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How machine learning can help us understand what we have grown in the dish 机器学习如何帮助我们理解我们在培养皿中生长的东西
IF 112.7 1区 生物学
Nature Reviews Molecular Cell Biology Pub Date : 2025-06-10 DOI: 10.1038/s41580-025-00868-7
Roser Vento-Tormo
{"title":"How machine learning can help us understand what we have grown in the dish","authors":"Roser Vento-Tormo","doi":"10.1038/s41580-025-00868-7","DOIUrl":"https://doi.org/10.1038/s41580-025-00868-7","url":null,"abstract":"A machine learning model was trained to quantify how closely neurons differentiated in a dish from stem cells resemble those found in the brain.","PeriodicalId":19051,"journal":{"name":"Nature Reviews Molecular Cell Biology","volume":"17 1","pages":""},"PeriodicalIF":112.7,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144252302","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Collective migration modes in development, tissue repair and cancer 发育、组织修复和癌症中的集体迁移模式
IF 112.7 1区 生物学
Nature Reviews Molecular Cell Biology Pub Date : 2025-06-05 DOI: 10.1038/s41580-025-00858-9
Kevin J. Cheung, Sally Horne-Badovinac
{"title":"Collective migration modes in development, tissue repair and cancer","authors":"Kevin J. Cheung, Sally Horne-Badovinac","doi":"10.1038/s41580-025-00858-9","DOIUrl":"https://doi.org/10.1038/s41580-025-00858-9","url":null,"abstract":"<p>Migrating cells have key functions in shaping tissues during development, repairing tissues after development and supporting cancer invasion and metastasis. In all these contexts, cells often maintain contact with their neighbours and move as a group, in a process termed collective migration. In this Review, we describe the elegant mechanisms used by collectively migrating cells in vivo to coordinate their movements and obtain directional information. We start by highlighting the diverse physiological roles that migrating collectives have within the body and then focus on dominant paradigms for the organization of migrating collectives including the roles of leader and follower cells, local cell–cell adhesion and signalling, and external guidance cues. By comparing collective migrations occurring during development and cancer, we bring into focus shared principles for collective cell movement and distinct strategies used by cancer cells for their own dispersal. Throughout, we pay particular attention to how migrating collectives display emergent properties not exhibited by individually migrating cells and how these properties provide the robustness needed for efficient cell movement.</p>","PeriodicalId":19051,"journal":{"name":"Nature Reviews Molecular Cell Biology","volume":"19 1","pages":""},"PeriodicalIF":112.7,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144228678","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Nucleosomes as blueprints of genome architecture 核小体是基因组结构的蓝图
IF 112.7 1区 生物学
Nature Reviews Molecular Cell Biology Pub Date : 2025-06-04 DOI: 10.1038/s41580-025-00866-9
Eytan Zlotorynski
{"title":"Nucleosomes as blueprints of genome architecture","authors":"Eytan Zlotorynski","doi":"10.1038/s41580-025-00866-9","DOIUrl":"https://doi.org/10.1038/s41580-025-00866-9","url":null,"abstract":"Nucleosomes — the basic unit of chromatin architecture — have intrinsic biophysical features of large-scale genome organization.","PeriodicalId":19051,"journal":{"name":"Nature Reviews Molecular Cell Biology","volume":"31 1","pages":""},"PeriodicalIF":112.7,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144211403","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Uncovering mRNA sequences that control translation initiation 揭示控制翻译起始的mRNA序列
IF 112.7 1区 生物学
Nature Reviews Molecular Cell Biology Pub Date : 2025-05-21 DOI: 10.1038/s41580-025-00862-z
Kyrillos S. Abdallah
{"title":"Uncovering mRNA sequences that control translation initiation","authors":"Kyrillos S. Abdallah","doi":"10.1038/s41580-025-00862-z","DOIUrl":"https://doi.org/10.1038/s41580-025-00862-z","url":null,"abstract":"In this Tools of the Trade article, Abdallah (Gilbert lab) describes the development of direct analysis of ribosome targeting (DART), a tool designed to explore 5' UTR sequences for their potential to efficiently initiate translation.","PeriodicalId":19051,"journal":{"name":"Nature Reviews Molecular Cell Biology","volume":"40 1","pages":""},"PeriodicalIF":112.7,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144104113","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Enabling RNA-compatible synthetic receptors through RNA editing 通过RNA编辑实现RNA兼容的合成受体
IF 112.7 1区 生物学
Nature Reviews Molecular Cell Biology Pub Date : 2025-05-21 DOI: 10.1038/s41580-025-00863-y
Xiaowei Zhang, Luis S. Mille-Fragoso
