GenBank Release 266.0
English
United States, Cabin John
The National Center for Biotechnology Information
数据描述
GenBank release 266.0 (4/25/2025) is now available on the NCBI FTP site. This release has 44.02 trillion bases and 5.68 billion records. The current release has: 257,038,531 traditional records containing 5,794,509,308,815 base pairs of sequence data 4,234,652,334 WGS records containing 37,294,058,110,495 base pairs of sequence data 996,759,705 bulk-oriented TSA records containing 852,869,986,922 base pairs of …
www.ncbi.nlm.nih.gov
IP: 130.14.29.110
加载中...
相关论文
278eIF6 deficiency alleviates colorectal cancer by modulating the gut microbiota and related metabolites
Shuai Yang•Jiawei Song•Zhenzhen Wang•Guang Peng•Linglin Tong等 11 人
Cell Death & Differentiation
2026
•2026/1/31
•00 p.1-14
eIF6 is overexpressed in multiple cancers. Previous work has showed that deficiency alters the gut microbiota. This study investigated the mechanism linking eIF6 deficiency, microbial dysbiosis, and colorectal cancer (CRC). eIF6 expression was assessed in human and mouse CRC samples. Functional assa...
GastroenteritisMicrobiology
10.1038/S41418-026-01674-0
ISSN:1350-9047
Conserved mechanism for vacuolar magnesium sequestration in yeast and plant cells
Tang Ren-Jie•Meng Su-Fang•Zheng Xiao-Jiang•Zhang Bin•Yang Yang等 10 人
Nature Plants
2022
•2022/1/27
•00 p.1-10
Magnesium (Mg2+) is an essential nutrient for all life forms. In fungal and plant cells, the majority of Mg2+ is stored in the vacuole but mechanisms for Mg2+ transport into the vacuolar store are not fully understood. Here we demonstrate that members of ancient conserved domain proteins (ACDPs) fro...
Plant breedingPlant cell biologyPlant sciences
10.1038/S41477-021-01087-6
ISSN:2055-0278
Gene duplication drives genome expansion in a major lineage of Thaumarchaeota
Paul O. Sheridan•Sebastien Raguideau•Christopher Quince•Jennifer Holden•Lihong Zhang等 7 人
Nature Communications
2020
•2020/10/30
•Vol.11 No.1 p.1-12
Ammonia-oxidising archaea of the phylum Thaumarchaeota are important organisms in the nitrogen cycle, but the mechanisms driving their radiation into diverse ecosystems remain underexplored. Here, existing thaumarchaeotal genomes are complemented with 12 genomes belonging to the previously under-sam...
Archaeal genomicsGenome evolutionMetagenomicsPhylogenetics
10.1038/S41467-020-19132-X
ISSN:2041-1723
A flavin-monooxygenase catalyzing oxepinone formation and the complete biosynthesis of vibralactone
Ke-Na Feng•Yue Zhang•Mingfang Zhang•Yan-Long Yang•Ji-Kai Liu等 7 人
Nature Communications
2023
•2023/6/10
•Vol.14 No.1 p.1-13
Oxepinone rings represent one of structurally unusual motifs of natural products and the biosynthesis of oxepinones is not fully understood. 1,5-Seco-vibralactone (3) features an oxepinone motif and is a stable metabolite isolated from mycelial cultures of the mushroom Boreostereum vibrans. Cyclizat...
BiosynthesisNatural product synthesisOxidoreductasesX-ray crystallography
10.1038/S41467-023-39108-X
ISSN:2041-1723
Cabotegravir and rilpivirine for treatment of HIV infection in Africa: week 96 results from the phase 3b randomized, open-label, noninferiority CARES trial
Cissy Kityo•Ivan K. Mambule•Joseph Musaazi•Simiso Sokhela•Henry Mugerwa等 20 人
Nature Medicine
2025
•2025/11/4
•00 p.1-10
Evaluation of the durable efficacy and safety of long-acting injectable therapy for HIV is needed in African populations. In a multicenter, open-label phase 3b trial, 512 African adults with HIV-1, stable on first-line oral therapy, with screening plasma viral load (VL) <50 copies ml−1 and withou...
Randomized controlled trialsTranslational research
10.1038/S41591-025-04041-7
ISSN:1078-8956
Biosynthesis of peptide–nucleobase hybrids in ribosomal peptides
Zeng-Fei Pei•Natalia M. Vior•Lingyang Zhu•Andrew W. Truman•Satish K. Nair
Nature Chemical Biology
2024
•2024/9/16
•00 p.1-12
The main biopolymers in nature are oligonucleotides and polypeptides. However, naturally occurring peptide–nucleobase hybrids are rare. Here we report the characterization of the founding member of a class of peptide–nucleobase hybrid natural products with a pyrimidone motif from a widely distribute...
BiosynthesisEnzymesPeptides
10.1038/S41589-024-01736-9
ISSN:1552-4450
Genetic assessment and Identification of genes related to characterization of Guangdong local goose breeds based on modern and historical genomes
Xing Zhang•Guiling Qiu•Dechun Huang•Zheng Ma•Jixiang Wei等 14 人
Communications Biology
2025
•2025/7/30
•Vol.8 No.1 p.1-12
Guangdong province has diverse local goose breeds with unique characteristics, but there is limited research on their genetic diversity, formation history and breed-specific genes. This study uses whole-genome sequencing to analyze 120 local geese representing four officially recognized breeds and t...
Animal breedingGenetic variation
10.1038/S42003-025-08550-6
ISSN:2399-3642
A 2.09 Mb fragment translocation on chromosome 6 causes abnormalities during meiosis and leads to less seed watermelon
Tian Shujuan•Ge Jie•Ai Gongli•Jiang Jiao•Liu Qiyan等 10 人
Horticulture Research
2021
•2021/12/1
•Vol.8 No.1 p.1-13
Seedlessness is a valuable agronomic trait in watermelon (Citrullus lanatus) breeding. Conventional less seed watermelons are mainly triploid, which has many disadvantages due to unbalanced genome content. Less seed watermelon can be achieved at the diploid level when certain reproductive genes are ...
Developmental biologyExperimental organisms
10.1038/S41438-021-00687-9
ISSN:2662-6810
l-theanine-targeted prefrontal cortex improves CUMS-induced depression via the gut-short-chain fatty acids-brain axis
Ying Peng•Tianxing Yu•Chunyin Qin•Feilong Li•Zhuoqi Xu等 11 人
Npj Science Of Food
2025
•2025/12/1
0Depression has emerged as a major global public health issue. l-theanine exerts notable anxiolytic and antidepressant effects mediated by its blood-brain barrier permeability as well as its anti-inflammatory and antioxidant properties. Nevertheless, the underlying mechanism of its key role remains e...
BiochemistryDiseasesDrug discoveryMicrobiologyNeuroscience
10.1038/S41538-025-00651-0
ISSN:2396-8370
TranDep: a transcriptomics atlas of depression
Xiaogang Zhong•Siwen Gui•Dongfang Wang•Yong He•Xiang Chen等 17 人
Molecular Psychiatry
2026
•2026/6/30
•00 p.1-10
Depression is a severe mental illness that poses substantial burdens on public health. Given that depression research is still challenged by its multifaceted pathogenesis, depicting the depression associated genetic regulatory networks is essential for understanding its mechanism, optimizing diagnos...
DepressionNeuroscience
10.1038/S41380-026-03726-W
ISSN:1359-4184
Iron restriction inside macrophages regulates pulmonary host defense against Rhizopus species
Angeliki M. Andrianaki•Irene Kyrmizi•Kalliopi Thanopoulou•Clara Baldin•Elias Drakos等 23 人
Nature Communications
2018
•2018/8/20
•Vol.9 No.1 p.1-17
Mucormycosis is a life-threatening respiratory fungal infection predominantly caused by Rhizopus species. Mucormycosis has incompletely understood pathogenesis, particularly how abnormalities in iron metabolism compromise immune responses. Here we show how, as opposed to other filamentous fungi, Rhi...
