Nature Communications最新文献_第10页

Taming large-scale genomic analyses via sparsified genomics

IF 16.6 1区综合性期刊

Nature Communications Pub Date : 2025-01-21 DOI: 10.1038/s41467-024-55762-1

Mohammed Alser, Julien Eudine, Onur Mutlu

{"title":"Taming large-scale genomic analyses via sparsified genomics","authors":"Mohammed Alser, Julien Eudine, Onur Mutlu","doi":"10.1038/s41467-024-55762-1","DOIUrl":"https://doi.org/10.1038/s41467-024-55762-1","url":null,"abstract":"Searching for similar genomic sequences is an essential and fundamental step in biomedical research. State-of-the-art computational methods performing such comparisons fail to cope with the exponential growth of genomic sequencing data. We introduce the concept of sparsified genomics where we systematically exclude a large number of bases from genomic sequences and enable faster and memory-efficient processing of the sparsified, shorter genomic sequences, while providing comparable accuracy to processing non-sparsified sequences. Sparsified genomics provides benefits to many genomic analyses and has broad applicability. Sparsifying genomic sequences accelerates the state-of-the-art read mapper (minimap2) by 2.57-5.38x, 1.13-2.78x, and 3.52-6.28x using real Illumina, HiFi, and ONT reads, respectively, while providing comparable memory footprint, 2x smaller index size, and more correctly detected variations compared to minimap2. Sparsifying genomic sequences makes containment search through very large genomes and large databases 72.7-75.88x (1.62-1.9x when indexing is preprocessed) faster and 723.3x more storage-efficient than searching through non-sparsified genomic sequences (with CMash and KMC3). Sparsifying genomic sequences enables robust microbiome discovery by providing 54.15-61.88x (1.58-1.71x when indexing is preprocessed) faster and 720x more storage-efficient taxonomic profiling of metagenomic samples over the state-of-the-art tool (Metalign).","PeriodicalId":19066,"journal":{"name":"Nature Communications","volume":"26 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142990621","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

Lactobacillus reuteri ZJ617 attenuates metabolic syndrome via microbiota-derived spermidine

IF 16.6 1区综合性期刊

Nature Communications Pub Date : 2025-01-21 DOI: 10.1038/s41467-025-56105-4

Yanfei Ma, Yifan Zhong, Wenjie Tang, Teresa G. Valencak, Jingliang Liu, Zhaoxi Deng, Jiangdi Mao, Daren Liu, Shanshan Wang, Yuhao Wang, Haifeng Wang

引用次数: 0

Time to HIV viral rebound and frequency of post-treatment control after analytical interruption of antiretroviral therapy: an individual data-based meta-analysis of 24 prospective studies

IF 16.6 1区综合性期刊

Nature Communications Pub Date : 2025-01-21 DOI: 10.1038/s41467-025-56116-1

Jesper D. Gunst, Jesal Gohil, Johanthan Z. Li, Ronald J. Bosch, Andrea Catherine Seamon White, Tae-Wook Chun, Beatriz Mothe, Kathleen Gittens, Lauren Praiss, Marie-Angélique De Scheerder, Linos Vandekerckhove, Kevin Escandón, Ann Thorkelson, Timothy Schacker, Devi SenGupta, Christian Brander, Emmanouil Papasavvas, Luis J. Montaner, Javier Martinez-Picado, Ruxandra Calin, Antonella Castagna, Camilla Muccini, Wesley de Jong, Lorna Leal, Felipe Garcia, Rob A. Gruters, Timothy Tipoe, John Frater, Ole S. Søgaard, Sarah Fidler

