Sequence Read Archive (SRA) data
English
United States, Cabin John
NLM National Library of Medicine 8600 Rockville
数据描述
The Sequence Read Archive (SRA) is the largest public repository offering high-throughput sequencing data accessible through NCBI servers and multiple cloud providers. It stores raw sequencing data and alignment information, facilitating scientific research by enhancing reproducibility and enabling new discoveries. The SRA accepts data from all areas of life, including metagenomic and environmental studies, providing a comprehensive resource for researchers across various disciplines.
www.ncbi.nlm.nih.gov
IP: 130.14.29.110
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10.1038/S41467-019-12505-X
ISSN:2041-1723
Chromosome-level genome assembly of the white-spotted sawyer Monochamus scutellatus (Coleoptera: Cerambycidae)
Sangil Kim•Brian D. Farrell
Scientific Data
2025
•2025/12/10
0The white-spotted sawyer, Monochamus scutellatus (Say) (Coleoptera: Cerambycidae), is an important vector of pinewood nematode (PWN), Bursaphelenchus xylophilus (Steiner and Buhrer) Nickle, in North America. While Monochamus species from the Palearctic region have been extensively studied for their ...
EntomologyEvolutionary geneticsMolecular ecology
10.1038/S41597-025-06258-0
ISSN:2052-4463
Profiling the molecular and physiological effects of senolytic treatment on aged mice identifies immune, fibrotic and metabolic remodeling
Jing Hou•Kai-Xuan Chen•Qiao-Ni Xiao•Chen Hu•Jie Wei等 20 人
Nature Aging
2026
•2026/6/17
•Vol.6 No.6 p.1281-1297
Although senolytics such as dasatinib and quercetin (D+Q) show promise in modulating aging, their tissue-specific efficacy and optimal intervention timing remain poorly understood. Given D+Q’s potential off-target effects, incomplete senescent cell clearance and associated hematologic side effects, ...
AgeingSenescence
10.1038/S43587-026-01130-1
ISSN:2662-8465
New insights into the molecular basis of spinal neurofibromatosis type 1
Paola Bettinaglio•Eleonora Mangano•Viviana Tritto•Roberta Bordoni•Rosina Paterra等 14 人
European Journal Of Human Genetics
2023
•2023/5/22
•00 p.1-8
Spinal neurofibromatosis (SNF) is a form of neurofibromatosis type 1 (NF1) characterized by bilateral neurofibromas involving all spinal roots. The pathogenic mechanisms determining the SNF form are currently unknown. To verify the presence of genetic variants possibly related to SNF or classic NF1,...
MutationTargeted resequencing
10.1038/S41431-023-01377-X
ISSN:1018-4813
Systematic analysis of cotranscriptional RNA folding using transcription elongation complex display
Skyler L. Kelly•Eric J. Strobel
Nature Communications
2025
•2025/3/10
•Vol.16 No.1 p.1-21
RNA can fold into structures that mediate diverse cellular functions. Understanding how RNA primary sequence directs the formation of functional structures requires methods that can comprehensively assess how changes in an RNA sequence affect its structure and function. Here we have developed a plat...
RiboswitchesRNATranscription
10.1038/S41467-025-57415-3
ISSN:2041-1723
A prospective study of the infant gut microbiome in relation to vaccine response
Moroishi Yuka•Gui Jiang•Nadeau Kari C.•Morrison Hilary G.•Madan Juliette等 6 人
Pediatric Research
2022
•2022/6/18
•00 p.1-7
The establishment of the gut microbiome plays a key symbiotic role in the developing immune system; however, its influence on vaccine response is yet uncertain. We prospectively investigated the composition and diversity of the early-life gut microbiome in relation to infant antibody response to two...
Medicine/Public Health, generalPediatricsPediatric Surgery
10.1038/S41390-022-02154-0
ISSN:0031-3998
Whole genome sequencing-based detection of extensively drug-resistant tuberculosis from Ethiopia
Getu Diriba•Hilina Mollalign•Abyot Meaza•Melak Getu•Betselot Zerihun等 27 人
Communications Medicine
2025
•2025/12/7
0Rapid and accurate detection of extensively drug-resistant tuberculosis is crucial for effective intervention. Next-generation sequencing technologies have been recommended to rapidly and accurately detect resistance to second-line anti-TB drugs. We deployed whole-genome sequencing to detect mutatio...
Clinical microbiologyTuberculosis
10.1038/S43856-025-01271-1
ISSN:2730-664X
Transcripts switched off at the stop of phloem unloading highlight the energy efficiency of sugar import in the ripening V. vinifera fruit
Savoi Stefania•Torregrosa Laurent•Romieu Charles
Horticulture Research
2021
•2021/9/1
•Vol.8 No.1 p.1-15
Transcriptomic changes at the cessation of sugar accumulation in the pericarp of Vitis vinifera were addressed on single berries re-synchronised according to their individual growth patterns. The net rates of water, sugars and K+ accumulation inferred from individual growth and solute concentration ...
MetabolismPlant developmentTranscriptomics
10.1038/S41438-021-00628-6
ISSN:2662-6810
A first-generation pediatric cancer dependency map
Neekesh V. Dharia•Guillaume Kugener•Lillian M. Guenther•Clare F. Malone•Adam D. Durbin等 26 人
Nature Genetics
2021
•2021/3/22
•00 p.1-10
Exciting therapeutic targets are emerging from CRISPR-based screens of high mutational-burden adult cancers. A key question, however, is whether functional genomic approaches will yield new targets in pediatric cancers, known for remarkably few mutations, which often encode proteins considered chall...
CancerFunctional genomicsHigh-throughput screening
10.1038/S41588-021-00819-W
ISSN:1061-4036
Vascular dysfunction caused by loss of Brn-3b/POU4F2 transcription factor in aortic vascular smooth muscle cells is linked to deregulation of calcium signalling pathways
Vaishaali Yogendran•Laura Mele•Oleksandra Prysyazhna•Vishwanie S. Budhram-Mahadeo
Cell Death & Disease
2023
•2023/11/25
•Vol.14 No.11 p.1-18
Phenotypic and functional changes in vascular smooth muscle cells (VSMCs) contribute significantly to cardiovascular diseases (CVD) but factors driving early adverse vascular changes are poorly understood. We report on novel and important roles for the Brn-3b/POU4F2 (Brn-3b) transcription factor (TF...
TranscriptionVascular diseases
10.1038/S41419-023-06306-W
ISSN:2041-4889
A ligand-gated strand displacement mechanism for ZTP riboswitch transcription control
Eric J. Strobel•Luyi Cheng•Katherine E. Berman•Paul D. Carlson•Julius B. Lucks
Nature Chemical Biology
2019
•2019/10/21
•Vol.15 No.11 p.1067-1076
Cotranscriptional folding is an obligate step of RNA biogenesis that can guide RNA structure formation and function through transient intermediate folds. This process is particularly important for transcriptional riboswitches in which the formation of ligand-dependent structures during transcription...
RiboswitchesRNAStructural biologyTranscription
10.1038/S41589-019-0382-7
ISSN:1552-4450
Mycorrhizal colonization of dryland tree establishment depends on soil microbial cooperation
Haiyun Zi•Zhe Hua•Yun Wang•Yangwenke Liao•Shuikuan Bei等 8 人
Nature Communications
2025
•2025/12/29
0Mycorrhizal fungi serve as fundamental agents in forest establishment and progression, underpinning critical ecosystem functions through symbiotic root associations. Drylands, which cover nearly half of Earth’s land, have limited forest establishment, and factors influencing mycorrhization in these ...
Microbial ecologySoil microbiology
10.1038/S41467-025-67797-Z
ISSN:2041-1723
The IDH1-R132H mutation aggravates cisplatin-induced acute kidney injury by promoting ferroptosis through disrupting NDUFA1 and FSP1 interaction
Kunmei Lai•Zhimin Chen•Siyi Lin•Keng Ye•Ying Yuan等 10 人
Cell Death & Differentiation
2024
•2024/9/22
•00 p.1-14
The IDH1-R132H mutation is implicated in the development of various tumors. Whether cisplatin, a common chemotherapeutic agent, induces more significant renal toxicity in individuals with the IDH1-R132H mutation remains unclear. In this study, we observed that the IDH1-R132H mutation exacerbates mit...
Disease geneticsKidney diseases
10.1038/S41418-024-01381-8
ISSN:1350-9047
Identification of antiviral RNAi regulators, ILF3/DHX9, recruit at ZIKV stem loop B to protect against ZIKV induced microcephaly
Zhiwei Lei•Yu Gu•Ying Liu•Hailiang Liu•Xiaohua Lu等 17 人
Nature Communications
2025
•2025/2/26
•Vol.16 No.1 p.1-18
Zika virus (ZIKV) is a member of the Flaviviridae family and causes congenital microcephaly and Guillain–Barré syndrome. Currently, there is a lack of approved vaccines or therapies against ZIKV infection. In this study, we profile vRNA‒host protein interactomes at ZIKV stem‒loop B (SLB) and reveal ...
Viral host responseVirus–host interactions
10.1038/S41467-025-56859-X
ISSN:2041-1723
Ethylene-independent functions of the ethylene precursor ACC in Marchantia polymorpha
Dongdong Li•Eduardo Flores-Sandoval•Uzair Ahtesham•Andrew Coleman•John M. Clay等 7 人
Nature Plants
2020
•2020/10/26
•Vol.6 No.11 p.1335-1344
The plant hormone ethylene has many roles in growth and development1. In seed plants, the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) is converted into ethylene by ACC oxidase (ACO), and treatment with ACC induces ethylene responses2. However, non-seed plants lack ACO homologues3–...
Plant evolutionPlant hormonesPlant signalling
10.1038/S41477-020-00784-Y
ISSN:2055-0278
Synergistic interplay of ABA and BR signal in regulating plant growth and adaptation
Qianqian Li•Fan Xu•Zhuo Chen•Zhenfeng Teng•Kai Sun等 15 人
Nature Plants
2021
•2021/7/5
•00 p.1-11
Complex antagonistic interactions between abscisic acid (ABA) and brassinosteroid (BR) signalling pathways have been widely documented. However, whether or how ABA interacts synergistically with BR in plants remains to be elucidated. Here, we report that low, but not high, concentration of ABA incre...
Plant hormonesPlant signalling
10.1038/S41477-021-00959-1
ISSN:2055-0278
An inferred fitness consequence map of the rice genome
Zoé Joly-Lopez•Adrian E. Platts•Brad Gulko•Jae Young Choi•Simon C. Groen等 8 人
Nature Plants
2020
•2020/2/10
•Vol.6 No.2 p.119-130
The extent to which sequence variation impacts plant fitness is poorly understood. High-resolution maps detailing the constraint acting on the genome, especially in regulatory sites, would be beneficial as functional annotation of noncoding sequences remains sparse. Here, we present a fitness conseq...
EvolutionPlant evolutionPlant molecular biologyPlant sciencesPopulation genetics
10.1038/S41477-019-0589-3
ISSN:2055-0278
Sliding-attention transformer neural architecture for predicting T cell receptor–antigen–human leucocyte antigen binding
Ziyan Feng•Jingyang Chen•Youlong Hai•Xuelian Pang•Kun Zheng等 16 人
Nature Machine Intelligence
2024
•2024/9/27
•00 p.1-15
Neoantigens are promising targets for immunotherapy by eliciting immune response and removing cancer cells with high specificity, low toxicity and ease of personalization. However, identifying effective neoantigens remains difficult because of the complex interactions among T cell receptors, antigen...
Computational biology and bioinformaticsImmunology
10.1038/S42256-024-00901-Y
ISSN:2522-5839
Roles of adenine methylation in the physiology of Lacticaseibacillus paracasei
Jie Zhao•Meng Zhang•Wenyan Hui•Yue Zhang•Jing Wang等 10 人
Nature Communications
2023
•2023/5/6
•Vol.14 No.1 p.1-12
Lacticaseibacillus paracasei is an economically important bacterial species, used in the food industry and as a probiotic. Here, we investigate the roles of N6-methyladenine (6mA) modification in L. paracasei using multi-omics and high-throughput chromosome conformation capture (Hi-C) analyses. The ...
Applied microbiologyBacterial genomicsDNA methylationFood microbiology
10.1038/S41467-023-38291-1
ISSN:2041-1723
The lactate receptor HCAR1 drives the recruitment of immunosuppressive PMN-MDSCs in colorectal cancer
Jiacheng He•Xiaolei Chai•Qiansen Zhang•Yang Wang•Yijie Wang等 38 人
Nature Immunology
2025
•2025/2/4
•Vol.26 No.3 p.391-403
Most patients with colorectal cancer do not achieve durable clinical benefits from immunotherapy, underscoring the existence of alternative immunosuppressive mechanisms. Here we found that activation of the lactate receptor HCAR1 signaling pathway induced the expression of chemokines CCL2 and CCL7 i...
Cancer therapy
10.1038/S41590-024-02068-5
ISSN:1529-2908
Multi-kingdom microbial signatures in excess body weight colorectal cancer based on global metagenomic analysis
Xinyue Zhu•Pingping Xu•Ruixin Zhu•Wenxing Gao•Wenjing Yin等 8 人
Communications Biology
2024
•2024/1/5
•Vol.7 No.1 p.1-14
Excess body weight (EBW) increases the risk of colorectal cancer (CRC) and is linked to lower colonoscopy compliance. Here, we extensively analyzed 981 metagenome samples from multiple cohorts to pinpoint the specific microbial signatures and their potential capability distinguishing EBW patients wi...
Cancer screeningClinical microbiology
10.1038/S42003-023-05714-0
ISSN:2399-3642
Hfq-binding small RNA PqsS regulates Pseudomonas aeruginosa pqs quorum sensing system and virulence
Tianyuan Jia•Xianbiao Bi•Menglu Li•Chenhui Zhang•Anmin Ren等 14 人
Npj Biofilms And Microbiomes
2024
•2024/9/11
•Vol.10 No.1 p.1-16
Pseudomonas aeruginosa is a widespread nosocomial pathogen with a significant to cause both severe planktonic acute and biofilm-related chronic infections. Small RNAs (sRNAs) are noncoding regulatory molecules that are stabilized by the RNA chaperone Hfq to trigger various virulence-related signalin...
Cellular microbiologyMicrobial geneticsPathogens
10.1038/S41522-024-00550-4
ISSN:2055-5008
Lentiviral gene therapy with reduced-intensity conditioning for sickle cell disease: a phase 1/2 trial
Michael Grimley•Stella M. Davies•Archana Shrestha•Amy Shova•Monika Asnani等 24 人
Nature Medicine
2025
•2025/5/26
•00 p.1-9
Autologous transplantation of gene-modified cells for treatment of sickle cell disease has involved myeloablative conditioning with associated cytopenias and toxicities. We report results of seven patients treated in a first-in-human phase 1/2 study for sickle cell disease using reduced-intensity co...
AnaemiaStem-cell researchTranslational research
10.1038/S41591-025-03662-2
ISSN:1078-8956
Trace metals induce microbial risk and antimicrobial resistance in biofilm in drinking water
Bowei Li•Ling Feng•Rakia Chouari•Sofia Samoili•Stefanos Giannakis
Npj Clean Water
2025
•2025/2/3
•Vol.8 No.1 p.1-12
This study investigated the changes in water quality and microbial risks resulting from trace metal pollutants in stagnant drinking water conditions using a 168-h experimental simulation and a metagenomic approach. The results showed that Fe(III) increased the water turbidity. Stagnation also caused...
Environmental chemistryEnvironmental monitoring
10.1038/S41545-025-00436-8
ISSN:2059-7037
Transcript errors generate amyloid-like proteins in huwman cells
Claire S. Chung•Yi Kou•Sarah J. Shemtov•Bert M. Verheijen•Ilse Flores等 31 人
Nature Communications
2024
•2024/10/7
•Vol.15 No.1 p.1-17
Aging is characterized by the accumulation of proteins that display amyloid-like behavior. However, the molecular mechanisms by which these proteins arise remain unclear. Here, we demonstrate that amyloid-like proteins are produced in a variety of human cell types, including stem cells, brain organo...
Mechanisms of diseaseProtein aggregationTranscription
10.1038/S41467-024-52886-2
ISSN:2041-1723
The interaction between STING and NCOA4 exacerbates lethal sepsis by orchestrating ferroptosis and inflammatory responses in macrophages
Wu Jie•Liu Qinjie•Zhang Xufei•Tan Miaomiao•Li Xuanheng等 13 人
Cell Death & Disease
2022
•2022/7/28
•Vol.13 No.7 p.1-17
The discovery of STING-related innate immunity has recently provided a deep mechanistic understanding of immunopathy. While the detrimental effects of STING during sepsis had been well documented, the exact mechanism by which STING causes lethal sepsis remains obscure. Through single-cell RNA sequen...
Bacterial infectionImmune cell death
10.1038/S41419-022-05115-X
ISSN:2041-4889
Brain expression quantitative trait locus and network analyses reveal downstream effects and putative drivers for brain-related diseases
de Klein Niek•Tsai Ellen A.•Vochteloo Martijn•Baird Denis•Huang Yunfeng等 21 人
Nature Genetics
2023
•2023/2/23
•Vol.55 No.3 p.377-388
Identification of therapeutic targets from genome-wide association studies (GWAS) requires insights into downstream functional consequences. We harmonized 8,613 RNA-sequencing samples from 14 brain datasets to create the MetaBrain resource and performed cis- and trans-expression quantitative trait l...
Gene expressionGene regulationTranscriptomics
10.1038/S41588-023-01300-6
ISSN:1061-4036
HIF1α-AS1 is a DNA:DNA:RNA triplex-forming lncRNA interacting with the HUSH complex
Leisegang Matthias S.•Bains Jasleen Kaur•Seredinski Sandra•Oo James A.•Krause Nina M.等 31 人
Nature Communications
2022
•2022/11/2
•Vol.13 No.1 p.1-20
DNA:DNA:RNA triplexes that are formed through Hoogsteen base-pairing of the RNA in the major groove of the DNA duplex have been observed in vitro, but the extent to which these interactions occur in cells and how they impact cellular functions remains elusive. Using a combination of bioinformatic te...
Cardiovascular biologyLong non-coding RNAsNucleic acids
10.1038/S41467-022-34252-2
ISSN:2041-1723
Genomic evidence for flies as carriers of zoonotic pathogens on dairy farms
Andrew J. Sommer•Joseph H. Skarlupka•Serafino Teseo•Saria Otani•Garret Suen等 7 人
Npj Biofilms And Microbiomes
2025
•2025/6/19
•Vol.11 No.1 p.1-11
Dairy farms are major reservoirs of zoonotic bacterial pathogens, which harbor antimicrobial resistance genes (ARGs), and raise critical questions about their dissemination on and off the farm environment. Here, we investigated the role of coprophagous muscid flies (Diptera: Muscidae) as carriers of...
MetagenomicsMicrobiomeSymbiosis
10.1038/S41522-025-00685-Y
ISSN:2055-5008
Identification of microbial markers across populations in early detection of colorectal cancer
Yuanqi Wu•Na Jiao•Ruixin Zhu•Yida Zhang•Dingfeng Wu等 15 人
Nature Communications
2021
•2021/5/24
•Vol.12 No.1 p.1-13
Associations between gut microbiota and colorectal cancer (CRC) have been widely investigated. However, the replicable markers for early-stage adenoma diagnosis across multiple populations remain elusive. Here, we perform an integrated analysis on 1056 public fecal samples, to identify adenoma-assoc...
Clinical microbiologyColorectal cancerDiagnostic markers
10.1038/S41467-021-23265-Y
ISSN:2041-1723
Engineered hypoxia-responsive albumin nanoparticles mediating mitophagy regulation for cancer therapy
Wenyan Wang•Shun-Yu Yao•Jingjing Luo•Chendi Ding•Qili Huang等 12 人
Nature Communications
2025
•2025/1/11
•Vol.16 No.1 p.1-22
Hypoxic tumors present a significant challenge in cancer therapy due to their ability to adaptation in low-oxygen environments, which supports tumor survival and resistance to treatment. Enhanced mitophagy, the selective degradation of mitochondria by autophagy, is a crucial mechanism that helps sus...
CancerDrug deliveryPolymer chemistryProteinsSupramolecular chemistry
10.1038/S41467-025-55905-Y
ISSN:2041-1723
The role of halophyte-induced saline fertile islands in soil microbial biogeochemical cycling across arid ecosystems
Shuai Zhao•Marcel G. A. van der Heijden•Samiran Banerjee•Jun-jie Liu•Hai-dong Gu等 11 人
Communications Biology
2024
•2024/8/29
•Vol.7 No.1 p.1-13
Halophyte shrubs, prevalent in arid regions globally, create saline fertile islands under their canopy. This study investigates the soil microbial communities and their energy utilization strategies associated with tamarisk shrubs in arid ecosystems. Shotgun sequencing revealed that high salinity in...
Element cyclesMicrobial ecology
10.1038/S42003-024-06741-1
ISSN:2399-3642
TSP50 deficiency in neural stem cells aggravates colitis in mice by altering intestinal microbiome
Xiaoli Li•Rong Jin•Zhaoxia Wang•Chunxue Niu•Zhenbo Song等 20 人
Npj Biofilms And Microbiomes
2025
•2025/6/3
•Vol.11 No.1 p.1-16
Inflammatory bowel disease (IBD) is a complex disease characterized by persistent chronic inflammation of the gastrointestinal tract and periodic episodes. Despite the increasing number of related studies, the detailed pathogenesis of IBD has not been elucidated. In recent years, host-microbiota int...
Applied microbiologyMicrobial genetics
10.1038/S41522-025-00737-3
ISSN:2055-5008
Molecular mechanism underlying miR-204-5p regulation of adipose-derived stem cells differentiation into cells from three germ layers
Zhimin Wang•Meiyu Bi•Xiaoshu Zhe•Xiao Wang•Bai Dai等 9 人
Cell Death Discovery
2024
•2024/2/22
•Vol.10 No.1 p.1-14
The limited differentiation ability of adipose-derived stem cells (ADSCs) limits their application in stem cell therapy and regenerative medicine. Here, we explore the molecular mechanism by which miR-204-5p regulates ADSCs differentiation into cells derived from the three germ layers (i.e., adipocy...
Cell biologyDifferentiationEpigeneticsMesenchymal stem cellsStem-cell differentiation
10.1038/S41420-024-01852-4
ISSN:2058-7716
Pathogenomic analyses of Shigella isolates inform factors limiting shigellosis prevention and control across LMICs
Bengtsson Rebecca J.•Simpkin Adam J.•Pulford Caisey V.•Low Ross•Rasko David A.等 10 人
Nature Microbiology
2022
•2022/1/31
•Vol.7 No.2 p.251-261
Shigella spp. are the leading bacterial cause of severe childhood diarrhoea in low- and middle-income countries (LMICs), are increasingly antimicrobial resistant and have no widely available licenced vaccine. We performed genomic analyses of 1,246 systematically collected shigellae sampled from seve...
Bacterial genomicsConjugate vaccines
10.1038/S41564-021-01054-Z
ISSN:2058-5276
The gut microbiome variability of a butterflyfish increases on severely degraded Caribbean reefs
Clever Friederike•Sourisse Jade M.•Preziosi Richard F.•Eisen Jonathan A.•Guerra E. Catalina Rodriguez等 10 人
Communications Biology
2022
•2022/7/30
•Vol.5 No.1 p.1-15
Environmental degradation has the potential to alter key mutualisms that underlie the structure and function of ecological communities. How microbial communities associated with fishes vary across populations and in relation to habitat characteristics remains largely unknown despite their fundamenta...
BiodiversityMetagenomicsMicrobial ecologyMicrobiome
10.1038/S42003-022-03679-0
ISSN:2399-3642
Experimental evolution of adaptive divergence under varying degrees of gene flow
Sergio Tusso•Bart P. S. Nieuwenhuis•Bernadette Weissensteiner•Simone Immler•Jochen B. W. Wolf
Nature Ecology & Evolution
2021
•2021/1/11
•Vol.5 No.3 p.338-349
Adaptive divergence is the key evolutionary process generating biodiversity by means of natural selection. Yet, the conditions under which it can arise in the presence of gene flow remain contentious. To address this question, we subjected 132 sexually reproducing fission yeast populations, sourced ...
Adaptive radiationEcological geneticsExperimental evolutionGenomics
10.1038/S41559-020-01363-2
ISSN:2397-334X
Metabolic reprogramming and mitochondrial dysfunction underlie β gonia arrest and niche cell dysfunction in sterile triploid oysters
Huihui Wang•Xi Lin•Chunxue Zheng•Hong Yu•Qi Li
Communications Biology
2025
•2025/11/23
0Complementary to the classical view that triploid sterility results from meiotic failure, female triploid pacific oysters exhibit partial sterility also characterized by the impairment of the differentiation of germ cells, forming β gonia. However, the molecular basis underlying this sterility remai...
DifferentiationOogenesis
10.1038/S42003-025-09202-5
ISSN:2399-3642
Evolutionary conservation of the fidelity of transcription
Chung Claire•Verheijen Bert M.•Navapanich Zoe•McGann Eric G.•Shemtov Sarah等 21 人
Nature Communications
2023
•2023/3/20
•Vol.14 No.1 p.1-15
Accurate transcription is required for the faithful expression of genetic information. However, relatively little is known about the molecular mechanisms that control the fidelity of transcription, or the conservation of these mechanisms across the tree of life. To address these issues, we measured ...
Evolutionary geneticsGene expressionMechanisms of diseaseMolecular evolution
10.1038/S41467-023-36525-W
ISSN:2041-1723
Insights into variation in meiosis from 31,228 human sperm genomes
Avery Davis Bell•Curtis J. Mello•James Nemesh•Sara A. Brumbaugh•Alec Wysoker等 6 人
Nature
2020
•2020/6/3
•Vol.583 No.7815 p.259-264
Meiosis, although essential for reproduction, is also variable and error-prone: rates of chromosome crossover vary among gametes, between the sexes, and among humans of the same sex, and chromosome missegregation leads to abnormal chromosome numbers (aneuploidy)1–8. To study diverse meiotic outcomes...
DNA sequencingGenetic variationGenomics
10.1038/S41586-020-2347-0
ISSN:0028-0836
Potential regulatory modules to integrate microgravity signals into flowering pathways in Arabidopsis thaliana grown in space
Junyan Xie•Jiachen Zhu•Lihua Wang•Yuwei Jiao•Yanhui Dou等 9 人
Npj Microgravity
2025
•2025/12/13
0Our previous studies suggested that FLOWERING LOCUS (FT) can integrate microgravity signals into the photoperiodic flowering pathway in Arabidopsis. However, the exact mechanisms remain unclear. In this study, we carried out transcriptomic analysis of wild-type (WT), gigantea (gi) mutant, CONSTANS o...
Developmental biologyMolecular biologyPlant sciences
10.1038/S41526-025-00539-Z
ISSN:2373-8065
Hypercompact adenine base editors based on transposase B guided by engineered RNA
Kim Do Yon•Chung Yuhee•Lee Yujin•Jeong Dongmin•Park Kwang-Hyun等 11 人
Nature Chemical Biology
2022
•2022/8/1
•00 p.1-9
Transposon-associated transposase B (TnpB) is deemed an ancestral protein for type V, Cas12 family members, and the closest ancestor to UnCas12f1. Previously, we reported a set of engineered guide RNAs supporting high indel efficiency for Cas12f1 in human cells. Here we suggest a new technology wher...
DNA metabolismEnzymesGeneticsNucleic acids
10.1038/S41589-022-01077-5
ISSN:1552-4450
Molecular characterization stratifies VQ myeloma cells into two clusters with distinct risk signatures and drug responses
Flietner Evan•Yu Mei•Poudel Govinda•Veltri Anthony J.•Zhou Yun等 15 人
Oncogene
2023
•2023/4/8
•00 p.1-12
Multiple myeloma (MM) is a cancer of malignant plasma cells in the bone marrow and extramedullary sites. We previously characterized a VQ model for human high-risk MM. The various VQ lines display different disease phenotypes and survival rates, suggesting significant intra-model variation. Here, we...
Cancer modelsMyeloma
10.1038/S41388-023-02684-9
ISSN:0950-9232
Cell-specific measurements show nitrogen fixation by particle-attached putative non-cyanobacterial diazotrophs in the North Pacific Subtropical Gyre
Harding Katie J.•Turk-Kubo Kendra A.•Mak Esther Wing Kwan•Weber Peter K.•Mayali Xavier等 6 人
Nature Communications
2022
•2022/11/15
•Vol.13 No.1 p.1-10
Biological nitrogen fixation is a major important source of nitrogen for low-nutrient surface oceanic waters. Nitrogen-fixing (diazotrophic) cyanobacteria are believed to be the primary contributors to this process, but the contribution of non-cyanobacterial diazotrophic organisms in oxygenated surf...