Fungal host responseFungal infectionFungal pathogenesisInfection
10.1038/S41467-018-05820-2
ISSN:2041-1723
Selective activator of human ClpP triggers cell cycle arrest to inhibit lung squamous cell carcinoma
Lin-Lin Zhou•Tao Zhang•Yun Xue•Chuan Yue•Yihui Pan等 13 人
Nature Communications
2023
•2023/11/3
•Vol.14 No.1 p.1-15
Chemo-activation of mitochondrial ClpP exhibits promising anticancer properties. However, we are currently unaware of any studies using selective and potent ClpP activators in lung squamous cell carcinoma. In this work, we report on such an activator, ZK53, which exhibits therapeutic effects on lung...
Drug discovery and developmentNon-small-cell lung cancerProteases
10.1038/S41467-023-42784-4
ISSN:2041-1723
Precise, predictable multi-nucleotide deletions in rice and wheat using APOBEC–Cas9
Shengxing Wang•Yuan Zong•Qiupeng Lin•Huawei Zhang•Zhuangzhuang Chai等 9 人
Nature Biotechnology
2020
•2020/6/29
•Vol.38 No.12 p.1460-1465
Short insertions and deletions can be produced in plant genomes using CRISPR–Cas editors, but reliable production of larger deletions in specific target sites has proven difficult to achieve. We report the development of a series of APOBEC–Cas9 fusion-induced deletion systems (AFIDs) that combine Ca...
BiotechnologyPlant biotechnologyPlant molecular biologyPlant sciences
10.1038/S41587-020-0566-4
ISSN:1087-0156
Robust mucosal SARS-CoV-2-specific T cells effectively combat COVID-19 and establish polyfunctional resident memory in patient lungs
Airu Zhu•Zhao Chen•Qihong Yan•Mei Jiang•Xuesong Liu等 42 人
Nature Immunology
2025
•2025/1/28
•Vol.26 No.3 p.459-472
Mucosal antigen-specific T cells are pivotal for pathogen clearance and immune modulation in respiratory infections. Dysregulated T cell responses exacerbate coronavirus disease 2019 severity, marked by cytokine storms and respiratory failure. Despite extensive description in peripheral blood, the c...
Adaptive immunityViral infection
10.1038/S41590-024-02072-9
ISSN:1529-2908
Deep sea cold seeps are a sink for mercury and source for methylmercury
Jiwei Li•Xiyang Dong•Yongjie Tang•Chuwen Zhang•Yali Yang等 13 人
Communications Earth & Environment
2024
•2024/6/14
•Vol.5 No.1 p.1-10
The effect of seafloor cold seeps on the biogeochemical cycling of mercury (Hg) remains enigmatic. Here we demonstrate substantial enrichments of mercury and methylmercury, along with the presence of microbes capable of metabolizing mercury in sediments of the Haima cold seep, South China Sea, by an...
Element cyclesMarine chemistry
10.1038/S43247-024-01484-7
ISSN:2662-4435
Enzymatic β-elimination in natural product O- and C-glycoside deglycosylation
Johannes Bitter•Martin Pfeiffer•Annika J. E. Borg•Kirill Kuhlmann•Tea Pavkov-Keller等 7 人
Nature Communications
2023
•2023/11/6
•Vol.14 No.1 p.1-17
Biological degradation of natural product glycosides involves, alongside hydrolysis, β-elimination for glycosidic bond cleavage. Here, we discover an O-glycoside β-eliminase (OGE) from Agrobacterium tumefaciens that converts the C3-oxidized O-β-d-glucoside of phloretin (a plant-derived flavonoid) in...
BiocatalysisEnzyme mechanismsEnzymesGlycosidesX-ray crystallography
10.1038/S41467-023-42750-0
ISSN:2041-1723
Microbial iron oxide respiration coupled to sulfide oxidation
Song-Can Chen•Xiao-Min Li•Nicola Battisti•Guoqing Guan•Maria A. Montoya等 13 人
Nature
2025
•2025/8/27
•00 p.1-9
Microorganisms have driven Earth’s sulfur cycle since the emergence of life1–6, yet the sulfur-cycling capacities of microorganisms and their integration with other element cycles remain incompletely understood. One such uncharacterized metabolism is the coupling of sulfide oxidation with iron(iii) ...
Element cyclesEnvironmental microbiology
10.1038/S41586-025-09467-0
ISSN:0028-0836
Transcriptional profiling of human microglia reveals grey–white matter heterogeneity and multiple sclerosis-associated changes
Marlijn van der Poel•Thomas Ulas•Mark R. Mizee•Cheng-Chih Hsiao•Suzanne S. M. Miedema等 12 人
Nature Communications
2019
•2019/3/13
•Vol.10 No.1 p.1-13
Here we report the transcriptional profile of human microglia, isolated from normal-appearing grey matter (GM) and white matter (WM) of multiple sclerosis (MS) and non-neurological control donors, to find possible early changes related to MS pathology. Microglia show a clear region-specific profile,...
MicrogliaMultiple sclerosisTranscriptomics
10.1038/S41467-019-08976-7
ISSN:2041-1723
Single-cell sequencing reveals increased LAMB3-positive basal keratinocytes and ZNF90-positive fibroblasts in autologous cultured epithelium
Weiling Lian•Xuanhao Zeng•Jian Li•Qing Zang•Yating Liu等 14 人
Communications Biology
2024
•2024/1/10
•Vol.7 No.1 p.1-13
Autologous cultured epithelium grafting (ACEG) presents a promising treatment for refractory vitiligo, yet concerns regarding infections and immunological reactions hinder its surgical use due to serum and feeder dependencies. Addressing this, we culture autologous epithelium under serum- and feeder...
BioinformaticsCellular signalling networksRegenerative medicineSkin stem cellsTissue engineering
10.1038/S42003-023-05747-5
ISSN:2399-3642
Auxin-producing bacteria promote barley rhizosheath formation
Feiyun Xu•Hanpeng Liao•Jinyong Yang•Yingjiao Zhang•Peng Yu等 18 人
Nature Communications
2023
•2023/9/19
•Vol.14 No.1 p.1-12
The rhizosheath, or the layer of soil closely adhering to roots, can help plants to tolerate drought under moderate soil drying conditions. Rhizosheath formation is the result of poorly understood interactions between root exudates, microbes, and soil conditions. Here, we study the roles played by t...
Microbial ecologyPlant symbiosisSoil microbiologySymbiosis
10.1038/S41467-023-40916-4
ISSN:2041-1723
Human adipose and umbilical cord mesenchymal stem cell-derived extracellular vesicles mitigate photoaging via TIMP1/Notch1
Huan Zhang•Xian Xiao•Liping Wang•Xianhao Shi•Nan Fu等 7 人
Signal Transduction And Targeted Therapy
2024
•2024/10/30
•Vol.9 No.1 p.1-17
UVB radiation induces oxidative stress, DNA damage, and inflammation, leading to skin wrinkling, compromised barrier function, and an increased risk of carcinogenesis. Addressing or preventing photoaging may offer a promising therapeutic avenue for these conditions. Recent research indicated that me...
Mesenchymal stem cellsSenescence
10.1038/S41392-024-01993-Z
ISSN:2059-3635
Monolignol acyltransferase for lignin p-hydroxybenzoylation in Populus
Zhao Yunjun•Yu Xiaohong•Lam Pui-Ying•Zhang Kewei•Tobimatsu Yuki等 6 人
Nature Plants
2021
•2021/8/5
•00 p.1-13
Plant lignification exhibits notable plasticity. Lignin in many species, including Populus spp., has long been known to be decorated with p-hydroxybenzoates. However, the molecular basis for such structural modification remains undetermined. Here, we report the identification and characterization of...
Cell wallSecondary metabolism
10.1038/S41477-021-00975-1
ISSN:2055-0278
Detection of a SARS-CoV-2 variant of concern in South Africa
Houriiyah Tegally•Eduan Wilkinson•Marta Giovanetti•Arash Iranzadeh•Vagner Fonseca等 47 人
Nature
2021
•2021/3/9
•00 p.1-6
Continued uncontrolled transmission of SARS-CoV-2 in many parts of the world is creating conditions for substantial evolutionary changes to the virus1,2. Here we describe a newly arisen lineage of SARS-CoV-2 (designated 501Y.V2; also known as B.1.351 or 20H) that is defined by eight mutations in the...