{"title":"Time to HIV viral rebound and frequency of post-treatment control after analytical interruption of antiretroviral therapy: an individual data-based meta-analysis of 24 prospective studies","authors":"Jesper D. Gunst, Jesal Gohil, Johanthan Z. Li, Ronald J. Bosch, Andrea Catherine Seamon White, Tae-Wook Chun, Beatriz Mothe, Kathleen Gittens, Lauren Praiss, Marie-Angélique De Scheerder, Linos Vandekerckhove, Kevin Escandón, Ann Thorkelson, Timothy Schacker, Devi SenGupta, Christian Brander, Emmanouil Papasavvas, Luis J. Montaner, Javier Martinez-Picado, Ruxandra Calin, Antonella Castagna, Camilla Muccini, Wesley de Jong, Lorna Leal, Felipe Garcia, Rob A. Gruters, Timothy Tipoe, John Frater, Ole S. Søgaard, Sarah Fidler","doi":"10.1038/s41467-025-56116-1","DOIUrl":"https://doi.org/10.1038/s41467-025-56116-1","url":null,"abstract":"The only current strategy to test efficacy of novel interventions for sustained HIV control without antiretroviral therapy (ART) among people with HIV (PWH) is through an analytical treatment interruption (ATI). Inclusion of ‘placebo’ controls in ATIs poses ethical, logistical, and economic challenges. To understand viral dynamics and rates of post-treatment control (PTC) after ATI among PWH receiving either placebo or no intervention, we undertook an individual-participant data meta-analysis. In total, 24 eligible prospective studies with 382 individuals with ≥5 plasma HIV RNA viral loads (pVLs) within the first 84 days post-ATI were included. Early-ART was defined as ART initiation within 6 months of HIV acquisition; others were classified as late-ART or unknown. Median age was 42 years, 91% male, 75% white, 45% received early-ART. Median time to pVL >50, >400, and >10,000 copies/mL was 16 days (interquartile range [IQR]:13–25), 21 (IQR:15–28), and 32 (IQR:20–35), respectively. PTC defined as pVL <50 copies/mL at day 84 occurred in 4% (n = 14) of participants (6% early-ART and 1% late-ART). Sustained PTC of pVL <50 copies/ml after 84 days is rare in PWH, especially in those starting ART late. Our findings inform future interventional HIV cure/remission trials on study size and design.","PeriodicalId":19066,"journal":{"name":"Nature Communications","volume":"46 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142992421","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

Noise amplification and ill-convergence of Richardson-Lucy deconvolution

IF 16.6 1区综合性期刊

Nature Communications Pub Date : 2025-01-21 DOI: 10.1038/s41467-025-56241-x

Yiming Liu, Spozmai Panezai, Yutong Wang, Sjoerd Stallinga

引用次数: 0

A high-valence bismuth(V) nanoplatform triggers cancer cell death and anti-tumor immune responses with exogenous excitation-free endogenous H2O2- and O2-independent ROS generation

IF 16.6 1区综合性期刊

Nature Communications Pub Date : 2025-01-20 DOI: 10.1038/s41467-025-56110-7

Yizhang Tang, Xujiang Yu, Liangrui He, Meng Tang, Wenji Yue, Ruitong Chen, Jie Zhao, Qi Pan, Wanwan Li

{"title":"A high-valence bismuth(V) nanoplatform triggers cancer cell death and anti-tumor immune responses with exogenous excitation-free endogenous H2O2- and O2-independent ROS generation","authors":"Yizhang Tang, Xujiang Yu, Liangrui He, Meng Tang, Wenji Yue, Ruitong Chen, Jie Zhao, Qi Pan, Wanwan Li","doi":"10.1038/s41467-025-56110-7","DOIUrl":"https://doi.org/10.1038/s41467-025-56110-7","url":null,"abstract":"Reactive oxygen species with evoked immunotherapy holds tremendous promise for cancer treatment but has limitations due to its dependence on exogenous excitation and/or endogenous H2O2 and O2. Here we report a versatile oxidizing pentavalent bismuth(V) nanoplatform (NaBiVO3-PEG) can generate reactive oxygen species in an excitation-free and H2O2- and O2-independent manner. Upon exposure to the tumor microenvironment, NaBiVO3-PEG undergoes continuous H+-accelerated hydrolysis with •OH and 1O2 generation through electron transfer-mediated BiV-to-BiIII conversion and lattice oxygen transformation. The simultaneous release of sodium counterions after endocytosis triggers caspase-1-mediated pyroptosis. NaBiVO3-PEG intratumorally administered initiates robust therapeutic efficacies against both primary and distant tumors and activates systemic immune responses to combat tumor metastasis. NaBiVO3-PEG intravenously administered can efficiently accumulate at the tumor site for further real-time computed tomography monitoring, immunotherapy, or alternative synergistic immune-radiotherapy. Overall, this work offers a nanomedicine based on high-valence bismuth(V) nanoplatform and underscores its great potential for cancer immunotherapy.","PeriodicalId":19066,"journal":{"name":"Nature Communications","volume":"84 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142990768","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