Marine biologyMarine microbiology
10.1038/S41467-022-34585-Y
ISSN:2041-1723
scRNA-seq reveals transcriptional plasticity of var gene expression in Plasmodium falciparum for host immune avoidance
Francesca Florini•Joseph E. Visone•Evi Hadjimichael•Shivali Malpotra•Christopher Nötzel等 7 人
Nature Microbiology
2025
•2025/5/16
•00 p.1-14
Plasmodium falciparum evades antibody recognition through transcriptional switching between members of the var gene family, which encodes the major virulence factor and surface antigen on infected red blood cells. Previous work with clonal P. falciparum populations revealed var gene expression profi...
Gene silencingParasite geneticsParasite immune evasion
10.1038/S41564-025-02008-5
ISSN:2058-5276
RNA G-quadruplex structure contributes to cold adaptation in plants
Yang Xiaofei•Yu Haopeng•Duncan Susan•Zhang Yueying•Cheema Jitender等 11 人
Nature Communications
2022
•2022/10/20
•Vol.13 No.1 p.1-9
Nucleotide composition is suggested to infer gene functionality and ecological adaptation of species to distinct environments. However, the underlying biological function of nucleotide composition dictating environmental adaptations is largely unknown. Here, we systematically analyze the nucleotide ...
Plant molecular biologyTranscriptomics
10.1038/S41467-022-34040-Y
ISSN:2041-1723
Selective sequestration of signalling proteins in a membraneless organelle reinforces the spatial regulation of asymmetry in Caulobacter crescentus
Keren Lasker•Lexy von Diezmann•Xiaofeng Zhou•Daniel G. Ahrens•Thomas H. Mann等 7 人
Nature Microbiology
2020
•2020/1/20
•Vol.5 No.3 p.418-429
Selective recruitment and concentration of signalling proteins within membraneless compartments is a ubiquitous mechanism for subcellular organization1–3. The dynamic flow of molecules into and out of these compartments occurs on faster timescales than for membrane-enclosed organelles, presenting a ...
BacteriaBacterial developmentBacterial transcriptionCell signallingSingle-molecule biophysics
10.1038/S41564-019-0647-7
ISSN:2058-5276
Enterotoxigenic Escherichia coli heat-labile toxin drives enteropathic changes in small intestinal epithelia
Sheikh Alaullah•Tumala Brunda•Vickers Tim J.•Martin John C.•Rosa Bruce A.等 15 人
Nature Communications
2022
•2022/11/12
•Vol.13 No.1 p.1-14
Enterotoxigenic E. coli (ETEC) produce heat-labile (LT) and/or heat-stable (ST) enterotoxins, and commonly cause diarrhea in resource-poor regions. ETEC have been linked repeatedly to sequelae in children including enteropathy, malnutrition, and growth impairment. Although cellular actions of ETEC e...
Bacterial toxinsCellular microbiologyMalnutrition
10.1038/S41467-022-34687-7
ISSN:2041-1723
ZNF410 represses fetal globin by singular control of CHD4
Divya S. Vinjamur•Qiuming Yao•Mitchel A. Cole•Connor McGuckin•Chunyan Ren等 11 人
Nature Genetics
2021
•2021/4/15
•Vol.53 No.5 p.719-728
Known fetal hemoglobin (HbF) silencers have potential on-target liabilities for rational β-hemoglobinopathy therapeutic inhibition. Here, through transcription factor (TF) CRISPR screening, we identify zinc-finger protein (ZNF) 410 as an HbF repressor. ZNF410 does not bind directly to the genes enco...
AnaemiaGene regulationHigh-throughput screening
10.1038/S41588-021-00843-W
ISSN:1061-4036
Identification of cancer-related mutations in human pluripotent stem cells using RNA-seq analysis
Lezmi Elyad•Benvenisty Nissim
Nature Protocols
2021
•2021/8/6
•00 p.1-16
Human pluripotent stem cells (hPSCs) are known to acquire genetic aberrations during in vitro propagation. In addition to recurrent chromosomal aberrations, it has recently been shown that these cells also gain point mutations in cancer-related genes, predominantly in TP53. The need for routine qual...
MutationPluripotent stem cellsRNA sequencingSoftware
10.1038/S41596-021-00591-5
ISSN:1754-2189
Missing microbial eukaryotes and misleading meta-omic conclusions
Arianna I. Krinos•Margaret Mars Brisbin•Sarah K. Hu•Natalie R. Cohen•Tatiana A. Rynearson等 8 人
Nature Communications
2024
•2024/11/14
•Vol.15 No.1 p.1-13
Meta-omics is commonly used for large-scale analyses of microbial eukaryotes, including species or taxonomic group distribution mapping, gene catalog construction, and inference on the functional roles and activities of microbial eukaryotes in situ. Here, we explore the potential pitfalls of common ...
Classification and taxonomyEnvironmental microbiologyMetagenomicsMicrobial ecology
10.1038/S41467-024-52212-W
ISSN:2041-1723
Circulation of Salmonella spp. between humans, animals and the environment in animal-owning households in Malawi
Catherine N. Wilson•Patrick Musicha•Mathew A. Beale•Yohane Diness•Oscar Kanjerwa等 19 人
Nature Communications
2025
•2025/11/12
•Vol.16 No.1 p.97030
Diverse salmonellae have the potential to cause disease and may be carried asymptomatically within the intestine of many vertebrate species. The relative contribution of human, animal, and environmental hosts to the transmission of Salmonella is unknown within and between households in low-income se...
Bacterial geneticsBacterial genomics
10.1038/S41467-025-65266-1
ISSN:2041-1723
Gut microbial ammonia enhances colonic acetylcholine levels to regulate intestinal motility
Hao Chen•Zhen Wang•Yiming Zhao•Wenyu Yang•Jing Huang等 6 人
Nature Microbiology
2026
•2026/2/20
•Vol.11 No.4 p.907-919
Intestinal motility is a function of the enteric nervous system involving secretion of the excitatory neurotransmitter acetylcholine (ACh). Although gut commensal bacteria are key regulators of intestinal physiology, the molecular mechanisms underlying microbial influence on intestinal peristalsis a...
Bacterial host responseIntestinal diseasesMetagenomicsMicrobiome
10.1038/S41564-026-02269-8
ISSN:2058-5276
Preclinical development of kinetin as a safe error-prone SARS-CoV-2 antiviral able to attenuate virus-induced inflammation
Souza Thiago Moreno L.•Pinho Vagner D.•Setim Cristina F.•Sacramento Carolina Q.•Marcon Rodrigo等 35 人
Nature Communications
2023
•2023/1/13
•Vol.14 No.1 p.1-17
Orally available antivirals against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are necessary because of the continuous circulation of new variants that challenge immunized individuals. Because severe COVID-19 is a virus-triggered immune and inflammatory dysfunction, molecules endow...
AntiviralsPharmacodynamicsRNASARS-CoV-2
10.1038/S41467-023-35928-Z
ISSN:2041-1723
Microplastic diversity increases the abundance of antibiotic resistance genes in soil
Yi-Fei Wang•Yan-Jie Liu•Yan-Mei Fu•Jia-Yang Xu•Tian-Lun Zhang等 10 人
Nature Communications
2024
•2024/11/12
•Vol.15 No.1 p.1-15
The impact of microplastics on antibiotic resistance has attracted widespread attention. However, previous studies primarily focused on the effects of individual microplastics. In reality, diverse microplastic types accumulate in soil, and it remains less well studied whether microplastic diversity ...
Antimicrobial resistanceEnvironmental impactEnvironmental microbiologySoil microbiology
10.1038/S41467-024-54237-7
ISSN:2041-1723
Commonality despite exceptional diversity in the baseline human antibody repertoire
Bryan Briney•Anne Inderbitzin•Collin Joyce•Dennis R. Burton
Nature
2019
•2019/1/21
•Vol.566 No.7744 p.393-397
In principle, humans can produce an antibody response to any non-self-antigen molecule in the appropriate context. This flexibility is achieved by the presence of a large repertoire of naive antibodies, the diversity of which is expanded by somatic hypermutation following antigen exposure1. The dive...
AntibodiesVDJ recombination
10.1038/S41586-019-0879-Y
ISSN:0028-0836
MARTX toxin of Vibrio vulnificus induces RBC phosphatidylserine exposure that can contribute to thrombosis
Chung Han Young•Bian Yiying•Lim Kyung-Min•Kim Byoung Sik•Choi Sang Ho
Nature Communications
2022
•2022/8/17
•Vol.13 No.1 p.1-12
V. vulnificus-infected patients suffer from hemolytic anemia and circulatory lesions, often accompanied by venous thrombosis. However, the pathophysiological mechanism of venous thrombosis associated with V. vulnificus infection remains largely unknown. Herein, V. vulnificus infection at the sub-hem...
Bacterial pathogenesisBacterial toxinsPathogens
10.1038/S41467-022-32599-0
ISSN:2041-1723
A splitCas9 phenotypic screen in Toxoplasma gondii identifies proteins involved in host cell egress and invasion
Li Wei•Grech Janessa•Stortz Johannes Felix•Gow Matthew•Periz Javier等 7 人
Nature Microbiology
2022
•2022/5/10
•00 p.1-14
Apicomplexan parasites, such as Toxoplasma gondii, have specific adaptations that enable invasion and exit from the host cell. Owing to the phylogenetic distance between apicomplexan parasites and model organisms, comparative genomics has limited capacity to infer gene functions. Further, although C...
Parasite biologyParasite genetics
10.1038/S41564-022-01114-Y
ISSN:2058-5276
CRISPR-based oligo recombineering prioritizes apicomplexan cysteines for drug discovery
Benns H. J.•Storch M.•Falco J. A.•Fisher F. R.•Tamaki F.等 17 人
Nature Microbiology
2022
•2022/10/20
•Vol.7 No.11 p.1891-1905
Nucleophilic amino acids are important in covalent drug development yet underutilized as anti-microbial targets. Chemoproteomic technologies have been developed to mine chemically accessible residues via their intrinsic reactivity towards electrophilic probes but cannot discern which chemically reac...
MutagenesisParasitologyProteomicsTarget identification
10.1038/S41564-022-01249-Y
ISSN:2058-5276
Recovery of human gut microbiota genomes with third-generation sequencing
Yanfei Li•Yueling Jin•Jianming Zhang•Haoying Pan•Lan Wu等 9 人
Cell Death & Disease
2021
•2021/6/2
•Vol.12 No.6 p.1-11
Human gut microbiota modulates normal physiological functions, such as maintenance of barrier homeostasis and modulation of metabolism, as well as various chronic diseases including type 2 diabetes and gastrointestinal cancer. Despite decades of research, the composition of the gut microbiota remain...
DNA sequencingMechanisms of disease
10.1038/S41419-021-03829-Y
ISSN:2041-4889
The power and promise of genetic mapping from Plasmodium falciparum crosses utilizing human liver-chimeric mice
Katrina A. Button-Simons•Sudhir Kumar•Nelly Carmago•Meseret T. Haile•Catherine Jett等 19 人
Communications Biology
2021
•2021/6/14
•Vol.4 No.1 p.1-13
Genetic crosses are most powerful for linkage analysis when progeny numbers are high, parental alleles segregate evenly and numbers of inbred progeny are minimized. We previously developed a novel genetic crossing platform for the human malaria parasite Plasmodium falciparum, an obligately sexual, h...
Genetic mappingParasite genetics
10.1038/S42003-021-02210-1
ISSN:2399-3642
Functional and structural diversification of incomplete phosphotransferase system in cellulose-degrading clostridia
Xu Tao•Tao Xuanyu•He Hongxi•Kempher Megan L.•Zhang Siping等 14 人
The Isme Journal
2023
•2023/3/10
•00 p.1-13
Carbohydrate utilization is critical to microbial survival. The phosphotransferase system (PTS) is a well-documented microbial system with a prominent role in carbohydrate metabolism, which can transport carbohydrates through forming a phosphorylation cascade and regulate metabolism by protein phosp...
Bacterial geneticsBacterial genomicsMetabolismStructural biology
10.1038/S41396-023-01392-2
ISSN:1751-7362
The ecological and developmental foundations of brood parasitism in a catfish
Martin Reichard•Radim Blažek•Matej Polačik•Tomáš Suchánek•Gernot K. Englmaier等 13 人
Nature Communications
2026
•2026/3/31
0Interspecific brood parasitism has evolved repeatedly from parental care. However, many non-avian brood-parasitic lineages have ancestors lacking parental care, leaving the foundations of brood parasitism in these lineages enigmatic. We examine ecological, reproductive, and developmental data from t...
Behavioural ecologyEvolutionary ecologyMimicry
10.1038/S41467-026-71179-4
ISSN:2041-1723
Altered oral microbiota and immune dysfunction in Chinese elderly patients with schizophrenia: a cross-sectional study
Zongxin Ling•Yiwen Cheng•Xia Liu•Xiumei Yan•Lingbin Wu等 11 人
Translational Psychiatry
2023
•2023/12/9
•Vol.13 No.1 p.1-12
Schizophrenia (SZ) is a complex psychiatric neurodevelopmental disorder with uncertain etiology and pathogenesis. Increasing evidence has recognized the key role of the gut microbiota in SZ. However, few studies have investigated the potential link between oral microbiota and SZ. We studied the tong...
Diagnostic markersSchizophrenia
10.1038/S41398-023-02682-1
ISSN:2158-3188
Quantitative evaluation of protective antibody response induced by hepatitis E vaccine in humans
Gui-Ping Wen•Linling He•Zi-Min Tang•Si-Ling Wang•Xu Zhang等 19 人
Nature Communications
2020
•2020/8/7
•Vol.11 No.1 p.1-13
Efficacy evaluation through human trials is crucial for advancing a vaccine candidate to clinics. Next-generation sequencing (NGS) can be used to quantify B cell repertoire response and trace antibody lineages during vaccination. Here, we demonstrate this application with a case study of Hecolin®, t...
Humoral immunityInfectious diseasesProtein vaccinesViral infection
10.1038/S41467-020-17737-W
ISSN:2041-1723
Paired analysis of host and pathogen genomes identifies determinants of human tuberculosis
Yang Luo•Chuan-Chin Huang•Nicole C. Howard•Xin Wang•Qingyun Liu等 19 人
Nature Communications
2024
•2024/11/29
•Vol.15 No.1 p.1-14
Infectious disease is the result of interactions between host and pathogen and can depend on genetic variations in both. We conduct a genome-to-genome study of paired human and Mycobacterium tuberculosis genomes from a cohort of 1556 tuberculosis patients in Lima, Peru. We identify an association be...
Disease geneticsTuberculosis
10.1038/S41467-024-54741-W
ISSN:2041-1723
The role of transposon inverted repeats in balancing drought tolerance and yield-related traits in maize
Sun Xiaopeng•Xiang Yanli•Dou Nannan•Zhang Hui•Pei Surui等 19 人
Nature Biotechnology
2022
•2022/10/13
•Vol.41 No.1 p.120-127
The genomic basis underlying the selection for environmental adaptation and yield-related traits in maize remains poorly understood. Here we carried out genome-wide profiling of the small RNA (sRNA) transcriptome (sRNAome) and transcriptome landscapes of a global maize diversity panel under dry and ...
AbioticData integrationGenetic variationRegulatory networksTranscriptomics
10.1038/S41587-022-01470-4
ISSN:1087-0156
The genomic landscape of molecular responses to natural drought stress in Panicum hallii
John T. Lovell•Jerry Jenkins•David B. Lowry•Sujan Mamidi•Avinash Sreedasyam等 27 人
Nature Communications
2018
•2018/12/6
•Vol.9 No.1 p.1-10
Environmental stress is a major driver of ecological community dynamics and agricultural productivity. This is especially true for soil water availability, because drought is the greatest abiotic inhibitor of worldwide crop yields. Here, we test the genetic basis of drought responses in the genetic ...
DroughtEvolutionary biologyGene regulatory networksGenome evolution
10.1038/S41467-018-07669-X
ISSN:2041-1723
Pathway-based signatures predict patient outcome, chemotherapy benefit and synthetic lethal dependencies in invasive lobular breast cancer
John Alexander•Koen Schipper•Sarah Nash•Rachel Brough•Harriet Kemp等 11 人
British Journal Of Cancer
2024
•2024/4/10
•00 p.1-13
Invasive Lobular Carcinoma (ILC) is a morphologically distinct breast cancer subtype that represents up to 15% of all breast cancers. Compared to Invasive Breast Carcinoma of No Special Type (IBC-NST), ILCs exhibit poorer long-term outcome and a unique pattern of metastasis. Despite these difference...
Breast cancerMachine learningPredictive markersPrognostic markers
10.1038/S41416-024-02679-7
ISSN:0007-0920
Plasmodium falciparum resistant to artemisinin and diagnostics have emerged in Ethiopia
Abebe A. Fola•Sindew M. Feleke•Hussein Mohammed•Bokretsion G. Brhane•Christopher M. Hennelly等 16 人
Nature Microbiology
2023
•2023/8/28
•00 p.1-9
Diagnosis and treatment of Plasmodium falciparum infections are required for effective malaria control and are pre-requisites for malaria elimination efforts; hence we need to monitor emergence, evolution and spread of drug- and diagnostics-resistant parasites. We deep sequenced key drug-resistance ...
Infectious-disease diagnosticsParasite genomics
10.1038/S41564-023-01461-4
ISSN:2058-5276
NR3C1-mediated epigenetic regulation suppresses astrocytic immune responses in mice
Seongwan Park•Hyeonji Park•Youkyeong Gloria Byun•Xiaolin Wei•Junghyun Eom等 10 人
Nature Communications
2025
•2025/9/22
•Vol.16 No.1 p.1-16
Astrocytes are critical contributors to brain disorders, yet the mechanisms underlying their selective vulnerability to specific diseases remain poorly understood. Here, we demonstrate that NR3C1 acts as a key regulator of early postnatal astrocyte development, shaping long-term immune responses in ...
EpigeneticsEpigenetics in the nervous systemGliogenesis
10.1038/S41467-025-64088-5
ISSN:2041-1723
Dietary cholesterol promotes steatohepatitis related hepatocellular carcinoma through dysregulated metabolism and calcium signaling
Jessie Qiaoyi Liang•Narcissus Teoh•Lixia Xu•Sharon Pok•Xiangchun Li等 15 人
Nature Communications
2018
•2018/10/26
•Vol.9 No.1 p.1-13
The underlining mechanisms of dietary cholesterol and nonalcoholic steatohepatitis (NASH) in contributing to hepatocellular carcinoma (HCC) remain undefined. Here we demonstrated that high-fat-non-cholesterol-fed mice developed simple steatosis, whilst high-fat-high-cholesterol-fed mice developed NA...
Cancer genomicsGenomics
10.1038/S41467-018-06931-6
ISSN:2041-1723
A novel c-Met/TRK inhibitor 1D228 efficiently inhibits tumor growth by targeting angiogenesis and tumor cell proliferation
Baijiao An•Wenyan Nie•Jinhui Hu•Yangyang Fan•Haoran Nie等 17 人
Cell Death & Disease
2023
•2023/11/9
•Vol.14 No.11 p.1-15
Multiple tumors are synergistically promoted by c-Met and TRK, and blocking their cross-signalling pathway may give better effects. In this study, we developed a tyrosine kinase inhibitor 1D228, which exhibited excellent anti-tumor activity by targeting c-Met and TRK. Models in vitro, 1D228 showed a...
Drug discovery and developmentKinasesTargeted therapies
10.1038/S41419-023-06246-5
ISSN:2041-4889
Combining mucosal microbiome and host multi-omics data shows prognostic potential in paediatric ulcerative colitis
Maria Kulecka•Jill O’Sullivan•Rachel Fitzgerald•Ana Velikonja•Chloe E. Huseyin等 20 人
Nature Communications
2025
•2025/8/4
•Vol.16 No.1 p.1-20
Current first-line treatments of paediatric ulcerative colitis (UC) maintain a 6-month remission in only half of the patients. Relapse prediction at diagnosis could enable earlier introduction of immunosuppressants. We collected intestinal biopsies from 56 treatment-naïve children, combining mucosal...
Data integrationMachine learningUlcerative colitis
10.1038/S41467-025-62533-Z
ISSN:2041-1723
A multi-tissue atlas of regulatory variants in cattle
Liu Shuli•Gao Yahui•Canela-Xandri Oriol•Wang Sheng•Yu Ying等 28 人
Nature Genetics
2022
•2022/8/11
•00 p.1-10
Characterization of genetic regulatory variants acting on livestock gene expression is essential for interpreting the molecular mechanisms underlying traits of economic value and for increasing the rate of genetic gain through artificial selection. Here we build a Cattle Genotype–Tissue Expression a...
Data miningGene expressionGene regulation
10.1038/S41588-022-01153-5
ISSN:1061-4036
Genetic diversity and comparative genomics across Leishmania (Viannia) species
Laura Natalia Gonzalez-Garcia•Maria Paula Rodriguez•Marcela Parra-Muñoz•Ana M. Clavijo•Laura Levy等 16 人
Communications Biology
2025
•2025/6/14
•Vol.8 No.1 p.1-14
Leishmaniasis is an important public health problem worldwide, with a broad spectrum of clinical and epidemiological features partly associated with the diversity and complex life cycle of the Leishmania parasites. This study analyzes genomic data from 205 Leishmania (Viannia) samples, including 65 ...
Genetic variationPathogens
10.1038/S42003-025-08331-1
ISSN:2399-3642
Historic transposon mobilisation waves create distinct pools of adaptive variants in a major crop pathogen
Tobias Baril•Guido Puccetti•Daniel Croll
Nature Communications
2025
•2025/11/12
•Vol.16 No.1 p.99610
Transposable elements (TEs) shape host-pathogen interactions and contribute to antimicrobial resistance, but how adaptive TEs arise in populations and how historical contingencies affect TE dynamics remains unclear. Fungal crop pathogens provide unique frameworks to address such questions due to spa...
Evolutionary geneticsFungal genomicsGenomicsMicrobial genetics
10.1038/S41467-025-64944-4
ISSN:2041-1723
Deciphering phenylalanine-derived salicylic acid biosynthesis in plants
Yukang Wang•Shuyan Song•Wenxuan Zhang•Qianwen Deng•Yanlei Feng等 31 人
Nature
2025
•2025/7/23
•00 p.1-10
Salicylic acid (SA) is a ubiquitous plant hormone with a long history in human civilization1,2. Because of the central role of SA in orchestrating plant pathogen defence, understanding SA biosynthesis is fundamental to plant immunity research and crop improvement. Isochorismate-derived SA biosynthes...
EnzymesMetabolomicsPlant hormonesPlant immunitySecondary metabolism
10.1038/S41586-025-09280-9
ISSN:0028-0836
Stomatal regulators are co-opted for seta development in the astomatous liverwort Marchantia polymorpha
Moriya Kenta C.•Shirakawa Makoto•Loue-Manifel Jeanne•Matsuda Yoriko•Lu Yen-Ting等 14 人
Nature Plants
2023
•2023/1/19
•Vol.9 No.2 p.302-314
The evolution of special types of cells requires the acquisition of new gene regulatory networks controlled by transcription factors (TFs). In stomatous plants, a TF module formed by subfamilies Ia and IIIb basic helix–loop–helix TFs (Ia-IIIb bHLH) regulates stomatal formation; however, how this mod...
Cell fatePlant evolution
10.1038/S41477-022-01325-5
ISSN:2055-0278
Reduced efficacy of HIV-1 integrase inhibitors in patients with drug resistance mutations in reverse transcriptase
Mark J. Siedner•Michelle A. Moorhouse•Bryony Simmons•Tulio de Oliveira•Richard Lessells等 13 人
Nature Communications
2020
•2020/12/1
•Vol.11 No.1 p.1-10
Little is known about the impact of pretreatment drug resistance (PDR) on the efficacy of second generation integrase inhibitors. We sequenced pretreatment plasma specimens from the ADVANCE trial (NCT03122262). Our primary outcome was 96-week virologic success, defined as a sustained viral load <100...
Molecular medicineRetrovirus
10.1038/S41467-020-19801-X
ISSN:2041-1723
A velocity-informed framework for resolving functional stratification in rare human stem cells
Justyna Jarczak•Mariusz Z. Ratajczak•Magdalena Kucia
Leukemia
2026
•2026/4/21
•00 p.1-12
Single-cell transcriptomics has transformed our understanding of stem cell biology; however, the analysis of extremely rare and quiescent populations remains limited by the low cell numbers and functional inaccessibility. Here, we present a velocity-informed framework to resolve transcriptional stra...
Cell signallingHaematopoietic stem cells
10.1038/S41375-026-02956-9
ISSN:0887-6924
Multimodal fusion of radio-pathology and proteogenomics identify integrated glioma subtypes with prognostic and therapeutic opportunities
Zaoqu Liu•Yushuai Wu•Hui Xu•Minkai Wang•Siyuan Weng等 37 人
Nature Communications
2025
•2025/4/13
•Vol.16 No.1 p.1-18
Integrating multimodal data can uncover causal features hidden in single-modality analyses, offering a comprehensive understanding of disease complexity. This study introduces a multimodal fusion subtyping (MOFS) framework that integrates radiological, pathological, genomic, transcriptomic, and prot...
Cancer genomicsCancer imagingCNS cancer
10.1038/S41467-025-58675-9
ISSN:2041-1723
Chimeric antigen receptor macrophages (CAR-M) sensitize HER2+ solid tumors to PD1 blockade in pre-clinical models
Stefano Pierini•Rashid Gabbasov•Maria Cecilia Oliveira-Nunes•Rehman Qureshi•Alison Worth等 31 人
Nature Communications
2025
•2025/1/15
•Vol.16 No.1 p.1-16
We previously developed human CAR macrophages (CAR-M) and demonstrated redirection of macrophage anti-tumor function leading to tumor control in immunodeficient xenograft models. Here, we develop clinically relevant fully immunocompetent syngeneic models to evaluate the potential for CAR-M to remode...
Antigen presentationCell delivery
10.1038/S41467-024-55770-1
ISSN:2041-1723
Targeting melanoma’s MCL1 bias unleashes the apoptotic potential of BRAF and ERK1/2 pathway inhibitors
Matthew J. Sale•Emma Minihane•Noel R. Monks•Rebecca Gilley•Frances M. Richards等 18 人
Nature Communications
2019
•2019/11/14
•Vol.10 No.1 p.1-19
BRAF and MEK1/2 inhibitors are effective in melanoma but resistance inevitably develops. Despite increasing the abundance of pro-apoptotic BIM and BMF, ERK1/2 pathway inhibition is predominantly cytostatic, reflecting residual pro-survival BCL2 family activity. Here, we show that uniquely low BCL-XL...
Cell deathCell signallingTargeted therapies
10.1038/S41467-019-12409-W
ISSN:2041-1723
Unveiling the hidden viral biodiversity and potential ecological functions with global coral holobiont virome database
Mengjie Wu•Xiaobin Wen•Shuchen Liu•Huu Hao Ngo•Zhonghua Cai等 6 人
Npj Biofilms And Microbiomes
2026
•2026/2/27
•Vol.12 No.1 p.770
Viruses are integral yet underexplored components of coral holobionts, with their roles in shaping microbial diversity, modulating symbioses, and contributing to Darwin’s paradox remaining largely unresolved. Here, we present the Global Coral Holobiont Virome Database (GCHVD), encompassing 76,755 vi...
Computational biology and bioinformaticsEcologyMicrobiology
10.1038/S41522-026-00944-6
ISSN:2055-5008
A multistage drug delivery approach for colorectal primary tumors and lymph node metastases
Yihang Yuan•Quanjun Lin•Hai-Yi Feng•Yunpeng Zhang•Xing Lai等 16 人
Nature Communications
2025
•2025/2/7
•Vol.16 No.1 p.1-19
The presence of lymph node (LN) metastases guides cancer staging and worsens prognoses. Incomplete lymphadenectomy of metastatic LNs may end up with disease recurrence, while excessive resection can result in increased postoperative complications with even no survival benefit. Thus, effective non-in...
