IF 64.8 1区综合性期刊

Nature Pub Date : 2025-07-23 DOI: 10.1038/d41586-025-02132-6

Charlotte Tupman

引用次数: 0

The deep sea is a globally connected habitat 深海是一个连接全球的栖息地

IF 64.8 1区综合性期刊

Nature Pub Date : 2025-07-23 DOI: 10.1038/d41586-025-02286-3

引用次数: 0

Integrated biotechnological and AI innovations for crop improvement 作物改良的综合生物技术和人工智能创新

IF 50.5 1区综合性期刊

Nature Pub Date : 2025-07-23 DOI: 10.1038/s41586-025-09122-8

Guotian Li, Linna An, Wanneng Yang, Lei Yang, Tong Wei, Jiawei Shi, Jianglin Wang, John H. Doonan, Kabin Xie, Alisdair R. Fernie, Evans S. Lagudah, Rod A. Wing, Caixia Gao

{"title":"Integrated biotechnological and AI innovations for crop improvement","authors":"Guotian Li, Linna An, Wanneng Yang, Lei Yang, Tong Wei, Jiawei Shi, Jianglin Wang, John H. Doonan, Kabin Xie, Alisdair R. Fernie, Evans S. Lagudah, Rod A. Wing, Caixia Gao","doi":"10.1038/s41586-025-09122-8","DOIUrl":"10.1038/s41586-025-09122-8","url":null,"abstract":"Crops provide food, clothing and other important products for the global population. To meet the demands of a growing population, substantial improvements are required in crop yield, quality and production sustainability. However, these goals are constrained by various environmental factors and limited genetic resources. Overcoming these limitations requires a paradigm shift in crop improvement by fully leveraging natural genetic diversity alongside biotechnological approaches such as genome editing and the heterologous expression of designed proteins, coupled with multimodal data integration. In this Review, we provide an in-depth analysis of integrated uses of omics technologies, genome editing, protein design and high-throughput phenotyping, in crop improvement, supported by artificial intelligence-enabled tools. We discuss the emerging applications and current challenges of these technologies in crop improvement. Finally, we present a perspective on how elite alleles generated through these technologies can be incorporated into the genomes of existing and de novo domesticated crops, aided by a proposed artificial intelligence model. We suggest that integrating these technologies with agricultural practices will lead to a new revolution in crop improvement, contributing to global food security in a sustainable manner. The integration of omics technologies, genome editing and protein design with artificial intelligence (AI) promises rapid advances in the field of crop improvement that will improve global food security.","PeriodicalId":18787,"journal":{"name":"Nature","volume":"643 8073","pages":"925-937"},"PeriodicalIF":50.5,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144688281","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Eye structure shapes neuron function in Drosophila motion vision 眼结构决定果蝇运动视觉的神经元功能

IF 64.8 1区综合性期刊

Nature Pub Date : 2025-07-23 DOI: 10.1038/s41586-025-09276-5

Arthur Zhao, Eyal Gruntman, Aljoscha Nern, Nirmala Iyer, Edward M. Rogers, Sanna Koskela, Igor Siwanowicz, Marisa Dreher, Miriam A. Flynn, Connor Laughland, Henrique Ludwig, Alexander Thomson, Cullen Moran, Bruck Gezahegn, Davi D. Bock, Michael B. Reiser

