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Artificial Intelligence Learns Protein Prediction. 人工智能学习蛋白质预测。
IF 6.9 2区 生物学 Q1 CELL BIOLOGY Pub Date : 2024-09-03 DOI: 10.1101/cshperspect.a041458
Michael Heinzinger, Burkhard Rost

From AlphaGO over StableDiffusion to ChatGPT, the recent decade of exponential advances in artificial intelligence (AI) has been altering life. In parallel, advances in computational biology are beginning to decode the language of life: AlphaFold2 leaped forward in protein structure prediction, and protein language models (pLMs) replaced expertise and evolutionary information from multiple sequence alignments with information learned from reoccurring patterns in databases of billions of proteins without experimental annotations other than the amino acid sequences. None of those tools could have been developed 10 years ago; all will increase the wealth of experimental data and speed up the cycle from idea to proof. AI is affecting molecular and medical biology at giant steps, and the most important might be the leap toward more powerful protein design.

从 AlphaGO 到 StableDiffusion,再到 ChatGPT,近十年来人工智能(AI)的指数级进步正在改变生活。与此同时,计算生物学的进步也开始解码生命的语言:AlphaFold2 在蛋白质结构预测方面突飞猛进,蛋白质语言模型(pLMs)取代了多序列比对中的专业知识和进化信息,取而代之的是从数十亿蛋白质数据库中除氨基酸序列外没有其他实验注释的重复出现模式中学习到的信息。这些工具都不可能在 10 年前开发出来;它们都将增加实验数据的财富,加快从想法到证明的周期。人工智能正在大步影响分子生物学和医学生物学,其中最重要的可能是向更强大的蛋白质设计跃进。
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引用次数: 0
The Ecology of Hybrid Incompatibilities. 杂交不相容的生态学。
IF 6.9 2区 生物学 Q1 CELL BIOLOGY Pub Date : 2024-09-03 DOI: 10.1101/cshperspect.a041440
Ken A Thompson, Yaniv Brandvain, Jenn M Coughlan, Kira E Delmore, Hannah Justen, Catherine R Linnen, Daniel Ortiz-Barrientos, Catherine A Rushworth, Hilde Schneemann, Molly Schumer, Rike Stelkens

Ecologically mediated selection against hybrids, caused by hybrid phenotypes fitting poorly into available niches, is typically viewed as distinct from selection caused by epistatic Dobzhansky-Muller hybrid incompatibilities. Here, we show how selection against transgressive phenotypes in hybrids manifests as incompatibility. After outlining our logic, we summarize current approaches for studying ecology-based selection on hybrids. We then quantitatively review QTL-mapping studies and find traits differing between parent taxa are typically polygenic. Next, we describe how verbal models of selection on hybrids translate to phenotypic and genetic fitness landscapes, highlighting emerging approaches for detecting polygenic incompatibilities. Finally, in a synthesis of published data, we report that trait transgression-and thus possibly extrinsic hybrid incompatibility in hybrids-escalates with the phenotypic divergence between parents. We discuss conceptual implications and conclude that studying the ecological basis of hybrid incompatibility will facilitate new discoveries about mechanisms of speciation.