Cancer modelsChemotherapyDrug deliveryDrug development
10.1038/S41467-025-56768-Z
ISSN:2041-1723
Tomato antiviral ubiquitin-proteasome system recognizes viral 59 kDa protein to confer tomato chlorosis virus resistance
Dan Zhao•Xiaoqian Liu•Hongbo Li•Tianchen Xia•Qi Jia等 16 人
Nature Communications
2026
•2026/1/31
•Vol.17 No.1 p.22290
Viral diseases critically impact crop yields, necessitating insights into plant-pathogen recognition and resistance. In tomato (Solanum lycopersicum), tomato chlorosis virus (ToCV) employs 59 kDa protein (p59) to facilitate movement and degrade the host Catalase1 (SlCAT1), disrupting redox home...
Effectors in plant pathologyPlant domesticationProteasome
10.1038/S41467-026-68832-3
ISSN:2041-1723
A fine-scale Arabidopsis chromatin landscape reveals chromatin conformation-associated transcriptional dynamics
Yueying Zhang•Qianli Dong•Zhen Wang•Qinzhe Liu•Haopeng Yu等 13 人
Nature Communications
2024
•2024/4/16
•Vol.15 No.1 p.1-13
Plants, as sessile organisms, deploy transcriptional dynamics for adapting to extreme growth conditions such as cold stress. Emerging evidence suggests that chromatin architecture contributes to transcriptional regulation. However, the relationship between chromatin architectural dynamics and transc...
AbioticChromatin structurePlant molecular biology
10.1038/S41467-024-47678-7
ISSN:2041-1723
Female-biased gene flow between two species of Darwin’s finches
Sangeet Lamichhaney•Fan Han•Matthew T. Webster•B. Rosemary Grant•Peter R. Grant等 6 人
Nature Ecology & Evolution
2020
•2020/5/4
•Vol.4 No.7 p.979-986
The mosaic nature of hybrid genomes is well recognized, but little is known of how they are shaped initially by patterns of breeding, selection, recombination and differential incompatibilities. On the small Galápagos island of Daphne Major, two species of Darwin’s finches, Geospiza fortis and G. sc...
Ecological geneticsEvolutionary ecology
10.1038/S41559-020-1183-9
ISSN:2397-334X
Structure-based prediction and characterization of photo-crosslinking in native protein–RNA complexes
Huijuan Feng•Xiang-Jun Lu•Suvrajit Maji•Linxi Liu•Dmytro Ustianenko等 7 人
Nature Communications
2024
•2024/3/13
•Vol.15 No.1 p.1-14
UV-crosslinking of protein and RNA in direct contacts has been widely used to study protein-RNA complexes while our understanding of the photo-crosslinking mechanisms remains poor. This knowledge gap is due to the challenge of precisely mapping the crosslink sites in protein and RNA simultaneously i...
Computational biology and bioinformaticsRNARNA-binding proteinsStructural biology
10.1038/S41467-024-46429-Y
ISSN:2041-1723
Nuclear farnesoid X receptor protects against bone loss by driving osteoblast differentiation through stabilizing RUNX2
Qi Dong•Haoyuan Fu•Wenxiao Li•Xinyu Ji•Yingchao Yin等 17 人
Bone Research
2025
•2025/1/30
•Vol.13 No.1 p.1-16
The delicate balance between bone formation by osteoblasts and bone resorption by osteoclasts maintains bone homeostasis. Nuclear receptors (NRs) are now understood to be crucial in bone physiology and pathology. However, the function of the Farnesoid X receptor (FXR), a member of the NR family, in ...
BonePathogenesis
10.1038/S41413-024-00394-W
ISSN:2095-6231
FEAST: fast expectation-maximization for microbial source tracking
Liat Shenhav•Mike Thompson•Tyler A. Joseph•Leah Briscoe•Ori Furman等 9 人
Nature Methods
2019
•2019/6/10
•Vol.16 No.7 p.627-632
A major challenge of analyzing the compositional structure of microbiome data is identifying its potential origins. Here, we introduce fast expectation-maximization microbial source tracking (FEAST), a ready-to-use scalable framework that can simultaneously estimate the contribution of thousands of ...
Computational biology and bioinformaticsEcologyMicrobiology
10.1038/S41592-019-0431-X
ISSN:1548-7091
Massively parallel genomic perturbations with multi-target CRISPR interrogates Cas9 activity and DNA repair at endogenous sites
Zou Roger S.•Marin-Gonzalez Alberto•Liu Yang•Liu Hans B.•Shen Leo等 9 人
Nature Cell Biology
2022
•2022/9/5
•Vol.24 No.9 p.1433-1444
Here we present an approach that combines a clustered regularly interspaced short palindromic repeats (CRISPR) system that simultaneously targets hundreds of epigenetically diverse endogenous genomic sites with high-throughput sequencing to measure Cas9 dynamics and cellular responses at scale. This...
CRISPR-Cas9 genome editingDNA damage responseDouble-strand DNA breaks
10.1038/S41556-022-00975-Z
ISSN:1465-7392
Molecular architecture of the developing mouse brain
La Manno Gioele•Siletti Kimberly•Furlan Alessandro•Gyllborg Daniel•Vinsland Elin等 14 人
Nature
2021
•2021/7/28
•00 p.1-5
The mammalian brain develops through a complex interplay of spatial cues generated by diffusible morphogens, cell–cell interactions and intrinsic genetic programs that result in probably more than a thousand distinct cell types. A complete understanding of this process requires a systematic characte...
Development of the nervous systemDevelopmental neurogenesisGlial developmentTranscriptomics
10.1038/S41586-021-03775-X
ISSN:0028-0836
Neurofibromin 1 in mushroom body neurons mediates circadian wake drive through activating cAMP–PKA signaling
Machado Almeida Pedro•Lago Solis Blanca•Stickley Luca•Feidler Alexis•Nagoshi Emi
Nature Communications
2021
•2021/10/1
•Vol.12 No.1 p.1-17
Various behavioral and cognitive states exhibit circadian variations in animals across phyla including Drosophila melanogaster, in which only ~0.1% of the brain’s neurons contain circadian clocks. Clock neurons transmit the timing information to a plethora of non-clock neurons via poorly understood ...
Circadian rhythms and sleepMolecular neuroscienceTranscriptomics
10.1038/S41467-021-26031-2
ISSN:2041-1723
Single-cell architecture of purinergic signaling in human cord blood hematopoietic stem and progenitor cells
M. Molenda•J. Jarczak•P. Kieszek•M. Z. Ratajczak•M. Kucia
Leukemia
2026
•2026/7/1
•00 p.1-11
Purinergic signaling has emerged as a key regulator of hematopoietic stem and progenitor cell (HSPC) trafficking, metabolism, and innate immune responsiveness. Our previous studies demonstrated that extracellular ATP promotes HSPC mobilization, homing, and engraftment by activating P2X purinergic re...
Haematopoietic stem cellsStem cells
10.1038/S41375-026-03031-Z
ISSN:0887-6924
Drinking water chlorination has minor effects on the intestinal flora and resistomes of Bangladeshi children
Nadimpalli Maya L.•Lanza Val F.•Montealegre Maria Camila•Sultana Sonia•Fuhrmeister Erica R.等 16 人
Nature Microbiology
2022
•2022/4/14
•00 p.1-10
Healthy development of the gut microbiome provides long-term health benefits. Children raised in countries with high infectious disease burdens are frequently exposed to diarrhoeal pathogens and antibiotics, which perturb gut microbiome assembly. A recent cluster-randomized trial leveraging >4,00...
Applied microbiologyPathogensRisk factors
10.1038/S41564-022-01101-3
ISSN:2058-5276
The Toxoplasma rhoptry protein ROP55 is a major virulence factor that prevents lytic host cell death
Margarida T. Grilo Ruivo•Ji-hun Shin•Todd Lenz•Stephanie Y. Matsuno•Katherine Olivia Yanes等 14 人
Nature Communications
2025
•2025/1/15
•Vol.16 No.1 p.1-19
Programmed-cell death is an antimicrobial defense mechanism that promotes clearance of intracellular pathogens. Toxoplasma counteracts host immune defenses by secreting effector proteins into host cells; however, how the parasite evades lytic cell death and the effectors involved remain poorly chara...
Antimicrobial responsesCell death and immune responseNecroptosisParasite host responseParasite immune evasion
10.1038/S41467-025-56128-X
ISSN:2041-1723
Tumour-wide RNA splicing aberrations generate actionable public neoantigens
Darwin W. Kwok•Nicholas O. Stevers•Iñaki Etxeberria•Takahide Nejo•Maggie Colton Cove等 31 人
Nature
2025
•2025/2/19
•Vol.639 No.8054 p.463-473
T cell-based immunotherapies hold promise in treating cancer by leveraging the immune system’s recognition of cancer-specific antigens1. However, their efficacy is limited in tumours with few somatic mutations and substantial intratumoural heterogeneity2–4. Here we introduce a previously uncharacter...
Cancer immunotherapyCNS cancerMHC class ITranslational immunologyTumour heterogeneity
10.1038/S41586-024-08552-0
ISSN:0028-0836
scCAD: Cluster decomposition-based anomaly detection for rare cell identification in single-cell expression data
Yunpei Xu•Shaokai Wang•Qilong Feng•Jiazhi Xia•Yaohang Li等 7 人
Nature Communications
2024
•2024/8/31
•Vol.15 No.1 p.1-20
Single-cell RNA sequencing (scRNA-seq) technologies have become essential tools for characterizing cellular landscapes within complex tissues. Large-scale single-cell transcriptomics holds great potential for identifying rare cell types critical to the pathogenesis of diseases and biological process...
BioinformaticsComputational modelsComputer scienceGene expression
10.1038/S41467-024-51891-9
ISSN:2041-1723
A multiomics approach to identify host-microbe alterations associated with infection severity in diabetic foot infections: a pilot study
Michael Radzieta•Fatemah Sadeghpour-Heravi•Timothy J. Peters•Honghua Hu•Karen Vickery等 10 人
Npj Biofilms And Microbiomes
2021
•2021/3/22
•Vol.7 No.1 p.1-12
Diabetic foot infections (DFIs) are a major cause of hospitalization and can lead to lower extremity amputation. In this pilot study, we used a multiomics approach to explore the host–microbe complex within DFIs. We observed minimal differences in the overall microbial composition between PEDIS infe...
BacteriologyClinical microbiologyMetagenomicsMicrobial geneticsMicrobiome
10.1038/S41522-021-00202-X
ISSN:2055-5008
Large DNA deletions occur during DNA repair at 20-fold lower frequency for base editors and prime editors than for Cas9 nucleases
Gue-Ho Hwang•Seok-Hoon Lee•Minsik Oh•Segi Kim•Omer Habib等 11 人
Nature Biomedical Engineering
2024
•2024/11/4
•00 p.1-14
When used to edit genomes, Cas9 nucleases produce targeted double-strand breaks in DNA. Subsequent DNA-repair pathways can induce large genomic deletions (larger than 100 bp), which constrains the applicability of genome editing. Here we show that Cas9-mediated double-strand breaks induce large dele...
CRISPR-Cas9 genome editingGenetic engineering
10.1038/S41551-024-01277-5
ISSN:2157-846X
Potential metabolic and genetic interaction among viruses, methanogen and methanotrophic archaea, and their syntrophic partners
Wang Long•Wang Yinzhao•Huang Xingyu•Ma Ruijie•Li Jiangtao等 8 人
Isme Communications
2022
•2022/6/28
•Vol.2 No.1 p.1-10
The metabolism of methane in anoxic ecosystems is mainly mediated by methanogens and methane-oxidizing archaea (MMA), key players in global carbon cycling. Viruses are vital in regulating their host fate and ecological function. However, our knowledge about the distribution and diversity of MMA viru...
Microbial ecology
10.1038/S43705-022-00135-2
ISSN:2730-6151
Breaking the durability barrier with d band optimized Cu Fe twin crystal nanozymes for long term suppression of Botrytis cinerea
Lu Liu•Hongsu Wang•Qianliao Zhou•Biao Dong•Xiaodi Niu
Nature Communications
2025
•2025/12/8
0Nanozymes that emulate the catalytic function of natural enzymes often suffer from self-depletion, limiting their long-term efficacy for practical applications. Here, we report an antifungal nanozyme composed of copper-iron nanocrystals (CuFe NCs) engineered through a Twinned Nanozyme Protection Str...
Antifungal agentsBiomaterials – cellsNanoparticles
10.1038/S41467-025-67095-8
ISSN:2041-1723
Protein phosphatase 2A inactivation induces microsatellite instability, neoantigen production and immune response
Yen Yu-Ting•Chien May•Wu Pei-Yi•Ho Chi-Chang•Ho Chun-Te等 10 人
Nature Communications
2021
•2021/12/15
•Vol.12 No.1 p.1-14
Microsatellite-instable (MSI), a predictive biomarker for immune checkpoint blockade (ICB) response, is caused by mismatch repair deficiency (MMRd) that occurs through genetic or epigenetic silencing of MMR genes. Here, we report a mechanism of MMRd and demonstrate that protein phosphatase 2A (PP2A)...
Cancer immunotherapyColon cancerGene silencingImmunoediting
10.1038/S41467-021-27620-X
ISSN:2041-1723
Antagonistic CLE peptide pathways shape root meristem tissue patterning
Hang Zhang•Qian Wang•Noel Blanco-Touriñán•Christian S. Hardtke
Nature Plants
2024
•2024/10/28
•00 p.1-9
Secreted CLAVATA3/EMBRYO SURROUNDING REGION (CLE) peptide ligands dimension the stem cell niche of Arabidopsis shoot meristems by signalling through redundant and cross-compensating CLAVATA1 (CLV1)-type receptor kinases. In the root meristem, the CLV1 homologues BARELY ANY MERISTEM 1 (BAM1) and BAM2...
Plant signallingPlant stem cellRoot apical meristem
10.1038/S41477-024-01838-1
ISSN:2055-0278
Identifying genomic data use with the Data Citation Explorer
Neil Byers•Charles Parker•Chris Beecroft•T. B. K. Reddy•Hugh Salamon等 7 人
Scientific Data
2024
•2024/11/6
•Vol.11 No.1 p.1-13
Increases in sequencing capacity, combined with rapid accumulation of publications and associated data resources, have increased the complexity of maintaining associations between literature and genomic data. As the volume of literature and data have exceeded the capacity of manual curation, automat...
GenomicsResearch data
10.1038/S41597-024-04049-7
ISSN:2052-4463
Super-enhancers orchestrate transcriptional dysregulation and metabolic reprogramming in uveal melanoma
Hui Pan•Weihuan Shao•Huixue Wang•Shengfang Ge•Lingyu Zhang等 8 人
Communications Biology
2025
•2025/6/23
•Vol.8 No.1 p.1-14
Uveal melanoma (UM) is the most common intraocular malignancy in adults and frequently metastasizes. Somatic mutations and chromatin aberrations have been implicated in the pathogenesis of this deadly disease. Despite rapid progress in elucidating the genetic landscape of UM, the epigenetic architec...
Cancer epigeneticsChromatin immunoprecipitationEye cancer
10.1038/S42003-025-08338-8
ISSN:2399-3642
Too big to purge: persistence of deleterious Mutations in Island populations of the European Barn Owl (Tyto alba)
Eléonore Lavanchy•Tristan Cumer•Alexandros Topaloudis•Anne-Lyse Ducrest•Céline Simon等 7 人
Heredity
2024
•2024/10/13
•00 p.1-13
A key aspect of assessing the risk of extinction/extirpation for a particular wild species or population is the status of inbreeding, but the origin of inbreeding and the current mutational load are also two crucial factors to consider when determining survival probability of a population. In this s...
ConsanguinityGenomicsInbreedingPopulation genetics
10.1038/S41437-024-00728-8
ISSN:0018-067X
Mechanism of fertilization-induced auxin synthesis in the endosperm for seed and fruit development
Guo Lei•Luo Xi•Li Muzi•Joldersma Dirk•Plunkert Madison等 6 人
Nature Communications
2022
•2022/7/9
•Vol.13 No.1 p.1-15
The dominance of flowering plants on earth is owed largely to the evolution of maternal tissues such as fruit and seedcoat that protect and disseminate the seeds. The mechanism of how fertilization triggers the development of these specialized maternal tissues is not well understood. A key event is ...
FruitingPlant developmentSeed development
10.1038/S41467-022-31656-Y
ISSN:2041-1723
Spatiotemporal variations in retrovirus-host interactions among Darwin’s finches
Hill Jason•Lillie Mette•Pettersson Mats E.•Rubin Carl-Johan•Grant B. Rosemary等 8 人
Nature Communications
2022
•2022/10/13
•Vol.13 No.1 p.1-8
Endogenous retroviruses (ERVs) are inherited remnants of retroviruses that colonized host germline over millions of years, providing a sampling of retroviral diversity across time. Here, we utilize the strength of Darwin’s finches, a system synonymous with evolutionary studies, for investigating ERV...
Genome evolutionMolecular evolutionPopulation genetics
10.1038/S41467-022-33723-W
ISSN:2041-1723
ViralCC retrieves complete viral genomes and virus-host pairs from metagenomic Hi-C data
Du Yuxuan•Fuhrman Jed A.•Sun Fengzhu
Nature Communications
2023
•2023/1/31
•Vol.14 No.1 p.1-11
The introduction of high-throughput chromosome conformation capture (Hi-C) into metagenomics enables reconstructing high-quality metagenome-assembled genomes (MAGs) from microbial communities. Despite recent advances in recovering eukaryotic, bacterial, and archaeal genomes using Hi-C contact maps, ...
Computational modelsMetagenomics
10.1038/S41467-023-35945-Y
ISSN:2041-1723
Two conserved epigenetic regulators prevent healthy ageing
Jie Yuan•Si-Yuan Chang•Shi-Gang Yin•Zhi-Yang Liu•Xiu Cheng等 16 人
Nature
2020
•2020/2/26
•Vol.579 No.7797 p.118-122
It has long been assumed that lifespan and healthspan correlate strongly, yet the two can be clearly dissociated1–6. Although there has been a global increase in human life expectancy, increasing longevity is rarely accompanied by an extended healthspan4,7. Thus, understanding the origin of healthy ...
AgeingNeural ageing
10.1038/S41586-020-2037-Y
ISSN:0028-0836
Tumor-specific lncRNA IGF1R-AS1 trans-regulates chromatin interactions associated with oncogenic MYC signaling
Yongyong Yang•Ting-You Wang•Joshua Fry•Yingming Li•Qingshu Meng等 27 人
Nature Communications
2026
•2026/3/19
0LncRNAs have emerged as pivotal regulators in the development and progression of various human cancers. However, understanding the precise mechanisms by which lncRNAs influence cancer progression remains a substantial challenge, largely due to their cell type- and tissue-specific expression patterns...
Cancer genomicsGene regulationGene regulatory networksProstate cancer
10.1038/S41467-026-70814-4
ISSN:2041-1723
Rising prevalence of Plasmodium falciparum Artemisinin partial resistance mutations in Ethiopia
Bokretsion G. Brhane•Abebe A. Fola•Helen Nigussie•Alec Leonetti•Moges Kassa等 20 人
Communications Medicine
2025
•2025/7/18
•Vol.5 No.1 p.1-11
Ethiopia aims to eliminate local malaria transmission by 2030, but rising malaria cases, due to different factors, present a challenge. Understanding the prevalence and distribution of artemisinin partial resistance (ART-R) and other markers related to partner drugs as well as parasite connectivity ...
DiseasesMolecular biology
10.1038/S43856-025-01008-0
ISSN:2730-664X
Gut microbiota–bile acid–interleukin-22 axis orchestrates polycystic ovary syndrome
Xinyu Qi•Chuyu Yun•Lulu Sun•Jialin Xia•Qing Wu等 22 人
Nature Medicine
2019
•2019/7/22
•Vol.25 No.8 p.1225-1233
Polycystic ovary syndrome (PCOS) is characterized by androgen excess, ovulatory dysfunction and polycystic ovaries1, and is often accompanied by insulin resistance2. The mechanism of ovulatory dysfunction and insulin resistance in PCOS remains elusive, thus limiting the development of therapeutics. ...
Endocrine reproductive disordersInfertility
10.1038/S41591-019-0509-0
ISSN:1078-8956
Linking differences in microbial network structure with changes in coral larval settlement
Abigail C. Turnlund•Inka Vanwonterghem•Emmanuelle S. Botté•Carly J. Randall•Christine Giuliano等 11 人
Isme Communications
2023
•2023/10/21
•Vol.3 No.1 p.1140
Coral cover and recruitment have decreased on reefs worldwide due to climate change-related disturbances. Achieving reliable coral larval settlement under aquaculture conditions is critical for reef restoration programmes; however, this can be challenging due to the lack of reliable and universal la...
Microbial ecologySymbiosisWater microbiology
10.1038/S43705-023-00320-X
ISSN:2730-6151
Marsupials have monoallelic MEST expression with a conserved antisense lncRNA but MEST is not imprinted
Teruhito Ishihara•Shunsuke Suzuki•Trent A. Newman•Jane C. Fenelon•Oliver W. Griffith等 7 人
Heredity
2023
•2023/11/11
•00 p.1-13
The imprinted isoform of the Mest gene in mice is involved in key mammalian traits such as placental and fetal growth, maternal care and mammary gland maturation. The imprinted isoform has a distinct differentially methylated region (DMR) at its promoter in eutherian mammals but in marsupials, there...
Evolutionary biologyEvolutionary geneticsMolecular evolution
10.1038/S41437-023-00656-Z
ISSN:0018-067X
Tyrosol blocks E. coli anaerobic biofilm formation via YbfA and FNR to increase antibiotic susceptibility
Ha-Young Choi•Won-Gon Kim
Nature Communications
2024
•2024/7/6
•Vol.15 No.1 p.1-20
Bacteria within mature biofilms are highly resistant to antibiotics than planktonic cells. Oxygen limitation contributes to antibiotic resistance in mature biofilms. Nitric oxide (NO) induces biofilm dispersal; however, low NO levels stimulate biofilm formation, an underexplored process. Here, we in...
AntibioticsBiofilms
10.1038/S41467-024-50116-3
ISSN:2041-1723
Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features
Natalya Yutin•Sean Benler•Sergei A. Shmakov•Yuri I. Wolf•Igor Tolstoy等 9 人
Nature Communications
2021
•2021/2/16
•Vol.12 No.1 p.1-11
CrAssphage is the most abundant human-associated virus and the founding member of a large group of bacteriophages, discovered in animal-associated and environmental metagenomes, that infect bacteria of the phylum Bacteroidetes. We analyze 4907 Circular Metagenome Assembled Genomes (cMAGs) of putativ...
EvolutionGenome informaticsPhage biology
10.1038/S41467-021-21350-W
ISSN:2041-1723
Concerted SUMO-targeted ubiquitin ligase activities of TOPORS and RNF4 are essential for stress management and cell proliferation
Julio C. Y. Liu•Leena Ackermann•Saskia Hoffmann•Zita Gál•Ivo A. Hendriks等 14 人
Nature Structural & Molecular Biology
2024
•2024/4/22
•00 p.1-13
Protein SUMOylation provides a principal driving force for cellular stress responses, including DNA–protein crosslink (DPC) repair and arsenic-induced PML body degradation. In this study, using genome-scale screens, we identified the human E3 ligase TOPORS as a key effector of SUMO-dependent DPC res...
DNA adductsHigh-throughput screeningSumoylationUbiquitin ligasesUbiquitylation
10.1038/S41594-024-01294-7
ISSN:1545-9993
Chronic circadian disruption modulates breast cancer stemness and immune microenvironment to drive metastasis in mice
Eva Hadadi•William Taylor•Xiao-Mei Li•Yetki Aslan•Marthe Villote等 13 人
Nature Communications
2020
•2020/6/24
•Vol.11 No.1 p.1-17
Breast cancer is the most common type of cancer worldwide and one of the major causes of cancer death in women. Epidemiological studies have established a link between night-shift work and increased cancer risk, suggesting that circadian disruption may play a role in carcinogenesis. Here, we aim to ...
Breast cancerCancer microenvironmentCancer stem cellsCircadian rhythms
10.1038/S41467-020-16890-6
ISSN:2041-1723
Persistent IDH mutations are not associated with increased relapse or death in patients with IDH-mutated acute myeloid leukemia undergoing allogeneic hematopoietic cell transplant with post-transplant cyclophosphamide
Niveditha Ravindra•Laura W. Dillon•Gege Gui•Matthew Smith•Lukasz P. Gondek等 9 人
Bone Marrow Transplantation
2024
•2024/1/5
•00 p.1-3
Cancer geneticsPrognosisTranslational research
10.1038/S41409-023-02189-9
ISSN:0268-3369
Pangenomic analysis of Chinese gastric cancer
Yu Yingyan•Zhang Zhen•Dong Xiaorui•Yang Ruixin•Duan Zhongqu等 27 人
Nature Communications
2022
•2022/9/15
•Vol.13 No.1 p.1-13
Pangenomic study might improve the completeness of human reference genome (GRCh38) and promote precision medicine. Here, we use an automated pipeline of human pangenomic analysis to build gastric cancer pan-genome for 185 paired deep sequencing data (370 samples), and characterize the gene presence-...
Cancer geneticsCancer genomicsGastric cancerGenome assembly algorithmsSurgical oncology
10.1038/S41467-022-33073-7
ISSN:2041-1723
Dynamic regulation of hypoxia-inducible factor-1α activity is essential for normal B cell development
Natalie Burrows•Rachael J. M. Bashford-Rogers•Vijesh J. Bhute•Ana Peñalver•John R. Ferdinand等 22 人
Nature Immunology
2020
•2020/8/31
•Vol.21 No.11 p.1408-1420
B lymphocyte development and selection are central to adaptive immunity and self-tolerance. These processes require B cell receptor (BCR) signaling and occur in bone marrow, an environment with variable hypoxia, but whether hypoxia-inducible factor (HIF) is involved is unknown. We show that HIF acti...
Adaptive immunityClonal selection
10.1038/S41590-020-0772-8
ISSN:1529-2908
Histidine kinase MHZ1/OsHK1 interacts with ethylene receptors to regulate root growth in rice
He Zhao•Kai-Xuan Duan•Biao Ma•Cui-Cui Yin•Yang Hu等 17 人
Nature Communications
2020
•2020/1/24
•Vol.11 No.1 p.1-13
Ethylene plays essential roles during adaptive responses to water-saturating environments in rice, but knowledge of its signaling mechanism remains limited. Here, through an analysis of a rice ethylene-response mutant mhz1, we show that MHZ1 positively modulates root ethylene responses. MHZ1 encodes...
Plant hormonesPlant sciences
10.1038/S41467-020-14313-0
ISSN:2041-1723
Three Near telomere-to-telomere Genomes for Gardenia jasminoides
Zhijun Zeng•Wenjie Lu•Chaohuang Liu•Xiang Zhang•Ziheng Yao等 12 人
Scientific Data
2026
•2026/4/23
0Gardenia jasminoides, an evergreen shrub in the Rubiaceae family, is widely cultivated across southern China, particularly in regions south of the Yangtze River. With a long history of use in traditional Chinese medicine, its fruits and flowers are valued for their rich diversity of bioactive compou...
GenomePlant breeding
10.1038/S41597-026-07169-4
ISSN:2052-4463
Seedling root system adaptation to water availability during maize domestication and global expansion
Peng Yu•Chunhui Li•Meng Li•Xiaoming He•Danning Wang等 38 人
Nature Genetics
2024
•2024/5/22
•00 p.1-12
The maize root system has been reshaped by indirect selection during global adaptation to new agricultural environments. In this study, we characterized the root systems of more than 9,000 global maize accessions and its wild relatives, defining the geographical signature and genomic basis of variat...
Genome-wide association studiesPlant geneticsPopulation genetics
10.1038/S41588-024-01761-3
ISSN:1061-4036
Biophotoelectrochemical process co-driven by dead microalgae and live bacteria
Chen Shanshan•Chen Jin•Zhang Lanlan•Huang Shaofu•Liu Xing等 10 人
The Isme Journal
2023
•2023/2/23
•00 p.1-8
Anaerobic reduction processes in natural waters can be promoted by dead microalgae that have been attributed to nutrient substances provided by the decomposition of dead microalgae for other microorganisms. However, previous reports have not considered that dead microalgae may also serve as photosen...
BiogeochemistryEnvironmental sciences
10.1038/S41396-023-01383-3
ISSN:1751-7362
Dark microbiome and extremely low organics in Atacama fossil delta unveil Mars life detection limits
Azua-Bustos Armando•Fairén Alberto G.•González-Silva Carlos•Prieto-Ballesteros Olga•Carrizo Daniel等 39 人
Nature Communications
2023
•2023/2/21
•Vol.14 No.1 p.1-14
Identifying unequivocal signs of life on Mars is one of the most important objectives for sending missions to the red planet. Here we report Red Stone, a 163-100 My alluvial fan–fan delta that formed under arid conditions in the Atacama Desert, rich in hematite and mudstones containing clays such as...
