Nature biotechnology最新文献_第6页

Electro-microbial production techno-economic viability and environmental implications 电微生物生产技术、经济可行性和环境影响

IF 46.9 1区生物学

Nature biotechnology Pub Date : 2025-04-22 DOI: 10.1038/s41587-025-02632-w

Samuel J. Lovat, Roee Ben-Nissan, Eliya Milshtein, Asaf Tzachor, Avi Flamholz, Dorian Leger, Elad Noor, Ron Milo

引用次数: 0

Detection of viral sequences at single-cell resolution identifies novel viruses associated with host gene expression changes 在单细胞分辨率下检测病毒序列可识别与宿主基因表达变化相关的新型病毒

IF 46.9 1区生物学

Nature biotechnology Pub Date : 2025-04-22 DOI: 10.1038/s41587-025-02614-y

Laura Luebbert, Delaney K. Sullivan, Maria Carilli, Kristján Eldjárn Hjörleifsson, Alexander Viloria Winnett, Tara Chari, Lior Pachter

{"title":"Detection of viral sequences at single-cell resolution identifies novel viruses associated with host gene expression changes","authors":"Laura Luebbert, Delaney K. Sullivan, Maria Carilli, Kristján Eldjárn Hjörleifsson, Alexander Viloria Winnett, Tara Chari, Lior Pachter","doi":"10.1038/s41587-025-02614-y","DOIUrl":"https://doi.org/10.1038/s41587-025-02614-y","url":null,"abstract":"The increasing use of high-throughput sequencing methods in research, agriculture and healthcare provides an opportunity for the cost-effective surveillance of viral diversity and investigation of virus–disease correlation. However, existing methods for identifying viruses in sequencing data rely on and are limited to reference genomes or cannot retain single-cell resolution through cell barcode tracking. We introduce a method that accurately and rapidly detects viral sequences in bulk and single-cell transcriptomics data based on the highly conserved RdRP protein, enabling the detection of over 100,000 RNA virus species. The analysis of viral presence and host gene expression in parallel at single-cell resolution allows for the characterization of host viromes and the identification of viral tropism and host responses. We apply our method to peripheral blood mononuclear cell data from rhesus macaques with Ebola virus disease and describe previously unknown putative viruses. Moreover, we are able to accurately predict viral presence in individual cells based on macaque gene expression.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"50 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2025-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143857453","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

QBEmax is a sequence-permuted and internally protected base editor QBEmax是一个序列排列和内部保护的碱基编辑器

IF 46.9 1区生物学

Nature biotechnology Pub Date : 2025-04-21 DOI: 10.1038/s41587-025-02641-9

Jiacheng Hu, Mengyue Guo, Qiang Gao, He Jia, Mingyang He, Zhiwei Wang, Lina Guo, Guanwen Liu, Quan Gao, Kevin Tianmeng Zhao

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Far-red chemigenetic kinase biosensors enable multiplexed and super-resolved imaging of signaling networks 远红色化学遗传激酶生物传感器实现信号网络的多路复用和超分辨率成像

IF 46.9 1区生物学

Nature biotechnology Pub Date : 2025-04-21 DOI: 10.1038/s41587-025-02642-8

Michelle S. Frei, Samantha A. Sanchez, Xinchang He, Longwei Liu, Falk Schneider, Zichen Wang, Hiroyuki Hakozaki, Yajuan Li, Anne C. Lyons, Theresa V. Rohm, Jerrold M. Olefsky, Lingyan Shi, Johannes Schöneberg, Scott E. Fraser, Sohum Mehta, Yingxiao Wang, Jin Zhang