生态学介导的针对杂交种的选择,是由杂交种的表型不能适应现有的生态位所引起的,通常被视为有别于由外显的多布赞斯基-穆勒杂交不兼容性所引起的选择。在这里,我们将展示针对杂交种转基因表型的选择是如何表现为不兼容性的。在概述了我们的逻辑之后,我们总结了目前研究基于生态学的杂交种选择的方法。然后,我们定量回顾了 QTL 图谱研究,发现亲本类群之间的性状差异通常是多基因的。接下来,我们描述了杂交种选择的口头模型如何转化为表型和遗传适应性景观,重点介绍了检测多基因不相容性的新兴方法。最后,综合已发表的数据,我们报告了性状变异--因此可能是杂交种的外在杂交不相容性--随着亲本之间表型差异的增加而增加。我们讨论了概念上的影响,并得出结论:研究杂交不相容性的生态基础将有助于发现物种分化的新机制。
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引用次数: 0
Cellular Contributions to Glymphatic and Lymphatic Waste Clearance in the Brain 细胞对大脑淋巴管和淋巴管废物清除的贡献
IF 7.2 2区 生物学 Q1 CELL BIOLOGY Pub Date : 2024-08-12 DOI: 10.1101/cshperspect.a041370
Leon C.D. Smyth, Natalie Beschorner, Maiken Nedergaard, Jonathan Kipnis
Cerebrospinal fluid (CSF) bathes and cushions the brain; however, it also serves a major role in the clearance of metabolic wastes and in the distribution of glucose, lipids, and amino acids. Unlike every other organ in the body, the brain parenchyma lacks a traditional lymphatic system to drain fluids and central nervous system (CNS) antigens. It was historically assumed that all brain wastes were removed by endogenous processing, such as phagocytosis and autophagy, while excess fluids drained directly into the blood. However, the twin discoveries of the glial-lymphatic (glymphatic) system and meningeal lymphatics have transformed our understanding of brain waste clearance. The glymphatic system describes the movement of fluids through the subarachnoid space (SAS), the influx along periarterial spaces into the brain parenchyma, and the ultimate efflux back into the SAS along perivenous spaces where it comes into direct contact with the meningeal lymphatics. The dura mater of the meninges contains a bona fide lymphatic network that can drain CSF that has entered the dura. Together, these pathways provide insights into the clearance of molecules and fluids from the brain, and show that the CNS is physically connected to the adaptive immune system. Here, we outline the glymphatic and lymphatic systems, and describe the cellular components that are important to their function.
脑脊液(CSF)是大脑的沐浴液和缓冲液,但它在清除代谢废物以及分配葡萄糖、脂类和氨基酸方面也发挥着重要作用。与身体的其他器官不同,脑实质缺乏传统的淋巴系统来排出体液和中枢神经系统(CNS)抗原。人们历来认为,所有脑废物都是通过吞噬和自噬等内源性处理方式清除的,而多余的体液则直接排入血液。然而,胶质-淋巴系统(glymphatic)和脑膜淋巴管的双重发现改变了我们对大脑废物清除的认识。淋巴系统描述了液体通过蛛网膜下腔(SAS)的运动,沿动脉周围间隙流入脑实质,并最终沿静脉周围间隙流回蛛网膜下腔,在那里与脑膜淋巴管直接接触。脑膜的硬脑膜包含一个真正的淋巴网络,可以引流进入硬脑膜的 CSF。这些途径共同揭示了脑内分子和液体的清除过程,并表明中枢神经系统与适应性免疫系统之间存在物理联系。在此,我们概述了甘液系统和淋巴系统,并描述了对其功能非常重要的细胞成分。
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引用次数: 0
The Diversity of Skeletal Muscle Fiber Types 骨骼肌纤维类型的多样性
IF 7.2 2区 生物学 Q1 CELL BIOLOGY Pub Date : 2024-08-12 DOI: 10.1101/cshperspect.a041477
Stefano Schiaffino, Francesco Chemello, Carlo Reggiani
The widespread presence of slow-red and fast-white muscles in all vertebrates supports the evolutionary advantage of having two types of motors available for animal movement—a slow economical motor used for most activities, and a fast energetically costly motor used for rapid movements and emergency actions, and actions that require a lot of force. Skeletal muscles are composed of multiple fiber types whose structural and functional properties have only in part been characterized. Further progress in this field is mainly occurring along two directions: Multiomics approaches are providing a global picture of the molecular composition of muscle fibers up to the single fiber and single nucleus level. Signaling studies are identifying many transcription factors and pathways controlling fiber-type specification. These new data should now be integrated into a wider whole-body context by defining the matching between muscle fiber and motor neuron heterogeneity in the neuromuscular system, as well as the relevance of muscle fiber types in systemic homeostatic functions, including metabolism and thermogenesis.
所有脊椎动物中都普遍存在慢红肌和快白肌,这证明了动物进化过程中拥有两种运动机能的优势:一种是用于大多数活动的经济型慢速运动机能,另一种是用于快速运动、紧急行动和需要很大力量的行动的高能耗快速运动机能。骨骼肌由多种纤维类型组成,其结构和功能特性只有部分得到了描述。该领域的进一步发展主要有两个方向:多组学方法提供了肌肉纤维分子组成的全貌,直至单个纤维和单个细胞核水平。信号研究正在确定许多转录因子和控制纤维类型规格的途径。现在应将这些新数据整合到更广泛的全身背景中,界定神经肌肉系统中肌纤维和运动神经元异质性之间的匹配关系,以及肌纤维类型与新陈代谢和产热等全身性平衡功能的相关性。
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引用次数: 0
Glial Origins of Inherited White Matter Disorders 遗传性白质疾病的神经胶质起源
IF 7.2 2区 生物学 Q1 CELL BIOLOGY Pub Date : 2024-08-12 DOI: 10.1101/cshperspect.a041457
Anjana Sevagamoorthy, Adeline Vanderver, Jamie L. Fraser, Jennifer Orthmann-Murphy
Inherited white matter disorders (IWMDs) are a phenotypically and genotypically heterogeneous group of disorders affecting the central nervous system (CNS) with or without peripheral neuropathy. They are classified either as leukodystrophies (LDs), with primary glial abnormalities, or genetic leukoencephalopathies (gLEs), where other CNS cells are involved. As a group, these disorders are common, with an incidence of 1 in 7500 births. However, IWMDs often go undiagnosed or suffer delayed or misdiagnosis due to their heterogeneous presentation. Many of these disorders present with lethal secondary manifestations that can be prevented through early disease recognition, periodic surveillance, and preventative management. Emerging therapeutics, including gene therapy trials for metachromatic leukodystrophy (MLD) and adrenoleukodystrophy (ALD), suggest disease progression may be slowed or even prevented if treated early. Therapies for IWMDs that target glial cells or the peripheral immune system may provide novel insights for treating acquired disorders of white matter.
