之后。该领域下一步的重要工作将是确定这些不同的小胶质细胞状态所发挥的功能作用,并以治疗为目标。
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引用次数: 0
Programmed Cell Death in Unicellular Versus Multicellular Organisms. 单细胞与多细胞生物的程序性细胞死亡。
IF 8.7 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2023-11-27 Epub Date: 2023-09-18 DOI: 10.1146/annurev-genet-033123-095833
Madhura Kulkarni, J Marie Hardwick

Programmed cell death (self-induced) is intrinsic to all cellular life forms, including unicellular organisms. However, cell death research has focused on animal models to understand cancer, degenerative disorders, and developmental processes. Recently delineated suicidal death mechanisms in bacteria and fungi have revealed ancient origins of animal cell death that are intertwined with immune mechanisms, allaying earlier doubts that self-inflicted cell death pathways exist in microorganisms. Approximately 20 mammalian death pathways have been partially characterized over the last 35 years. By contrast, more than 100 death mechanisms have been identified in bacteria and a few fungi in recent years. However, cell death is nearly unstudied in most human pathogenic microbes that cause major public health burdens. Here, we consider how the current understanding of programmed cell death arose through animal studies and how recently uncovered microbial cell death mechanisms in fungi and bacteria resemble and differ from mechanisms of mammalian cell death.

程序性细胞死亡(自我诱导)是包括单细胞生物在内的所有细胞生命形式所固有的。然而,细胞死亡研究主要集中在动物模型上,以了解癌症、退行性疾病和发育过程。最近在细菌和真菌中描述的自杀死亡机制揭示了与免疫机制交织在一起的动物细胞死亡的古老起源,减轻了早期对微生物中存在自我造成的细胞死亡途径的怀疑。在过去的35年里,大约有20种哺乳动物的死亡途径得到了部分表征。相比之下,近年来在细菌和一些真菌中发现了100多种死亡机制。然而,在大多数造成重大公共卫生负担的人类致病微生物中,细胞死亡几乎没有得到研究。在这里,我们考虑目前对程序性细胞死亡的理解是如何通过动物研究产生的,以及最近发现的真菌和细菌中的微生物细胞死亡机制与哺乳动物细胞死亡机制的相似和不同之处。
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引用次数: 0
Leveraging Single-Cell Populations to Uncover the Genetic Basis of Complex Traits. 利用单细胞群体揭示复杂性状的遗传基础。
IF 11.1 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2023-11-27 Epub Date: 2023-08-10 DOI: 10.1146/annurev-genet-022123-110824
Mark A A Minow, Alexandre P Marand, Robert J Schmitz

The ease and throughput of single-cell genomics have steadily improved, and its current trajectory suggests that surveying single-cell populations will become routine. We discuss the merger of quantitative genetics with single-cell genomics and emphasize how this synergizes with advantages intrinsic to plants. Single-cell population genomics provides increased detection resolution when mapping variants that control molecular traits, including gene expression or chromatin accessibility. Additionally, single-cell population genomics reveals the cell types in which variants act and, when combined with organism-level phenotype measurements, unveils which cellular contexts impact higher-order traits. Emerging technologies, notably multiomics, can facilitate the measurement of both genetic changes and genomic traits in single cells, enabling single-cell genetic experiments. The implementation of single-cell genetics will advance the investigation of the genetic architecture of complex molecular traits and provide new experimental paradigms to study eukaryotic genetics.