Construction and iterative redesign of synXVI a 903 kb synthetic Saccharomyces cerevisiae chromosome

IF 16.6 1区综合性期刊

Nature Communications Pub Date : 2025-01-20 DOI: 10.1038/s41467-024-55318-3

Hugh D. Goold, Heinrich Kroukamp, Paige E. Erpf, Yu Zhao, Philip Kelso, Julie Calame, John J. B. Timmins, Elizabeth L. I. Wightman, Kai Peng, Alexander C. Carpenter, Briardo Llorente, Carmen Hawthorne, Samuel Clay, Niël van Wyk, Elizabeth L. Daniel, Fergus Harrison, Felix Meier, Robert D. Willows, Yizhi Cai, Roy S. K. Walker, Xin Xu, Monica I. Espinosa, Giovanni Stracquadanio, Joel S. Bader, Leslie A. Mitchell, Jef D. Boeke, Thomas C. Williams, Ian T. Paulsen, Isak S. Pretorius

{"title":"Construction and iterative redesign of synXVI a 903 kb synthetic Saccharomyces cerevisiae chromosome","authors":"Hugh D. Goold, Heinrich Kroukamp, Paige E. Erpf, Yu Zhao, Philip Kelso, Julie Calame, John J. B. Timmins, Elizabeth L. I. Wightman, Kai Peng, Alexander C. Carpenter, Briardo Llorente, Carmen Hawthorne, Samuel Clay, Niël van Wyk, Elizabeth L. Daniel, Fergus Harrison, Felix Meier, Robert D. Willows, Yizhi Cai, Roy S. K. Walker, Xin Xu, Monica I. Espinosa, Giovanni Stracquadanio, Joel S. Bader, Leslie A. Mitchell, Jef D. Boeke, Thomas C. Williams, Ian T. Paulsen, Isak S. Pretorius","doi":"10.1038/s41467-024-55318-3","DOIUrl":"https://doi.org/10.1038/s41467-024-55318-3","url":null,"abstract":"The Sc2.0 global consortium to design and construct a synthetic genome based on the Saccharomyces cerevisiae genome commenced in 2006, comprising 16 synthetic chromosomes and a new-to-nature tRNA neochromosome. In this paper we describe assembly and debugging of the 902,994-bp synthetic Saccharomyces cerevisiae chromosome synXVI of the Sc2.0 project. Application of the CRISPR D-BUGS protocol identified defective loci, which were modified to improve sporulation and recover wild-type like growth when grown on glycerol as a sole carbon source when grown at 37˚C. LoxPsym sites inserted downstream of dubious open reading frames impacted the 5’ UTR of genes required for optimal growth and were identified as a systematic cause of defective growth. Based on lessons learned from analysis of Sc2.0 defects and synXVI, an in-silico redesign of the synXVI chromosome was performed, which can be used as a blueprint for future synthetic yeast genome designs. The in-silico redesign of synXVI includes reduced PCR tag frequency, modified chunk and megachunk termini, and adjustments to allocation of loxPsym sites and TAA stop codons to dubious ORFs. This redesign provides a roadmap into applications of Sc2.0 strategies in non-yeast organisms.","PeriodicalId":19066,"journal":{"name":"Nature Communications","volume":"57 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142989976","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

Instantaneous self-recovery and ultra-low detection limit hydrogel electronic sensor for temporomandibular disorders intelligent diagnosis

IF 16.6 1区综合性期刊

Nature Communications Pub Date : 2025-01-20 DOI: 10.1038/s41467-025-55996-7

Yujie Yan, Lixia Yu, Xuefeng Zhang, Qi Han, Zhixin Yang, Xingyuan Lu, Jiongke Wang, Hao Xu, Qianming Chen, Hang Zhao