遗传性白质疾病(IWMDs)是一组表型和基因型异质性疾病,影响中枢神经系统(CNS),伴有或不伴有周围神经病变。它们可分为原发性神经胶质异常的白质营养不良症(LDs)和累及其他中枢神经系统细胞的遗传性脑白质病(gLEs)。作为一类常见疾病,这些疾病的发病率为每 7500 名新生儿中就有 1 例。然而,由于表现各异,IWMD 常常得不到诊断,或被延误或误诊。许多这类疾病会出现致命的继发性表现,而通过早期疾病识别、定期监测和预防性管理,这些表现是可以避免的。新出现的治疗方法,包括针对变色性白质营养不良症(MLD)和肾上腺白质营养不良症(ALD)的基因治疗试验表明,如果早期治疗,可以减缓甚至预防疾病的发展。针对神经胶质细胞或外周免疫系统的 IWMDs 疗法可能会为治疗后天性白质疾病提供新的见解。
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引用次数: 0
Autophagy in Skeletal Muscle 骨骼肌中的自噬作用
IF 7.2 2区 生物学 Q1 CELL BIOLOGY Pub Date : 2024-08-12 DOI: 10.1101/cshperspect.a041565
Anais Franco-Romero, Marco Sandri, Stefano Schiaffino
Skeletal muscle fibers possess, like all cells of our body, an evolutionary conserved autophagy machinery, which allows them to segregate unfolded proteins and damaged organelles within autophagosomes, and to induce fusion of autophagosomes with lysosomes, leading to degradation of those altered cell constituents. This process may be selective for specific cell components, as in the case of glycogen (glycophagy) or organelles, as with mitochondria (mitophagy). The autophagic flux is activated by fasting, and contributes with the proteasome to provide the organism with amino acids required for survival. Autophagy is also essential for the normal turnover of muscle proteins and organelles, as shown by the degenerative changes induced by genetic block of the autophagic mechanism, and in several myopathies. Autophagy is enhanced in muscle by exercise and impaired during aging, suggesting that aging-dependent muscle dysfunction could be delayed by boosting autophagy.
骨骼肌纤维与人体所有细胞一样,拥有进化保守的自噬机制,可将未折叠蛋白质和受损细胞器分离到自噬体中,并诱导自噬体与溶酶体融合,从而降解这些发生变化的细胞成分。这一过程可能对特定的细胞成分具有选择性,如糖原(糖吞噬)或细胞器,如线粒体(线粒体吞噬)。禁食会激活自噬通量,并与蛋白酶体一起为生物体提供生存所需的氨基酸。自噬对于肌肉蛋白质和细胞器的正常周转也是必不可少的,自噬机制的基因阻断所诱发的退行性变化以及多种肌病都证明了这一点。肌肉中的自噬功能在运动时会增强,而在衰老过程中则会减弱,这表明通过增强自噬功能可以延缓依赖衰老的肌肉功能障碍。
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引用次数: 0
The Myotendinous Junction—Form and Function 肌腱接头--形态与功能
IF 7.2 2区 生物学 Q1 CELL BIOLOGY Pub Date : 2024-08-12 DOI: 10.1101/cshperspect.a041500
Abigail L. Mackey
A critical link in the chain of force transmission from muscle fiber cross-bridge to bone is the interface between muscle and tendon—the myotendinous junction (MTJ). To meet the challenge of connecting these two tissues, the MTJ is specialized molecularly and morphologically. Distinct transcriptional profiles are evident for the myonuclei at the myofiber tips and a population of mononuclear tendon cells at the MTJ, demonstrating support from both sides in MTJ maintenance. Paradoxically, despite this high degree of specialization, the MTJ remains susceptible to strain (rupture) injury and is often associated with failed tissue healing. Incomplete understanding of the nature of the MTJ and the elements contributing to its plasticity hinder tackling this unsolved clinical challenge. The goal of this review is to summarize key structural and molecular features of the MTJ, discuss MTJ adaptation in response to mechanical (un)loading, aging, and injury, and highlight the major unanswered questions surrounding the MTJ.
从肌纤维横桥到骨骼的力传递链中的一个关键环节是肌肉和肌腱之间的界面--肌腱连接处(MTJ)。为了应对连接这两种组织的挑战,MTJ 在分子和形态上都进行了特化。肌纤维顶端的肌核和MTJ处的单核肌腱细胞群明显具有不同的转录特征,这表明MTJ的维持得到了双方的支持。令人啼笑皆非的是,尽管MTJ高度特化,但它仍然容易受到应变(断裂)损伤,并经常与组织愈合失败有关。对 MTJ 的性质及其可塑性因素的不完全了解阻碍了这一悬而未决的临床难题的解决。本综述旨在总结 MTJ 的主要结构和分子特征,讨论 MTJ 对机械(非)加载、老化和损伤的适应性,并强调有关 MTJ 的主要未解之谜。
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引用次数: 0
The Nodes of Ranvier: Mechanisms of Assembly and Maintenance 兰维耶结节:组装和维护机制
IF 7.2 2区 生物学 Q1 CELL BIOLOGY Pub Date : 2024-08-12 DOI: 10.1101/cshperspect.a041361
Matthew N. Rasband, Elior Peles
Action potential propagation along myelinated axons requires clustered voltage-gated sodium and potassium channels. These channels must be restricted to nodes of Ranvier where the action potential is regenerated. Several mechanisms have evolved to facilitate and ensure the correct assembly and stabilization of these essential axonal domains. This review highlights the current understanding of the axon-intrinsic and glial-extrinsic mechanisms that control the formation and maintenance of the nodes of Ranvier in both the peripheral (PNS) and central (CNS) nervous systems.
髓鞘轴突的动作电位传播需要电压门控钠和钾通道的聚集。这些通道必须限制在再生动作电位的 Ranvier 节上。为了促进和确保这些重要轴突结构域的正确组装和稳定,已经形成了多种机制。本综述将重点介绍目前对轴突内在机制和神经胶质外在机制的理解,这些机制控制着外周(PNS)和中枢(CNS)神经系统中兰维耶结的形成和维持。
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引用次数: 0
Astrocyte Regulation of Synapse Formation, Maturation, and Elimination. 星形胶质细胞对突触形成、成熟和消除的调控作用
IF 6.9 2区 生物学 Q1 CELL BIOLOGY Pub Date : 2024-08-01 DOI: 10.1101/cshperspect.a041352
Won-Suk Chung, Katherine T Baldwin, Nicola J Allen