单细胞基因组学的易用性和吞吐量稳步提高,其目前的轨迹表明,调查单细胞群体将成为常规。我们讨论了数量遗传学与单细胞基因组学的合并,并强调了这如何与植物固有的优势协同作用。单细胞群体基因组学在绘制控制分子性状的变异时提供了更高的检测分辨率,包括基因表达或染色质可及性。此外,单细胞群体基因组学揭示了变异作用的细胞类型,当与生物体水平的表型测量相结合时,揭示了哪些细胞背景影响高阶性状。新兴技术,特别是多组学,可以促进单细胞遗传变化和基因组特征的测量,使单细胞遗传实验成为可能。单细胞遗传学的实现将推动复杂分子性状遗传结构的研究,为真核生物遗传学研究提供新的实验范式。
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引用次数: 0
Integrating Complex Life Cycles in Comparative Developmental Biology. 比较发育生物学中复杂生命周期的整合。
IF 11.1 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2023-11-27 Epub Date: 2023-08-16 DOI: 10.1146/annurev-genet-071719-020641
Laurent Formery, Christopher J Lowe

The goal of comparative developmental biology is identifying mechanistic differences in embryonic development between different taxa and how these evolutionary changes have led to morphological and organizational differences in adult body plans. Much of this work has focused on direct-developing species in which the adult forms straight from the embryo and embryonic modifications have direct effects on the adult. However, most animal lineages are defined by indirect development, in which the embryo gives rise to a larval body plan and the adult forms by transformation of the larva. Historically, much of our understanding of complex life cycles is viewed through the lenses of ecology and zoology. In this review, we discuss the importance of establishing developmental rather than morphological or ecological criteria for defining developmental mode and explicitly considering the evolutionary implications of incorporating complex life cycles into broad developmental comparisons of embryos across metazoans.

比较发育生物学的目标是确定不同类群之间胚胎发育的机制差异,以及这些进化变化如何导致成人身体计划的形态和组织差异。这方面的工作主要集中在直接发育的物种上,在这些物种中,成体直接从胚胎形成,胚胎的修饰对成体有直接的影响。然而,大多数动物谱系是通过间接发育来确定的,在间接发育中,胚胎产生幼虫体计划,并通过幼虫的转化产生成虫形式。从历史上看,我们对复杂生命周期的理解大多是通过生态学和动物学的视角来看待的。在这篇综述中,我们讨论了建立发育而不是形态学或生态学标准来定义发育模式的重要性,并明确考虑了将复杂生命周期纳入后生动物胚胎发育比较的进化意义。
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引用次数: 0
RNA Repair: Hiding in Plain Sight. RNA修复:隐藏在视线之中。
IF 11.1 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2023-11-27 Epub Date: 2023-09-18 DOI: 10.1146/annurev-genet-071719-021856
Stewart Shuman

Enzymes that phosphorylate, dephosphorylate, and ligate RNA 5' and 3' ends were discovered more than half a century ago and were eventually shown to repair purposeful site-specific endonucleolytic breaks in the RNA phosphodiester backbone. The pace of discovery and characterization of new candidate RNA repair activities in taxa from all phylogenetic domains greatly exceeds our understanding of the biological pathways in which they act. The key questions anent RNA break repair in vivo are (a) identifying the triggers, agents, and targets of RNA cleavage and (b) determining whether RNA repair results in restoration of the original RNA, modification of the RNA (by loss or gain at the ends), or rearrangements of the broken RNA segments (i.e., RNA recombination). This review provides a perspective on the discovery, mechanisms, and physiology of purposeful RNA break repair, highlighting exemplary repair pathways (e.g., tRNA restriction-repair and tRNA splicing) for which genetics has figured prominently in their elucidation.

对RNA 5′和3′端进行磷酸化、去磷酸化和连接的酶在半个多世纪前被发现,并最终被证明可以修复RNA磷酸二酯主链中有目的的位点特异性核内溶断裂。在所有系统发育域的分类群中,新的候选RNA修复活性的发现和表征的速度大大超出了我们对它们起作用的生物学途径的理解。体内RNA断裂修复的关键问题是(a)确定RNA切割的触发因素、媒介和目标,以及(b)确定RNA修复是否导致原始RNA的恢复、RNA的修饰(通过末端的损失或获得)或断裂RNA片段的重排(即RNA重组)。这篇综述提供了有目的的RNA断裂修复的发现、机制和生理学的观点,强调了典型的修复途径(例如,tRNA限制性修复和tRNA剪接),其中遗传学在它们的阐明中起着重要作用。
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引用次数: 0
Pooled Genome-Scale CRISPR Screens in Single Cells. 单个细胞的基因组级CRISPR筛选。
IF 11.1 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2023-11-27 Epub Date: 2023-08-10 DOI: 10.1146/annurev-genet-072920-013842
Daniel Schraivogel, Lars M Steinmetz, Leopold Parts