{"title":"Instantaneous self-recovery and ultra-low detection limit hydrogel electronic sensor for temporomandibular disorders intelligent diagnosis","authors":"Yujie Yan, Lixia Yu, Xuefeng Zhang, Qi Han, Zhixin Yang, Xingyuan Lu, Jiongke Wang, Hao Xu, Qianming Chen, Hang Zhao","doi":"10.1038/s41467-025-55996-7","DOIUrl":"https://doi.org/10.1038/s41467-025-55996-7","url":null,"abstract":"Temporomandibular disorders (TMD) intelligent diagnosis promises to elevate clinical efficiency and facilitate timely TMD management for patients. However, development of TMD intelligent diagnostic tools with high accuracy and sensitivity presents challenges, particularly in sensing minute deformations and ensuring rapid self-recovery. Here we report a biocompatible hydrogel electronic sensor with instantaneous self-recovery (within 2.1 s) and ultra-low detection limit (0.005% strain). It could efficiently diagnose disc displacement with reduction (DDwR) with satisfactory accuracy of 90.00%, and also had a clear indication of the typical clinical manifestations of DDwR and the timing of temporomandibular joint (TMJ) clicking, with a sensitivity of up to 100% in human compared to the diagnostic criteria for TMD (DC/TMD). Furthermore, a predictive model based on waveform features achieved 84.4% accuracy and 86% sensitivity, reducing dependence on physicians. In summary, the hydrogel sensor is expected to become a radiation-free, non-invasive, practical and effective tool for future TMD diagnosis.","PeriodicalId":19066,"journal":{"name":"Nature Communications","volume":"47 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142989926","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

Fast 3D printing of fine, continuous, and soft fibers via embedded solvent exchange 通过嵌入式溶剂交换快速 3D 打印细纤维、连续纤维和软纤维

IF 16.6 1区综合性期刊

Nature Communications Pub Date : 2025-01-20 DOI: 10.1038/s41467-025-55972-1

Wonsik Eom, Mohammad Tanver Hossain, Vidush Parasramka, Jeongmin Kim, Ryan W. Y. Siu, Kate A. Sanders, Dakota Piorkowski, Andrew Lowe, Hyun Gi Koh, Michael F. L. De Volder, Douglas S. Fudge, Randy H. Ewoldt, Sameh H. Tawfick

{"title":"Fast 3D printing of fine, continuous, and soft fibers via embedded solvent exchange","authors":"Wonsik Eom, Mohammad Tanver Hossain, Vidush Parasramka, Jeongmin Kim, Ryan W. Y. Siu, Kate A. Sanders, Dakota Piorkowski, Andrew Lowe, Hyun Gi Koh, Michael F. L. De Volder, Douglas S. Fudge, Randy H. Ewoldt, Sameh H. Tawfick","doi":"10.1038/s41467-025-55972-1","DOIUrl":"https://doi.org/10.1038/s41467-025-55972-1","url":null,"abstract":"Nature uses fibrous structures for sensing and structural functions as observed in hairs, whiskers, stereocilia, spider silks, and hagfish slime thread skeins. Here, we demonstrate multi-nozzle printing of 3D hair arrays having freeform trajectories at a very high rate, with fiber diameters as fine as 1.5 µm, continuous lengths reaching tens of centimeters, and a wide range of materials with elastic moduli from 5 MPa to 3500 MPa. This is achieved via 3D printing by rapid solvent exchange in high yield stress micro granular gel, leading to radial solidification of the extruded polymer filament at a rate of 2.33 μm/s. This process extrudes filaments at 5 mm/s, which is 500,000 times faster than meniscus printing owing to the rapid solidification which prevents capillarity-induced fiber breakage. This study demonstrates the potential of 3D printing by rapid solvent exchange as a fast and scalable process for replicating natural fibrous structures for use in biomimetic functions.","PeriodicalId":19066,"journal":{"name":"Nature Communications","volume":"31 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142989975","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