EpidemiologyMolecular evolutionSARS-CoV-2
10.1038/S41586-021-03402-9
ISSN:0028-0836
The role of gene duplication and paralog specialisation in the evolution of the mammalian PRPS complex
Bibek R. Karki•Austin C. MacMillan•Sara Vicente-Muñoz•Kenneth D. Greis•Lindsey E. Romick等 6 人
Nature Communications
2025
•2025/7/8
•Vol.16 No.1 p.1-18
The phosphoribosyl pyrophosphate synthetase (PRPS) enzyme catalyzes a chokepoint reaction in nucleotide production, making it essential for life. Here, we show that the presence of multiple PRPS-encoding genes is a hallmark trait of eukaryotes, and we find that gains or losses of paralogs are associ...
Evolutionary geneticsMolecular evolutionMultienzyme complexes
10.1038/S41467-025-61216-Z
ISSN:2041-1723
Carbon fixation and energy metabolisms of a subseafloor olivine biofilm
Amy R. Smith•Brandon Kieft•Ryan Mueller•Martin R. Fisk•Olivia U. Mason等 7 人
The Isme Journal
2019
•2019/3/12
•Vol.13 No.7 p.1737-1749
Earth’s largest aquifer ecosystem resides in igneous oceanic crust, where chemosynthesis and water-rock reactions provide the carbon and energy that support an active deep biosphere. The Calvin Cycle is the predominant carbon fixation pathway in cool, oxic, crust; however, the energy and carbon meta...
BiogeochemistryMetagenomics
10.1038/S41396-019-0385-0
ISSN:1751-7362
A spatial hierarchical network learning framework for drug repositioning allowing interpretation from macro to micro scale
Zhonghao Ren•Xiangxiang Zeng•Yizhen Lao•Heping Zheng•Zhuhong You等 7 人
Communications Biology
2024
•2024/10/30
•Vol.7 No.1 p.1-18
Biomedical network learning offers fresh prospects for expediting drug repositioning. However, traditional network architectures struggle to quantify the relationship between micro-scale drug spatial structures and corresponding macro-scale biomedical networks, limiting their ability to capture key ...
Biochemical reaction networksComputational chemistryComputational modelsVirtual screening
10.1038/S42003-024-07107-3
ISSN:2399-3642
Multiple system biology approaches reveals the role of the hsa-miR-21 in increasing risk of neurological disorders in patients suffering from hypertension
Sanjana Mishra•Prekshi Garg•Mala Trivedi•Prachi Srivastava
Journal Of Human Hypertension
2025
•2025/5/20
•00 p.1-10
Hypertension is a prevalent disease that substantially elevates the risk of neurological disorders such as dementia, stroke and Parkinson’s disease. MicroRNAs (miRNAs) play a critical role in the regulation of gene expression related to brain function and disorders. Understanding the involvement of ...
HypertensionLifestyle modification
10.1038/S41371-025-01027-3
ISSN:1476-5527
Repeated species radiations in the recent evolution of the key marine phytoplankton lineage Gephyrocapsa
El Mahdi Bendif•Bruno Nevado•Edgar L. Y. Wong•Kyoko Hagino•Ian Probert等 8 人
Nature Communications
2019
•2019/9/17
•Vol.10 No.1 p.1-9
Phytoplankton account for nearly half of global primary productivity and strongly affect the global carbon cycle, yet little is known about the forces that drive the evolution of these keystone microscopic organisms. Here we combine morphometric data from the fossil record of the ubiquitous coccolit...
Adaptive radiationEvolutionary geneticsMarine biologyPalaeontology
10.1038/S41467-019-12169-7
ISSN:2041-1723
Bridge RNAs direct programmable recombination of target and donor DNA
Matthew G. Durrant•Nicholas T. Perry•James J. Pai•Aditya R. Jangid•Januka S. Athukoralage等 11 人
Nature
2024
•2024/6/26
•Vol.630 No.8018 p.984-993
Genomic rearrangements, encompassing mutational changes in the genome such as insertions, deletions or inversions, are essential for genetic diversity. These rearrangements are typically orchestrated by enzymes that are involved in fundamental DNA repair processes, such as homologous recombination, ...
DNA recombinationMicrobial geneticsNon-coding RNAsTransposition
10.1038/S41586-024-07552-4
ISSN:0028-0836
Environmental DNA monitoring of oncogenic viral shedding and genomic profiling of sea turtle fibropapillomatosis reveals unusual viral dynamics
Jessica A. Farrell•Kelsey Yetsko•Liam Whitmore•Jenny Whilde•Catherine B. Eastman等 12 人
Communications Biology
2021
•2021/5/12
•Vol.4 No.1 p.1-17
Pathogen-induced cancers account for 15% of human tumors and are a growing concern for endangered wildlife. Fibropapillomatosis is an expanding virally and environmentally co-induced sea turtle tumor epizootic. Chelonid herpesvirus 5 (ChHV5) is implicated as a causative virus, but its transmission m...
HerpetologyTumour virus infections
10.1038/S42003-021-02085-2
ISSN:2399-3642
Chloroplast and whole-genome sequencing shed light on the evolutionary history and phenotypic diversification of peanuts
Zheng Zheng•Ziqi Sun•Feiyan Qi•Yuanjin Fang•Ke Lin等 29 人
Nature Genetics
2024
•2024/8/13
•00 p.1-10
Cultivated peanut (Arachis hypogaea L.) is a widely grown oilseed crop worldwide; however, the events leading to its origin and diversification are not fully understood. Here by combining chloroplast and whole-genome sequence data from a large germplasm collection, we show that the two subspecies of...
DNA sequencingGenome-wide association studies
10.1038/S41588-024-01876-7
ISSN:1061-4036
Comparative activity of sulbactam and sulbactam/durlobactam against carbapenem-resistant A. baumannii isolates producing OXA-23 or OXA-23 plus PER-1 enzymes
Hasan Cenk Mirza•Aylin Üsküdar Güçlü•Sezin Ünlü•Süleyman Yalçın
The Journal Of Antibiotics
2026
•2026/4/10
•00 p.1-8
Our objective was to compare the in vitro activity of sulbactam and sulbactam/durlobactam against carbapenem-resistant A. baumannii isolates carrying blaOXA−23 or both blaOXA−23 and blaPER-1 genes. We also aimed to investigate the possible mechanisms of resistance in sulbactam/durlobactam resistant ...
AntibioticsBacteriology
10.1038/S41429-026-00919-X
ISSN:0021-8820
Bet hedging in a unicellular microalga
Si Tang•Yaqing Liu•Jianming Zhu•Xueyu Cheng•Lu Liu等 8 人
Nature Communications
2024
•2024/3/7
•Vol.15 No.1 p.1-13
Understanding how organisms have adapted to persist in unpredictable environments is a fundamental goal in biology. Bet hedging, an evolutionary adaptation observed from microbes to humans, facilitates reproduction and population persistence in randomly fluctuating environments. Despite its prevalen...
Evolutionary theoryMicrobial ecology
10.1038/S41467-024-46297-6
ISSN:2041-1723
Blood DNA virome associates with autoimmune diseases and COVID-19
Noah Sasa•Shohei Kojima•Rie Koide•Takanori Hasegawa•Ho Namkoong等 132 人
Nature Genetics
2025
•2025/1/3
•Vol.57 No.1 p.65-79
Aberrant immune responses to viral pathogens contribute to pathogenesis, but our understanding of pathological immune responses caused by viruses within the human virome, especially at a population scale, remains limited. We analyzed whole-genome sequencing datasets of 6,321 Japanese individuals, in...
Autoimmune diseasesImmunogeneticsInfectious diseasesMicrobial genetics
10.1038/S41588-024-02022-Z
ISSN:1061-4036
TIR immune signalling is blocked by phosphorylation to maintain plant growth
Jun Li•Sisi Chen•Bo Yu•Qingzhong Li•Ruijia Liu等 8 人
Nature Plants
2025
•2025/6/9
•00 p.1-12
Toll/interleukin-1 receptor (TIR) domain proteins are immune signalling components and function as NAD+-cleaving enzymes to activate defence responses. In plants, TIR activation triggers cell death and severely represses growth, especially under osmotic stress, while in animals, it promotes axon deg...