Assigning functions to genes and learning how to control their expression are part of the foundation of cell biology and therapeutic development. An efficient and unbiased method to accomplish this is genetic screening, which historically required laborious clone generation and phenotyping and is still limited by scale today. The rapid technological progress on modulating gene function with CRISPR-Cas and measuring it in individual cells has now relaxed the major experimental constraints and enabled pooled screening with complex readouts from single cells. Here, we review the principles and practical considerations for pooled single-cell CRISPR screening. We discuss perturbation strategies, experimental model systems, matching the perturbation to the individual cells, reading out cell phenotypes, and data analysis. Our focus is on single-cell RNA sequencing and cell sorting-based readouts, including image-enabled cell sorting. We expect this transformative approach to fuel biomedical research for the next several decades.

赋予基因功能并学习如何控制它们的表达是细胞生物学和治疗发展的基础。实现这一目标的一种有效和公正的方法是遗传筛选,这在历史上需要费力的克隆生成和表型分析,今天仍然受到规模的限制。利用CRISPR-Cas调节基因功能并在单个细胞中测量基因功能方面的快速技术进步,现在已经放宽了主要的实验限制,并使单个细胞的复杂读数的集合筛选成为可能。在这里,我们回顾了合并单细胞CRISPR筛选的原则和实际考虑因素。我们讨论了扰动策略、实验模型系统、与单个细胞的扰动匹配、读出细胞表型和数据分析。我们的重点是单细胞RNA测序和基于细胞分选的读数,包括启用图像的细胞分选。我们期望这种变革性的方法能够在未来几十年推动生物医学研究。
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引用次数: 0
Unlocking the Complex Cell Biology of Coral-Dinoflagellate Symbiosis: A Model Systems Approach. 解开珊瑚-鞭毛藻共生的复杂细胞生物学:模型系统方法。
IF 11.1 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2023-11-27 Epub Date: 2023-09-18 DOI: 10.1146/annurev-genet-072320-125436
Marie R Jacobovitz, Elizabeth A Hambleton, Annika Guse

Symbiotic interactions occur in all domains of life, providing organisms with resources to adapt to new habitats. A prime example is the endosymbiosis between corals and photosynthetic dinoflagellates. Eukaryotic dinoflagellate symbionts reside inside coral cells and transfer essential nutrients to their hosts, driving the productivity of the most biodiverse marine ecosystem. Recent advances in molecular and genomic characterization have revealed symbiosis-specific genes and mechanisms shared among symbiotic cnidarians. In this review, we focus on the cellular and molecular processes that underpin the interaction between symbiont and host. We discuss symbiont acquisition via phagocytosis, modulation of host innate immunity, symbiont integration into host cell metabolism, and nutrient exchange as a fundamental aspect of stable symbiotic associations. We emphasize the importance of using model systems to dissect the cellular complexity of endosymbiosis, which ultimately serves as the basis for understanding its ecology and capacity to adapt in the face of climate change.