{"title":"Far-red chemigenetic kinase biosensors enable multiplexed and super-resolved imaging of signaling networks","authors":"Michelle S. Frei, Samantha A. Sanchez, Xinchang He, Longwei Liu, Falk Schneider, Zichen Wang, Hiroyuki Hakozaki, Yajuan Li, Anne C. Lyons, Theresa V. Rohm, Jerrold M. Olefsky, Lingyan Shi, Johannes Schöneberg, Scott E. Fraser, Sohum Mehta, Yingxiao Wang, Jin Zhang","doi":"10.1038/s41587-025-02642-8","DOIUrl":"https://doi.org/10.1038/s41587-025-02642-8","url":null,"abstract":"Fluorescent biosensors have advanced biomedical research by enabling direct live-cell measurements of signaling activities. However, current technology offers limited resolution and dimensionality, impeding our ability to resolve and interrogate spatiotemporally regulated networks of signaling activities. Here we introduce highly sensitive chemigenetic kinase activity biosensors that combine the genetically encodable self-labeling tag, HaloTag7, with far-red-emitting synthetic fluorophores. This technology enables both four-dimensional activity imaging and functional super-resolution imaging using stimulated emission depletion and other high-resolution microscopy techniques, permitting signaling activity to be detected across scales with the necessary resolution. Stimulated emission depletion imaging enabled the investigation of protein kinase A activity at individual clathrin-coated pits. We further demonstrate imaging of up to five analytes in single living cells, an increase in the dimensionality of biosensor multiplexing. Multiplexed imaging of cellular responses to the activation of different G-protein-coupled receptors (GPCRs) allowed quantitative measurements of spatiotemporal network states downstream of individual GPCR–ligand pairs.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"14 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143853117","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}

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Author Correction: Precise, predictable multi-nucleotide deletions in rice and wheat using APOBEC–Cas9 作者更正：使用apobecc - cas9对水稻和小麦进行精确、可预测的多核苷酸缺失

IF 46.9 1区生物学

Nature biotechnology Pub Date : 2025-04-17 DOI: 10.1038/s41587-025-02674-0

Shengxing Wang, Yuan Zong, Qiupeng Lin, Huawei Zhang, Zhuangzhuang Chai, Dandan Zhang, Kunling Chen, Jin-Long Qiu, Caixia Gao

引用次数: 0

AI tool adjusts for ancestral bias in genetic data 人工智能工具可调整遗传数据中的祖先偏差

IF 46.9 1区生物学

Nature biotechnology Pub Date : 2025-04-14 DOI: 10.1038/s41587-025-02651-7

Iris Marchal

{"title":"AI tool adjusts for ancestral bias in genetic data","authors":"Iris Marchal","doi":"10.1038/s41587-025-02651-7","DOIUrl":"https://doi.org/10.1038/s41587-025-02651-7","url":null,"abstract":"Human ancestry has a considerable impact on gene expression, but genomic datasets for disease analysis severely underrepresent non-European populations, thereby limiting the advancement of precision medicine. In a paper in Nature Communications, Smith et al. introduce a machine learning tool to mitigate the effects of ancestral bias in transcriptomic data.The tool, called PhyloFrame, creates ancestry-aware signatures of disease by integrating population genomics data with smaller, disease-relevant training datasets. PhyloFrame uses a logistic regression model with LASSO penalty to obtain an initial set of disease-relevant genes. It then uses population genomics data to help compensate for data distribution shifts caused by human ancestry differences. In short, PhyloFrame projects the initial disease signature onto a functional interaction network, extending the network to include the first and second neighbors of each signature gene. This new set is then filtered by a statistic defined as enhanced allele frequency (EAF) — which captures population-specific allelic enrichment in healthy tissue — to identify ancestrally diverse genes that interact with the original signature. From each ancestry, a selected subset of genes with high EAF and gene expression variability in the training data are added to the PhyloFrame signature. Retraining the model with the forced inclusion of these equitable genes results in a signature of disease that generalizes to all populations, even if not represented in the training data.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"7 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143831851","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

People 人

IF 46.9 1区生物学

Nature biotechnology Pub Date : 2025-04-14 DOI: 10.1038/s41587-025-02637-5

引用次数: 0

Not just obesity: GLP-1 receptor agonists advance on addiction 不仅仅是肥胖症GLP-1 受体激动剂在戒毒方面取得进展

IF 46.9 1区生物学

Nature biotechnology Pub Date : 2025-04-14 DOI: 10.1038/s41587-025-02644-6

引用次数: 0

Spotlight on cancer immunotherapies 聚焦癌症免疫疗法

IF 46.9 1区生物学

Nature biotechnology Pub Date : 2025-04-14 DOI: 10.1038/s41587-025-02645-5