{"title":"Enabling RNA-compatible synthetic receptors through RNA editing","authors":"Xiaowei Zhang, Luis S. Mille-Fragoso","doi":"10.1038/s41580-025-00863-y","DOIUrl":"https://doi.org/10.1038/s41580-025-00863-y","url":null,"abstract":"In this Tools of the Trade article, Zhang and Mille-Fragoso (Gao lab) describe a synthetic receptor platform that is activated by the binding of specific ligands, which triggers RNA editing, enabling the translation of an output protein.","PeriodicalId":19051,"journal":{"name":"Nature Reviews Molecular Cell Biology","volume":"135 1","pages":""},"PeriodicalIF":112.7,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144104100","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Structure, regulation and assembly of the photosynthetic electron transport chain 光合作用电子传递链的结构、调节和组装
IF 112.7 1区 生物学
Nature Reviews Molecular Cell Biology Pub Date : 2025-05-21 DOI: 10.1038/s41580-025-00847-y
Matthew P. Johnson
{"title":"Structure, regulation and assembly of the photosynthetic electron transport chain","authors":"Matthew P. Johnson","doi":"10.1038/s41580-025-00847-y","DOIUrl":"https://doi.org/10.1038/s41580-025-00847-y","url":null,"abstract":"<p>The electron transfer chain of chloroplast thylakoid membranes uses solar energy to split water into electrons and protons, creating energetic gradients that drive the formation of photosynthetic fuel in the form of NADPH and ATP. These metabolites are then used to power the fixation of carbon dioxide into biomass through the Calvin–Benson–Bassham cycle in the chloroplast stroma. Recent advances in molecular genetics, structural biology and spectroscopy have provided an unprecedented understanding of the molecular events involved in photosynthetic electron transfer from photon capture to ATP production. Specifically, we have gained insights into the assembly of the photosynthetic complexes into larger supercomplexes, thylakoid membrane organization and the mechanisms underpinning efficient light harvesting, photoprotection and oxygen evolution. In this Review, I focus on the angiosperm plant thylakoid system, outlining our current knowledge on the structure, function, regulation and assembly of each component of the photosynthetic chain. I explain how solar energy is harvested and converted into chemical energy by the photosynthetic electron transfer chain, how its components are integrated into a complex membrane macrostructure and how this organization contributes to regulation and photoprotection.</p>","PeriodicalId":19051,"journal":{"name":"Nature Reviews Molecular Cell Biology","volume":"262 1","pages":""},"PeriodicalIF":112.7,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144113689","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Functions and therapeutic applications of pseudouridylation 假尿嘧啶化的功能和治疗应用
IF 112.7 1区 生物学
Nature Reviews Molecular Cell Biology Pub Date : 2025-05-20 DOI: 10.1038/s41580-025-00852-1
Nan Luo, Qiang Huang, Meiling Zhang, Chengqi Yi
{"title":"Functions and therapeutic applications of pseudouridylation","authors":"Nan Luo, Qiang Huang, Meiling Zhang, Chengqi Yi","doi":"10.1038/s41580-025-00852-1","DOIUrl":"https://doi.org/10.1038/s41580-025-00852-1","url":null,"abstract":"<p>The success of using pseudouridine (Ψ) and its methylation derivative in mRNA vaccines against SARS-CoV-2 has sparked a renewed interest in this RNA modification, known as the ‘fifth nucleotide’ of RNA. In this Review, we discuss the emerging functions of pseudouridylation in gene regulation, focusing on how pseudouridine in mRNA, tRNA and ribosomal RNA (rRNA) regulates translation. We also discuss the effects of pseudouridylation on RNA secondary structure, pre-mRNA splicing, and in vitro mRNA stability. In addition to nuclear-genome-encoded RNAs, pseudouridine is also present in mitochondria-encoded rRNA, mRNA and tRNA, where it has different distributions and functions compared with their nuclear counterparts. We then discuss the therapeutic potential of programmable pseudouridylation and mRNA vaccine optimization through pseudouridylation. Lastly, we briefly describe the latest quantitative pseudouridine detection methods. We posit that pseudouridine is a highly promising modification that merits further epitranscriptomics investigation and therapeutic application.</p>","PeriodicalId":19051,"journal":{"name":"Nature Reviews Molecular Cell Biology","volume":"39 1","pages":""},"PeriodicalIF":112.7,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144097188","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
N-glycan-dependent protein maturation and quality control in the ER 内质网中n-聚糖依赖蛋白的成熟和质量控制
IF 112.7 1区 生物学
Nature Reviews Molecular Cell Biology Pub Date : 2025-05-19 DOI: 10.1038/s41580-025-00855-y
Kevin P. Guay, Wen-Chuan Chou, Nathan P. Canniff, Kylie B. Paul, Daniel N. Hebert