Asymmetric projection of introspection reveals a behavioural and neural mechanism for interindividual social coordination 内省的非对称投射揭示了个体间社会协调的行为和神经机制

IF 16.6 1区综合性期刊

Nature Communications Pub Date : 2025-01-20 DOI: 10.1038/s41467-024-55202-0

Kentaro Miyamoto, Caroline Harbison, Shiho Tanaka, Marina Saito, Shuyi Luo, Sara Matsui, Pranav Sankhe, Ali Mahmoodi, Mingming Lin, Nadescha Trudel, Nicholas Shea, Matthew F. S. Rushworth

{"title":"Asymmetric projection of introspection reveals a behavioural and neural mechanism for interindividual social coordination","authors":"Kentaro Miyamoto, Caroline Harbison, Shiho Tanaka, Marina Saito, Shuyi Luo, Sara Matsui, Pranav Sankhe, Ali Mahmoodi, Mingming Lin, Nadescha Trudel, Nicholas Shea, Matthew F. S. Rushworth","doi":"10.1038/s41467-024-55202-0","DOIUrl":"https://doi.org/10.1038/s41467-024-55202-0","url":null,"abstract":"When we collaborate with others to tackle novel problems, we anticipate how they will perform their part of the task to coordinate behavior effectively. We might estimate how well someone else will perform by extrapolating from estimates of how well we ourselves would perform. This account predicts that our metacognitive model should make accurate predictions when projected onto people as good as, or worse than, us but not on those whose abilities exceed our own. We demonstrate just such a pattern and that it leads to worse coordination when working with people more skilled than ourselves. Metacognitive projection is associated with a specific activity pattern in anterior lateral prefrontal cortex (alPFC47). Manipulation of alPFC47 activity altered metacognitive projection and impaired interpersonal social coordination. By contrast, monitoring of other individuals’ observable performance and outcomes is associated with a distinct pattern of activity in the posterior temporal parietal junction (TPJp).","PeriodicalId":19066,"journal":{"name":"Nature Communications","volume":"27 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142989979","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

Unveiling pelagic-benthic coupling associated with the biological carbon pump in the Fram Strait (Arctic Ocean)

IF 16.6 1区综合性期刊

Nature Communications Pub Date : 2025-01-20 DOI: 10.1038/s41467-024-55221-x

Simon Ramondenc, Damien Eveillard, Katja Metfies, Morten H. Iversen, Eva-Maria Nöthig, Dieter Piepenburg, Christiane Hasemann, Thomas Soltwedel

{"title":"Unveiling pelagic-benthic coupling associated with the biological carbon pump in the Fram Strait (Arctic Ocean)","authors":"Simon Ramondenc, Damien Eveillard, Katja Metfies, Morten H. Iversen, Eva-Maria Nöthig, Dieter Piepenburg, Christiane Hasemann, Thomas Soltwedel","doi":"10.1038/s41467-024-55221-x","DOIUrl":"https://doi.org/10.1038/s41467-024-55221-x","url":null,"abstract":"Settling aggregates transport organic matter from the ocean surface to the deep sea and seafloor. Though plankton communities impact carbon export, how specific organisms and their interactions affect export efficiency is unknown. Looking at 15 years of eDNA sequences (18S-V4) from settling and sedimented organic matter in the Fram Strait, here we observe that most phylogenetic groups were transferred from pelagic to benthic ecosystems. Chaetoceros socialis, sea-ice diatoms, Radiolaria, and Chaetognatha are critical components of vertical carbon flux to 200 m depth. In contrast, the diatom C. socialis alone is essential for the amount of organic carbon reaching the seafloor. Spatiotemporal changes in community composition show decreasing diatom abundance during warm anomalies, which would reduce the efficiency of a diatom-driven biological carbon pump. Interestingly, several parasites are also tightly associated with carbon flux and show a strong vertical connectivity, suggesting a potential role in sedimentation processes involving their hosts, especially through interactions with resting spores, which could have implications for pelagic-benthic coupling and overall ecosystem functioning.","PeriodicalId":19066,"journal":{"name":"Nature Communications","volume":"9 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142989978","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