AstrobiologySoil microbiology
10.1038/S41467-023-36172-1
ISSN:2041-1723
Changes in the skin microbiome associated with squamous cell carcinoma in transplant recipients
Krueger Annika•Zaugg Julian•Lachner Nancy•Bialasiewicz Seweryn•Lin Lynlee L.等 11 人
Isme Communications
2022
•2022/2/1
•Vol.2 No.1 p.1-10
Actinic keratoses (AK) arise in severely photo-damaged skin and can progress to squamous cell carcinomas (SCC). AK and SCC are common in Caucasian populations, and immunosuppressed individuals have a markedly higher risk of developing SCC. An overabundance of Staphylococcus aureus has been reported ...
Bacterial geneticsClinical microbiology
10.1038/S43705-022-00095-7
ISSN:2730-6151
The histone methyltransferase ASH1L protects against bone loss by inhibiting osteoclastogenesis
Xiaoli Zhao•Shuai Lin•Hangjiang Ren•Shenghui Sun•Liyun Zheng等 7 人
Cell Death & Differentiation
2024
•2024/3/2
•00 p.1-13
Absent, small, or homeotic1-like (ASH1L) is a histone lysine methyltransferase that generally functions as a transcriptional activator in controlling cell fate. So far, its physiological relevance in bone homeostasis and osteoclast differentiation remains elusive. Here, by conditional deleting Ash1l...
EpigeneticsGene regulationMetabolic disorders
10.1038/S41418-024-01274-W
ISSN:1350-9047
Global impact of unproductive splicing on human gene expression
Benjamin Fair•Carlos F. Buen Abad Najar•Junxing Zhao•Stephanie Lozano•Austin Reilly等 9 人
Nature Genetics
2024
•2024/9/2
•00 p.1-11
Alternative splicing (AS) in human genes is widely viewed as a mechanism for enhancing proteomic diversity. AS can also impact gene expression levels without increasing protein diversity by producing ‘unproductive’ transcripts that are targeted for rapid degradation by nonsense-mediated decay (NMD)....
Gene regulationTranscriptomics
10.1038/S41588-024-01872-X
ISSN:1061-4036
Synergistic effects of ferulic acid and wogonin on cholestatic liver injury via gut microbiota modulation
Xin Luo•Ting Mao•Xi Wang•Peng Cheng•Mingyuan Liu等 11 人
Npj Biofilms And Microbiomes
2025
•2025/12/18
•Vol.11 No.1 p.2310
Cholestasis, a bile flow disorder common to many liver diseases, currently lacks effective treatments. Emerging evidence links gut microbiota disturbances to cholestatic liver injury. Here, an antibiotic cocktail (ABX)-treated mouse model confirmed the indispensable role of the intestinal microbiota...
DiseasesGastroenterologyMicrobiology
10.1038/S41522-025-00862-Z
ISSN:2055-5008
High-protein diet prevents fat mass increase after dieting by counteracting Lactobacillus-enhanced lipid absorption
Zhong Wuling•Wang Hui•Yang Yale•Zhang Yali•Lai Hejin等 17 人
Nature Metabolism
2022
•2022/12/1
•Vol.4 No.12 p.1713-1731
Dietary restriction is widely used to reduce fat mass and lose weight in individuals with or without obesity; however, weight regain after dieting is still a big challenge, and the underlying mechanisms remain largely elusive. Here we show that refeeding after various types of dieting induces quick ...
Fat metabolismMetabolismObesity
10.1038/S42255-022-00687-6
ISSN:2522-5812
Spatial transcriptome atlas reveals pulmonary microstructure-specific COVID-19 gene signatures in cynomolgus macaques
Taehwan Oh•Green Kim•Seung Ho Baek•YoungMin Woo•Bon-Sang Koo等 14 人
Communications Biology
2023
•2023/8/28
•Vol.6 No.1 p.1-11
Characterizing the host response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the molecular level is necessary to understand viral pathogenesis and identify clinically relevant biomarkers. However, in humans, the pulmonary host response during disease onset remains poorly under...
InfectionPathogenesis
10.1038/S42003-023-05253-8
ISSN:2399-3642
Plant flavones enrich rhizosphere Oxalobacteraceae to improve maize performance under nitrogen deprivation
Peng Yu•Xiaoming He•Marcel Baer•Stien Beirinckx•Tian Tian等 20 人
Nature Plants
2021
•2021/4/8
•Vol.7 No.4 p.481-499
Beneficial interactions between plant roots and rhizosphere microorganisms are pivotal for plant fitness. Nevertheless, the molecular mechanisms controlling the feedback between root architecture and microbial community structure remain elusive in maize. Here, we demonstrate that transcriptomic grad...
GenomicsMicrobiologyPlant development
10.1038/S41477-021-00897-Y
ISSN:2055-0278
A joint NCBI and EMBL-EBI transcript set for clinical genomics and research
Morales Joannella•Pujar Shashikant•Loveland Jane E.•Astashyn Alex•Bennett Ruth等 40 人
Nature
2022
•2022/4/6
•00 p.1-6
Comprehensive genome annotation is essential to understand the impact of clinically relevant variants. However, the absence of a standard for clinical reporting and browser display complicates the process of consistent interpretation and reporting. To address these challenges, Ensembl/GENCODE1 and R...
Clinical geneticsDatabasesGenome informaticsSequence annotationStandards
10.1038/S41586-022-04558-8
ISSN:0028-0836
Analysis of genome and methylation changes in Chinese indigenous chickens over time provides insight into species conservation
Zeng Tao•Yin Jianmei•Feng Peishi•Han Feiran•Tian Yong等 26 人
Communications Biology
2022
•2022/9/12
•Vol.5 No.1 p.1-11
Conservation of natural resources is a vital and challenging task. Numerous animal genetic resources have been effectively conserved worldwide. However, the effectiveness of conservation programmes and the variation information of species have rarely been evaluated. Here, we performed whole-genome a...
BiodiversityConservation biologyDNA sequencing
10.1038/S42003-022-03907-7
ISSN:2399-3642
Ordered and deterministic cancer genome evolution after p53 loss
Baslan Timour•Morris John P.•Zhao Zhen•Reyes Jose•Ho Yu-Jui等 31 人
Nature
2022
•2022/8/17
•Vol.608 No.7924 p.795-802
Although p53 inactivation promotes genomic instability1 and presents a route to malignancy for more than half of all human cancers2,3, the patterns through which heterogenous TP53 (encoding human p53) mutant genomes emerge and influence tumorigenesis remain poorly understood. Here, in a mouse model ...
Cancer geneticsCancer genomics
10.1038/S41586-022-05082-5
ISSN:0028-0836
Comprehensive proteogenomic characterization reveals clinically relevant molecular subtypes associated with medulloblastoma progression
Seong-Min Park•Kyung-Hee Kim•Jong Hyuk Yoon•Fulvio D’Angelo•Seung Ah Choi等 38 人
Experimental & Molecular Medicine
2026
•2026/6/5
•00 p.1-15
Current treatment strategies for medulloblastoma remain ineffective owing to extensive tumor heterogeneity. We generated five platforms of omics data including liquid chromatography and mass spectrometry-based proteome and performed integrated multi-omic characterization to improve the conventional ...
AutophagyCancer metabolismCancer microenvironmentInflammation
10.1038/S12276-026-01732-0
ISSN:2092-6413
Evolution of Phytophthora infestans on its potato host since the Irish potato famine
Allison Coomber•Amanda Saville•Jean Beagle Ristaino
Nature Communications
2024
•2024/8/5
•Vol.15 No.1 p.1-12
Phytophthora infestans is a major oomycete plant pathogen, responsible for potato late blight, which led to the Irish Potato Famine from 1845–1852. Since then, potatoes resistant to this disease have been bred and deployed worldwide. Their resistance (R) genes recognize pathogen effectors responsibl...
Effectors in plant pathologyPlant evolutionPopulation genetics
10.1038/S41467-024-50749-4
ISSN:2041-1723
Gut microbiota impacts bone via Bacteroides vulgatus-valeric acid-related pathways
Xu Lin•Hong-Mei Xiao•Hui-Min Liu•Wan-Qiang Lv•Jonathan Greenbaum等 32 人
Nature Communications
2023
•2023/10/27
•Vol.14 No.1 p.1-17
Although the gut microbiota has been reported to influence osteoporosis risk, the individual species involved, and underlying mechanisms, remain largely unknown. We performed integrative analyses in a Chinese cohort of peri-/post-menopausal women with metagenomics/targeted metabolomics/whole-genome ...
Applied microbiologyOsteoporosisPredictive markersRisk factors
10.1038/S41467-023-42005-Y
ISSN:2041-1723
ARID1A mutations protect follicular lymphoma from FAS-dependent immune surveillance by reducing RUNX3/ETS1-driven FAS-expression
Martina Antoniolli•Maria Solovey•Johannes Adrian Hildebrand•Tabea Freyholdt•Carolin Dorothea Strobl等 25 人
Cell Death & Differentiation
2025
•2025/1/23
•00 p.1-12
The cell death receptor FAS and its ligand (FASLG) play crucial roles in the selection of B cells during the germinal center (GC) reaction. Failure to eliminate potentially harmful B cells via FAS can lead to lymphoproliferation and the development of B cell malignancies. The classic form of fo...
Cancer microenvironmentCell death and immune responseHaematological diseases
10.1038/S41418-025-01445-3
ISSN:1350-9047
Generation and comparative analysis of an Itga8-CreERT2 mouse with preferential activity in vascular smooth muscle cells
Warthi Ganesh•Faulkner Jessica L.•Doja Jaser•Ghanam Amr R.•Gao Pan等 22 人
Nature Cardiovascular Research
2022
•2022/11/11
•Vol.1 No.11 p.1084-1100
All current smooth muscle cell (SMC) Cre mice similarly recombine floxed alleles in vascular and visceral SMCs. Here we present an Itga8-CreERT2 knock-in mouse and compare its activity with a Myh11-CreERT2 mouse. Both Cre drivers demonstrate equivalent recombination in vascular SMCs. However, Myh11-...
Cardiovascular biologyGenetic engineeringGenetics
10.1038/S44161-022-00162-1
ISSN:2731-0590
Co-transcriptional folding orchestrates sequential multi-effector sensing by a glycine tandem riboswitch
Rosa A. Romero•Adrien Chauvier•Serena S. Teh•Vincent A. Reed•Sicheng Zhang等 9 人
Nature Communications
2026
•2026/2/14
•Vol.17 No.1 p.27790
Riboswitches are non-coding RNA motifs that regulate gene expression in response to ligand binding. The glycine tandem riboswitch (GTR) contains two glycine aptamers that interact extensively, driving conformational changes in the downstream expression platform to control gene expression. Despite nu...
RiboswitchesRNA
10.1038/S41467-026-69648-X
ISSN:2041-1723
DNA nicks induce mutational signatures associated with BRCA1 deficiency
Feng Yi-Li•Liu Qian•Chen Ruo-Dan•Liu Si-Cheng•Huang Zhi-Cheng等 8 人
Nature Communications
2022
•2022/7/25
•Vol.13 No.1 p.1-15
Analysis of human cancer genome sequences has revealed specific mutational signatures associated with BRCA1-deficient tumors, but the underlying mechanisms remain poorly understood. Here, we show that one-ended DNA double strand breaks (DSBs) converted from CRISPR/Cas9-induced nicks by DNA replicati...
Cancer geneticsDNA
10.1038/S41467-022-32011-X
ISSN:2041-1723
Acinetobacter baylyi regulates type IV pilus synthesis by employing two extension motors and a motor protein inhibitor
Courtney K. Ellison•Triana N. Dalia•Catherine A. Klancher•Joshua W. Shaevitz•Zemer Gitai等 6 人
Nature Communications
2021
•2021/6/18
•Vol.12 No.1 p.1-9
Bacteria use extracellular appendages called type IV pili (T4P) for diverse behaviors including DNA uptake, surface sensing, virulence, protein secretion, and twitching motility. Dynamic extension and retraction of T4P is essential for their function, and T4P extension is thought to occur through th...
Bacterial geneticsBacterial transformation
10.1038/S41467-021-24124-6
ISSN:2041-1723
Postnatal supplementation with alarmins S100a8/a9 ameliorates malnutrition-induced neonate enteropathy in mice
Lisa Perruzza•Julia Heckmann•Tanja Rezzonico Jost•Matteo Raneri•Simone Guglielmetti等 14 人
Nature Communications
2024
•2024/10/4
•Vol.15 No.1 p.1-16
Malnutrition is linked to 45% of global childhood mortality, however, the impact of maternal malnutrition on the child’s health remains elusive. Previous studies suggested that maternal malnutrition does not affect breast milk composition. Yet, malnourished children often develop a so-called environ...
Chronic inflammationGastroenteritisMalnutrition
10.1038/S41467-024-52829-X
ISSN:2041-1723
Integrated microbiota and metabolite profiles link Crohn’s disease to sulfur metabolism
Amira Metwaly•Andreas Dunkel•Nadine Waldschmitt•Abilash Chakravarthy Durai Raj•Ilias Lagkouvardos等 15 人
Nature Communications
2020
•2020/8/28
•Vol.11 No.1 p.1-15
Gut microbial and metabolite alterations have been linked to the pathogenesis of inflammatory bowel diseases. Here we perform a multi-omics microbiome and metabolite analysis of a longitudinal cohort of Crohn’s disease patients undergoing autologous hematopoietic stem cell transplantation, and inves...
DiseasesMicrobiologyMolecular biology
10.1038/S41467-020-17956-1
ISSN:2041-1723
Domain insertion permissibility-guided engineering of allostery in ion channels
Willow Coyote-Maestas•Yungui He•Chad L. Myers•Daniel Schmidt
Nature Communications
2019
•2019/1/17
•Vol.10 No.1 p.1-14
Allostery is a fundamental principle of protein regulation that remains hard to engineer, particularly in membrane proteins such as ion channels. Here we use human Inward Rectifier K+ Channel Kir2.1 to map site-specific permissibility to the insertion of domains with different biophysical properties...
Molecular conformationPotassium channelsProtein function predictions
10.1038/S41467-018-08171-0
ISSN:2041-1723
Malat-1-PRC2-EZH1 interaction supports adaptive oxidative stress dependent epigenome remodeling in skeletal myotubes
El Said Nadine Hosny•Della Valle Francesco•Liu Peng•Paytuví-Gallart Andreu•Adroub Sabir等 7 人
Cell Death & Disease
2021
•2021/9/16
•Vol.12 No.10 p.1-10
PRC2-mediated epigenetic function involves the interaction with long non-coding RNAs (lncRNAs). Although the identity of some of these RNAs has been elucidated in the context of developmental programs, their counterparts in postmitotic adult tissue homeostasis remain uncharacterized. To this aim, we...
Gene silencingLong non-coding RNAs
10.1038/S41419-021-04082-Z
ISSN:2041-4889
Efficient base editing for multiple genes and loci in pigs using base editors
Jingke Xie•Weikai Ge•Nan Li•Qishuai Liu•Fangbing Chen等 23 人
Nature Communications
2019
•2019/6/28
•Vol.10 No.1 p.1-13
Cytosine base editors (CBEs) enable programmable C-to-T conversion without DNA double-stranded breaks and homology-directed repair in a variety of organisms, which exhibit great potential for agricultural and biomedical applications. However, all reported cases only involved C-to-T substitution at a...
CRISPR-Cas9 genome editingGenetic engineering
10.1038/S41467-019-10421-8
ISSN:2041-1723
Structural and mechanistic insights into the dual-nuclease defense protein Upx as an anti-phage system
Ruimin Zhou•Yingcan Liu•Qian Zhang•Zhenning Yin•Jiajing Tong等 18 人
Nature Communications
2026
•2026/3/9
0Nucleic acid degradation is a common strategy for prokaryotic anti-phage systems, as exemplified by the CRISPR-Cas system. The PD-(D/E)-XK nucleases constitute a widely distributed family in these defenses. Notably, most members exhibit a single nuclease domain, while variants containing dual nuclea...
BacteriophagesCryoelectron microscopyPhage biologyVirus–host interactions
10.1038/S41467-026-70435-X
ISSN:2041-1723
Selection against domestication alleles in introduced rabbit populations
Pedro Andrade•Joel M. Alves•Paulo Pereira•Carl-Johan Rubin•Eugénio Silva等 22 人
Nature Ecology & Evolution
2024
•2024/6/21
•00 p.1-13
Humans have moved domestic animals around the globe for thousands of years. These have occasionally established feral populations in nature, often with devastating ecological consequences. To understand how natural selection shapes re-adaptation into the wild, we investigated one of the most success...
Conservation genomicsEcological geneticsEvolutionary geneticsGenetic variationInvasive species
10.1038/S41559-024-02443-3
ISSN:2397-334X
Effects of iron supplements and iron-containing micronutrient powders on the gut microbiome in Bangladeshi infants: a randomized controlled trial
Andrew Baldi•Sabine Braat•Mohammed Imrul Hasan•Cavan Bennett•Marilou Barrios等 19 人
Nature Communications
2024
•2024/10/5
•Vol.15 No.1 p.1-12
Anemia is highly prevalent globally, especially in young children in low-income countries, where it often overlaps with a high burden of diarrheal disease. Distribution of iron interventions (as supplements or iron-containing multiple micronutrient powders, MNPs) is a key anemia reduction strategy. ...
AnaemiaMetagenomicsMicrobiomePaediatric research
10.1038/S41467-024-53013-X
ISSN:2041-1723
Acarbose enhances the efficacy of immunotherapy against solid tumours by modulating the gut microbiota
Shi-Long Zhang•Xin Wang•Qing-Qing Cai•Chen Chen•Zheng-Yan Zhang等 10 人
Nature Metabolism
2024
•2024/9/25
•00 p.1-19
The crucial role of gut microbiota in shaping immunotherapy outcomes has prompted investigations into potential modulators. Here we show that oral administration of acarbose significantly increases the anti-tumour response to anti-PD-1 therapy in female tumour-bearing mice. Acarbose modulates the gu...
CancerCancer immunotherapyMetabolismMicrobiomeTumour immunology
10.1038/S42255-024-01137-1
ISSN:2522-5812
Intracerebral fate of organic and inorganic nanoparticles is dependent on microglial extracellular vesicle function
Jinchao Gao•Qingxiang Song•Xiao Gu•Gan Jiang•Jialin Huang等 12 人
Nature Nanotechnology
2023
•2023/12/29
•00 p.1-11
Nanoparticles (NPs) represent an important advance for delivering diagnostic and therapeutic agents across the blood–brain barrier. However, NP clearance is critical for safety and therapeutic applicability. Here we report on a study of the clearance of model organic and inorganic NPs from the brain...
BiotechnologyNanoparticles
10.1038/S41565-023-01551-8
ISSN:1748-3387
Giant tortoise genomes provide insights into longevity and age-related disease
Víctor Quesada•Sandra Freitas-Rodríguez•Joshua Miller•José G. Pérez-Silva•Zi-Feng Jiang等 35 人
Nature Ecology & Evolution
2018
•2018/12/3
•Vol.3 No.1 p.87-95
Giant tortoises are among the longest-lived vertebrate animals and, as such, provide an excellent model to study traits like longevity and age-related diseases. However, genomic and molecular evolutionary information on giant tortoises is scarce. Here, we describe a global analysis of the genomes of...
Comparative genomicsMolecular evolution
10.1038/S41559-018-0733-X
ISSN:2397-334X
Distance-decay reveals contrasting effects of land-use types on arthropod community homogenisation
Orsi Decker•Johannes Uhler•Sarah Redlich•Anne Chao•Mareike Kortmann等 16 人
Nature Communications
2026
•2026/1/15
•Vol.17 No.1 p.7630
Homogenisation caused by intensive land-use is one of the drivers of global biodiversity decline. However, the contribution of land-use intensity to insect diversity loss is still largely untested. Therefore, we compare the rate of species homogenisation of ~12.000 arthropod species (using Barcode I...
BiodiversityCommunity ecology
10.1038/S41467-025-67612-9
ISSN:2041-1723
Spatially resolved single-cell analyses of human meningioma identify novel cell states influencing tumor microenvironment and progression
Alexander P. Landry•Leeor S. Yefet•Justin Z. Wang•Andrew Ajisebutu•Chloe Gui等 18 人
Nature Genetics
2026
•2026/6/9
•Vol.58 No.6 p.1383-1395
Recent advances in our understanding of the molecular landscape of meningioma have generated new insights into the biology and heterogeneity of this disease, with demonstrated clinical value. However, there remains a need to understand tumor-intrinsic heterogeneity at single-cell resolution to infor...
CNS cancerComputational biology and bioinformatics
10.1038/S41588-026-02615-W
ISSN:1061-4036
CD301b+ macrophage: the new booster for activating bone regeneration in periodontitis treatment
Can Wang•Qin Zhao•Chen Chen•Jiaojiao Li•Jing Zhang等 9 人
International Journal Of Oral Science
2023
•2023/5/17
•Vol.15 No.1 p.1-12
Periodontal bone regeneration is a major challenge in the treatment of periodontitis. Currently the main obstacle is the difficulty of restoring the regenerative vitality of periodontal osteoblast lineages suppressed by inflammation, via conventional treatment. CD301b+ macrophages were recently iden...
PeriodontitisTissue engineering
10.1038/S41368-023-00225-4
ISSN:2049-3169
Evolution of Pseudomonas aeruginosa toward higher fitness under standard laboratory conditions
Igor Grekov•Janne Gesine Thöming•Adrian Kordes•Susanne Häussler
The Isme Journal
2020
•2020/12/3
•Vol.15 No.4 p.1165-1177
Identifying genetic factors that contribute to the evolution of adaptive phenotypes in pathogenic bacteria is key to understanding the establishment of infectious diseases. In this study, we performed mutation accumulation experiments to record the frequency of mutations and their effect on fitness ...
Bacterial geneticsBiofilmsFunctional genomicsMolecular evolutionTranscriptomics
10.1038/S41396-020-00841-6
ISSN:1751-7362
General transcription factor from Escherichia coli with a distinct mechanism of action
Nikita Vasilyev•Mengjie M. J. Liu•Vitaly Epshtein•Ilya Shamovsky•Evgeny Nudler
Nature Structural & Molecular Biology
2024
•2024/1/4
•00 p.1-9
Gene expression in Escherichia coli is controlled by well-established mechanisms that activate or repress transcription. Here, we identify CedA as an unconventional transcription factor specifically associated with the RNA polymerase (RNAP) σ70 holoenzyme. Structural and biochemical analysis of CedA...
Cellular microbiologyCryoelectron microscopyMass spectrometryTranscriptional regulatory elements
10.1038/S41594-023-01154-W
ISSN:1545-9993
Long-read transcript sequencing identifies differential isoform expression in the entorhinal cortex in a transgenic model of tau pathology
Szi Kay Leung•Rosemary A. Bamford•Aaron R. Jeffries•Isabel Castanho•Barry Chioza等 15 人
Nature Communications
2024
•2024/8/2
•Vol.15 No.1 p.1-19
Increasing evidence suggests that alternative splicing plays an important role in Alzheimer’s disease (AD) pathology. We used long-read sequencing in combination with a novel bioinformatics tool (FICLE) to profile transcript diversity in the entorhinal cortex of female transgenic (TG) mice harboring...
Diseases of the nervous systemTranscriptomics
10.1038/S41467-024-50486-8
ISSN:2041-1723
SoxC and MmpReg promote blastema formation in whole-body regeneration of fragmenting potworms Enchytraeus japonensis
Toshiyuki Fujita•Naoya Aoki•Chihiro Mori•Koichi J. Homma•Shinji Yamaguchi
Nature Communications
2024
•2024/8/22
•Vol.15 No.1 p.1-18
Regeneration in many animals involves the formation of a blastema, which differentiates and organizes into the appropriate missing body parts. Although the mechanisms underlying blastema formation are often fundamental to regeneration biology, information on the cellular and molecular basis of blast...
Regeneration
10.1038/S41467-024-50865-1
ISSN:2041-1723
Biotin-dependent cell envelope remodelling is required for Mycobacterium abscessus survival in lung infection
Sullivan Mark R.•McGowen Kerry•Liu Qiang•Akusobi Chidiebere•Young David C.等 12 人
Nature Microbiology
2023
•2023/1/19
•Vol.8 No.3 p.481-497
Mycobacterium abscessus is an emerging pathogen causing lung infection predominantly in patients with underlying structural abnormalities or lung disease and is resistant to most frontline antibiotics. As the pathogenic mechanisms of M. abscessus in the context of the lung are not well-understood, w...
Bacterial geneticsBacterial host responsePathogens
10.1038/S41564-022-01307-5
ISSN:2058-5276
Tumor microbiome diversity influences papillary thyroid cancer invasion
Yuan Lijuan•Yang Ping•Wei Gang•Hu Xi’e•Chen Songhao等 9 人
Communications Biology
2022
•2022/8/24
•Vol.5 No.1 p.1-9
Papillary thyroid carcinoma (PTC) has a high incidence, and its proper treatment remains challenging. Therefore, identifying PTC progression markers is essential. Here, using 16S RNA sequences, we analyzed the PTC intratumor microbiome and its role in tumor progression. Substantial microbial abundan...
MicrobiomeThyroid cancerThyroid diseases
10.1038/S42003-022-03814-X
ISSN:2399-3642
The Fanconi anemia core complex promotes CtIP-dependent end resection to drive homologous recombination at DNA double-strand breaks
Bert van de Kooij•Fenna J. van der Wal•Magdalena B. Rother•Wouter W. Wiegant•Pau Creixell等 12 人
Nature Communications
2024
•2024/8/16
•Vol.15 No.1 p.1-17
During the repair of interstrand crosslinks (ICLs) a DNA double-strand break (DSB) is generated. The Fanconi anemia (FA) core complex, which is recruited to ICLs, promotes high-fidelity repair of this DSB by homologous recombination (HR). However, whether the FA core complex also promotes HR at ICL-...
Double-strand DNA breaksHomologous recombination
10.1038/S41467-024-51090-6
ISSN:2041-1723
Cytidine deaminases APOBEC3C and APOBEC3D promote DNA replication stress resistance in pancreatic cancer cells
Tajinder Ubhi•Olga Zaslaver•Andrew T. Quaile•Dennis Plenker•Pinjiang Cao等 17 人
Nature Cancer
2024
•2024/3/6
•00 p.1-21
Gemcitabine is a potent inhibitor of DNA replication and is a mainstay therapeutic for diverse cancers, particularly pancreatic ductal adenocarcinoma (PDAC). However, most tumors remain refractory to gemcitabine therapies. Here, to define the cancer cell response to gemcitabine, we performed genome-...
CancerCancer modelsDNA damage response
10.1038/S43018-024-00742-Z
ISSN:2662-1347
ZDHHC11-mediated palmitoylation alleviates chondrocyte senescence and serves as a therapeutic target for osteoarthritis
Kefan Wang•Wei He•Zhe Gong•Jun Gao•Tianyou Gao等 12 人
Nature Aging
2025
•2025/9/30
•00 p.1-19
Osteoarthritis (OA) is a whole-joint disorder that interferes with the quality of life in older individuals. Here we report that ZDHHC11 is highly expressed in articular chondrocytes but is downregulated in the degenerated cartilage of aged mice and patients with OA. ZDHHC11 prevents chondrocyte sen...
AgeingMechanisms of diseasePost-translational modificationsSenescence
10.1038/S43587-025-00968-1
ISSN:2662-8465
A Pseudomonas aeruginosa small RNA regulates chronic and acute infection
Pengbo Cao•Derek Fleming•Dina A. Moustafa•Stephen K. Dolan•Kayla H. Szymanik等 12 人
Nature
2023
•2023/5/24
•00 p.1-7
The ability to switch between different lifestyles allows bacterial pathogens to thrive in diverse ecological niches1,2. However, a molecular understanding of their lifestyle changes within the human host is lacking. Here, by directly examining bacterial gene expression in human-derived samples, we ...
Bacterial geneticsBacterial pathogenesisPathogensSmall RNAs
10.1038/S41586-023-06111-7
ISSN:0028-0836
Single-cell multi-omics identifies chronic inflammation as a driver of TP53-mutant leukemic evolution
Alba Rodriguez-Meira•Ruggiero Norfo•Sean Wen•Agathe L. Chédeville•Haseeb Rahman等 34 人
Nature Genetics
2023
•2023/9/4
•Vol.55 No.9 p.1531-1541
Understanding the genetic and nongenetic determinants of tumor protein 53 (TP53)-mutation-driven clonal evolution and subsequent transformation is a crucial step toward the design of rational therapeutic strategies. Here we carry out allelic resolution single-cell multi-omic analysis of hematopoieti...