{"title":"Eye structure shapes neuron function in Drosophila motion vision","authors":"Arthur Zhao, Eyal Gruntman, Aljoscha Nern, Nirmala Iyer, Edward M. Rogers, Sanna Koskela, Igor Siwanowicz, Marisa Dreher, Miriam A. Flynn, Connor Laughland, Henrique Ludwig, Alexander Thomson, Cullen Moran, Bruck Gezahegn, Davi D. Bock, Michael B. Reiser","doi":"10.1038/s41586-025-09276-5","DOIUrl":"https://doi.org/10.1038/s41586-025-09276-5","url":null,"abstract":"Many animals use vision to navigate their environment. The pattern of changes that self-motion induces in the visual scene, referred to as optic flow1, is first estimated in local patches by directionally selective neurons2,3,4. However, how arrays of directionally selective neurons, each responsive to motion in a preferred direction at specific retinal positions, are organized to support robust decoding of optic flow by downstream circuits is unclear. Understanding this global organization requires mapping fine, local features of neurons across an animal’s field of view3. In Drosophila, the asymmetrical dendrites of the T4 and T5 directionally selective neurons establish their preferred direction, which makes it possible to predict directional tuning from anatomy4,5. Here we show that the organization of the compound eye shapes the systematic variation in the preferred directions of directionally selective neurons across the entire visual field. To estimate the preferred directions across the visual field, we reconstructed hundreds of T4 neurons in an electron-microscopy volume of the full adult fly brain6, and discovered unexpectedly stereotypical dendritic arborizations. We then used whole-head micro-computed-tomography scans to map the viewing directions of all compound eye facets, and found a non-uniform sampling of visual space that explains the spatial variation in preferred directions. Our findings show that the global organization of the directionally selective neurons’ preferred directions is determined mainly by the fly’s compound eye, revealing the intimate connections between eye structure, functional properties of neurons and locomotion control.","PeriodicalId":18787,"journal":{"name":"Nature","volume":"711 1","pages":""},"PeriodicalIF":64.8,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144693862","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Complete biosynthesis of salicylic acid from phenylalanine in plants. 植物中苯丙氨酸完全生物合成水杨酸。

IF 64.8 1区综合性期刊

Nature Pub Date : 2025-07-23 DOI: 10.1038/s41586-025-09175-9

Bao Zhu,Yanjun Zhang,Rong Gao,Zhihua Wu,Wei Zhang,Chao Zhang,Penghong Zhang,Can Ye,Linbo Yao,Ying Jin,Hui Mao,Peiyao Tou,Peng Huang,Jiangzhe Zhao,Qiao Zhao,Chang-Jun Liu,Kewei Zhang

{"title":"Complete biosynthesis of salicylic acid from phenylalanine in plants.","authors":"Bao Zhu,Yanjun Zhang,Rong Gao,Zhihua Wu,Wei Zhang,Chao Zhang,Penghong Zhang,Can Ye,Linbo Yao,Ying Jin,Hui Mao,Peiyao Tou,Peng Huang,Jiangzhe Zhao,Qiao Zhao,Chang-Jun Liu,Kewei Zhang","doi":"10.1038/s41586-025-09175-9","DOIUrl":"https://doi.org/10.1038/s41586-025-09175-9","url":null,"abstract":"Salicylic acid (SA) is a pivotal phytohormone for plant responses to biotic and abiotic stresses. Plants have evolved two pathways to produce SA: the isochorismate synthase and phenylalanine ammonia lyase (PAL) pathways1. Whereas the isochorismate synthase pathway has been fully identified2-4, the PAL pathway remains incomplete. Here we report the full characterization of the PAL pathway for SA biosynthesis via functional analysis of rice (Oryza sativa) SA-DEFICIENT GENE 1 (OSD1) to OSD4. The cinnamoyl-coenzyme A (CoA) ligase OSD1 catalyses the conversion of trans-cinnamic acid to cinnamoyl-CoA, which is subsequently transformed to benzoyl-CoA via the β-oxidative pathway in peroxisomes. The resulting benzoyl-CoA is further converted to benzyl benzoate by the peroxisomal benzoyltransferase OSD2. Benzyl benzoate is subsequently hydroxylated to benzyl salicylate by the endoplasmic reticulum membrane-resident cytochrome P450 OSD3, which is ultimately hydrolysed to salicylic acid by the cytoplasmic carboxylesterase OSD4. Evolutionary analyses reveal that the PAL pathway was first assembled before the divergence of gymnosperms and has been conserved in most seed plants. Activation of the PAL pathway in rice significantly enhances salicylic acid levels and plant immunity. Completion of the PAL pathway provides critical insights into the primary salicylic acid biosynthetic pathway across plant species and offers a precise target for modulating crop immunity.","PeriodicalId":18787,"journal":{"name":"Nature","volume":"18 1","pages":""},"PeriodicalIF":64.8,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144693487","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Precisely defining disease variant effects in CRISPR-edited single cells. 在crispr编辑的单细胞中精确定义疾病变异效应。