Astrocytes play an integral role in the development, maturation, and refinement of neuronal circuits. Astrocytes secrete proteins and lipids that instruct the formation of new synapses and induce the maturation of existing synapses. Through contact-mediated signaling, astrocytes can regulate the formation and state of synapses within their domain. Through phagocytosis, astrocytes participate in the elimination of excess synaptic connections. In this work, we will review key findings on the molecular mechanisms of astrocyte-synapse interaction with a focus on astrocyte-secreted factors, contact-mediated mechanisms, and synapse elimination. We will discuss this in the context of typical brain development and maintenance, as well as consider the consequences of dysfunction in these pathways in neurological disorders, highlighting a role for astrocytes in health and disease.

星形胶质细胞在神经元回路的发育、成熟和完善过程中发挥着不可或缺的作用。星形胶质细胞分泌的蛋白质和脂质可指示新突触的形成,并诱导现有突触的成熟。通过接触介导的信号传递,星形胶质细胞可以调节其领域内突触的形成和状态。通过吞噬作用,星形胶质细胞参与消除多余的突触连接。在这项研究中,我们将回顾星形胶质细胞与突触相互作用分子机制的主要发现,重点是星形胶质细胞分泌的因子、接触介导的机制和突触消除。我们将在典型的大脑发育和维持的背景下讨论这个问题,并考虑这些途径的功能障碍在神经系统疾病中的后果,强调星形胶质细胞在健康和疾病中的作用。
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引用次数: 0
The Biology of Lipids. 脂质生物学
IF 6.9 2区 生物学 Q1 CELL BIOLOGY Pub Date : 2024-08-01 DOI: 10.1101/cshperspect.a041713
Robert G Parton, Kai Simons

Lipids are the defining features of cellular membranes. They act collectively to form a variety of different structures, and understanding their complex behavior represents an early example of systems biology. A multidisciplinary approach is needed to analyse the functions of lipids in biological systems, and new work is providing fascinating insights into their roles in membrane biology, metabolism, signaling, subcellular dynamics and various disease processes.

脂质是细胞膜的决定性特征。它们共同作用形成各种不同的结构,了解它们的复杂行为是系统生物学的早期范例。要分析脂质在生物系统中的功能,需要采用多学科的方法,而新的研究成果为我们提供了关于脂质在膜生物学、新陈代谢、信号传递、亚细胞动力学和各种疾病过程中的作用的精彩见解。
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引用次数: 0
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Cold Spring Harbor perspectives in biology
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