Cancer stem cellsLeukaemiaTranscriptomics
10.1038/S41588-023-01480-1
ISSN:1061-4036
Genetic regulation of gene expression across multiple tissues in chickens
Dailu Guan•Zhonghao Bai•Xiaoning Zhu•Conghao Zhong•Yali Hou等 62 人
Nature Genetics
2025
•2025/4/8
•00 p.1-11
The chicken is a valuable model for understanding fundamental biology and vertebrate evolution and is a major global source of nutrient-dense and lean protein. Despite being the first non-mammalian amniote to have its genome sequenced, a systematic characterization of functional variation on the chi...
Data miningGene regulation
10.1038/S41588-025-02155-9
ISSN:1061-4036
Revisiting the intrinsic mycobiome in pancreatic cancer
Ashley A. Fletcher•Matthew S. Kelly•Austin M. Eckhoff•Peter J. Allen
Nature
2023
•2023/8/2
•Vol.620 No.7972 p.1-6
Cancer microenvironmentMicrobiomePancreatic cancer
10.1038/S41586-023-06292-1
ISSN:0028-0836
The chromatin network helps prevent cancer-associated mutagenesis at transcription-replication conflicts
Aleix Bayona-Feliu•Emilia Herrera-Moyano•Nibal Badra-Fajardo•Iván Galván-Femenía•María Eugenia Soler-Oliva等 6 人
Nature Communications
2023
•2023/10/28
•Vol.14 No.1 p.1-16
Genome instability is a feature of cancer cells, transcription being an important source of DNA damage. This is in large part associated with R-loops, which hamper replication, especially at head-on transcription-replication conflicts (TRCs). Here we show that TRCs trigger a DNA Damage Response (DDR...
Cancer epigeneticsCancer genomicsEpigeneticsGenomic instability
10.1038/S41467-023-42653-0
ISSN:2041-1723
Correlational networking guides the discovery of unclustered lanthipeptide protease-encoding genes
Xue Dan•Older Ethan A.•Zhong Zheng•Shang Zhuo•Chen Nanzhu等 16 人
Nature Communications
2022
•2022/3/28
•Vol.13 No.1 p.1-14
Bacterial natural product biosynthetic genes, canonically clustered, have been increasingly found to rely on hidden enzymes encoded elsewhere in the genome for completion of biosynthesis. The study and application of lanthipeptides are frequently hindered by unclustered protease genes required for f...
BiosynthesisNatural products
10.1038/S41467-022-29325-1
ISSN:2041-1723
Initial community composition determines the long-term dynamics of a microbial cross-feeding interaction by modulating niche availability
Dolinšek Jan•Ramoneda Josep•Johnson David R.
Isme Communications
2022
•2022/8/24
•Vol.2 No.1 p.1-10
Multi-step substrate consumption pathways can promote microbial biodiversity via cross-feeding. If one cell type preferentially consumes a primary substrate rather than the subsequently formed intermediates, then other cell types can specialize in consuming the intermediates. While this mechanism fo...
Microbial ecology
10.1038/S43705-022-00160-1
ISSN:2730-6151
Unravelling bovine preadipocyte differentiation and their three-dimensional cultivation for cellular agriculture
Apeksha Bharatgiri Goswami•Laurence Don Wai Luu•Joanna M. Biazik•Mark S. Rybchyn•Johannes le Coutre
Npj Science Of Food
2025
•2025/11/25
•Vol.9 No.1 p.2530
Cultured meat is an attractive concept to address environmental and ethical issues of livestock farming. Replication of conventional meat requires fat tissue, for flavour, texture, and mouthfeel. However, cultured meat production is limited by the lack of bovine adipogenic cells that are both prolif...
Biological techniquesBiotechnologyCell biologyMolecular biology
10.1038/S41538-025-00616-3
ISSN:2396-8370
Berberine attenuates choline-induced atherosclerosis by inhibiting trimethylamine and trimethylamine- N -oxide production via manipulating the gut microbiome
Xingxing Li•Chunyan Su•Zhibo Jiang•Yuxin Yang•Yue Zhang等 12 人
Npj Biofilms And Microbiomes
2021
•2021/4/16
•Vol.7 No.1 p.1-14
Trimethylamine-N-oxide (TMAO), a derivative from the gut microbiota metabolite trimethylamine (TMA), has been identified to be an independent risk factor for promoting atherosclerosis. Evidences suggest that berberine (BBR) could be used to treat obesity, diabetes and atherosclerosis, however, its m...
Health careMicrobiome
10.1038/S41522-021-00205-8
ISSN:2055-5008
Spatial genomic, biochemical and cellular mechanisms underlying meningioma heterogeneity and evolution
Calixto-Hope G. Lucas•Kanish Mirchia•Kyounghee Seo•Hinda Najem•William C. Chen等 19 人
Nature Genetics
2024
•2024/5/17
•00 p.1-13
Intratumor heterogeneity underlies cancer evolution and treatment resistance, but targetable mechanisms driving intratumor heterogeneity are poorly understood. Meningiomas are the most common primary intracranial tumors and are resistant to all medical therapies, and high-grade meningiomas have sign...
CNS cancerEpigeneticsPersonalized medicineTranscriptomics
10.1038/S41588-024-01747-1
ISSN:1061-4036
Deep convolutional neural networks for accurate somatic mutation detection
Sayed Mohammad Ebrahim Sahraeian•Ruolin Liu•Bayo Lau•Karl Podesta•Marghoob Mohiyuddin等 6 人
Nature Communications
2019
•2019/3/4
•Vol.10 No.1 p.1-10
Accurate detection of somatic mutations is still a challenge in cancer analysis. Here we present NeuSomatic, the first convolutional neural network approach for somatic mutation detection, which significantly outperforms previous methods on different sequencing platforms, sequencing strategies, and ...
Cancer genomicsGenomicsMachine learning
10.1038/S41467-019-09027-X
ISSN:2041-1723
Fast and accurate metagenotyping of the human gut microbiome with GT-Pro
Shi Zhou Jason•Dimitrov Boris•Zhao Chunyu•Nayfach Stephen•Pollard Katherine S.
Nature Biotechnology
2021
•2021/12/23
•00 p.1-10
Single nucleotide polymorphisms (SNPs) in metagenomics are used to quantify population structure, track strains and identify genetic determinants of microbial phenotypes. However, existing alignment-based approaches for metagenomic SNP detection require high-performance computing and enough read cov...
Genome informaticsSoftware
10.1038/S41587-021-01102-3
ISSN:1087-0156
A high-quality chromosome-scale genome assembly of the wild sorghum (Sorghum virgatum)
Xiaojian Fang•Leina Zhou•Zhongwei Lin
Scientific Data
2025
•2025/9/30
•Vol.12 No.1 p.1-5
Sorghum virgatum (Sv) is a wild subspecies of sorghum (Sorghum bicolor ssp. Verticilliflorum (L.) Moench). We employed Hi-C sequencing and HiFi technology in this study, successfully assembly a high-quality genome for Sv. This assembled genome is 795 Mb in total and scaffold N50 is 62.47 Mb. Within ...
Computational biology and bioinformaticsPlant sciences
10.1038/S41597-025-05907-8
ISSN:2052-4463
Comparative pathogenicity of SARS-CoV-2 Omicron subvariants including BA.1, BA.2, and BA.5
Tomokazu Tamura•Daichi Yamasoba•Yoshitaka Oda•Jumpei Ito•Tomoko Kamasaki等 28 人
Communications Biology
2023
•2023/7/24
•Vol.6 No.1 p.1-12
The unremitting emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants necessitates ongoing control measures. Given its rapid spread, the new Omicron subvariant BA.5 requires urgent characterization. Here, we comprehensively analyzed BA.5 with the other Omicron variants B...
PathogensSARS-CoV-2Virology
10.1038/S42003-023-05081-W
ISSN:2399-3642
Detecting and phasing minor single-nucleotide variants from long-read sequencing data
Zhixing Feng•Jose C. Clemente•Brandon Wong•Eric E. Schadt
Nature Communications
2021
•2021/5/24
•Vol.12 No.1 p.1-13
Cellular genetic heterogeneity is common in many biological conditions including cancer, microbiome, and co-infection of multiple pathogens. Detecting and phasing minor variants play an instrumental role in deciphering cellular genetic heterogeneity, but they are still difficult tasks because of tec...
Computational biology and bioinformaticsNext-generation sequencingStatistical methods
10.1038/S41467-021-23289-4
ISSN:2041-1723
Candida albicans promotes tooth decay by inducing oral microbial dysbiosis
Qian Du•Biao Ren•Jinzhi He•Xian Peng•Qiang Guo等 12 人
The Isme Journal
2020
•2020/11/4
•Vol.15 No.3 p.894-908
Candida albicans has been detected in root carious lesions. The current study aimed to explore the action of this fungal species on the microbial ecology and the pathogenesis of root caries. Here, by analyzing C. albicans in supragingival dental plaque collected from root carious lesions and sound r...
BacteriaBiofilmsFungi
10.1038/S41396-020-00823-8
ISSN:1751-7362
Pentatricopeptide repeat poly(A) binding protein KPAF4 stabilizes mitochondrial mRNAs in Trypanosoma brucei
Mikhail V. Mesitov•Tian Yu•Takuma Suematsu•Francois M. Sement•Liye Zhang等 8 人
Nature Communications
2019
•2019/1/11
•Vol.10 No.1 p.1-15
In Trypanosoma brucei, most mitochondrial mRNAs undergo editing, and 3′ adenylation and uridylation. The internal sequence changes and terminal extensions are coordinated: pre-editing addition of the short (A) tail protects the edited transcript against 3′-5′ degradation, while post-editing A/U-tail...
Parasite biologyRNARNA decayRNA editing
10.1038/S41467-018-08137-2
ISSN:2041-1723
Bridging of host-microbiota tryptophan partitioning by the serotonin pathway in fungal pneumonia
Giorgia Renga•Fiorella D’Onofrio•Marilena Pariano•Roberta Galarini•Carolina Barola等 17 人
Nature Communications
2023
•2023/9/16
•Vol.14 No.1 p.1-21
The aromatic amino acid L-tryptophan (Trp) is essentially metabolized along the host and microbial pathways. While much is known about the role played by downstream metabolites of each pathways in intestinal homeostasis, their role in lung immune homeostasis is underappreciated. Here we have examine...
Cystic fibrosisFungal infectionMicrobiome
10.1038/S41467-023-41536-8
ISSN:2041-1723
Fecal microbial transplantation and fiber supplementation in patients with severe obesity and metabolic syndrome: a randomized double-blind, placebo-controlled phase 2 trial
Valentin Mocanu•Zhengxiao Zhang•Edward C. Deehan•Dina H. Kao•Naomi Hotte等 10 人
Nature Medicine
2021
•2021/7/5
•00 p.1-8
Fecal microbial transplantation (FMT) from lean donors to patients with obesity has been associated with metabolic benefits, yet results so far have been inconsistent. In this study, we tested the application of daily fiber supplementation as an adjunct to FMT therapy to modulate cardiometabolic out...
Metabolic syndromeMicrobiome
10.1038/S41591-021-01399-2
ISSN:1078-8956
Custom microfluidic chip design enables cost-effective three-dimensional spatiotemporal transcriptomics with a wide field of view
Junjie Zhu•Kun Pang•Beiyu Hu•Ruiqiao He•Ning Wang等 8 人
Nature Genetics
2024
•2024/9/10
•00 p.1-12
Spatial transcriptomic techniques offer unprecedented insights into the molecular organization of complex tissues. However, integrating cost-effectiveness, high throughput, a wide field of view and compatibility with three-dimensional (3D) volumes has been challenging. Here we introduce microfluidic...
Gene expressionGene expression analysis
10.1038/S41588-024-01906-4
ISSN:1061-4036
Population-wide DNA methylation polymorphisms at single-nucleotide resolution in 207 cotton accessions reveal epigenomic contributions to complex traits
Ting Zhao•Xueying Guan•Yan Hu•Ziqian Zhang•Han Yang等 30 人
Cell Research
2024
•2024/10/17
•00 p.1-14
DNA methylation plays multiple regulatory roles in crop development. However, the relationships of methylation polymorphisms with genetic polymorphisms, gene expression, and phenotypic variation in natural crop populations remain largely unknown. Here, we surveyed high-quality methylomes, transcript...
DNA methylationPlant molecular biology
10.1038/S41422-024-01027-X
ISSN:1748-7838
The relationship between the gut microbiome and the risk of respiratory infections among newborns
Moroishi Yuka•Gui Jiang•Hoen Anne G.•Morrison Hilary G.•Baker Emily R.等 10 人
Communications Medicine
2022
•2022/7/14
•Vol.2 No.1 p.1-8
Emerging evidence points to a critical role of the developing gut microbiome in immune maturation and infant health; however, prospective studies are lacking. We examined the occurrence of infections and associated symptoms during the first year of life in relation to the infant gut microbiome at si...
BiomarkersEpidemiologyMicrobiomePaediatric research
10.1038/S43856-022-00152-1
ISSN:2730-664X
Dynamic O-GlcNAcylation governs long-range chromatin interactions in V(D)J recombination during early B-cell development
Bong Chan Jeon•Yu-Ji Kim•Ae Kyung Park•Mi-Ran Song•Ki Myeong Na等 12 人
Cellular & Molecular Immunology
2024
•2024/12/3
•00 p.1-15
V(D)J recombination secures the production of functional immunoglobulin (Ig) genes and antibody diversity during the early stages of B-cell development through long-distance interactions mediated by cis-regulatory elements and trans-acting factors. O-GlcNAcylation is a dynamic and reversible posttra...
AntibodiesVDJ recombination
10.1038/S41423-024-01236-9
ISSN:2042-0226
Long-lasting memory of jasmonic acid-dependent immunity requires DNA demethylation and ARGONAUTE1
Wilkinson S. W.•Hannan Parker A.•Muench A.•Wilson R. S.•Hooshmand K.等 15 人
Nature Plants
2023
•2023/1/5
•Vol.9 No.1 p.81-95
Stress can have long-lasting impacts on plants. Here we report the long-term effects of the stress hormone jasmonic acid (JA) on the defence phenotype, transcriptome and DNA methylome of Arabidopsis. Three weeks after transient JA signalling, 5-week-old plants retained induced resistance (IR) agains...
BioticDNA methylationHerbivoryJasmonic acidMicrobe
10.1038/S41477-022-01313-9
ISSN:2055-0278
Characterization and structural basis of a lethal mouse-adapted SARS-CoV-2
Sun Shihui•Gu Hongjing•Cao Lei•Chen Qi•Ye Qing等 30 人
Nature Communications
2021
•2021/9/27
•Vol.12 No.1 p.1-16
There is an urgent need for animal models to study SARS-CoV-2 pathogenicity. Here, we generate and characterize a novel mouse-adapted SARS-CoV-2 strain, MASCp36, that causes severe respiratory symptoms, and mortality. Our model exhibits age- and gender-related mortality akin to severe COVID-19. Deep...
PathogensSARS-CoV-2Structural biologyVirus–host interactions
10.1038/S41467-021-25903-X
ISSN:2041-1723
Pervasive population genomic consequences of genome duplication in Arabidopsis arenosa
Patrick Monnahan•Filip Kolář•Pierre Baduel•Christian Sailer•Jordan Koch等 17 人
Nature Ecology & Evolution
2019
•2019/2/25
•Vol.3 No.3 p.457-468
Ploidy-variable species allow direct inference of the effects of chromosome copy number on fundamental evolutionary processes. While an abundance of theoretical work suggests polyploidy should leave distinct population genomic signatures, empirical data remains sparse. We sequenced ~300 individuals ...
Evolutionary geneticsPlant evolutionPopulation genetics
10.1038/S41559-019-0807-4
ISSN:2397-334X
Mutated lncRNA increase the risk of type 2 diabetes by promoting β cell dysfunction and insulin resistance
Guo Wan-Hui•Guo Qi•Liu Ya-Lin•Yan Dan-Dan•Jin Li等 9 人
Cell Death & Disease
2022
•2022/10/27
•Vol.13 No.10 p.1-14
Islet β cell dysfunction and insulin resistance are the main pathogenesis of type 2 diabetes (T2D), but the mechanism remains unclear. Here we identify a rs3819316 C > T mutation in lncRNA Reg1cp mainly expressed in islets associated with an increased risk of T2D. Analyses in 16,113 Chinese adult...
Long non-coding RNAsMechanisms of diseaseType 2 diabetes
10.1038/S41419-022-05348-W
ISSN:2041-4889
Engineered triple inhibitory receptor resistance improves anti-tumor CAR-T cell performance via CD56
Fan Zou•Lijuan Lu•Jun Liu•Baijin Xia•Wanying Zhang等 14 人
Nature Communications
2019
•2019/9/11
•Vol.10 No.1 p.1-14
The inhibitory receptors PD-1, Tim-3, and Lag-3 are highly expressed on tumor-infiltrating lymphocytes and compromise their antitumor activity. For efficient cancer immunotherapy, it is important to prevent chimeric antigen receptor T (CAR-T)-cell exhaustion. Here we downregulate these three checkpo...
Cancer therapyCytotoxic T cellsImmunotherapy
10.1038/S41467-019-11893-4
ISSN:2041-1723
Activation of AMPK by GLP-1R agonists mitigates Alzheimer-related phenotypes in transgenic mice
Yun Zhang•Huaqiu Chen•Yijia Feng•Mingjing Liu•Zhi Lu等 17 人
Nature Aging
2025
•2025/5/20
•00 p.1-17
Individuals with type 2 diabetes mellitus have an increased risk of developing Alzheimer’s disease (AD). GLP-1 receptor agonists (GLP-1RAs) are used for glycemic control in diabetes and show potential neuroprotective properties, but their effects on AD and the underlying mechanisms are not well unde...
Alzheimer's diseaseDrug discovery
10.1038/S43587-025-00869-3
ISSN:2662-8465
MetaCC allows scalable and integrative analyses of both long-read and short-read metagenomic Hi-C data
Yuxuan Du•Fengzhu Sun
Nature Communications
2023
•2023/10/6
•Vol.14 No.1 p.1-12
Metagenomic Hi-C (metaHi-C) can identify contig-to-contig relationships with respect to their proximity within the same physical cell. Shotgun libraries in metaHi-C experiments can be constructed by next-generation sequencing (short-read metaHi-C) or more recent third-generation sequencing (long-rea...
Computational modelsComputational platforms and environmentsMetagenomicsSoftwareStatistical methods
10.1038/S41467-023-41209-6
ISSN:2041-1723
Multi-omic analysis reveals significantly mutated genes and DDX3X as a sex-specific tumor suppressor in cutaneous melanoma
Rached Alkallas•Mathieu Lajoie•Dan Moldoveanu•Karen Vo Hoang•Philippe Lefrançois等 12 人
Nature Cancer
2020
•2020/6/22
•Vol.1 No.6 p.635-652
The high background tumor mutation burden in cutaneous melanoma limits the ability to identify significantly mutated genes (SMGs) that drive this cancer. To address this, we performed a mutation significance study of over 1,000 melanoma exomes, combined with a multi-omic analysis of 470 cases from T...
CancerCancer genomicsMelanoma
10.1038/S43018-020-0077-8
ISSN:2662-1347
A soybean cyst nematode suppresses microbial plant symbionts using a lipochitooligosaccharide-hydrolysing enzyme
Wei Chen•Di Wang•Shaoyong Ke•Yangrong Cao•Wensheng Xiang等 7 人
Nature Microbiology
2024
•2024/6/17
•00 p.1-13
Cyst nematodes are the most damaging species of plant-parasitic nematodes. They antagonize the colonization of beneficial microbial symbionts that are important for nutrient acquisition of plants. The molecular mechanism of the antagonism, however, remains elusive. Here, through biochemical combined...
Arbuscular mycorrhizaParasitismRhizobial symbiosis
10.1038/S41564-024-01727-5
ISSN:2058-5276
Haplotype-resolved genome analyses of a heterozygous diploid potato
Qian Zhou•Dié Tang•Wu Huang•Zhongmin Yang•Yu Zhang等 12 人
Nature Genetics
2020
•2020/9/28
•Vol.52 No.10 p.1018-1023
Potato (Solanum tuberosum L.) is the most important tuber crop worldwide. Efforts are underway to transform the crop from a clonally propagated tetraploid into a seed-propagated, inbred-line-based hybrid, but this process requires a better understanding of potato genome. Here, we report the 1.67-Gb ...
GeneticsGenomicsPlant breedingPlant geneticsSequencing
10.1038/S41588-020-0699-X
ISSN:1061-4036
Evolution of placental invasion and cancer metastasis are causally linked
Kshitiz•Junaid Afzal•Jamie D. Maziarz•Archer Hamidzadeh•Cong Liang等 16 人
Nature Ecology & Evolution
2019
•2019/11/25
•Vol.3 No.12 p.1743-1753
Among mammals, placental invasion is correlated with vulnerability to malignancy. Animals with more invasive placentation (for example, humans) are more vulnerable to malignancy. To explain this correlation, we propose the hypothesis of ‘Evolved Levels of Invasibility’ proposing that the evolution o...
Cancer genomicsEvolutionary developmental biology
10.1038/S41559-019-1046-4
ISSN:2397-334X
Triticum population sequencing provides insights into wheat adaptation
Yao Zhou•Xuebo Zhao•Yiwen Li•Jun Xu•Aoyue Bi等 17 人
Nature Genetics
2020
•2020/10/26
•Vol.52 No.12 p.1412-1422
Bread wheat expanded its habitat from a core area of the Fertile Crescent to global environments within ~10,000 years. The genetic mechanisms of this remarkable evolutionary success are not well understood. By whole-genome sequencing of populations from 25 subspecies within the genera Triticum and A...
Genome informaticsGenomicsPlant geneticsPopulation genetics
10.1038/S41588-020-00722-W
ISSN:1061-4036
Nanoparticle delivery of a prodrug-activating bacterial enzyme leads to anti-tumor responses
Sebastian G. Huayamares•Liming Lian•Regina Rab•Yuning Hou•Afsane Radmand等 20 人
Nature Communications
2025
•2025/4/12
•Vol.16 No.1 p.1-14
Most cancer patients diagnosed with late-stage head and neck squamous cell carcinoma are treated with chemoradiotherapy, which can lead to toxicity. One potential alternative is tumor-limited conversion of a prodrug into its cytotoxic form. We reason this could be achieved by transient and tumor-spe...
Drug deliveryHead and neck cancerHigh-throughput screeningNanotechnology in cancer
10.1038/S41467-025-58548-1
ISSN:2041-1723
Coupling chemical mutagenesis to next generation sequencing for the identification of drug resistance mutations in Leishmania
Arijit Bhattacharya•Philippe Leprohon•Sophia Bigot•Prasad Kottayil Padmanabhan•Angana Mukherjee等 10 人
Nature Communications
2019
•2019/12/9
•Vol.10 No.1 p.1-14
Current genome-wide screens allow system-wide study of drug resistance but detecting small nucleotide variants (SNVs) is challenging. Here, we use chemical mutagenesis, drug selection and next generation sequencing to characterize miltefosine and paromomycin resistant clones of the parasite Leishman...
Antimicrobial resistanceKinasesParasite genomicsParasitic infection
10.1038/S41467-019-13344-6
ISSN:2041-1723
Microbial abundance, activity and population genomic profiling with mOTUs2
Alessio Milanese•Daniel R Mende•Lucas Paoli•Guillem Salazar•Hans-Joachim Ruscheweyh等 18 人
Nature Communications
2019
•2019/3/4
•Vol.10 No.1 p.1-11
Metagenomic sequencing has greatly improved our ability to profile the composition of environmental and host-associated microbial communities. However, the dependency of most methods on reference genomes, which are currently unavailable for a substantial fraction of microbial species, introduces est...
MicrobiomeSoftware
10.1038/S41467-019-08844-4
ISSN:2041-1723
Integrated omics in Drosophila uncover a circadian kinome
Chenwei Wang•Ke Shui•Shanshan Ma•Shaofeng Lin•Ying Zhang等 12 人
Nature Communications
2020
•2020/6/1
•Vol.11 No.1 p.1-15
Most organisms on the earth exhibit circadian rhythms in behavior and physiology, which are driven by endogenous clocks. Phosphorylation plays a central role in timing the clock, but how this contributes to overt rhythms is unclear. Here we conduct phosphoproteomics in conjunction with transcriptomi...
Computational biology and bioinformaticsGeneticsSystems biology
10.1038/S41467-020-16514-Z
ISSN:2041-1723
Schistosoma mansoni treatment reduces HIV entry into cervical CD4+ T cells and induces IFN-I pathways
Sergey Yegorov•Vineet Joag•Ronald M. Galiwango•Sara V. Good•Juliet Mpendo等 10 人
Nature Communications
2019
•2019/5/24
•Vol.10 No.1 p.1-12
Schistosoma mansoni (Sm) infection has been linked with an increased risk of HIV acquisition in women. Therefore, defining the mechanism(s) by which Sm alters HIV susceptibility might lead to new HIV prevention strategies. Here, we analyze the impact of standard Sm therapy in HIV-uninfected Sm+ Ugan...
Clinical microbiologyHIV infectionsMucosal immunologyParasitic infection
10.1038/S41467-019-09900-9
ISSN:2041-1723
Nanoparticle hydrogel system delivery of miR-494-3p to improve tendon healing by targeting CXXC4
Gu Heng Wang•Lei Wang•Lei Sheng•Hua Jian Shan•Wei Gang Zhu等 9 人
Gene Therapy
2025
•2025/7/9
•00 p.1-10
Due to the poor healing capacity of tendons, the healing process is slow, with a risk of re-rupture post-injury. In this study, we found that miR-494-3p was one of the miRNAs with significant expression differences after tendon injury by sequencing in the rat Achilles tendon injury model. There...
Drug deliveryTrauma
10.1038/S41434-025-00543-8
ISSN:0969-7128
Cas9 activates the p53 pathway and selects for p53-inactivating mutations
Oana M. Enache•Veronica Rendo•Mai Abdusamad•Daniel Lam•Desiree Davison等 16 人
Nature Genetics
2020
•2020/5/18
•Vol.52 No.7 p.662-668
Cas9 is commonly introduced into cell lines to enable CRISPR–Cas9-mediated genome editing. Here, we studied the genetic and transcriptional consequences of Cas9 expression itself. Gene expression profiling of 165 pairs of human cancer cell lines and their Cas9-expressing derivatives revealed upregul...
CancerGenetics
10.1038/S41588-020-0623-4
ISSN:1061-4036
Revisiting the initial steps of sexual development in the malaria parasite Plasmodium falciparum
Cristina Bancells•Oriol Llorà-Batlle•Asaf Poran•Christopher Nötzel•Núria Rovira-Graells等 8 人
Nature Microbiology
2018
•2018/11/26
•Vol.4 No.1 p.144-154
Human to vector transmission of malaria requires that some blood-stage parasites abandon asexual growth and convert into non-replicating sexual forms called gametocytes. The initial steps of gametocytogenesis remain largely uncharacterized. Here, we study this part of the malaria life cycle in Plasm...
Cell-cycle exitEpigeneticsMalariaParasite biology
10.1038/S41564-018-0291-7
ISSN:2058-5276
Single-component multilayered self-assembling nanoparticles presenting rationally designed glycoprotein trimers as Ebola virus vaccines
Linling He•Anshul Chaudhary•Xiaohe Lin•Cindy Sou•Tanwee Alkutkar等 13 人
Nature Communications
2021
•2021/5/11
•Vol.12 No.1 p.1-18
Ebola virus (EBOV) glycoprotein (GP) can be recognized by neutralizing antibodies (NAbs) and is the main target for vaccine design. Here, we first investigate the contribution of the stalk and heptad repeat 1-C (HR1C) regions to GP metastability. Specific stalk and HR1C modifications in a mucin-dele...
Humoral immunityProtein vaccinesX-ray crystallography
10.1038/S41467-021-22867-W
ISSN:2041-1723
Rare jackpot individuals drive rapid adaptation in Threespine Stickleback
Alexander Kwakye•Kerry Reid•Matthew A. Wund•David C. Heins•Michael A. Bell等 6 人
Nature Communications
2026
•2026/3/30
0Recombination has long been considered the primary mechanism to bring beneficial alleles together, which can increase the speed of adaptation from standing genetic variation. Recombination is fundamental to the transporter hypothesis proposed to explain precise parallel adaptation in Threespine Stic...