DroughtEffectors in plant pathology
10.1038/S41477-025-02012-X
ISSN:2055-0278
SARS-CoV-2 infection of human lung epithelial cells induces TMPRSS-mediated acute fibrin deposition
Rachel Erickson•Chang Huang•Cameron Allen•Joanna Ireland•Gwynne Roth等 18 人
Nature Communications
2023
•2023/10/11
•Vol.14 No.1 p.1-15
Severe COVID-associated lung injury is a major confounding factor of hospitalizations and death with no effective treatments. Here, we describe a non-classical fibrin clotting mechanism mediated by SARS-CoV-2 infected primary lung but not other susceptible epithelial cells. This infection-induced fi...
InfectionSARS-CoV-2Viral infection
10.1038/S41467-023-42140-6
ISSN:2041-1723
scRNA-seq generates a molecular map of emerging cell subtypes after sciatic nerve injury in rats
Lovatt Ditte•Tamburino Alex•Krasowska-Zoladek Alicja•Sanoja Raul•Li Lixia等 8 人
Communications Biology
2022
•2022/10/19
•Vol.5 No.1 p.1-17
Patients with peripheral nerve injury, viral infection or metabolic disorder often suffer neuropathic pain due to inadequate pharmacological options for relief. Developing novel therapies has been challenged by incomplete mechanistic understanding of the cellular microenvironment in sensory nerve th...
NeuroscienceTranscriptomics
10.1038/S42003-022-03970-0
ISSN:2399-3642
Ecology and molecular targets of hypermutation in the global microbiome
Simon Roux•Blair G. Paul•Sarah C. Bagby•Stephen Nayfach•Michelle A. Allen等 19 人
Nature Communications
2021
•2021/5/24
•Vol.12 No.1 p.1-12
Changes in the sequence of an organism’s genome, i.e., mutations, are the raw material of evolution. The frequency and location of mutations can be constrained by specific molecular mechanisms, such as diversity-generating retroelements (DGRs). DGRs have been characterized from cultivated bacteria a...
Environmental microbiologyMolecular evolutionPhage biology
10.1038/S41467-021-23402-7
ISSN:2041-1723
Combining AI to reveal CCDC3-mediated pathways of colorectal cancer liver metastasis
Runze Huang•Qinyu Liu•Xin Jin•Xuanci Bai•Yibin Wu等 12 人
Npj Digital Medicine
2026
•2026/3/7
0In colorectal cancer liver metastases, chromosomal instability (CIN) serves as a critical hallmark linked to tumor aggressiveness and poor prognosis. This study integrated single-cell RNA sequencing, weighted gene co-expression network analysis, and non-negative matrix factorization to construct a c...
CancerComputational biology and bioinformaticsOncology
10.1038/S41746-026-02457-0
ISSN:2398-6352
PDK1-dependent metabolic reprogramming regulates stemness and tumorigenicity of osteosarcoma stem cells through ATF3
Kazuya Tokumura•Kazuya Fukasawa•Jiro Ichikawa•Koki Sadamori•Manami Hiraiwa等 6 人
Cell Death & Disease
2025
•2025/7/29
•Vol.16 No.1 p.1-14
Osteosarcoma stem cells (OSCs) are characterized by their self-renewal and multilineage differentiation abilities, contributing to osteosarcoma malignancy. The Warburg effect describes cancer cells’ preference for glycolysis over mitochondrial oxidative phosphorylation (OXPHOS) for energy production...
Bone cancer
10.1038/S41419-025-07903-7
ISSN:2041-4889
Molecular characterization of a marine turtle tumor epizootic, profiling external, internal and postsurgical regrowth tumors
Kelsey Yetsko•Jessica A. Farrell•Nicholas B. Blackburn•Liam Whitmore•Maximilian R. Stammnitz等 21 人
Communications Biology
2021
•2021/2/1
•Vol.4 No.1 p.1-16
Sea turtle populations are under threat from an epizootic tumor disease (animal epidemic) known as fibropapillomatosis. Fibropapillomatosis continues to spread geographically, with prevalence of the disease also growing at many longer-affected sites globally. However, we do not yet understand the pr...
CancerCancer genomicsCancer modelsConservation biologyEcology
10.1038/S42003-021-01656-7
ISSN:2399-3642
Neutralizing antibodies reveal cryptic vulnerabilities and interdomain crosstalk in the porcine deltacoronavirus spike protein
Wenjuan Du•Oliver Debski-Antoniak•Dubravka Drabek•Rien van Haperen•Melissa van Dortmondt等 11 人
Nature Communications
2024
•2024/6/22
•Vol.15 No.1 p.1-13
Porcine deltacoronavirus (PDCoV) is an emerging enteric pathogen that has recently been detected in humans. Despite this zoonotic concern, the antigenic structure of PDCoV remains unknown. The virus relies on its spike (S) protein for cell entry, making it a prime target for neutralizing antibodies....
AntibodiesCryoelectron microscopyViral immune evasion
10.1038/S41467-024-49693-0
ISSN:2041-1723
A dual-target molecular mechanism of pyrethrum repellency against mosquitoes
Feng Liu•Qiang Wang•Peng Xu•Felipe Andreazza•Wilson R. Valbon等 19 人
Nature Communications
2021
•2021/5/5
•Vol.12 No.1 p.1-9
Pyrethrum extracts from flower heads of Chrysanthemum spp. have been used worldwide in insecticides and repellents. While the molecular mechanisms of its insecticidal action are known, the molecular basis of pyrethrum repellency remains a mystery. In this study, we find that the principal components...
NeurosciencePhysiology
10.1038/S41467-021-22847-0
ISSN:2041-1723
ADP binding by the Culex quinquefasciatus mosquito D7 salivary protein enhances blood feeding on mammals
Ines Martin-Martin•Andrew Paige•Paola Carolina Valenzuela Leon•Apostolos G. Gittis•Olivia Kern等 11 人
Nature Communications
2020
•2020/6/9
•Vol.11 No.1 p.1-15
During blood-feeding, mosquito saliva is injected into the skin to facilitate blood meal acquisition. D7 proteins are among the most abundant components of the mosquito saliva. Here we report the ligand binding specificity and physiological relevance of two D7 long proteins from Culex quinquefasciat...
EntomologyNucleotide-binding proteinsX-ray crystallography
10.1038/S41467-020-16665-Z
ISSN:2041-1723
ABA-independent PP2C-binding in PYLs traces to bacterial origins and persists in land plants
Tianjiao Lu•Qingzhong Li•Tao Hu•Wenqi Li•Yafei Lu等 7 人
Nature Communications
2025
•2025/12/16
•Vol.16 No.1 p.112610
Land plants have evolved strategies to survive water deficiency. Among these adaptations, the “drying without dying” strategy evolved in early land plants and is maintained in the desiccated seeds of angiosperms. This process is regulated by a family of ABA receptors known as the PYR/PYL/RCAR (PYL) ...
AbioticPlant hormonesPlant signalling
10.1038/S41467-025-66141-9
ISSN:2041-1723
Phage-plasmids promote recombination and emergence of phages and plasmids
Eugen Pfeifer•Eduardo P. C. Rocha
Nature Communications
2024
•2024/2/20
•Vol.15 No.1 p.1-13
Phages and plasmids are regarded as distinct types of mobile genetic elements that drive bacterial evolution by horizontal gene transfer. However, the distinction between both types is blurred by the existence of elements known as prophage-plasmids or phage-plasmids, which transfer horizontally betw...
BacteriophagesData processingMolecular evolutionPhage biology
10.1038/S41467-024-45757-3
ISSN:2041-1723
The structure of the teleost Immunoglobulin M core provides insights on polymeric antibody evolution, assembly, and function
Mengfan Lyu•Andrey G. Malyutin•Beth M. Stadtmueller
Nature Communications
2023
•2023/11/21
•Vol.14 No.1 p.1-14
Polymeric (p) immunoglobulins (Igs) serve broad functions during vertebrate immune responses. Typically, pIgs contain between two and six Ig monomers, each with two antigen binding fragments and one fragment crystallization (Fc). In addition, many pIgs assemble with a joining-chain (JC); however, th...
AntibodiesCryoelectron microscopyImmunogenetics
10.1038/S41467-023-43240-Z
ISSN:2041-1723
High-efficiency leucoplast transit peptides for manipulating plastid protein production
Chiung-Chih Chu•Chia-Ying Han•Hsou-min Li
Nature Plants
2025
•2025/6/13
•00 p.1-9
Plastids develop into nutrient-storing leucoplasts in seeds and roots. Efficient protein delivery is essential to modify biosynthetic processes in leucoplasts for human needs, but no effective transit peptide for leucoplasts is currently available. Here, using an in vitro leucoplast import system, w...