{"title":"N-glycan-dependent protein maturation and quality control in the ER","authors":"Kevin P. Guay, Wen-Chuan Chou, Nathan P. Canniff, Kylie B. Paul, Daniel N. Hebert","doi":"10.1038/s41580-025-00855-y","DOIUrl":"https://doi.org/10.1038/s41580-025-00855-y","url":null,"abstract":"<p>The vast majority of proteins that traverse the mammalian secretory pathway become N-glycosylated in the endoplasmic reticulum (ER). The bulky glycan protein modifications, which are conserved in fungi and humans, act as maturation and quality-control tags. In this Review, we discuss findings published in the past decade that have rapidly expanded our understanding of the transfer and processing of N-glycans, as well as their role in protein maturation, quality control and trafficking in the ER, facilitated by structural insights into the addition of N-glycans by the oligosaccharyltransferases A and B (OST-A and OST-B). These findings suggest that N-glycans serve as reporters of the folding status of secretory proteins as they traverse the ER, enabling the lectin chaperones to guide their maturation. We also explore how the emergence of co-translational glycosylation and the expansion of the glycoproteostasis network in metazoans has expanded the role of N-glycans in early protein-maturation events and quality control.</p>","PeriodicalId":19051,"journal":{"name":"Nature Reviews Molecular Cell Biology","volume":"130 1","pages":""},"PeriodicalIF":112.7,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144097136","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Mechanisms of auxin action in plant growth and development 生长素在植物生长发育中的作用机制
IF 112.7 1区 生物学
Nature Reviews Molecular Cell Biology Pub Date : 2025-05-19 DOI: 10.1038/s41580-025-00851-2
Steffen Vanneste, Yuanrong Pei, Jiří Friml
{"title":"Mechanisms of auxin action in plant growth and development","authors":"Steffen Vanneste, Yuanrong Pei, Jiří Friml","doi":"10.1038/s41580-025-00851-2","DOIUrl":"https://doi.org/10.1038/s41580-025-00851-2","url":null,"abstract":"<p>The phytohormone auxin is a major signal coordinating growth and development in plants. The variety of its effects arises from its ability to form local auxin maxima and gradients within tissues, generated through directional cell-to-cell transport and elaborate metabolic control. These auxin distribution patterns instruct cells in a context-dependent manner to undergo predefined developmental transitions. In this Review, we discuss advances in auxin action at the level of homeostasis and signalling. We highlight key insights into the structural basis of PIN-mediated intercellular auxin transport and explore two novel non-transcriptional auxin signalling mechanisms: one involving intracellular Ca<sup>2+</sup> transients and another involving cell-surface auxin perception that mediates global, ultrafast phosphorylation. Furthermore, we examine emerging evidence indicating the involvement of cyclic adenosine monophosphate as a second messenger in the transcriptional auxin response. Together, these recent developments in auxin research have profoundly deepened our understanding of the complex and diverse activities of auxin in plant growth and development.</p>","PeriodicalId":19051,"journal":{"name":"Nature Reviews Molecular Cell Biology","volume":"17 1","pages":""},"PeriodicalIF":112.7,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144087863","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Molecular machineries shaping the mitochondrial inner membrane 形成线粒体内膜的分子机制
IF 112.7 1区 生物学
Nature Reviews Molecular Cell Biology Pub Date : 2025-05-14 DOI: 10.1038/s41580-025-00854-z
Oliver Daumke, Martin van der Laan
{"title":"Molecular machineries shaping the mitochondrial inner membrane","authors":"Oliver Daumke, Martin van der Laan","doi":"10.1038/s41580-025-00854-z","DOIUrl":"https://doi.org/10.1038/s41580-025-00854-z","url":null,"abstract":"<p>Mitochondria display intricately shaped deep invaginations of the mitochondrial inner membrane (MIM) termed cristae. This peculiar membrane architecture is essential for diverse mitochondrial functions, such as oxidative phosphorylation or the biosynthesis of cellular building blocks. Conserved protein nano-machineries such as F<sub>1</sub>F<sub>o</sub>-ATP synthase oligomers and the mitochondrial contact site and cristae organizing system (MICOS) act as adaptable protein–lipid scaffolds controlling MIM biogenesis and its dynamic remodelling. Signal-dependent rearrangements of cristae architecture and MIM fusion events are governed by the dynamin-like GTPase optic atrophy 1 (OPA1). Recent groundbreaking structural insights into these nano-machineries have considerably advanced our understanding of the functional architecture of mitochondria. In this Review, we discuss how the MIM-shaping machineries cooperate to control cristae and crista junction dynamics, including MIM fusion, in response to cellular signalling pathways. We also explore how mutations affecting MIM-shaping machineries compromise mitochondrial functions.</p>","PeriodicalId":19051,"journal":{"name":"Nature Reviews Molecular Cell Biology","volume":"29 1","pages":""},"PeriodicalIF":112.7,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143979572","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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