Evolutionary biologyEvolutionary geneticsMolecular evolution
10.1038/S41467-026-71236-Y
ISSN:2041-1723
Determinants of genetic variation across eco-evolutionary scales in pinnipeds
Claire R. Peart•Sergio Tusso•Saurabh D. Pophaly•Fidel Botero-Castro•Chi-Chih Wu等 22 人
Nature Ecology & Evolution
2020
•2020/6/8
•Vol.4 No.8 p.1095-1104
The effective size of a population (Ne), which determines its level of neutral variability, is a key evolutionary parameter. Ne can substantially depart from census sizes of present-day breeding populations (NC) as a result of past demographic changes, variation in life-history traits and selection ...
BiodiversityConservation biologyEcological geneticsEvolutionary ecologyPopulation genetics
10.1038/S41559-020-1215-5
ISSN:2397-334X
Rapid transmission and tight bottlenecks constrain the evolution of highly transmissible SARS-CoV-2 variants
Bendall Emily E.•Callear Amy P.•Getz Amy•Goforth Kendra•Edwards Drew等 8 人
Nature Communications
2023
•2023/1/17
•Vol.14 No.1 p.1-7
Transmission bottlenecks limit the spread of novel mutations and reduce the efficiency of selection along a transmission chain. While increased force of infection, receptor binding, or immune evasion may influence bottleneck size, the relationship between transmissibility and the transmission bottle...
SARS-CoV-2Viral genetics
10.1038/S41467-023-36001-5
ISSN:2041-1723
rMATS-turbo: an efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data
Yuanyuan Wang•Zhijie Xie•Eric Kutschera•Jenea I. Adams•Kathryn E. Kadash-Edmondson等 6 人
Nature Protocols
2024
•2024/2/23
•00 p.1-22
Pre-mRNA alternative splicing is a prevalent mechanism for diversifying eukaryotic transcriptomes and proteomes. Regulated alternative splicing plays a role in many biological processes, and dysregulated alternative splicing is a feature of many human diseases. Short-read RNA sequencing (RNA-seq) is...
BioinformaticsSoftwareTranscriptomics
10.1038/S41596-023-00944-2
ISSN:1754-2189
Sequence and chemical specificity define the functional landscape of intrinsically disordered regions
Iris Langstein-Skora•Andrea Schmid•Frauke Huth•Drin Shabani•Lorenz Spechtenhauser等 21 人
Nature Cell Biology
2026
•2026/2/12
•Vol.28 No.2 p.323-337
Intrinsically disordered regions (IDRs) pervasively engage in essential molecular functions, yet they are often poorly conserved as assessed by sequence alignment. To explore the seeming paradox of how sequence variability is compatible with persistent function, we examined the functional determinan...
BiochemistryChromatin remodellingChromosomesMolecular biophysics
10.1038/S41556-025-01867-8
ISSN:1465-7392
Memory regulatory T cells reprogram into protective TFH cell-like effectors in recurrent malaria
Nana Appiah Essel Charles-Chess•Anthony A. Ruberto•Carson Bowers•Clyde Schmidt-Silva•Nyamekye Obeng-Adjei等 12 人
Nature Immunology
2026
•2026/6/22
•00 p.1-15
Although people living in malaria-endemic areas experience repeated infections with Plasmodium, the role of regulatory T (Treg) cells in recurrent malaria remains poorly understood. During a primary infection with Plasmodium, Treg cells suppress protective immunity by inhibiting germinal center (GC)...
Epigenetics in immune cellsImmunological memoryMalaria
10.1038/S41590-026-02537-Z
ISSN:1529-2908
Ecology and evolution of chlamydial symbionts of arthropods
Halter Tamara•Köstlbacher Stephan•Collingro Astrid•Sixt Barbara S.•Tönshoff Elena R.等 8 人
Isme Communications
2022
•2022/5/24
•Vol.2 No.1 p.1-11
The phylum Chlamydiae consists of obligate intracellular bacteria including major human pathogens and diverse environmental representatives. Here we investigated the Rhabdochlamydiaceae, which is predicted to be the largest and most diverse chlamydial family, with the few described members known to ...
Bacterial evolutionBacterial genomicsSymbiosis
10.1038/S43705-022-00124-5
ISSN:2730-6151
STRaM: A genetic framework for improved cell product provenance for research and clinical translations
Binglin Li•Chi Le•Wen Lei•Yingqi Zhou•Ying Zhang等 23 人
Communications Biology
2025
•2025/8/15
•Vol.8 No.1 p.1-20
Multiple assessment checks are required to handle the increasingly complex engineered-cell and cell-line provenance. To manage the biosafety and efficacy demands, we developed a bioinformatic pipeline for de novo profiling of short tandem repeats and mutations (STRaM) to identify and track homologou...
Cancer genomicsPersonalized medicine
10.1038/S42003-025-08547-1
ISSN:2399-3642
Pan-cancer pervasive upregulation of 3′ UTR splicing drives tumourigenesis
Chan Jia Jia•Zhang Bin•Chew Xiao Hong•Salhi Adil•Kwok Zhi Hao等 48 人
Nature Cell Biology
2022
•2022/5/26
•00 p.1-12
Most mammalian genes generate messenger RNAs with variable untranslated regions (UTRs) that are important post-transcriptional regulators. In cancer, shortening at 3′ UTR ends via alternative polyadenylation can activate oncogenes. However, internal 3′ UTR splicing remains poorly understood as splic...
CancerGene regulatory networksRNA splicingSystems analysis
10.1038/S41556-022-00913-Z
ISSN:1465-7392
A deep learning and large language hybrid workflow for omics interpretation
Dachao Tang•Chi Zhang•Weizhi Zhang•Funian Lu•Leming Xiao等 18 人
Nature Biomedical Engineering
2026
•2026/1/8
•00 p.1-22
Profiling molecular panorama from massive omics data identifies regulatory networks in cells but requires mechanistic interpretation and experimental follow up. Here we combine deep learning and large language model reasoning to develop a hybrid workflow for omics interpretation, called LyMOI. LyMOI...
AutophagyBioinformaticsData miningMachine learningTargeted therapies
10.1038/S41551-025-01576-5
ISSN:2157-846X
Adaptive laboratory evolution in S. cerevisiae highlights role of transcription factors in fungal xenobiotic resistance
Ottilie Sabine•Luth Madeline R.•Hellemann Erich•Goldgof Gregory M.•Vigil Eddy等 32 人
Communications Biology
2022
•2022/2/11
•Vol.5 No.1 p.1-14
In vitro evolution and whole genome analysis were used to comprehensively identify the genetic determinants of chemical resistance in Saccharomyces cerevisiae. Sequence analysis identified many genes contributing to the resistance phenotype as well as numerous amino acids in potential targets that m...
Evolutionary biologyTarget identification
10.1038/S42003-022-03076-7
ISSN:2399-3642
Defining the biogeographical map and potential bacterial translocation of microbiome in human ‘surface organs’
Jun-Jun She•Wei-Xin Liu•Xiao-Ming Ding•Gang Guo•Jing Han等 16 人
Nature Communications
2024
•2024/1/10
•Vol.15 No.1 p.1-12
The microbiome in a specific human organ has been well-studied, but few reports have investigated the multi-organ microbiome as a whole. Here, we aim to analyse the intra-individual inter-organ and intra-organ microbiome in deceased humans. We collected 1608 samples from 53 sites of 7 surface organs...
Clinical microbiologyMetagenomicsMicrobial ecologyMicrobiome
10.1038/S41467-024-44720-6
ISSN:2041-1723
Characterization of the genomic landscape and actionable mutations in Chinese breast cancers by clinical sequencing
Guan-Tian Lang•Yi-Zhou Jiang•Jin-Xiu Shi•Fan Yang•Xiao-Guang Li等 28 人
Nature Communications
2020
•2020/11/10
•Vol.11 No.1 p.1-13
The remarkable advances in next-generation sequencing technology have enabled the wide usage of sequencing as a clinical tool. To promote the advance of precision oncology for breast cancer in China, here we report a large-scale prospective clinical sequencing program using the Fudan-BC panel, and c...
Breast cancerCancer genetics
10.1038/S41467-020-19342-3
ISSN:2041-1723
Functional synapses between neurons and small cell lung cancer
Vignesh Sakthivelu•Anna Schmitt•Franka Odenthal•Kristiano Ndoci•Marian Touet等 75 人
Nature
2025
•2025/9/10
•00 p.1-11
Small cell lung cancer (SCLC) is a highly aggressive type of lung cancer, characterized by rapid proliferation, early metastatic spread, frequent early relapse and a high mortality rate1–3. Recent evidence has suggested that innervation has an important role in the development and progression o...
Cancer genomicsCancer microenvironmentNeuroscienceSmall-cell lung cancerTargeted therapies
10.1038/S41586-025-09434-9
ISSN:0028-0836
Community use of oral antibiotics transiently reprofiles the intestinal microbiome in young Bangladeshi children
Andrew Baldi•Sabine Braat•Mohammed Imrul Hasan•Cavan Bennett•Marilou Barrios等 18 人
Nature Communications
2024
•2024/8/14
•Vol.15 No.1 p.1-11
Antibiotics may alter the gut microbiome, and this is one of the mechanisms by which antimicrobial resistance may be promoted. Suboptimal antimicrobial stewardship in Asia has been linked to antimicrobial resistance. We aim to examine the relationship between oral antibiotic use and composition and ...
Antimicrobial resistanceEpidemiologyMicrobiota
10.1038/S41467-024-51326-5
ISSN:2041-1723
Response of iPSC-derived neurons from individuals with treatment-resistant depression to (2 R,6 R)-hydroxynorketamine and reelin: an exploratory study
Jenessa N. Johnston•Peixiong Yuan•Bashkim Kadriu•Nirmala Akula•Brandi Quintanilla等 14 人
Translational Psychiatry
2025
•2025/11/18
0Treatment-resistant depression (TRD) is associated with worse clinical outcomes and longer course of illness. However, TRD is more difficult to model in animal phenotypes, suggesting that other experimental and translational models must be considered to properly address and research novel therapeuti...
DepressionDrug discoveryStem cells
10.1038/S41398-025-03724-6
ISSN:2158-3188
Phyllosphere microbiome induces host metabolic defence against rice false-smut disease
Liu Xiaoyu•Matsumoto Haruna•Lv Tianxing•Zhan Chengfang•Fang Hongda等 15 人
Nature Microbiology
2023
•2023/5/4
•00 p.1-15
Mutualistic interactions between host plants and their microbiota have the potential to provide disease resistance. Most research has focused on the rhizosphere, but it is unclear how the microbiome associated with the aerial surface of plants protects against infection. Here we identify a metabolic...
Applied microbiologyMicrobiologyMicrobiome
10.1038/S41564-023-01379-X
ISSN:2058-5276
Genomic epidemiology reveals geographical clustering of multidrug-resistant Escherichia coli ST131 associated with bacteraemia in Wales
Rhys T. White•Matthew J. Bull•Clare R. Barker•Julie M. Arnott•Mandy Wootton等 12 人
Nature Communications
2024
•2024/2/14
•Vol.15 No.1 p.1-10
Antibiotic resistance is a significant global public health concern. Uropathogenic Escherichia coli sequence type (ST)131, a widely prevalent multidrug-resistant clone, is frequently associated with bacteraemia. This study investigates third-generation cephalosporin resistance in bloodstream infecti...
Bacterial evolutionEpidemiologyPhylogeneticsPhylogeny
10.1038/S41467-024-45608-1
ISSN:2041-1723
Intestinal fungal signatures and their impact on immune checkpoint inhibitor efficacy: a multi-cohort meta-analysis
Lei Zhang•Ding-Ding Zhou•Jia Feng•Zhi-Jun Liao•Xian-Long Shu等 11 人
Npj Biofilms And Microbiomes
2025
•2025/9/26
•Vol.11 No.1 p.1-13
Gut microbiota influence on the effectiveness of immune checkpoint inhibitors (ICIs), but research on fungi—an essential component of the microbiome—has been limited. This multi-cohort meta-analysis of 976 fecal metagenomes across 8 cohorts, representing melanoma, non-small cell lung cancer (NSCLC),...
Clinical microbiologyMetagenomicsMicrobiota
10.1038/S41522-025-00827-2
ISSN:2055-5008
Fungal community composition predicts forest carbon storage at a continental scale
Mark A. Anthony•Leho Tedersoo•Bruno De Vos•Luc Croisé•Henning Meesenburg等 32 人
Nature Communications
2024
•2024/3/16
•Vol.15 No.1 p.1-13
Forest soils harbor hyper-diverse microbial communities which fundamentally regulate carbon and nutrient cycling across the globe. Directly testing hypotheses on how microbiome diversity is linked to forest carbon storage has been difficult, due to a lack of paired data on microbiome diversity and i...
Ecosystem ecologyMicrobial ecologyPlant symbiosis
10.1038/S41467-024-46792-W
ISSN:2041-1723
Tyrosine-protein kinase Yes controls endothelial junctional plasticity and barrier integrity by regulating VE-cadherin phosphorylation and endocytosis
Jin Yi•Ding Yindi•Richards Mark•Kaakinen Mika•Giese Wolfgang等 24 人
Nature Cardiovascular Research
2022
•2022/12/7
•Vol.1 No.12 p.1156-1173
Vascular endothelial (VE)-cadherin in endothelial adherens junctions is an essential component of the vascular barrier, critical for tissue homeostasis and implicated in diseases such as cancer and retinopathies. Inhibitors of Src cytoplasmic tyrosine kinase have been applied to suppress VE-cadherin...
AngiogenesisCadherinsPhosphorylation
10.1038/S44161-022-00172-Z
ISSN:2731-0590
Aged bone marrow macrophages drive systemic aging and age-related dysfunction via extracellular vesicle-mediated induction of paracrine senescence
Jing Hou•Kai-Xuan Chen•Chen He•Xiao-Xiao Li•Mei Huang等 19 人
Nature Aging
2024
•2024/9/12
•00 p.1-20
The accumulation and systemic propagation of senescent cells contributes to physiological aging and age-related pathology. However, which cell types are most susceptible to the aged milieu and could be responsible for the propagation of senescence has remained unclear. Here we found that physiologic...
AgeingEndocrine system and metabolic diseasesInflammationSenescence
10.1038/S43587-024-00694-0
ISSN:2662-8465
Investigating RNA editing in deep transcriptome datasets with REDItools and REDIportal
Claudio Lo Giudice•Marco Antonio Tangaro•Graziano Pesole•Ernesto Picardi
Nature Protocols
2020
•2020/1/29
•Vol.15 No.3 p.1098-1131
RNA editing is a widespread post-transcriptional mechanism able to modify transcripts through insertions/deletions or base substitutions. It is prominent in mammals, in which millions of adenosines are deaminated to inosines by members of the ADAR family of enzymes. A-to-I RNA editing has a plethora...
BioinformaticsHigh-throughput screeningMolecular biologyTranscriptomics
10.1038/S41596-019-0279-7
ISSN:1754-2189
Contrasting genomic epidemiology between sympatric Plasmodium falciparum and Plasmodium vivax populations
Philipp Schwabl•Flavia Camponovo•Collette Clementson•Angela M. Early•Margaret Laws等 16 人
Nature Communications
2024
•2024/9/30
•Vol.15 No.1 p.1-12
The malaria parasites Plasmodium falciparum and Plasmodium vivax differ in key biological processes and associated clinical effects, but consequences on population-level transmission dynamics are difficult to predict. This co-endemic malaria study from Guyana details important epidemiological contra...
EpidemiologyMalariaMicrobial geneticsMolecular ecologyParasite genomics
10.1038/S41467-024-52545-6
ISSN:2041-1723
Structural insights into the assembly and evolution of a complex bacterial flagellar motor
Xueyin Feng•Shoichi Tachiyama•Jing He•Siqi Zhu•Hang Zhao等 14 人
Nature Microbiology
2026
•2026/1/9
•Vol.11 No.3 p.770-785
Knowledge of bacterial flagella has largely come from studies of the simpler motors of Escherichia coli and Salmonella enterica. However, many bacteria harbour more complex motors. The function, mechanisms and evolution associated with such auxiliary motor structures are unclear. Here we deploy stru...
Bacterial secretionBacteriology
10.1038/S41564-025-02248-5
ISSN:2058-5276
Structural variant evolution after telomere crisis
Sally M. Dewhurst•Xiaotong Yao•Joel Rosiene•Huasong Tian•Julie Behr等 9 人
Nature Communications
2021
•2021/4/7
•Vol.12 No.1 p.1-17
Telomere crisis contributes to cancer genome evolution, yet only a subset of cancers display breakage-fusion-bridge (BFB) cycles and chromothripsis, hallmarks of experimental telomere crisis identified in previous studies. We examine the spectrum of structural variants (SVs) instigated by natural te...
Cancer genomicsTelomeres
10.1038/S41467-021-21933-7
ISSN:2041-1723
EBP1 potentiates amyloid β pathology by regulating γ-secretase
Byeong-Seong Kim•Inwoo Hwang•Hyo Rim Ko•Young Kwan Kim•Hee Jin Kim等 18 人
Nature Aging
2025
•2025/1/8
•00 p.1-18
The abnormal deposition of amyloid β (Aβ), produced by proteolytic cleavage events of amyloid precursor protein involving the protease γ-secretase and subsequent polymerization into amyloid plaques, plays a key role in the neuropathology of Alzheimer’s disease (AD). Here we show that ErbB3 binding p...
AgeingAlzheimer's diseaseExperimental models of diseaseNeural ageing
10.1038/S43587-024-00790-1
ISSN:2662-8465
Rapid improvement of domestication traits in an orphan crop by genome editing
Zachary H. Lemmon•Nathan T. Reem•Justin Dalrymple•Sebastian Soyk•Kerry E. Swartwood等 8 人
Nature Plants
2018
•2018/10/1
•Vol.4 No.10 p.766-770
Genome editing holds great promise for increasing crop productivity, and there is particular interest in advancing breeding in orphan crops, which are often burdened by undesirable characteristics resembling wild relatives. We developed genomic resources and efficient transformation in the orphan So...
BioinformaticsCRISPR-Cas9 genome editingComparative genomicsNon-model organismsTransgenic organisms
10.1038/S41477-018-0259-X
ISSN:2055-0278
SerpinE1 drives a cell-autonomous pathogenic signaling in Hutchinson–Gilford progeria syndrome
Catarinella Giorgia•Nicoletti Chiara•Bracaglia Andrea•Procopio Paola•Salvatori Illari等 11 人
Cell Death & Disease
2022
•2022/8/26
•Vol.13 No.8 p.1-12
Hutchinson–Gilford progeria syndrome (HGPS) is a rare, fatal disease caused by Lamin A mutation, leading to altered nuclear architecture, loss of peripheral heterochromatin and deregulated gene expression. HGPS patients eventually die by coronary artery disease and cardiovascular alterations. Yet, h...
AtherosclerosisDNA damage responseMechanisms of diseaseSenescenceTarget identification
10.1038/S41419-022-05168-Y
ISSN:2041-4889
Impact of intensive control on malaria population genomics under elimination settings in Southeast Asia
Xue Li•Grace A. Arya•Aung Myint Thu•Jordi Landier•Daniel M. Parker等 11 人
Nature Microbiology
2026
•2026/4/13
•00 p.1-13
The malaria elimination programme in Kayin State (Myanmar) uses malaria posts for rapid detection and treatment, together with mass drug administration in high-transmission villages, which has reduced transmission by 97%. Here we examine the impact of control on parasite genomic parameters to inform...
MalariaParasite genomics
10.1038/S41564-026-02327-1
ISSN:2058-5276
Effect of nanoparticle-mediated delivery of SFRP4 siRNA for treating Dupuytren disease
Jin Rujue•Zhu Weigang•Xu Jiajun•Gu Jianhui•Deng Aidong
Gene Therapy
2022
•2022/3/28
•00 p.1-10
Dupuytren disease (DD) is a progressive fibrous proliferative disease. It invades the palmar aponeurosis and extends to the finger fascia, eventually leading to flexion contracture of the metacarpophalangeal or interphalangeal joint. At present, surgical resection and the local injection of collagen...
Gene expressionGene therapyRNAi
10.1038/S41434-022-00330-9
ISSN:0969-7128
A synthetic antibiotic class with a deeply-optimized design for overcoming bacterial resistance
Jin Feng•Youle Zheng•Wanqing Ma•Defeng Weng•Dapeng Peng等 8 人
Nature Communications
2024
•2024/7/18
•Vol.15 No.1 p.1-16
The lack of new drugs that are effective against antibiotic-resistant bacteria has caused increasing concern in global public health. Based on this study, we report development of a modified antimicrobial drug through structure-based drug design (SBDD) and modular synthesis. The optimal modified com...
AntibioticsAntimicrobial resistanceStructure-based drug design
10.1038/S41467-024-50453-3
ISSN:2041-1723
Symbiont population control by host-symbiont metabolic interaction in Symbiodiniaceae-cnidarian associations
Tingting Xiang•Erik Lehnert•Robert E. Jinkerson•Sophie Clowez•Rick G. Kim等 8 人
Nature Communications
2020
•2020/1/8
•Vol.11 No.1 p.1-9
In cnidarian-Symbiodiniaceae symbioses, algal endosymbiont population control within the host is needed to sustain a symbiotic relationship. However, the molecular mechanisms that underlie such population control are unclear. Here we show that a cnidarian host uses nitrogen limitation as a primary m...
CoevolutionMarine biologyMicrobial ecologyMolecular ecology
10.1038/S41467-019-13963-Z
ISSN:2041-1723
Immunoregulatory role of the gut microbiota in inflammatory depression
Penghong Liu•Zhifen Liu•Jizhi Wang•Junyan Wang•Mingxue Gao等 14 人
Nature Communications
2024
•2024/4/8
•Vol.15 No.1 p.1-17
Inflammatory depression is a treatment-resistant subtype of depression. A causal role of the gut microbiota as a source of low-grade inflammation remains unclear. Here, as part of an observational trial, we first analyze the gut microbiota composition in the stool, inflammatory factors and short-cha...
DepressionDiagnostic markers
10.1038/S41467-024-47273-W
ISSN:2041-1723
Selection signatures and population dynamics of transposable elements in lima bean
Daniela Lozano-Arce•Tatiana García•Laura Natalia Gonzalez-Garcia•Romain Guyot•Maria Isabel Chacón-Sánchez等 6 人
Communications Biology
2023
•2023/8/2
•Vol.6 No.1 p.1-13
The domestication process in lima bean (Phaseolus lunatus L.) involves two independent events, within the Mesoamerican and Andean gene pools. This makes lima bean an excellent model to understand convergent evolution. The mechanisms of adaptation followed by Mesoamerican and Andean landraces are lar...
Agricultural geneticsEcological geneticsEvolutionary genetics
10.1038/S42003-023-05144-Y
ISSN:2399-3642
Unique plastisphere viromes with habitat-dependent potential for modulating global methane cycle
Xue-Peng Chen•Dong Zhu•Shu-Yue Liu•Ming-Ming Sun•Mao Ye等 10 人
Nature Communications
2025
•2025/8/29
•Vol.16 No.1 p.1-19
Plastispheres, novel niches in the Anthropocene, harbor microbial communities with unique functional signatures. As the most abundant biological entity on Earth, viruses are key regulators of microbial community composition and metabolism. However, little is known about viral communities and their f...
BacteriophagesElement cyclesMicrobial ecology
10.1038/S41467-025-63215-6
ISSN:2041-1723
Rational design of uncleaved prefusion-closed trimer vaccines for human respiratory syncytial virus and metapneumovirus
Yi-Zong Lee•Jerome Han•Yi-Nan Zhang•Garrett Ward•Keegan Braz Gomes等 10 人
Nature Communications
2024
•2024/11/16
•Vol.15 No.1 p.1-25
Respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) cause human respiratory diseases and are major targets for vaccine development. In this study, we design uncleaved prefusion-closed (UFC) trimers for the fusion protein (F) of both viruses by examining mutations critical to F metasta...
Protein vaccinesVirologyX-ray crystallography
10.1038/S41467-024-54287-X
ISSN:2041-1723
Carbapenems drive the collateral resistance to ceftaroline in cystic fibrosis patients with MRSA
Maria Celeste Varela•Melanie Roch•Agustina Taglialegna•Scott W. Long•Matthew Ojeda Saavedra等 11 人
Communications Biology
2020
•2020/10/22
•Vol.3 No.1 p.1-10
Chronic airways infection with methicillin-resistant Staphylococcus aureus (MRSA) is associated with worse respiratory disease cystic fibrosis (CF) patients. Ceftaroline is a cephalosporin that inhibits the penicillin-binding protein (PBP2a) uniquely produced by MRSA. We analyzed 335 S. aureus isola...
MicrobiologyPreclinical research
10.1038/S42003-020-01313-5
ISSN:2399-3642
Unveiling novel double-negative prostate cancer subtypes through single-cell RNA sequencing analysis
Siyuan Cheng•Lin Li•Yunshin Yeh•Yingli Shi•Omar Franco等 7 人
Npj Precision Oncology
2024
•2024/8/2
•Vol.8 No.1 p.1-10
Recent advancements in single-cell RNA sequencing (scRNAseq) have facilitated the discovery of previously unrecognized subtypes within prostate cancer (PCa), offering new insights into cancer heterogeneity and progression. In this study, we integrated scRNAseq data from multiple studies, comprising ...
Prostate cancerTumour heterogeneity
10.1038/S41698-024-00667-X
ISSN:2397-768X
Context transcription factors establish cooperative environments and mediate enhancer communication
Judith F. Kribelbauer-Swietek•Olga Pushkarev•Vincent Gardeux•Katerina Faltejskova•Julie Russeil等 7 人
Nature Genetics
2024
•2024/10/3
•00 p.1-14
Many enhancers control gene expression by assembling regulatory factor clusters, also referred to as condensates. This process is vital for facilitating enhancer communication and establishing cellular identity. However, how DNA sequence and transcription factor (TF) binding instruct the formation o...
Computational biology and bioinformaticsFunctional genomicsGene regulationMolecular biology
10.1038/S41588-024-01892-7
ISSN:1061-4036
DNA damage sensitivity of SWI/SNF-deficient cells depends on TFIIH subunit p62/GTF2H1
Cristina Ribeiro-Silva•Özge Z. Aydin•Raquel Mesquita-Ribeiro•Jana Slyskova•Angela Helfricht等 9 人
Nature Communications
2018
•2018/10/4
•Vol.9 No.1 p.1-14
Mutations in SWI/SNF genes are amongst the most common across all human cancers, but efficient therapeutic approaches that exploit vulnerabilities caused by SWI/SNF mutations are currently lacking. Here, we show that the SWI/SNF ATPases BRM/SMARCA2 and BRG1/SMARCA4 promote the expression of p62/GTF2...
DNA damage responseNucleotide excision repair
10.1038/S41467-018-06402-Y
ISSN:2041-1723
ALKBH5-Mediated ITGB1 m6A Modification in Ovarian Cancer Progression and Immune Evasion
Zheng He•Dalu Wang•Weijia Zhao•Mingyue Ma•Cheng Du
Npj Precision Oncology
2025
•2025/12/9
0Ovarian cancer (OC) is the deadliest gynecologic malignancy, with immune evasion contributing to its poor prognosis. This study reveals that the m6A demethylase ALKBH5 enhances OC progression and immune escape by regulating ITGB1 expression. Using bulk and single-cell RNA sequencing, deep learning, ...
HIPPO signallingOvarian cancer
10.1038/S41698-025-01127-W
ISSN:2397-768X
Genome-wide association studies demonstrate that TASP1 contributes to increased muscle fiber diameter
Dapeng Liu•Wenlei Fan•Yaxi Xu•Simeng Yu•Wenjing Liu等 9 人
Heredity
2021
•2021/3/25
•00 p.1-9
Muscle fiber diameter is an economically important trait because it affects meat yield and quality. However, the genetic basis underlying muscle fiber diameter has not been determined. In this study, we collected THREE muscular histological phenotypes in 479 ducks from an F2 segregating population g...
Gene expressionGenome-wide association studies
10.1038/S41437-021-00425-W
ISSN:0018-067X
A multi-omics integrative network map of maize
Han Linqian•Zhong Wanshun•Qian Jia•Jin Minliang•Tian Peng等 35 人
Nature Genetics
2022
•2022/12/29
•Vol.55 No.1 p.144-153
Networks are powerful tools to uncover functional roles of genes in phenotypic variation at a system-wide scale. Here, we constructed a maize network map that contains the genomic, transcriptomic, translatomic and proteomic networks across maize development. This map comprises over 2.8 million edges...