IF 64.8 1区综合性期刊

Nature Pub Date : 2025-07-23 DOI: 10.1038/s41586-025-09313-3

Yuriy Baglaenko,Zepeng Mu,Michelle Curtis,Hafsa M Mire,Vidyashree Jayanthi,Majd Al Suqri,Cassidy Liu,Ryan Agnew,Aparna Nathan,Annelise Yoo Mah-Som,David R Liu,Gregory A Newby,Soumya Raychaudhuri

{"title":"Precisely defining disease variant effects in CRISPR-edited single cells.","authors":"Yuriy Baglaenko,Zepeng Mu,Michelle Curtis,Hafsa M Mire,Vidyashree Jayanthi,Majd Al Suqri,Cassidy Liu,Ryan Agnew,Aparna Nathan,Annelise Yoo Mah-Som,David R Liu,Gregory A Newby,Soumya Raychaudhuri","doi":"10.1038/s41586-025-09313-3","DOIUrl":"https://doi.org/10.1038/s41586-025-09313-3","url":null,"abstract":"Genetic studies have identified thousands of individual disease-associated non-coding alleles, but the identification of the causal alleles and their functions remains a critical bottleneck1. CRISPR-Cas editing has enabled targeted modification of DNA to introduce and test disease alleles. However, the combination of inefficient editing, heterogeneous editing outcomes in individual cells and nonspecific transcriptional changes caused by editing and culturing conditions limits the ability to detect the functional consequences of disease alleles2,3. To overcome these challenges, we present a multi-omic single-cell sequencing approach that directly identifies genomic DNA edits, assays the transcriptome and measures cell-surface protein expression. We apply this approach to investigate the effects of gene disruption, deletions in regulatory regions, non-coding single-nucleotide polymorphism alleles and multiplexed editing. We identify the effects of individual single-nucleotide polymorphisms, including the state-specific effects of an IL2RA autoimmune variant in primary human T cells. Multimodal functional genomic single-cell assays, including DNA sequencing, enable the identification of causal variation in primary human cells and bridge a crucial gap in our understanding of complex human diseases.","PeriodicalId":18787,"journal":{"name":"Nature","volume":"17 1","pages":""},"PeriodicalIF":64.8,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144693176","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Molecule eases neurological symptoms of mitochondrial deficiency in coenzyme Q10 分子缓解辅酶Q10线粒体缺乏的神经症状

IF 64.8 1区综合性期刊

Nature Pub Date : 2025-07-23 DOI: 10.1038/d41586-025-02289-0

引用次数: 0

Contextualizing ancient texts with generative neural networks. 用生成神经网络对古代文本进行语境化。

IF 64.8 1区综合性期刊

Nature Pub Date : 2025-07-23 DOI: 10.1038/s41586-025-09292-5

Yannis Assael,Thea Sommerschield,Alison Cooley,Brendan Shillingford,John Pavlopoulos,Priyanka Suresh,Bailey Herms,Justin Grayston,Benjamin Maynard,Nicholas Dietrich,Robbe Wulgaert,Jonathan Prag,Alex Mullen,Shakir Mohamed