共生相互作用发生在生命的所有领域,为生物体提供适应新栖息地的资源。一个主要的例子是珊瑚和光合鞭毛藻之间的内共生。真核鞭毛藻共生体居住在珊瑚细胞内,并将必需的营养物质传递给宿主,推动了最具生物多样性的海洋生态系统的生产力。分子和基因组特征的最新进展揭示了共生刺胞动物之间共享的共生特异性基因和机制。在本文中,我们将重点介绍共生体与宿主相互作用的细胞和分子过程。我们讨论了通过吞噬获得共生体,宿主先天免疫的调节,共生体融入宿主细胞代谢,以及作为稳定共生关系的基本方面的营养交换。我们强调使用模型系统来剖析内共生的细胞复杂性的重要性,这最终将成为了解其生态和适应气候变化能力的基础。
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引用次数: 0
Interplay Between Antimicrobial Resistance and Global Environmental Change. 抗菌素耐药性与全球环境变化的相互作用。
IF 11.1 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2023-11-27 Epub Date: 2023-09-14 DOI: 10.1146/annurev-genet-022123-113904
María Mercedes Zambrano

Antibiotic resistance genes predate the therapeutic uses of antibiotics. However, the current antimicrobial resistance crisis stems from our extensive use of antibiotics and the generation of environmental stressors that impose new selective pressure on microbes and drive the evolution of resistant pathogens that now threaten human health. Similar to climate change, this global threat results from human activities that change habitats and natural microbiomes, which in turn interact with human-associated ecosystems and lead to adverse impacts on human health. Human activities that alter our planet at global scales exacerbate the current resistance crisis and exemplify our central role in large-scale changes in which we are both protagonists and architects of our success but also casualties of unanticipated collateral outcomes. As cognizant participants in this ongoing planetary experiment, we are driven to understand and find strategies to curb the ongoing crises of resistance and climate change.

抗生素耐药基因早于抗生素的治疗用途。然而,目前的抗菌素耐药性危机源于我们广泛使用抗生素和环境压力源的产生,这些压力源对微生物施加了新的选择压力,并推动耐药病原体的进化,现在威胁着人类健康。与气候变化类似,这一全球性威胁源于改变栖息地和自然微生物群的人类活动,而这些活动又与与人类有关的生态系统相互作用,对人类健康产生不利影响。人类活动在全球范围内改变了我们的星球,加剧了目前的耐药性危机,并证明了我们在大规模变革中的核心作用。在这些变革中,我们既是成功的主角和建筑师,也是意外附带结果的受害者。作为这个正在进行的全球实验的参与者,我们被驱使去理解和找到遏制持续的耐药性和气候变化危机的策略。
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引用次数: 0
Induced Pluripotent Stem Cells in Disease Biology and the Evidence for Their In Vitro Utility. 诱导多能干细胞在疾病生物学中的应用及其体外应用证据。
IF 11.1 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2023-11-27 Epub Date: 2023-09-14 DOI: 10.1146/annurev-genet-022123-090319
Ayodeji Adegunsoye, Natalia M Gonzales, Yoav Gilad

Many human phenotypes are impossible to recapitulate in model organisms or immortalized human cell lines. Induced pluripotent stem cells (iPSCs) offer a way to study disease mechanisms in a variety of differentiated cell types while circumventing ethical and practical issues associated with finite tissue sources and postmortem states. Here, we discuss the broad utility of iPSCs in genetic medicine and describe how they are being used to study musculoskeletal, pulmonary, neurologic, and cardiac phenotypes. We summarize the particular challenges presented by each organ system and describe how iPSC models are being used to address them. Finally, we discuss emerging iPSC-derived organoid models and the potential value that they can bring to studies of human disease.

许多人类表型不可能在模式生物或永生化的人类细胞系中重现。诱导多能干细胞(iPSCs)为研究多种分化细胞类型的疾病机制提供了一种方法,同时避免了与有限组织来源和死后状态相关的伦理和实践问题。在这里,我们讨论了多能干细胞在遗传医学中的广泛应用,并描述了它们如何被用于研究肌肉骨骼、肺、神经和心脏表型。我们总结了每个器官系统提出的特殊挑战,并描述了如何使用iPSC模型来解决这些挑战。最后,我们讨论了新兴的ipsc衍生类器官模型及其对人类疾病研究的潜在价值。
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引用次数: 0
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Annual review of genetics
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