Molecular engineering in plantsPlant cell biology
10.1038/S41477-025-02020-X
ISSN:2055-0278
A scalable platform to discover antimicrobials of ribosomal origin
Ayikpoe Richard S.•Shi Chengyou•Battiste Alexander J.•Eslami Sara M.•Ramesh Sangeetha等 19 人
Nature Communications
2022
•2022/10/17
•Vol.13 No.1 p.1-15
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a promising source of new antimicrobials in the face of rising antibiotic resistance. Here, we report a scalable platform that combines high-throughput bioinformatics with automated biosynthetic gene cluster refactoring f...
Natural productsPeptidesStructure elucidationSynthetic biology
10.1038/S41467-022-33890-W
ISSN:2041-1723
Deep mining reveals the diversity of endogenous viral elements in vertebrate genomes
Jose Gabriel Nino Barreat•Aris Katzourakis
Nature Microbiology
2024
•2024/10/22
•Vol.9 No.11 p.3013-3024
Integration of viruses into host genomes can give rise to endogenous viral elements (EVEs), which provide insights into viral diversity, host range and evolution. A systematic search for EVEs is becoming computationally challenging given the available genomic data. We used a cloud-computing approach...
EcologyEvolution
10.1038/S41564-024-01825-4
ISSN:2058-5276
Detection of hidden antibiotic resistance through real-time genomics
Ela Sauerborn•Nancy Carolina Corredor•Tim Reska•Albert Perlas•Samir Vargas da Fonseca Atum等 10 人
Nature Communications
2024
•2024/6/28
•Vol.15 No.1 p.1-8
Real-time genomics through nanopore sequencing holds the promise of fast antibiotic resistance prediction directly in the clinical setting. However, concerns about the accuracy of genomics-based resistance predictions persist, particularly when compared to traditional, clinically established diagnos...
Antimicrobial resistanceBacterial geneticsBacterial infectionMedical genomics
10.1038/S41467-024-49851-4
ISSN:2041-1723
Differential gut transmission of IncP plasmid clades involving hypervirulent Klebsiella pneumoniae reveals plasmid-specific ecological adaptation
Melvin Yong•Wen Wen Low•Swapnil Mishra•Galain Williams•Steven Mileto等 14 人
Nature Communications
2025
•2025/12/10
0Conjugative plasmids can drive the global spread of antimicrobial resistance (AMR) in Enterobacterales. Hypervirulent Klebsiella pneumoniae (hvKp) increasingly acquire AMR plasmids, raising concern about convergent hypervirulent drug-resistant clones. Yet little is known about plasmid transmission d...
Bacterial evolutionBacterial infection
10.1038/S41467-025-66413-4
ISSN:2041-1723
A clinically practical model for the preoperative prediction of lymph node metastasis in bladder cancer: a multicohort study
Junlin Lu•Jiajian Lai•Kanghua Xiao•Shengmeng Peng•Yangjie Zhang等 12 人
British Journal Of Cancer
2023
•2023/8/4
•00 p.1-10
The aim of this study was to construct a clinically practical model to precisely predict lymph node (LN) metastasis in bladder cancer patients. Four independent cohorts were included. The least absolute shrinkage and selection operator regression with multivariate logistic regression were applied. T...
Bladder cancerPredictive markers
10.1038/S41416-023-02383-Y
ISSN:0007-0920
Ultrasensitive and visual detection of SARS-CoV-2 using all-in-one dual CRISPR-Cas12a assay
Xiong Ding•Kun Yin•Ziyue Li•Rajesh V. Lalla•Enrique Ballesteros等 7 人
Nature Communications
2020
•2020/9/18
•Vol.11 No.1 p.1-10
The recent outbreak of novel coronavirus (SARS-CoV-2) causing COVID-19 disease spreads rapidly in the world. Rapid and early detection of SARS-CoV-2 facilitates early intervention and prevents the disease spread. Here, we present an All-In-One Dual CRISPR-Cas12a (AIOD-CRISPR) assay for one-pot, ultr...
Analytical biochemistryAssay systemsBiochemical assaysGenetic testingInfectious diseases
10.1038/S41467-020-18575-6
ISSN:2041-1723
A single transcription factor facilitates an insect host combating Bacillus thuringiensis infection while maintaining fitness
Guo Zhaojiang•Guo Le•Qin Jianying•Ye Fan•Sun Dan等 12 人
Nature Communications
2022
•2022/10/12
•Vol.13 No.1 p.1-15
Maintaining fitness during pathogen infection is vital for host survival as an excessive response can be as detrimental as the infection itself. Fitness costs are frequently associated with insect hosts countering the toxic effect of the entomopathogenic bacterium Bacillus thuringiensis (Bt), which ...
Bacterial host responseBacterial toxinsEntomologyGene regulation
10.1038/S41467-022-33706-X
ISSN:2041-1723
The role of nitric oxide synthase in biofilm formation by Staphylococcus aureus
Yi Huang•Yu Cheng•Yingying Shi•Xiaoqiong Wang•Samira Khodi Aghmiuni等 9 人
Npj Biofilms And Microbiomes
2025
•2025/12/18
0Staphylococcus aureus is capable of colonizing diverse environments and forming biofilms. In this study, we found that the knockout of NO synthase (NOS) impaired biofilm integrity, resulting in weakened biofilms. We found the deletion of the nos reduced intracellular NO levels, which subsequently al...
BiochemistryMicrobiology
10.1038/S41522-025-00870-Z
ISSN:2055-5008
Entamoeba and Giardia parasites implicated as hosts of CRESS viruses
Cormac M. Kinsella•Aldert Bart•Martin Deijs•Patricia Broekhuizen•Joanna Kaczorowska等 9 人
Nature Communications
2020
•2020/9/15
•Vol.11 No.1 p.1-10
Metagenomic techniques have enabled genome sequencing of unknown viruses without isolation in cell culture, but information on the virus host is often lacking, preventing viral characterisation. High-throughput methods capable of identifying virus hosts based on genomic data alone would aid evaluati...
Parasite genomicsPhylogeneticsViral evolutionViral host response
10.1038/S41467-020-18474-W
ISSN:2041-1723
Genomic insights into the evolution of Echinochloa species as weed and orphan crop
Wu Dongya•Shen Enhui•Jiang Bowen•Feng Yu•Tang Wei等 32 人
Nature Communications
2022
•2022/2/3
•Vol.13 No.1 p.1-16
As one of the great survivors of the plant kingdom, barnyard grasses (Echinochloa spp.) are the most noxious and common weeds in paddy ecosystems. Meanwhile, at least two Echinochloa species have been domesticated and cultivated as millets. In order to better understand the genomic forces driving th...
Agricultural geneticsComparative genomicsGenome evolutionPlant evolution
10.1038/S41467-022-28359-9
ISSN:2041-1723
Methanotrophic Methanoperedens archaea host diverse and interacting extrachromosomal elements
Ling-Dong Shi•Jacob West-Roberts•Marie C. Schoelmerich•Petar I. Penev•LinXing Chen等 9 人
Nature Microbiology
2024
•2024/6/25
•00 p.1-12
Methane emissions are mitigated by anaerobic methane-oxidizing archaea, including Methanoperedens. Some Methanoperedens host huge extrachromosomal genetic elements (ECEs) called Borgs that may modulate their activity, yet the broader diversity of Methanoperedens ECEs is understudied. Here we report ...
BiodiversityEnvironmental sciencesMicrobiology
10.1038/S41564-024-01740-8
ISSN:2058-5276
Integrated proteogenomic characterization of ampullary adenocarcinoma
Qiao Zhang•Xiaomeng Xu•Dongxian Jiang•Yunzhi Wang•Haixing Wang等 19 人
Cell Discovery
2025
•2025/1/7
•Vol.11 No.1 p.1-25
Ampullary adenocarcinoma (AMPAC) is a rare and heterogeneous malignancy. Here we performed a comprehensive proteogenomic analysis of 198 samples from Chinese AMPAC patients and duodenum patients. Genomic data illustrate that 4q loss causes fatty acid accumulation and cell proliferation. Proteomic an...