{"title":"Contextualizing ancient texts with generative neural networks.","authors":"Yannis Assael,Thea Sommerschield,Alison Cooley,Brendan Shillingford,John Pavlopoulos,Priyanka Suresh,Bailey Herms,Justin Grayston,Benjamin Maynard,Nicholas Dietrich,Robbe Wulgaert,Jonathan Prag,Alex Mullen,Shakir Mohamed","doi":"10.1038/s41586-025-09292-5","DOIUrl":"https://doi.org/10.1038/s41586-025-09292-5","url":null,"abstract":"Human history is born in writing. Inscriptions are among the earliest written forms, and offer direct insights into the thought, language and history of ancient civilizations. Historians capture these insights by identifying parallels-inscriptions with shared phrasing, function or cultural setting-to enable the contextualization of texts within broader historical frameworks, and perform key tasks such as restoration and geographical or chronological attribution1. However, current digital methods are restricted to literal matches and narrow historical scopes. Here we introduce Aeneas, a generative neural network for contextualizing ancient texts. Aeneas retrieves textual and contextual parallels, leverages visual inputs, handles arbitrary-length text restoration, and advances the state of the art in key tasks. To evaluate its impact, we conduct a large study with historians using outputs from Aeneas as research starting points. The historians find the parallels retrieved by Aeneas to be useful research starting points in 90% of cases, improving their confidence in key tasks by 44%. Restoration and geographical attribution tasks yielded superior results when historians were paired with Aeneas, outperforming both humans and artificial intelligence alone. For dating, Aeneas achieved a 13-year distance from ground-truth ranges. We demonstrate Aeneas' contribution to historical workflows through analysis of key traits in the renowned Roman inscription Res Gestae Divi Augusti, showing how integrating science and humanities can create transformative tools to assist historians and advance our understanding of the past.","PeriodicalId":18787,"journal":{"name":"Nature","volume":"18 1","pages":""},"PeriodicalIF":64.8,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144693183","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A gut sense for a microbial pattern regulates feeding. 肠道对微生物模式的感知调节着摄食。

IF 64.8 1区综合性期刊

Nature Pub Date : 2025-07-23 DOI: 10.1038/s41586-025-09301-7

Winston W Liu,Naama Reicher,Emily Alway,Laura E Rupprecht,Peter Weng,Chloe Schaefgen,Marguerita E Klein,Jorge A Villalobos,Carlos Puerto-Hernandez,Yolanda Graciela Kiesling Altún,Amanda Carbajal,José Alfredo Aguayo-Guerrero,Alam Coss,Atharva Sahasrabudhe,Polina Anikeeva,Alan de Araujo,Avnika Bali,Guillaume de Lartigue,Elvi Gil-Lievana,Ranier Gutierrez,Edward A Miao,John F Rawls,M Maya Kaelberer,Diego V Bohórquez

{"title":"A gut sense for a microbial pattern regulates feeding.","authors":"Winston W Liu,Naama Reicher,Emily Alway,Laura E Rupprecht,Peter Weng,Chloe Schaefgen,Marguerita E Klein,Jorge A Villalobos,Carlos Puerto-Hernandez,Yolanda Graciela Kiesling Altún,Amanda Carbajal,José Alfredo Aguayo-Guerrero,Alam Coss,Atharva Sahasrabudhe,Polina Anikeeva,Alan de Araujo,Avnika Bali,Guillaume de Lartigue,Elvi Gil-Lievana,Ranier Gutierrez,Edward A Miao,John F Rawls,M Maya Kaelberer,Diego V Bohórquez","doi":"10.1038/s41586-025-09301-7","DOIUrl":"https://doi.org/10.1038/s41586-025-09301-7","url":null,"abstract":"To coexist with its resident microorganisms, the host must have a sense to adjust its behaviour in response to them. In the intestine, a sense for nutrients transduced to the brain through neuroepithelial circuits guides appetitive choices1-5. However, a sense that allows the host to respond in real time to stimuli arising from resident gut microorganisms remains to be uncovered. Here we show that in the mouse colon, the ubiquitous microbial pattern flagellin-a unifying feature across phyla6-stimulates Toll-like receptor 5 (TLR5) in peptide YY (PYY)-labelled colonic neuropod cells. This stimulation leads to PYY release onto NPY2R vagal nodose neurons to regulate feeding. Mice lacking TLR5 in these cells eat more and gain more weight than controls. We found that flagellin does not act on the nerve directly. Instead, flagellin stimulates neuropod cells from the colonic lumen to reduce feeding through a gut-brain sensory neural circuit. Moreover, flagellin reduces feeding independent of immune responses, metabolic changes or the presence of gut microbiota. This sense enables the host to adjust its behaviour in response to a molecular pattern from its resident microorganisms. We call this sense at the interface of the biota and the brain the neurobiotic sense7.","PeriodicalId":18787,"journal":{"name":"Nature","volume":"120 1","pages":""},"PeriodicalIF":64.8,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144693190","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The last parliament 上届议会

IF 64.8 1区综合性期刊

Nature Pub Date : 2025-07-23 DOI: 10.1038/d41586-025-02246-x

引用次数: 0

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