Gene expression profilingGene regulationPlant geneticsPopulation geneticsSystems analysis
10.1038/S41588-022-01262-1
ISSN:1061-4036
Copy number deletion of PLA2G4A affects the susceptibility and clinical phenotypes of schizophrenia
Zibo Gao•Xinru Guo•Zhouyang Sun•Songyu Wu•Qianyi Wang等 8 人
Schizophrenia
2024
•2024/5/30
•Vol.10 No.1 p.1-8
Phospholipase A2(PLA2) superfamily is recognized as being involved in the pathogenesis of schizophrenia by affecting lipid homeostasis in cell membranes. We hypothesized that PLA2 gene copy number variation (CNV) may affect PLA2 enzyme expression and be associated with schizophrenia risk. This study...
Epigenetics in the nervous systemSchizophrenia
10.1038/S41537-024-00474-0
ISSN:2754-6993
Dual RNA-seq identifies human mucosal immunity protein Mucin-13 as a hallmark of Plasmodium exoerythrocytic infection
Gregory M. LaMonte•Pamela Orjuela-Sanchez•Jaeson Calla•Lawrence T. Wang•Shangzhong Li等 15 人
Nature Communications
2019
•2019/1/30
•Vol.10 No.1 p.1-13
The exoerythrocytic stage of Plasmodium infection is a critical window for prophylactic intervention. Using genome-wide dual RNA sequencing of flow-sorted infected and uninfected hepatoma cells we show that the human mucosal immunity gene, mucin-13 (MUC13), is strongly upregulated during Plasmodium ...
MalariaParasite geneticsParasite host responseRNA sequencing
10.1038/S41467-019-08349-0
ISSN:2041-1723
Wireworm (Coleoptera: Elateridae) genomic analysis reveals putative cryptic species, population structure, and adaptation to pest control
Kimberly R. Andrews•Alida Gerritsen•Arash Rashed•David W. Crowder•Silvia I. Rondon等 13 人
Communications Biology
2020
•2020/9/7
•Vol.3 No.1 p.1-13
The larvae of click beetles (Coleoptera: Elateridae), known as “wireworms,” are agricultural pests that pose a substantial economic threat worldwide. We produced one of the first wireworm genome assemblies (Limonius californicus), and investigated population structure and phylogenetic relationships ...
BiogeographyMolecular ecologyPhylogeneticsPopulation genetics
10.1038/S42003-020-01169-9
ISSN:2399-3642
Functional analysis of the human miRNome in non-small cell lung cancer unveils a novel miR-92b-3p/NOTCH3 axis that drives tumor progression
Roberto Cuttano•Miriam Kuku Afanga•Francesca Longo•Nicole Di Cillo•Valentina Melocchi等 10 人
Cell Death & Disease
2026
•2026/4/8
0Lung cancer remains the leading cause of cancer-related mortality worldwide. MicroRNAs, endogenous non-coding RNA of ~22 nucleotides, play key regulatory roles in lung cancer–related mechanisms and represent promising diagnostic and prognostic biomarkers, as well as potential therapeutic agents. How...
miRNAsNon-small-cell lung cancer
10.1038/S41419-026-08709-X
ISSN:2041-4889
Haplotype-resolved assembly of a pig genome using single-sperm sequencing
Yongchao Niu•Xinhao Fan•Yalan Yang•Jiang Li•Jinmin Lian等 9 人
Communications Biology
2024
•2024/6/18
•Vol.7 No.1 p.1-9
Single gamete cell sequencing together with long-read sequencing can reliably produce chromosome-level phased genomes. In this study, we employed PacBio HiFi and Hi-C sequencing on a male Landrace pig, coupled with single-sperm sequencing of its 102 sperm cells. A haplotype assembly method was devel...
GenomeGenomics
10.1038/S42003-024-06397-X
ISSN:2399-3642
The vaginal microbiota associates with the regression of untreated cervical intraepithelial neoplasia 2 lesions
Anita Mitra•David A. MacIntyre•George Ntritsos•Ann Smith•Konstantinos K. Tsilidis等 9 人
Nature Communications
2020
•2020/4/24
•Vol.11 No.1 p.1-13
Emerging evidence suggests associations between the vaginal microbiota (VMB) composition, human papillomavirus (HPV) infection, and cervical intraepithelial neoplasia (CIN); however, causal inference remains uncertain. Here, we use bacterial DNA sequencing from serially collected vaginal samples fro...
Cancer preventionCervical cancerMicrobiome
10.1038/S41467-020-15856-Y
ISSN:2041-1723
Tecovirimat is effective against human monkeypox virus in vitro at nanomolar concentrations
Frenois-Veyrat Gaëlle•Gallardo Franck•Gorgé Olivier•Marcheteau Elie•Ferraris Olivier等 18 人
Nature Microbiology
2022
•2022/11/7
•Vol.7 No.12 p.1951-1955
The ongoing monkeypox virus (MPXV) outbreak is the largest ever recorded outside of Africa. We isolated and sequenced a virus from the first clinical MPXV case diagnosed in France (May 2022). We report that tecovirimat (ST-246), a US Food and Drug Administration approved drug, is efficacious against...
Antiviral agentsPox virusViral infection
10.1038/S41564-022-01269-8
ISSN:2058-5276
Heritable microbiome variation is correlated with source environment in locally adapted maize varieties
Xiaoming He•Danning Wang•Yong Jiang•Meng Li•Manuel Delgado-Baquerizo等 27 人
Nature Plants
2024
•2024/3/21
•00 p.1-20
Beneficial interactions with microorganisms are pivotal for crop performance and resilience. However, it remains unclear how heritable the microbiome is with respect to the host plant genotype and to what extent host genetic mechanisms can modulate plant–microbiota interactions in the face of enviro...
AbioticPlant developmentPlant genetics
10.1038/S41477-024-01654-7
ISSN:2055-0278
Greenland melt drives continuous export of methane from the ice-sheet bed
Guillaume Lamarche-Gagnon•Jemma L. Wadham•Barbara Sherwood Lollar•Sandra Arndt•Peer Fietzek等 15 人
Nature
2019
•2019/1/2
•Vol.565 No.7737 p.73-77
Ice sheets are currently ignored in global methane budgets1,2. Although ice sheets have been proposed to contain large reserves of methane that may contribute to a rise in atmospheric methane concentration if released during periods of rapid ice retreat3,4, no data exist on the current methane footp...
AttributionCarbon cycleCryospheric scienceHydrology
10.1038/S41586-018-0800-0
ISSN:0028-0836
Upregulation of CPNE7 in mesenchymal stromal cells promotes oral squamous cell carcinoma metastasis through the NF-κB pathway
Ji Xiaoli•Sun Tianyong•Xie Shang•Qian Hua•Song lixiang等 8 人
Cell Death Discovery
2021
•2021/10/14
•Vol.7 No.1 p.1-11
A remarkable shift in Mesenchymal stromal cells (MSCs) plays an important role in cancer metastasis, but the molecular mechanism is still unclear. CPNE7, a calcium-dependent phospholipid-binding protein, mediates signal transduction and metastasis in many tumours. Here, we demonstrated that MSCs der...
Oral cancer detection
10.1038/S41420-021-00684-W
ISSN:2058-7716
An interpretable RNA foundation model for exploring functional RNA motifs in plants
Haopeng Yu•Heng Yang•Wenqing Sun•Zongyun Yan•Xiaofei Yang等 8 人
Nature Machine Intelligence
2024
•2024/12/9
•00 p.1-10
The complex ‘language’ of plant RNA encodes a vast array of biological regulatory elements that orchestrate crucial aspects of plant growth, development and adaptation to environmental stresses. Recent advancements in foundation models (FMs) have demonstrated their unprecedented potential to deciphe...
Computational modelsMachine learningPlant molecular biology
10.1038/S42256-024-00946-Z
ISSN:2522-5839
Metabolic network remodelling enhances yeast’s fitness on xylose using aerobic glycolysis
Li Xiaowei•Wang Yanyan•Li Gang•Liu Quanli•Pereira Rui等 7 人
Nature Catalysis
2021
•2021/9/16
•Vol.4 No.9 p.783-796
The reprogramming of metabolism in response to switching the carbon source from glucose to non-preferred carbon sources is well-studied for yeast. However, understanding how metabolic networks respond to utilize a non-natural carbon source such as xylose is limited due to the incomplete knowledge of...
BiosynthesisCell growthMetabolic engineeringSustainabilitySynthetic biology
10.1038/S41929-021-00670-6
ISSN:2520-1158
Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa
Caisey V. Pulford•Blanca M. Perez-Sepulveda•Rocío Canals•Jessica A. Bevington•Rebecca J. Bengtsson等 31 人
Nature Microbiology
2020
•2020/12/21
•Vol.6 No.3 p.327-338
Bloodstream infections caused by nontyphoidal Salmonella are a major public health concern in Africa, causing ~49,600 deaths every year. The most common Salmonella enterica pathovariant associated with invasive nontyphoidal Salmonella disease is Salmonella Typhimurium sequence type (ST)313. It has b...
Computational biology and bioinformaticsGenome informaticsMolecular evolutionPhylogeneticsPhylogeny
10.1038/S41564-020-00836-1
ISSN:2058-5276
Transcriptome and physiological analyses provide insights into the leaf epicuticular wax accumulation mechanism in yellowhorn
Yang Zhao•Xiaojuan Liu•Mengke Wang•Quanxin Bi•Yifan Cui等 6 人
Horticulture Research
2021
•2021/6/1
•Vol.8 No.1 p.1-13
Plantations and production of yellowhorn, one of the most important woody oil and urban greening trees widely cultivated in northern China, have gradually become limited by drought stress. The epicuticular wax layer plays a key role in the protection of yellowhorn trees from drought and other stress...
DroughtMetabolomics
10.1038/S41438-021-00564-5
ISSN:2662-6810
Chloroquine resistance evolution in Plasmodium falciparum is mediated by the putative amino acid transporter AAT1
Alfred Amambua-Ngwa•Katrina A. Button-Simons•Xue Li•Sudhir Kumar•Katelyn Vendrely Brenneman等 28 人
Nature Microbiology
2023
•2023/5/11
•00 p.1-14
Malaria parasites break down host haemoglobin into peptides and amino acids in the digestive vacuole for export to the parasite cytoplasm for growth: interrupting this process is central to the mode of action of several antimalarial drugs. Mutations in the chloroquine (CQ) resistance transporter, pf...
MalariaParasite genetics
10.1038/S41564-023-01377-Z
ISSN:2058-5276
The NONRATT023402.2/rno-miR-3065-5p/NGFR axis affects levodopa-induced dyskinesia in a rat model of Parkinson’s disease
Qiao Wang•Huizhi Wang•Wenjia Meng•Chong Liu•Renpeng Li等 13 人
Cell Death Discovery
2023
•2023/9/15
•Vol.9 No.1 p.1-14
Levodopa-induced dyskinesia (LID) is a common motor complication in Parkinson’s disease. However, few studies have focused on the pathogenesis of LID at the transcriptional level. NONRATT023402.2, a long non-coding RNA (lncRNA) that may be related to LID was discovered in our previous study and char...
Epigenetics and behaviourParkinson's disease
10.1038/S41420-023-01644-2
ISSN:2058-7716
DHH1/DDX6-like RNA helicases maintain ephemeral half-lives of stress-response mRNAs
Thanin Chantarachot•Reed S. Sorenson•Maureen Hummel•Haiyan Ke•Alek T. Kettenburg等 11 人
Nature Plants
2020
•2020/6/1
•Vol.6 No.6 p.675-685
Gene transcription is counterbalanced by messenger RNA decay processes that regulate transcript quality and quantity. We show here that the evolutionarily conserved DHH1/DDX6-like RNA hellicases of Arabidopsis thaliana control the ephemerality of a subset of cellular mRNAs. These RNA helicases co-lo...
Plant cell biologyPlant molecular biology
10.1038/S41477-020-0681-8
ISSN:2055-0278
Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission
Aggarwal Dinesh•Warne Ben•Jahun Aminu S.•Hamilton William L.•Fieldman Thomas等 40 人
Nature Communications
2022
•2022/2/8
•Vol.13 No.1 p.1-16
Understanding SARS-CoV-2 transmission in higher education settings is important to limit spread between students, and into at-risk populations. In this study, we sequenced 482 SARS-CoV-2 isolates from the University of Cambridge from 5 October to 6 December 2020. We perform a detailed phylogenetic c...
EpidemiologySARS-CoV-2Viral epidemiologyViral geneticsViral transmission
10.1038/S41467-021-27942-W
ISSN:2041-1723
Distinct ossification trade-offs illuminate the shoulder girdle reconfiguration at the water-to-land transition
Janet Wei•Thomas W. P. Wood•Kathleen Flaherty•Olivia E. Fitch•Shahid Ali等 16 人
Nature Communications
2025
•2025/5/29
•Vol.16 No.1 p.1-16
The mechanisms of the pectoral girdle transformation at the origin of terrestrial locomotion in vertebrates remain an outstanding problem. The loss of intramembranous bones and the enlargement of endochondral bones resulted in the disarticulation of the pectoral girdle from the skull and the formati...
Evolutionary developmental biologyEvolutionary geneticsMorphogenesis
10.1038/S41467-025-60236-Z
ISSN:2041-1723
Modular one-pot assembly of CRISPR arrays enables library generation and reveals factors influencing crRNA biogenesis
Chunyu Liao•Fani Ttofali•Rebecca A. Slotkowski•Steven R. Denny•Taylor D. Cecil等 8 人
Nature Communications
2019
•2019/7/3
•Vol.10 No.1 p.1-14
CRISPR-Cas systems inherently multiplex through CRISPR arrays—whether to defend against different invaders or mediate multi-target editing, regulation, imaging, or sensing. However, arrays remain difficult to generate due to their reoccurring repeat sequences. Here, we report a modular, one-pot sche...
BiotechnologyCRISPR-Cas systemsMicrobiologySmall RNAs
10.1038/S41467-019-10747-3
ISSN:2041-1723
Design and testing of a humanized porcine donor for xenotransplantation
Ranjith P. Anand•Jacob V. Layer•David Heja•Takayuki Hirose•Grace Lassiter等 60 人
Nature
2023
•2023/10/11
•Vol.622 No.7982 p.393-401
Recent human decedent model studies1,2 and compassionate xenograft use3 have explored the promise of porcine organs for human transplantation. To proceed to human studies, a clinically ready porcine donor must be engineered and its xenograft successfully tested in nonhuman primates. Here we describe...
Preclinical researchSynthetic biology
10.1038/S41586-023-06594-4
ISSN:0028-0836
Oral fungal dysbiosis and systemic immune dysfunction in Chinese patients with schizophrenia
Xia Liu•Zongxin Ling•Yiwen Cheng•Lingbin Wu•Li Shao等 12 人
Translational Psychiatry
2024
•2024/11/21
•Vol.14 No.1 p.1-12
Oral microbial dysbiosis contributes to the development of schizophrenia (SZ). While numerous studies have investigated alterations in the oral bacterial microbiota among SZ patients, investigations into the fungal microbiota, another integral component of the oral microbiota, are scarce. In this cr...
Diagnostic markersSchizophrenia
10.1038/S41398-024-03183-5
ISSN:2158-3188
Inhibiting glucocorticoid receptors enhances adult spinal cord neural stem cell activity and improves outcomes in spinal cord injury
Xuefeng Zhang•Siyuan Zhou•Shengyu Tang•Xiaotong Hou•Yonghui Cai等 6 人
Communications Biology
2026
•2026/3/23
0The spinal cord injury (SCI) microenvironment undergoes significant biochemical changes that influence the behavior of endogenous neural stem/progenitor cells (NSPCs), including elevated glucocorticoid levels. Here, we investigate the effects of glucocorticoids on NSPCs in the adult mouse spinal cor...
Adult neurogenesisNeural stem cells
10.1038/S42003-026-09901-7
ISSN:2399-3642
A streamlined solution for processing, elucidating and quality control of cyclobutane pyrimidine dimer sequencing data
Quanhu Sheng•Hui Yu•Mingrui Duan•Scott Ness•Jiapeng He等 10 人
Nature Protocols
2021
•2021/3/17
•00 p.1-23
UV radiation may lead to melanoma and nonmelanoma skin cancers by causing helix-distorting DNA damage such as cyclobutane pyrimidine dimers (CPDs). These DNA lesions, if located in important genes and not repaired promptly, are mutagenic and may eventually result in carcinogenesis. Examining CPD for...
Cancer genomicsComputational biology and bioinformaticsSoftware
10.1038/S41596-021-00496-3
ISSN:1754-2189
Gut microbiota-derived l-theanine promotes host branched-chain amino acid catabolism
Youxia Wang•Bingnan Liu•Ziyi Han•Peng Bin•Wenjie Tang等 11 人
Nature Microbiology
2026
•2026/1/14
•Vol.11 No.2 p.507-521
Elevated levels of serum branched-chain amino acids (BCAA) are linked to various metabolic disorders such as obesity, insulin resistance and type 2 diabetes. Although gut microbiota can regulate circulating BCAA levels via direct transformation, here we uncover an indirect mechanism that influences ...
BacteriaDiseases
10.1038/S41564-025-02236-9
ISSN:2058-5276
Pan-active imidazolopiperazine antimalarials target the Plasmodium falciparum intracellular secretory pathway
Gregory M. LaMonte•Frances Rocamora•Danushka S. Marapana•Nina F. Gnädig•Sabine Ottilie等 26 人
Nature Communications
2020
•2020/4/14
•Vol.11 No.1 p.1-15
A promising new compound class for treating human malaria is the imidazolopiperazines (IZP) class. IZP compounds KAF156 (Ganaplacide) and GNF179 are effective against Plasmodium symptomatic asexual blood-stage infections, and are able to prevent transmission and block infection in animal models. But...
Endoplasmic reticulumTarget identification
10.1038/S41467-020-15440-4
ISSN:2041-1723
Isolation and characterization of a pangolin-borne HKU4-related coronavirus that potentially infects human-DPP4-transgenic mice
Luo-Yuan Xia•Zhen-Fei Wang•Xiao-Ming Cui•Yuan-Guo Li•Run-Ze Ye等 18 人
Nature Communications
2024
•2024/2/5
•Vol.15 No.1 p.1-12
We recently detected a HKU4-related coronavirus in subgenus Merbecovirus (named pangolin-CoV-HKU4-P251T) from a Malayan pangolin1. Here we report isolation and characterization of pangolin-CoV-HKU4-P251T, the genome sequence of which is closest to that of a coronavirus from the greater bamboo bat (T...
MousePathogensViral reservoirsVirology
10.1038/S41467-024-45453-2
ISSN:2041-1723
Flexible genes establish widespread bacteriophage pan-genomes in cryoconite hole ecosystems
Christopher M. Bellas•Declan C. Schroeder•Arwyn Edwards•Gary Barker•Alexandre M. Anesio
Nature Communications
2020
•2020/9/2
•Vol.11 No.1 p.1-10
Bacteriophage genomes rapidly evolve via mutation and horizontal gene transfer to counter evolving bacterial host defenses; such arms race dynamics should lead to divergence between phages from similar, geographically isolated ecosystems. However, near-identical phage genomes can reoccur over large ...
MetagenomicsPhage biologyViral evolutionVirus–host interactions
10.1038/S41467-020-18236-8
ISSN:2041-1723
CRISPR-mediated gene correction links the ATP7A M1311V mutations with amyotrophic lateral sclerosis pathogenesis in one individual
Yeomin Yun•Sung-Ah Hong•Ka-Kyung Kim•Daye Baek•Dongsu Lee等 20 人
Communications Biology
2020
•2020/1/20
•Vol.3 No.1 p.1-10
Amyotrophic lateral sclerosis (ALS) is a severe disease causing motor neuron death, but a complete cure has not been developed and related genes have not been defined in more than 80% of cases. Here we compared whole genome sequencing results from a male ALS patient and his healthy parents to identi...
Amyotrophic lateral sclerosisCRISPR-Cas9 genome editing
10.1038/S42003-020-0755-1
ISSN:2399-3642
Shigella infection is facilitated by interaction of human enteric α-defensin 5 with colonic epithelial receptor P2Y11
Dan Xu•Mengyao Guo•Xin Xu•Gan Luo•Yaxin Liu等 21 人
Nature Microbiology
2025
•2025/2/3
•Vol.10 No.2 p.509-526
Human enteric α-defensin 5 (HD5) is an immune system peptide that acts as an important antimicrobial factor but is also known to promote pathogen infections by enhancing adhesion of the pathogens. The mechanistic basis of these conflicting functions is unknown. Here we show that HD5 induces abundant...
Cellular microbiologyInfectionPathogens
10.1038/S41564-024-01901-9
ISSN:2058-5276
Dirigent gene editing of gossypol enantiomers for toxicity-depleted cotton seeds
Lin Jia-Ling•Fang Xin•Li Jian-Xu•Chen Zhi-Wen•Wu Wen-Kai等 14 人
Nature Plants
2023
•2023/3/16
•00 p.1-11
Axial chirality of biaryls can generate varied bioactivities. Gossypol is a binaphthyl compound made by cotton plants. Of its two axially chiral isomers, (−)-gossypol is the bioactive form in mammals and has antispermatogenic activity, and its accumulation in cotton seeds poses health concerns. Here...
Plant evolutionSecondary metabolismTransgenic plants
10.1038/S41477-023-01376-2
ISSN:2055-0278
Molecular classification to refine surgical and radiotherapeutic decision-making in meningioma
Justin Z. Wang•Vikas Patil•Alexander P. Landry•Chloe Gui•Andrew Ajisebutu等 37 人
Nature Medicine
2024
•2024/8/21
•00 p.1-11
Treatment of the tumor and dural margin with surgery and sometimes radiation are cornerstones of therapy for meningioma. Molecular classifications have provided insights into the biology of disease; however, response to treatment remains heterogeneous. In this study, we used retrospective data on 2,...
CNS cancerTranslational research
10.1038/S41591-024-03167-4
ISSN:1078-8956
Aspergillus cvjetkovicii protects against phytopathogens through interspecies chemical signalling in the phyllosphere
Xiaoyan Fan•Haruna Matsumoto•Haorong Xu•Hongda Fang•Qianqian Pan等 16 人
Nature Microbiology
2024
•2024/8/5
•00 p.1-15
Resident microbiota produces small molecules that influence the chemical microenvironments on leaves, but its signalling roles in pathogen defence are not yet well understood. Here we show that Aspergillus cvjetkovicii, enriched in rice leaf microbiota, subverts Rhizoctonia solani infections via sma...
Applied microbiologyMicrobiomePlant signalling
10.1038/S41564-024-01781-Z
ISSN:2058-5276
Epigenetic inheritance is unfaithful at intermediately methylated CpG sites
Amir D. Hay•Noah J. Kessler•Daniel Gebert•Nozomi Takahashi•Hugo Tavares等 7 人
Nature Communications
2023
•2023/9/2
•Vol.14 No.1 p.1-11
DNA methylation at the CpG dinucleotide is considered a stable epigenetic mark due to its presumed long-term inheritance through clonal expansion. Here, we perform high-throughput bisulfite sequencing on clonally derived somatic cell lines to quantitatively measure methylation inheritance at the nuc...
DNA methylationEpigenetic memory
10.1038/S41467-023-40845-2
ISSN:2041-1723
Sequential structure probing of cotranscriptional RNA folding intermediates
Courtney E. Szyjka•Skyler L. Kelly•Eric J. Strobel
Nature Communications
2025
•2025/6/1
•Vol.16 No.1 p.1-18
Cotranscriptional RNA folding pathways typically involve the sequential formation of folding intermediates. Existing methods for cotranscriptional RNA structure probing map the structure of nascent RNA in the context of a terminally arrested transcription elongation complex. Consequently, the rearra...
RiboswitchesRNATranscription
10.1038/S41467-025-60425-W
ISSN:2041-1723
Astrocyte reactivity and inflammation-induced depression-like behaviors are regulated by Orai1 calcium channels
Michaela M. Novakovic•Kirill S. Korshunov•Rogan A. Grant•Megan E. Martin•Hiam A. Valencia等 8 人
Nature Communications
2023
•2023/9/7
•Vol.14 No.1 p.1-20
Astrocytes contribute to brain inflammation in neurological disorders but the molecular mechanisms controlling astrocyte reactivity and their relationship to neuroinflammatory endpoints are complex and poorly understood. In this study, we assessed the role of the calcium channel, Orai1, for astrocyt...
AstrocyteCalcium signallingIon channels in the nervous system
10.1038/S41467-023-40968-6
ISSN:2041-1723
Aglycosylated antibody-producing mice for aglycosylated antibody-lectin coupled immunoassay for the quantification of tumor markers (ALIQUAT)
Nan-Ee Lee•Sun Hee Kim•Dae-Yeul Yu•Eui-Jeon Woo•Myung-Il Kim等 9 人
Communications Biology
2020
•2020/10/30
•Vol.3 No.1 p.1-13
Targeting aberrant glycoforms has been validated for in vitro cancer diagnostic development, and several assays are currently in routine clinical use. Because N-glycans in Fc region of antibodies show cross-reactivity with various lectins, high-quality aglycosylated antibodies are exceptionally impo...
Biochemical assaysDiagnostic markersGenetic engineeringMouse
10.1038/S42003-020-01363-9
ISSN:2399-3642
Whole-exome mutational landscape of neuroendocrine carcinomas of the gallbladder
Fatao Liu•Yongsheng Li•Dongjian Ying•Shimei Qiu•Yong He等 17 人
Signal Transduction And Targeted Therapy
2021
•2021/2/10
•Vol.6 No.1 p.1-12
Neuroendocrine carcinoma (NEC) of the gallbladder (GB-NEC) is a rare but extremely malignant subtype of gallbladder cancer (GBC). The genetic and molecular signatures of GB-NEC are poorly understood; thus, molecular targeting is currently unavailable. In the present study, we applied whole-exome seq...
Cancer genomicsGastrointestinal cancer
10.1038/S41392-020-00412-3
ISSN:2059-3635
Clinically relevant atovaquone-resistant human malaria parasites fail to transmit by mosquito
Victoria A. Balta•Deborah Stiffler•Abeer Sayeed•Abhai K. Tripathi•Rubayet Elahi等 18 人
Nature Communications
2023
•2023/10/12
•Vol.14 No.1 p.1-9
Long-acting injectable medications, such as atovaquone, offer the prospect of a “chemical vaccine” for malaria, combining drug efficacy with vaccine durability. However, selection and transmission of drug-resistant parasites is of concern. Laboratory studies have indicated that atovaquone resistance...
Antiparasitic agentsMalariaParasitologyTranslational research
10.1038/S41467-023-42030-X
ISSN:2041-1723
The small CRL4CSA ubiquitin ligase component DDA1 regulates transcription-coupled repair dynamics
Diana A. Llerena Schiffmacher•Shun-Hsiao Lee•Katarzyna W. Kliza•Arjan F. Theil•Masaki Akita等 20 人
Nature Communications
2024
•2024/7/29
•Vol.15 No.1 p.1-17
Transcription-blocking DNA lesions are specifically targeted by transcription-coupled nucleotide excision repair (TC-NER), which removes a broad spectrum of DNA lesions to preserve transcriptional output and thereby cellular homeostasis to counteract aging. TC-NER is initiated by the stalling of RNA...
DNA damage responseNucleotide excision repair
10.1038/S41467-024-50584-7
ISSN:2041-1723
Arctic plant-fungus interaction networks show major rewiring with environmental variation
Bastien Parisy•Niels M. Schmidt•Alyssa R. Cirtwill•Edith Villa-Galaviz•Mikko Tiusanen等 11 人
Communications Earth & Environment
2024
•2024/11/23
•Vol.5 No.1 p.1-9
Global environmental change may lead to changes in community structure and in species interactions, ultimately changing ecosystem functioning. Focusing on spatial variation in fungus–plant interactions across the rapidly changing Arctic, we quantified variation in the identity of interaction partner...
Ecological networksFood webs
10.1038/S43247-024-01902-W
ISSN:2662-4435
Multi-kingdom microbiota analyses identify bacterial–fungal interactions and biomarkers of colorectal cancer across cohorts
Liu Ning-Ning•Jiao Na•Tan Jing-Cong•Wang Ziliang•Wu Dingfeng等 21 人
Nature Microbiology
2022
•2022/1/27
•Vol.7 No.2 p.238-250
Despite recent progress in our understanding of the association between the gut microbiome and colorectal cancer (CRC), multi-kingdom gut microbiome dysbiosis in CRC across cohorts is unexplored. We investigated four-kingdom microbiota alterations using CRC metagenomic datasets of 1,368 samples from...