Gastrointestinal cancerMolecular biology
10.1038/S41421-024-00742-4
ISSN:2056-5968
Glycine max NNL1 restricts symbiotic compatibility with widely distributed bradyrhizobia via root hair infection
Bao Zhang•Mengdi Wang•Yifang Sun•Peng Zhao•Chang Liu等 31 人
Nature Plants
2021
•2021/1/15
•Vol.7 No.1 p.73-86
Symbiosis between soybean (Glycine max) and rhizobia is essential for efficient nitrogen fixation. Rhizobial effectors secreted through the type-III secretion system are key for mediating the interactions between plants and rhizobia, but the molecular mechanism remains largely unknown. Here, our gen...
AgricultureEvolutionGeneticsPlant sciencesScientific community
10.1038/S41477-020-00832-7
ISSN:2055-0278
Quercetin alleviates endothelial dysfunction in preeclampsia by inhibiting ferroptosis and inflammation through EGFR binding
Meiting Shi•Lu Sun•Jiachun Wei•Yao Shen•Jian Wang等 13 人
Communications Biology
2025
•2025/1/20
•Vol.8 No.1 p.1-15
Preeclampsia (PE) is a pregnancy-specific complication and there remains no effective treatment. Given the limitations on medication use during pregnancy, exploring natural, safe, and effective drugs for PE is worthwhile. We investigate the causal relationship between ferroptosis, inflammation, and ...
Experimental models of diseaseTarget validation
10.1038/S42003-025-07547-5
ISSN:2399-3642
Lycium barbarum polysaccharide modulates gut microbiota to alleviate rheumatoid arthritis in a rat model
Lai Wenjia•Wang Chunyan•Lai Renfa•Peng Xichun•Luo Jianming
Npj Science Of Food
2022
•2022/7/21
•Vol.6 No.1 p.1-10
Rheumatoid arthritis (RA) seriously impairs the quality of life of sufferers. It has been shown that Lycium barbarum polysaccharide (LBP), a natural active indigestible ingredient with medicinal and edible functions, can effectively relieve RA, however, whether this effect is related to gut microbio...
MicrobiomePolysaccharides
10.1038/S41538-022-00149-Z
ISSN:2396-8370
Genetic and clinical variables act synergistically to impact neurodevelopmental outcomes in children with single ventricle heart disease
Thomas A. Miller•Edgar J. Hernandez•J. William Gaynor•Mark W. Russell•Jane W. Newburger等 23 人
Communications Medicine
2023
•2023/9/27
•Vol.3 No.1 p.1-9
Recent large-scale sequencing efforts have shed light on the genetic contribution to the etiology of congenital heart defects (CHD); however, the relative impact of genetics on clinical outcomes remains less understood. Outcomes analyses using genetics are complicated by the intrinsic severity of th...
CardiologyGenetics
10.1038/S43856-023-00361-2
ISSN:2730-664X
Antiviral type III CRISPR signalling via conjugation of ATP and SAM
Haotian Chi•Ville Hoikkala•Sabine Grüschow•Shirley Graham•Sally Shirran等 6 人
Nature
2023
•2023/10/18
•00 p.1-8
CRISPR systems are widespread in the prokaryotic world, providing adaptive immunity against mobile genetic elements1,2. Type III CRISPR systems, with the signature gene cas10, use CRISPR RNA to detect non-self RNA, activating the enzymatic Cas10 subunit to defend the cell against mobile genetic elem...
BacteriaBacteriophagesEnzyme mechanismsRNA
10.1038/S41586-023-06620-5
ISSN:0028-0836
Profiles of antibiotic resistome risk in diverse water environments
Yiwen Yang•Shuang Cai•Chunhao Mo•Junjie Dong•Sheng Chen等 6 人
Communications Earth & Environment
2025
•2025/2/27
•Vol.6 No.1 p.1-10
The water environment is considered to be a reservoir for antibiotic resistant bacteria and antibiotic resistance genes. However, profiles of antibiotic resistome risk in different water environments remain largely underexplored. Here we found that the number, abundance and risk of antibiotic resist...
Environmental monitoringMicrobial ecology
10.1038/S43247-025-02139-X
ISSN:2662-4435
Genomics-driven discovery of superior alleles and genes for yellow rust resistance in wheat
Jianhui Wu•Shengwei Ma•Jianqing Niu•Weihang Sun•Haitao Dong等 24 人
Nature Genetics
2025
•2025/7/22
•00 p.1-11
Yellow rust (YR), caused by Puccinia striiformis f. sp. tritici, poses a significant threat to wheat production worldwide. Breeding resistant cultivars is crucial for managing this disease. However, our understanding of the genetic mechanisms underlying YR resistance remains fragmented. To address t...
DNA sequencingPlant breedingPlant genetics
10.1038/S41588-025-02259-2
ISSN:1061-4036
Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution
Nina Dombrowski•Tom A. Williams•Jiarui Sun•Benjamin J. Woodcroft•Jun-Hoe Lee等 8 人
Nature Communications
2020
•2020/8/7
•Vol.11 No.1 p.1-15
The recently discovered DPANN archaea are a potentially deep-branching, monophyletic radiation of organisms with small cells and genomes. However, the monophyly and early emergence of the various DPANN clades and their role in life’s evolution are debated. Here, we reconstructed and analysed genomes...
Archaeal evolutionComputational biology and bioinformaticsPhylogeneticsPhylogenomics
10.1038/S41467-020-17408-W
ISSN:2041-1723
Genetic diversity of H9N2 avian influenza viruses in poultry across China and implications for zoonotic transmission
Jing Yang•Juan Li•Ju Sun•Jiaming Li•Guanghua Fu等 28 人
Nature Microbiology
2025
•2025/6/3
•Vol.10 No.6 p.1378-1392
Nationwide surveillance of avian influenza viruses (AIVs) in live poultry markets across China has occurred since 2014, providing a resource for AIV prevalence and genetic diversity studies. Here we report that 3,237 of 18,425 samples from poultry were AIV positive (17.57%) between 2019 and 2023, wi...
Influenza virus
10.1038/S41564-025-02002-X
ISSN:2058-5276
A conserved immunogenic and vulnerable site on the coronavirus spike protein delineated by cross-reactive monoclonal antibodies
Chunyan Wang•Rien van Haperen•Javier Gutiérrez-Álvarez•Wentao Li•Nisreen M. A. Okba等 18 人
Nature Communications
2021
•2021/3/17
•Vol.12 No.1 p.1-15
The coronavirus spike glycoprotein, located on the virion surface, is the key mediator of cell entry and the focus for development of protective antibodies and vaccines. Structural studies show exposed sites on the spike trimer that might be targeted by antibodies with cross-species specificity. Her...
SARS-CoV-2Viral infection
10.1038/S41467-021-21968-W
ISSN:2041-1723
Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis
Franziska Saul•Mathias Scharmann•Takanori Wakatake•Sitaram Rajaraman•André Marques等 22 人
Nature Plants
2023
•2023/11/23
•00 p.1-16
Subgenome dominance after whole-genome duplication generates distinction in gene number and expression at the level of chromosome sets, but it remains unclear how this process may be involved in evolutionary novelty. Here we generated a chromosome-scale genome assembly of the Asian pitcher plant Nep...
GeneticsPlant sciences
10.1038/S41477-023-01562-2
ISSN:2055-0278
Multiple strategies association revealed functional candidate FASN gene for fatty acid composition in cattle
Bo Zhu•Tianzhen Wang•Qunhao Niu•Zezhao Wang•El Hamidi Hay等 14 人
Communications Biology
2025
•2025/2/10
•Vol.8 No.1 p.1-12
Fatty acid composition (FA) is an important indicator of meat quality in beef cattle. We investigated potential functional candidate genes for FA in beef cattle by integrating genomic and transcriptomic dataset through multiple strategies. In this study, we observed 65 SNPs overlapping with five can...
Animal breedingQuantitative trait
10.1038/S42003-025-07604-Z
ISSN:2399-3642
Genomics of soil depth niche partitioning in the Thaumarchaeota family Gagatemarchaeaceae
Paul O. Sheridan•Yiyu Meng•Tom A. Williams•Cécile Gubry-Rangin
Nature Communications
2023
•2023/11/11
•Vol.14 No.1 p.1-14
Knowledge of deeply-rooted non-ammonia oxidising Thaumarchaeota lineages from terrestrial environments is scarce, despite their abundance in acidic soils. Here, 15 new deeply-rooted thaumarchaeotal genomes were assembled from acidic topsoils (0-15 cm) and subsoils (30-60 cm), corresponding to two ge...
Archaeal evolutionArchaeal genomicsMicrobial ecologyMolecular evolution
10.1038/S41467-023-43196-0
ISSN:2041-1723
Cyclic di-GMP suppresses cancer metastasis by targeting proteasome 26S subunit non-ATPase 3 independently of STING
Jieqiong Wang•Alexander Mrozek•Kewen Hu•Hanyu You•Sarah E. Traverse等 10 人
Signal Transduction And Targeted Therapy
2026
•2026/2/4
•Vol.11 No.1 p.440
Cancer metastasis is the primary cause of cancer-related mortality, yet effective treatments remain limited. There is an urgent need to develop novel therapeutic strategies to combat metastasis. In this study, we demonstrate that the bacterial intracellular signaling molecule cyclic di-GMP (c-di-GMP...
Breast cancerTarget identification
10.1038/S41392-025-02553-9
ISSN:2059-3635
Antibiotic contamination and antimicrobial resistance dynamics in the urban sewage microbiome in India
Deepjyoti Paul•Daizee Talukdar•Ramani Shyam Kapuganti•Vaishali Gupta•Lekshmi Narendrakumar等 23 人
Nature Communications
2025
•2025/12/29
0The emergence and spread of antimicrobial resistance (AMR) in clinically important bacterial pathogens has severely compromised the effectiveness of commonly used antibiotics in healthcare. Acquisition and transmission of AMR genes (ARGs) are often facilitated by sublethal concentrations of antibiot...
Antimicrobial resistanceGenetics researchMobile elements
10.1038/S41467-025-68034-3
ISSN:2041-1723
Detecting and quantifying circular RNAs in terabyte-scale RNA-seq datasets with CIRI3
Xin Zheng•Jinyang Zhang•Lipu Song•Xiang Jennie Li•Fangqing Zhao等 6 人
Nature Biotechnology
2025
•2025/10/1
•00 p.1-7
To address recent challenges in circular RNA (circRNA) analysis, we present CIRI3, a tool for circRNA detection and quantification in terabyte-scale RNA-sequencing datasets. Using dynamic multithreaded task partitioning and a blocking search strategy for junction reads, CIRI3 is an order of magnitud...
Data miningGene expression
10.1038/S41587-025-02835-1
ISSN:1087-0156
Expanding anaerobic alkane metabolism in the domain of Archaea
Yinzhao Wang•Gunter Wegener•Jialin Hou•Fengping Wang•Xiang Xiao
Nature Microbiology
2019
•2019/3/4
•Vol.4 No.4 p.595-602
Methanogenesis and anaerobic methane oxidation through methyl-coenzyme M reductase (MCR) as a key enzyme have been suggested to be basal pathways of archaea1. How widespread MCR-based alkane metabolism is among archaea, where it occurs and how it evolved remain elusive. Here, we performed a global s...
ArchaeaArchaeal biologyMetagenomics
10.1038/S41564-019-0364-2
ISSN:2058-5276
Plagued by a cryptic clock: insight and issues from the global phylogeny of Yersinia pestis
Eaton Katherine•Featherstone Leo•Duchene Sebastian•Carmichael Ann G.•Varlık Nükhet等 8 人
Communications Biology
2023
•2023/1/19
•Vol.6 No.1 p.1-13
Plague has an enigmatic history as a zoonotic pathogen. This infectious disease will unexpectedly appear in human populations and disappear just as suddenly. As a result, a long-standing line of inquiry has been to estimate when and where plague appeared in the past. However, there have been signifi...
PhylogeneticsPhylogeny
10.1038/S42003-022-04394-6
ISSN:2399-3642
The correlation between CpG methylation and gene expression is driven by sequence variants
Olafur Andri Stefansson•Brynja Dogg Sigurpalsdottir•Solvi Rognvaldsson•Gisli Hreinn Halldorsson•Kristinn Juliusson等 32 人
Nature Genetics
2024
•2024/7/24
•Vol.56 No.8 p.1624-1631
Gene promoter and enhancer sequences are bound by transcription factors and are depleted of methylated CpG sites (cytosines preceding guanines in DNA). The absence of methylated CpGs in these sequences typically correlates with increased gene expression, indicating a regulatory role for methylation....
DNA sequencingEpigeneticsGene expressionGenome-wide association studiesGenomics
10.1038/S41588-024-01851-2
ISSN:1061-4036
Sixteen novel lineages of SARS-CoV-2 in South Africa
Houriiyah Tegally•Eduan Wilkinson•Richard J. Lessells•Jennifer Giandhari•Sureshnee Pillay等 31 人
Nature Medicine
2021
•2021/2/2
•Vol.27 No.3 p.440-446
The first severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in South Africa was identified on 5 March 2020, and by 26 March the country was in full lockdown (Oxford stringency index of 90)1. Despite the early response, by November 2020, over 785,000 people in South Africa were i...
Genetics researchPhylogenetics
10.1038/S41591-021-01255-3
ISSN:1078-8956
Evolutionary genomics of anthroponosis in Cryptosporidium
Johanna L. Nader•Thomas C. Mathers•Ben J. Ward•Justin A. Pachebat•Martin T. Swain等 10 人
Nature Microbiology
2019
•2019/3/4
•Vol.4 No.5 p.826-836
Human cryptosporidiosis is the leading protozoan cause of diarrhoeal mortality worldwide, and a preponderance of infections is caused by Cryptosporidium hominis and C. parvum. Both species consist of several subtypes with distinct geographical distributions and host preferences (that is, generalist ...
EpidemiologyEvolutionary geneticsParasite evolutionParasite geneticsParasite genomics
10.1038/S41564-019-0377-X
ISSN:2058-5276
Machine learning discovery of missing links that mediate alternative branches to plant alkaloids
Vavricka Christopher J.•Takahashi Shunsuke•Watanabe Naoki•Takenaka Musashi•Matsuda Mami等 15 人
Nature Communications
2022
•2022/3/16
•Vol.13 No.1 p.1-14
Engineering the microbial production of secondary metabolites is limited by the known reactions of correctly annotated enzymes. Therefore, the machine learning discovery of specialized enzymes offers great potential to expand the range of biosynthesis pathways. Benzylisoquinoline alkaloid production...
EnzymesMachine learningMetabolic engineeringSynthetic biology
10.1038/S41467-022-28883-8
ISSN:2041-1723
Genomic diversity and transmission patterns of Yersinia pestis in Inner Mongolia Autonomous Region, China
Xiujuan Zuo•Fang Liu•Yanhong Hu•Xuezhi Huang•Yan Guo等 14 人
Communications Biology
2024
•2024/11/9
•Vol.7 No.1 p.1-8
According to WHO, plague, caused by Yersinia pestis, has resurged since 2000. Inner Mongolia, harboring a quarter of China’s plague foci, has accounted for 80% of national plague cases in the past five years. Despite its pivotal role in Chinese plague epidemiology, the genetic diversity and transmis...
Evolutionary biologyGenetic variationPathogens
10.1038/S42003-024-07190-6
ISSN:2399-3642
Bioremediation of complex organic pollutants by engineered Vibrio natriegens
Cong Su•Haotian Cui•Weiwei Wang•Yong Liu•Zhenyu Cheng等 16 人
Nature
2025
•2025/5/7
•00 p.1-10
Industrial wastewater, petroleum pollution and plastic contamination are significant threats to global marine biosecurity because of their toxic, mutagenic and persistent nature1. The use of microorganisms in bioremediation has been constrained by the complexity of organic pollutants and limited tol...
Environmental biotechnologyWater microbiology
10.1038/S41586-025-08947-7
ISSN:0028-0836
A comparative genomics multitool for scientific discovery and conservation
Nature
2020
•2020/11/11
•Vol.587 No.7833 p.240-245
The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe a whole-genome alignment of 240 species of considerable phylogenetic diversity,...