Computational modelsMicrobiome
10.1038/S41564-021-01030-7
ISSN:2058-5276
Characterization of Cme and Yme thermostable Cas12a orthologs
Fuchs Ryan T.•Curcuru Jennifer L.•Mabuchi Megumu•Noireterre Audrey•Weigele Peter R.等 7 人
Communications Biology
2022
•2022/4/6
•Vol.5 No.1 p.1-16
CRISPR-Cas12a proteins are RNA-guided endonucleases that cleave invading DNA containing target sequences adjacent to protospacer adjacent motifs (PAM). Cas12a orthologs have been repurposed for genome editing in non-native organisms by reprogramming them with guide RNAs to target specific sites in g...
CRISPR-Cas9 genome editingNucleases
10.1038/S42003-022-03275-2
ISSN:2399-3642
Pangenomics reveals alternative environmental lifestyles among chlamydiae
Stephan Köstlbacher•Astrid Collingro•Tamara Halter•Frederik Schulz•Sean P. Jungbluth等 6 人
Nature Communications
2021
•2021/6/29
•Vol.12 No.1 p.1-15
Chlamydiae are highly successful strictly intracellular bacteria associated with diverse eukaryotic hosts. Here we analyzed metagenome-assembled genomes of the “Genomes from Earth’s Microbiomes” initiative from diverse environmental samples, which almost double the known phylogenetic diversity of th...
MetagenomicsMicrobial ecologySymbiosis
10.1038/S41467-021-24294-3
ISSN:2041-1723
Phylogeny resolved, metabolism revealed: functional radiation within a widespread and divergent clade of sponge symbionts
Jessica A. Taylor•Giorgia Palladino•Bernd Wemheuer•Georg Steinert•Detmer Sipkema等 7 人
The Isme Journal
2020
•2020/10/3
•Vol.15 No.2 p.503-519
The symbiosis between bacteria and sponges has arguably the longest evolutionary history for any extant metazoan lineage, yet little is known about bacterial evolution or adaptation in this process. An example of often dominant and widespread bacterial symbionts of sponges is a clade of uncultured a...
Microbial ecologySymbiosis
10.1038/S41396-020-00791-Z
ISSN:1751-7362
ESRP1-regulated isoform switching of LRRFIP2 determines metastasis of gastric cancer
Lee Jihee•Pang Kyoungwha•Kim Junil•Hong Eunji•Lee Jeeyun等 15 人
Nature Communications
2022
•2022/10/28
•Vol.13 No.1 p.1-15
Although accumulating evidence indicates that alternative splicing is aberrantly altered in many cancers, the functional mechanism remains to be elucidated. Here, we show that epithelial and mesenchymal isoform switches of leucine-rich repeat Fli-I-interacting protein 2 (LRRFIP2) regulated by epithe...
Gastric cancerMetastasis
10.1038/S41467-022-33786-9
ISSN:2041-1723
Acarbose redirects gut microbiome utilization of dietary carbohydrates to suppress anaphylaxis in mice
Kyosuke Yakabe•Yukinobu Inoue•Yuki Yanagisawa•Shungo Imai•Shunnosuke Suwa等 20 人
Nature Microbiology
2026
•2026/5/12
•00 p.1-14
Microbiota-accessible carbohydrates modulate host immunity by shaping gut microbial composition and metabolism. However, their role in modulating the microbiota to influence allergic responses is unclear. Here we show that a widely used antidiabetic agent, the α-glucosidase inhibitor acarbose, redir...
AllergyMicrobiomeMolecular medicine
10.1038/S41564-026-02350-2
ISSN:2058-5276
MRP3 is a sex determining gene in the diatom Pseudo-nitzschia multistriata
Monia T. Russo•Laura Vitale•Laura Entrambasaguas•Konstantinos Anestis•Neri Fattorini等 13 人
Nature Communications
2018
•2018/11/28
•Vol.9 No.1 p.1-10
A broad diversity of sex-determining systems has evolved in eukaryotes. However, information on the mechanisms of sex determination for unicellular microalgae is limited, including for diatoms, key-players of ocean food webs. Here we report the identification of a mating type (MT) determining gene f...
Evolutionary geneticsGene regulationGenetic association study
10.1038/S41467-018-07496-0
ISSN:2041-1723
Observation of coordinated RNA folding events by systematic cotranscriptional RNA structure probing
Courtney E. Szyjka•Eric J. Strobel
Nature Communications
2023
•2023/11/29
•Vol.14 No.1 p.1-22
RNA begins to fold as it is transcribed by an RNA polymerase. Consequently, RNA folding is constrained by the direction and rate of transcription. Understanding how RNA folds into secondary and tertiary structures therefore requires methods for determining the structure of cotranscriptional folding ...
RiboswitchesRNATranscription
10.1038/S41467-023-43395-9
ISSN:2041-1723
Sequence-based genetic mapping of Cynodon dactylon Pers. reveals new insights into genome evolution in Poaceae
Tilin Fang•Hongxu Dong•Shuhao Yu•Justin Q. Moss•Charles H. Fontanier等 8 人
Communications Biology
2020
•2020/7/9
•Vol.3 No.1 p.1-10
Bermudagrass (Cynodon dactylon Pers.) is an important warm-season perennial used extensively for turf, forage, soil conservation and remediation worldwide. However, limited genomic information has hindered the application of molecular tools towards understanding genome evolution and in breeding new ...
Agricultural geneticsEvolutionary genetics
10.1038/S42003-020-1086-Y
ISSN:2399-3642
Digital multiplex ligation assay for highly multiplexed screening of β-lactamase-encoding genes in bacterial isolates
Manu Tamminen•Jenny Spaak•Lea Caduff•Hanna Schiff•Ramon Lang等 8 人
Communications Biology
2020
•2020/5/25
•Vol.3 No.1 p.1-6
Increasing incidence of antibiotic resistance in clinical and environmental settings calls for increased scalability in their surveillance. Current screening technologies are limited by the number of samples and genes that can easily be screened. We demonstrate here digital multiplex ligation assay ...
Bacterial genesHigh-throughput screening
10.1038/S42003-020-0980-7
ISSN:2399-3642
Targetable lesions and proteomes predict therapy sensitivity through disease evolution in pediatric acute lymphoblastic leukemia
Amanda C. Lorentzian•Jenna Rever•Enes K. Ergin•Meiyun Guo•Neha M. Akella等 10 人
Nature Communications
2023
•2023/11/21
•Vol.14 No.1 p.1-14
Childhood acute lymphoblastic leukemia (ALL) genomes show that relapses often arise from subclonal outgrowths. However, the impact of clonal evolution on the actionable proteome and response to targeted therapy is not known. Here, we present a comprehensive retrospective analysis of paired ALL diagn...
Cancer genomicsLeukaemiaNext-generation sequencingPaediatric cancerProteomics
10.1038/S41467-023-42701-9
ISSN:2041-1723
Multiplatform genomic profiling and magnetic resonance imaging identify mechanisms underlying intratumor heterogeneity in meningioma
Stephen T. Magill•Harish N. Vasudevan•Kyounghee Seo•Javier E. Villanueva-Meyer•Abrar Choudhury等 23 人
Nature Communications
2020
•2020/9/23
•Vol.11 No.1 p.1-15
Meningiomas are the most common primary intracranial tumors, but the molecular drivers of meningioma tumorigenesis are poorly understood. We hypothesized that investigating intratumor heterogeneity in meningiomas would elucidate biologic drivers and reveal new targets for molecular therapy. To test ...
Cancer epigeneticsCNS cancerGene regulatory networksTumour heterogeneity
10.1038/S41467-020-18582-7
ISSN:2041-1723
NINJ1 ubiquitination by TRIM72 protects against plasma membrane rupture and AKI-CKD progression
Keng Ye•Siyi Lin•Caiming Chen•Zhimin Chen•Kongwen Lin等 11 人
Cell Death & Differentiation
2026
•2026/4/27
•00 p.1-14
The progression of acute kidney injury (AKI) to chronic kidney disease (CKD) remains a major clinical challenge. It is primarily triggered by renal tubular epithelial cell (RTEC) death that leads to persistent sterile inflammation, maladaptive repair and irreversible renal fibrosis. A pivotal event ...
Cell death and immune responseKidney diseases
10.1038/S41418-026-01746-1
ISSN:1350-9047
Genomic insights into diverse bacterial taxa that degrade extracellular DNA in marine sediments
Kenneth Wasmund•Claus Pelikan•Arno Schintlmeister•Michael Wagner•Margarete Watzka等 14 人
Nature Microbiology
2021
•2021/6/14
•00 p.1-14
Extracellular DNA is a major macromolecule in global element cycles, and is a particularly crucial phosphorus, nitrogen and carbon source for microorganisms in the seafloor. Nevertheless, the identities, ecophysiology and genetic features of DNA-foraging microorganisms in marine sediments are largel...
Environmental microbiologyEnvironmental sciences
10.1038/S41564-021-00917-9
ISSN:2058-5276
Population genomics unravels the Holocene history of bread wheat and its relatives
Zhao Xuebo•Guo Yafei•Kang Lipeng•Yin Changbin•Bi Aoyue等 19 人
Nature Plants
2023
•2023/3/16
•Vol.9 No.3 p.403-419
Deep knowledge of crop biodiversity is essential to improving global food security. Despite bread wheat serving as a keystone crop worldwide, the population history of bread wheat and its relatives, both cultivated and wild, remains elusive. By analysing whole-genome sequences of 795 wheat accession...
GenomicsPopulation genetics
10.1038/S41477-023-01367-3
ISSN:2055-0278
Gibberellic acid induced parthenocarpic ‘Honeycrisp’ apples ( Malus domestica ) exhibit reduced ovary width and lower acidity
Kelsey D. Galimba•Daniel G. Bullock•Chris Dardick•Zhongchi Liu•Ann M. Callahan
Horticulture Research
2019
•2019/4/6
•Vol.6 No.1 p.1-13
Fruit set and development are dependent on auxin, gibberellin, and cytokinin, which cause parthenocarpic development in many species when applied ectopically. Commercial sprays containing these hormones are used to improve apple fruit set, size, and shape, but have been implicated negatively in othe...
Agricultural geneticsFruitingGibberellinsPlant molecular biology
10.1038/S41438-019-0124-8
ISSN:2052-7276
Integrative iTRAQ-based proteomic and transcriptomic analysis reveals the accumulation patterns of key metabolites associated with oil quality during seed ripening of Camellia oleifera
Zhouchen Ye•Jing Yu•Wuping Yan•Junfeng Zhang•Dongmei Yang等 9 人
Horticulture Research
2021
•2021/7/1
•Vol.8 No.1 p.1-26
Camellia oleifera (C. oleifera) is one of the four major woody oil-bearing crops in the world and has relatively high ecological, economic, and medicinal value. Its seeds undergo a series of complex physiological and biochemical changes during ripening, which is mainly manifested as the accumulation...
Plant molecular biologyTranscriptomics
10.1038/S41438-021-00591-2
ISSN:2662-6810
LncRNA DILA1 inhibits Cyclin D1 degradation and contributes to tamoxifen resistance in breast cancer
Qianfeng Shi•Yudong Li•Shunying Li•Liang Jin•Hongna Lai等 15 人
Nature Communications
2020
•2020/11/2
•Vol.11 No.1 p.1-15
Cyclin D1 is one of the most important oncoproteins that drives cancer cell proliferation and associates with tamoxifen resistance in breast cancer. Here, we identify a lncRNA, DILA1, which interacts with Cyclin D1 and is overexpressed in tamoxifen-resistant breast cancer cells. Mechanistically, DIL...
CancerMolecular biology
10.1038/S41467-020-19349-W
ISSN:2041-1723
Large-scale multi-omics unveils host–microbiome interactions driving root development and nitrogen acquisition
Nannan Li•Guoliang Li•Xiaofang Huang•Lige Ma•Danning Wang等 27 人
Nature Plants
2026
•2026/2/3
•Vol.12 No.2 p.319-336
The rhizosphere microbiome plays a crucial role in determining plant performance and fitness. Nevertheless, regulatory mechanisms linking host genetic variation, root gene regulation and microbiome assembly—and their collective influence on plant nutritional traits—remain poorly understood. Here we ...
Genetic association studyMicrobiologyPlant developmentPlant genetics
10.1038/S41477-025-02210-7
ISSN:2055-0278
Methane-dependent complete denitrification by a single Methylomirabilis bacterium
Xiangwu Yao•Jiaqi Wang•Mingyue He•Zishu Liu•Yuxiang Zhao等 11 人
Nature Microbiology
2024
•2024/1/16
•00 p.1-13
Methane-dependent nitrate and nitrite removal in anoxic environments is thought to rely on syntrophy between ANME-2d archaea and bacteria in the genus ‘Candidatus Methylomirabilis’. Here we enriched and purified a single Methylomirabilis from paddy soil fed with nitrate and methane, which is capable...
BiogeochemistryWater microbiology
10.1038/S41564-023-01578-6
ISSN:2058-5276
Trimethoprim resistance in surface and wastewater is mediated by contrasting variants of the dfrB gene
David Kneis•Claudèle Lemay-St-Denis•Stella Cellier-Goetghebeur•Alan X. Elena•Thomas U. Berendonk等 7 人
The Isme Journal
2023
•2023/6/27
•Vol.17 No.9 p.1455-1466
Trimethoprim (TMP) is a low-cost, widely prescribed antibiotic. Its effectiveness is increasingly challenged by the spread of genes coding for TMP-resistant dihydrofolate reductases: dfrA, and the lesser-known, evolutionarily unrelated dfrB. Despite recent reports of novel variants conferring high l...
AntibioticsMetagenomicsWater microbiology
10.1038/S41396-023-01460-7
ISSN:1751-7362
Deep mutational scanning of the Trypanosoma brucei developmental regulator RBP6 reveals an essential disordered region influenced by positive residues
Saúl Rojas-Sánchez•Nikolay G. Kolev•Christian Tschudi
Nature Communications
2025
•2025/1/30
•Vol.16 No.1 p.1-13
To regain infectivity, Trypanosoma brucei, the pathogen causing Human and Animal African trypanosomiasis, undergoes a complex developmental program within the tsetse fly known as metacyclogenesis. RNA-binding protein 6 (RBP6) is a potent orchestrator of this process, however, an understanding of its...
Molecular biologyPathogenesis
10.1038/S41467-025-56553-Y
ISSN:2041-1723
Almond snacking modulates gut microbiome and metabolome in association with improved cardiometabolic and inflammatory markers
Gwoncheol Park•Katelyn Johnson•Katelyn Miller•Saurabh Kadyan•Saiful Singar等 13 人
Npj Science Of Food
2025
•2025/3/20
•Vol.9 No.1 p.1-14
Western-style dietary patterns have been linked with obesity and associated metabolic disorders and gut dysbiosis, whereas prudent dietary and snacking choices mitigate these predispositions. Using a multi-omics approach, we investigated how almond snacking counters gut imbalances linked to adiposit...
MetagenomicsMicrobiomeNutrition
10.1038/S41538-025-00403-0
ISSN:2396-8370
Effect of a spore-based Mannheimia haemolytica vaccine on immune responses and respiratory microbiota in sheep
Muhammed Salah Uddin•José Ortiz Guluarte•Timothy D. Schwinghamer•Daniel R. Barreda•Tim A. McAllister等 7 人
Npj Vaccines
2026
•2026/7/10
•Vol.11 No.1 p.1440
Mannheimia haemolytica is an opportunistic pathogen associated with respiratory disease in ruminants. Current vaccines provide incomplete protection, highlighting the need for improved immunization strategies. In this study, a mucosal vaccine was developed using Bacillus subtilis spores as an adjuva...
DiseasesImmunologyMicrobiology
10.1038/S41541-026-01415-X
ISSN:2059-0105
Flexible and cost-effective genomic surveillance of P. falciparum malaria with targeted nanopore sequencing
Mariateresa de Cesare•Mulenga Mwenda•Anna E. Jeffreys•Jacob Chirwa•Chris Drakeley等 19 人
Nature Communications
2024
•2024/2/15
•Vol.15 No.1 p.1-16
Genomic surveillance of Plasmodium falciparum malaria can provide policy-relevant information about antimalarial drug resistance, diagnostic test failure, and the evolution of vaccine targets. Yet the large and low complexity genome of P. falciparum complicates the development of genomic methods, wh...
DiagnosisMalariaParasite genetics
10.1038/S41467-024-45688-Z
ISSN:2041-1723
A single-cell mass cytometry-based atlas of the developing mouse brain
Amy L. Van Deusen•Sushanth Kumar•O. Yipkin Calhan•Sarah M. Goggin•Jiachen Shi等 11 人
Nature Neuroscience
2024
•2024/12/18
•00 p.1-15
Development of the mammalian brain requires precise molecular changes across diverse cell lineages. While single-cell RNA abundances in the developing brain have been characterized by single-cell RNA sequencing (scRNA-seq), single-cell protein abundances have not been characterized. To address this ...
Cell type diversityCellular neuroscienceDevelopmental neurogenesisGliogenesisNeural progenitors
10.1038/S41593-024-01786-1
ISSN:1097-6256
Ancient marine sediment DNA reveals diatom transition in Antarctica
Armbrecht Linda•Weber Michael E.•Raymo Maureen E.•Peck Victoria L.•Williams Trevor等 34 人
Nature Communications
2022
•2022/10/2
•Vol.13 No.1 p.1-14
Antarctica is one of the most vulnerable regions to climate change on Earth and studying the past and present responses of this polar marine ecosystem to environmental change is a matter of urgency. Sedimentary ancient DNA (sedaDNA) analysis can provide such insights into past ecosystem-wide changes...
BiodiversityMarine biologyMetagenomicsPalaeoceanographyPalaeoecology
10.1038/S41467-022-33494-4
ISSN:2041-1723
Whole-genome sequencing identifies ADGRG6 enhancer mutations and FRS2 duplications as angiogenesis-related drivers in bladder cancer
Song Wu•Tong Ou•Nianzeng Xing•Jiang Lu•Shengqing Wan等 10 人
Nature Communications
2019
•2019/2/12
•Vol.10 No.1 p.1-12
Bladder cancer is one of the most common and highly vascularized cancers. To better understand its genomic structure and underlying etiology, we conduct whole-genome and targeted sequencing in urothelial bladder carcinomas (UBCs, the most common type of bladder cancer). Recurrent mutations in noncod...
Bladder cancerTumour angiogenesis
10.1038/S41467-019-08576-5
ISSN:2041-1723
Conserved DNA architect couples chloroplast development to cell cycle in developing cotyledons
Xiushun Wang•Zhao Zhang•Ting Cao•Wenjing An•Jiarui Zhang等 13 人
Nature Plants
2026
•2026/4/17
•00 p.1-17
Light orchestrates cotyledon greening and growth by coordinating chloroplast development with cell division and expansion, yet the molecular integrator of these processes remains unknown. Here we identify RDE (REGULATOR OF DG1 EXPRESSION), a conserved DNA architectural factor that synchronizes thyla...
Light responsesPlant development
10.1038/S41477-026-02280-1
ISSN:2055-0278
Probing ion channel functional architecture and domain recombination compatibility by massively parallel domain insertion profiling
Coyote-Maestas Willow•Nedrud David•Suma Antonio•He Yungui•Matreyek Kenneth A.等 9 人
Nature Communications
2021
•2021/12/8
•Vol.12 No.1 p.1-16
Protein domains are the basic units of protein structure and function. Comparative analysis of genomes and proteomes showed that domain recombination is a main driver of multidomain protein functional diversification and some of the constraining genomic mechanisms are known. Much less is known about...
Molecular biophysicsPotassium channelsProtein design
10.1038/S41467-021-27342-0
ISSN:2041-1723
Cross-protection and cross-feeding between Klebsiella pneumoniae and Acinetobacter baumannii promotes their co-existence
Semenec Lucie•Cain Amy K.•Dawson Catherine J.•Liu Qi•Dinh Hue等 11 人
Nature Communications
2023
•2023/2/9
•Vol.14 No.1 p.1-18
Acinetobacter baumannii and Klebsiella pneumoniae are opportunistic pathogens frequently co-isolated from polymicrobial infections. The infections where these pathogens co-exist can be more severe and recalcitrant to therapy than infections caused by either species alone, however there is a lack of ...
Microbial communitiesMicrobiologyPathogens
10.1038/S41467-023-36252-2
ISSN:2041-1723
Aberrant expression of a novel circular RNA in pancreatic cancer
Takahiro Seimiya•Motoyuki Otsuka•Takuma Iwata•Eri Tanaka•Kazuma Sekiba等 10 人
Journal Of Human Genetics
2020
•2020/9/3
•Vol.66 No.2 p.181-191
Circular RNAs (circRNAs) are single-stranded, covalently closed RNA molecules that are produced from pre-mRNAs through a process known as back-splicing. Although circRNAs are expressed under specific conditions, current understanding of their comprehensive expression status is still limited. Here, w...
Cancer geneticsTranscriptomics
10.1038/S10038-020-00826-5
ISSN:1434-5161
Impact of antibiotics on off-target infant gut microbiota and resistance genes in cohort studies
Lebeaux Rebecca M.•Madan Juliette C.•Nguyen Quang P.•Coker Modupe O.•Dade Erika F.等 12 人
Pediatric Research
2022
•2022/5/14
•00 p.1-10
Young children are frequently exposed to antibiotics, with the potential for collateral consequences to the gut microbiome. The impact of antibiotic exposures to off-target microbes (i.e., bacteria not targeted by treatment) and antibiotic resistance genes (ARGs) is poorly understood. We used metage...
Medicine/Public Health, generalPediatricsPediatric Surgery
10.1038/S41390-022-02104-W
ISSN:0031-3998
A study of transposable element-associated structural variations (TASVs) using a de novo-assembled Korean genome
Seyoung Mun•Songmi Kim•Wooseok Lee•Keunsoo Kang•Thomas J. Meyer等 8 人
Experimental & Molecular Medicine
2021
•2021/4/8
•Vol.53 No.4 p.615-630
Advances in next-generation sequencing (NGS) technology have made personal genome sequencing possible, and indeed, many individual human genomes have now been sequenced. Comparisons of these individual genomes have revealed substantial genomic differences between human populations as well as between...
Comparative genomicsMobile elementsNext-generation sequencing
10.1038/S12276-021-00586-Y
ISSN:1226-3613
Highly drug resistant clone of Salmonella Kentucky ST198 in clinical infections and poultry in Zimbabwe
Tapfumanei Mashe•Gaetan Thilliez•Blessmore V. Chaibva•Pimlapas Leekitcharoenphon•Matt Bawn等 21 人
Npj Antimicrobials And Resistance
2023
•2023/6/16
•Vol.1 No.1 p.1-11
A highly multidrug-resistant strain of Salmonella enterica serotype Kentucky (S. Kentucky) of sequence type (ST)198 emerged in North Africa and has since spread widely. To investigate the genetic diversity and phylogenetic relationship of S. Kentucky in Zimbabwe and identify potential sources of inf...
Bacterial genesPathogens
10.1038/S44259-023-00003-6
ISSN:2731-8745
Nuclear genome of Bulinus truncatus, an intermediate host of the carcinogenic human blood fluke Schistosoma haematobium
Young Neil D.•Stroehlein Andreas J.•Wang Tao•Korhonen Pasi K.•Mentink-Kane Margaret等 8 人
Nature Communications
2022
•2022/2/21
•Vol.13 No.1 p.1-15
Some snails act as intermediate hosts (vectors) for parasitic flatworms (flukes) that cause neglected tropical diseases, such as schistosomiases. Schistosoma haematobium is a blood fluke that causes urogenital schistosomiasis and induces bladder cancer and increased risk of HIV infection. Understand...
GenomeParasite genomicsZoology
10.1038/S41467-022-28634-9
ISSN:2041-1723
FOXJ1 mediates taxane resistance through regulation of microtubule dynamics
Fang Xie•Ada Gjyrezi•Daniel Fein•Maryam Labaf•Larysa Poluben等 15 人
Nature Communications
2026
•2026/2/14
•Vol.17 No.1 p.27630
Docetaxel is the first-line chemotherapy for metastatic prostate cancer (PC), but clinically meaningful mechanisms of resistance remain to be established. Here we show, in an in vivo model of docetaxel resistant PC patient-derived xenografts, increased expression of genes that drive development of m...
Molecular biologyProstate cancer
10.1038/S41467-026-69556-0
ISSN:2041-1723
Three chromosome-level duck genome assemblies provide insights into genomic variation during domestication
Zhu Feng•Yin Zhong-Tao•Wang Zheng•Smith Jacqueline•Zhang Fan等 22 人
Nature Communications
2021
•2021/10/11
•Vol.12 No.1 p.1-11
Domestic ducks are raised for meat, eggs and feather down, and almost all varieties are descended from the Mallard (Anas platyrhynchos). Here, we report chromosome-level high-quality genome assemblies for meat and laying duck breeds, and the Mallard. Our new genomic databases contain annotations for...
Agricultural geneticsGenomics
10.1038/S41467-021-26272-1
ISSN:2041-1723
Functional and metabolic alterations of gut microbiota in children with new-onset type 1 diabetes
Yuan Xiaoxiao•Wang Ruirui•Han Bing•Sun ChengJun•Chen Ruimin等 27 人
Nature Communications
2022
•2022/10/26
•Vol.13 No.1 p.1-16
Gut dysbiosis has been linked to type 1 diabetes (T1D); however, microbial capacity in T1D remains unclear. Here, we integratively profiled gut microbial functional and metabolic alterations in children with new-onset T1D in independent cohorts and investigated the underlying mechanisms. In T1D, the...
MetagenomicsType 1 diabetes
10.1038/S41467-022-33656-4
ISSN:2041-1723
Parallel evolutionary paths to produce more than one Pseudomonas aeruginosa biofilm phenotype
Janne G. Thöming•Jürgen Tomasch•Matthias Preusse•Michal Koska•Nora Grahl等 10 人
Npj Biofilms And Microbiomes
2020
•2020/1/10
•Vol.6 No.1 p.1-13
Studying parallel evolution of similar traits in independent within-species lineages provides an opportunity to address evolutionary predictability of molecular changes underlying adaptation. In this study, we monitored biofilm forming capabilities, motility, and virulence phenotypes of a plethora o...
BiofilmsNext-generation sequencing
10.1038/S41522-019-0113-6
ISSN:2055-5008
Ubiquitin proteolysis of a CDK-related kinase regulates titan cell formation and virulence in the fungal pathogen Cryptococcus neoformans
Cao Chengjun•Wang Keyi•Wang Yina•Liu Tong-Bao•Rivera Amariliz等 6 人
Nature Communications
2022
•2022/10/27
•Vol.13 No.1 p.1-16
Fungal pathogens often undergo morphological switches, including cell size changes, to adapt to the host environment and cause disease. The pathogenic yeast Cryptococcus neoformans forms so-called ‘titan cells’ during infection. Titan cells are large, polyploid, display alterations in cell wall and ...
Fungal geneticsFungal pathogenesisPathogensUbiquitin ligases
10.1038/S41467-022-34151-6
ISSN:2041-1723
Tandem gene duplications contributed to high-level azole resistance in a rapidly expanding Candida tropicalis population
Xin Fan•Rong-Chen Dai•Shu Zhang•Yuan-Yuan Geng•Mei Kang等 12 人
Nature Communications
2023
•2023/12/15
•Vol.14 No.1 p.1-18
Invasive diseases caused by the globally distributed commensal yeast Candida tropicalis are associated with mortality rates of greater than 50%. Notable increases of azole resistance have been observed in this species, particularly within Asia-Pacific regions. Here, we carried out a genetic populati...
Fungal genomicsFungal infectionGenetic variation
10.1038/S41467-023-43380-2
ISSN:2041-1723
PUM1-TRAF3 fusion protein activates non-canonical NF-κB signaling via rescued NIK in biliary tract cancer
Dawoon E. Jung•Mi-Kyoung Seo•Jung Hyun Jo•Kahee Kim•Chanyang Kim等 10 人
Npj Precision Oncology
2024
•2024/8/1
•Vol.8 No.1 p.1-14
Discovery and verification of diagnostic or therapeutic biomarkers for biliary tract cancer (BTC) is challenging owing to the low prevalence of the disease. Here, we identified and investigated the clinical impact of a fusion gene, Pumilio1-tumor necrosis factor receptor-associated factor 3 (PUM1-TR...
Bile duct cancerPrognostic markers
10.1038/S41698-024-00654-2
ISSN:2397-768X