Comparative genomicsEcological geneticsEvolutionary geneticsGenome informaticsPhylogenetics
10.1038/S41586-020-2876-6
ISSN:0028-0836
A system-level approach identifies HIF-2α as a critical regulator of chondrosarcoma progression
Hyeonkyeong Kim•Yongsik Cho•Hyeon-Seop Kim•Donghyun Kang•Donghyeon Cheon等 12 人
Nature Communications
2020
•2020/10/6
•Vol.11 No.1 p.1-16
Chondrosarcomas, malignant cartilaginous neoplasms, are capable of transitioning to highly aggressive, metastatic, and treatment-refractory states, resulting in significant patient mortality. Here, we aim to uncover the transcriptional program directing such tumor progression in chondrosarcomas. We ...
SarcomaTargeted therapies
10.1038/S41467-020-18817-7
ISSN:2041-1723
Rats exhibit age-related mosaic loss of chromosome Y
Orta Alberto H.•Bush Stephen J.•Gutiérrez-Mariscal Mariana•Castro-Obregón Susana•Jaimes-Hoy Lorraine等 15 人
Communications Biology
2021
•2021/12/21
•Vol.4 No.1 p.1-8
Mosaic loss of the Y chromosome (LOY) is the most frequent chromosomal aberration in aging men and is strongly correlated with mortality and disease. To date, studies of LOY have only been performed in humans, and so it is unclear whether LOY is a natural consequence of our relatively long lifespan ...
DNA sequencingGenomic instabilityGenomics
10.1038/S42003-021-02936-Y
ISSN:2399-3642
An ancestral SARS-CoV-2 vaccine induces anti-Omicron variants antibodies by hypermutation
Seoryeong Park•Jaewon Choi•Yonghee Lee•Jinsung Noh•Namphil Kim等 17 人
Nature Communications
2024
•2024/4/20
•Vol.15 No.1 p.1-9
The immune escape of Omicron variants significantly subsides by the third dose of an mRNA vaccine. However, it is unclear how Omicron variant-neutralizing antibodies develop under repeated vaccination. We analyze blood samples from 41 BNT162b2 vaccinees following the course of three injections and a...
AntibodiesRNA vaccinesSARS-CoV-2Somatic hypermutation
10.1038/S41467-024-47743-1
ISSN:2041-1723
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
Biodiversity of the beneficial soil-borne fungi steered by Trichoderma-amended biofertilizers stimulates plant production
Yan Wang•Zhengyang Liu•Xinyi Hao•Ziqi Wang•Zhe Wang等 12 人
Npj Biofilms And Microbiomes
2023
•2023/7/5
•Vol.9 No.1 p.1-9
The soil microbiota is critical to plant performance. Improving the ability of plant-associated soil probiotics is thus essential for establishing dependable and sustainable crop yields. Although fertilizer applications may provide an effective way of steering soil microbes, it is still unknown how ...
Applied microbiologyMicrobiome
10.1038/S41522-023-00416-1
ISSN:2055-5008
A distinct Acyl-CoA binding protein (ACBP6) shapes tissue plasticity during nutrient adaptation in Drosophila
Xiaotong Li•Jason Karpac
Nature Communications
2023
•2023/11/21
•Vol.14 No.1 p.1-17
Nutrient availability is a major selective force in the evolution of metazoa, and thus plasticity in tissue function and morphology is shaped by adaptive responses to nutrient changes. Utilizing Drosophila, we reveal that distinct calibration of acyl-CoA metabolism, mediated by Acbp6 (Acyl-CoA bindi...
Cell proliferationHomeostasisIntestinal stem cells
10.1038/S41467-023-43362-4
ISSN:2041-1723
Pediococcus acidilactici GR-5 alleviates hyperuricemia by degrading purine nucleosides and improving gut microbiota metabolism
Jing Ji•Zi-Yi An•Aman Khan•Liang Peng•Sourabh Kulshreshtha等 10 人
Npj Science Of Food
2025
•2025/8/23
•Vol.9 No.1 p.1-16
Reducing intestinal absorption by degrading purine nucleosides has been shown to alleviate hyperuricemia (HUA). The probiotic Pediococcus acidilactici GR-5, derived from the traditional food “Jiangshui”, achieved efficient degradation of purine nucleosides through its unique purine nucleoside phosph...
Applied microbiologyEndocrine system and metabolic diseases
10.1038/S41538-025-00556-Y
ISSN:2396-8370
Efficacy of FERscore in predicting sensitivity to ferroptosis inducers in breast cancer
Kaimin Hu•Jili Qiu•Yue Hu•Yanyan Wang•Chengcheng Yu等 6 人
Npj Breast Cancer
2024
•2024/8/20
•Vol.10 No.1 p.1-12
Recent studies have highlighted the potential of ferroptosis in treating breast cancer. However, the efficacy of ferroptosis induction in the most common subtype, estrogen receptor-positive (ER + ) breast cancer, remains inadequately explored. This study unveils that both short-term and long-term tr...
Cancer therapeutic resistancePredictive markers
10.1038/S41523-024-00685-9
ISSN:2374-4677
Oral and gut dysbiosis leads to functional alterations in Parkinson’s disease
Jo Sungyang•Kang Woorim•Hwang Yun Su•Lee Seung Hyun•Park Kye Won等 15 人
Npj Parkinson's Disease
2022
•2022/7/7
•Vol.8 No.1 p.1-12
Although several studies have identified a distinct gut microbial composition in Parkinson’s disease (PD), few studies have investigated the oral microbiome or functional alteration of the microbiome in PD. We aimed to investigate the connection between the oral and gut microbiome and the functional...
Parkinson's disease
10.1038/S41531-022-00351-6
ISSN:2373-8057
LorBin: efficient binning of long-read metagenomes by multiscale adaptive clustering and evaluation
Wei Xue•Zuo Liu•Yaozhong Zhang•Waseem Raza•Yarong Li等 15 人
Nature Communications
2025
•2025/10/24
•Vol.16 No.1 p.1-14
Long-read sequencing has transformed metagenomics and improved the quality of metagenome-assembled genomes (MAGs). However, current binning methods struggle with identifying unknown species and managing imbalanced species distributions. Here, we present LorBin, an unsupervised binner specially desig...
Computational biology and bioinformaticsMetagenomics
10.1038/S41467-025-64916-8
ISSN:2041-1723
Incorporating genetic load contributes to predicting Arabidopsis thaliana’s response to climate change
Juan Jiang•Jia-Fu Chen•Xin-Tong Li•Li Wang•Jian-Feng Mao等 7 人
Nature Communications
2025
•2025/3/20
•Vol.16 No.1 p.1-12
Understanding how species respond to climate change can facilitate species conservation and crop breeding. Current prediction frameworks about population vulnerability focused on predicting range shifts or local adaptation but ignored genetic load, which is also crucial for adaptation. By analyzing ...
Conservation biologyEvolutionary geneticsMolecular evolutionPopulation genetics
10.1038/S41467-025-58021-Z
ISSN:2041-1723
Soil microbiome manipulation triggers direct and possible indirect suppression against Ralstonia solanacearum and Fusarium oxysporum
Xuhui Deng•Na Zhang•Zongzhuan Shen•Chengzhi Zhu•Hongjun Liu等 9 人
Npj Biofilms And Microbiomes
2021
•2021/4/12
•Vol.7 No.1 p.1-10
Soil microbiome manipulation can potentially reduce the use of pesticides by improving the ability of soils to resist or recover from pathogen infestation, thus generating natural suppressiveness. We simulated disturbance through soil fumigation and investigated how the subsequent application of bio...
MicrobiomePathogens
10.1038/S41522-021-00204-9
ISSN:2055-5008
Inhibition of CBP synergizes with the RNA-dependent mechanisms of Azacitidine by limiting protein synthesis
Diesch Jeannine•Le Pannérer Marguerite-Marie•Winkler René•Casquero Raquel•Muhar Matthias等 18 人
Nature Communications
2021
•2021/10/18
•Vol.12 No.1 p.1-13
The nucleotide analogue azacitidine (AZA) is currently the best treatment option for patients with high-risk myelodysplastic syndromes (MDS). However, only half of treated patients respond and of these almost all eventually relapse. New treatment options are urgently needed to improve the clinical m...
Acute myeloid leukaemiaMyelodysplastic syndrome
10.1038/S41467-021-26258-Z
ISSN:2041-1723
Recruitment of Cdc48 to chloroplasts by a UBX-domain protein in chloroplast-associated protein degradation
Na Li•R. Paul Jarvis
Nature Plants
2024
•2024/8/19
•00 p.1-18
The translocon at the outer chloroplast membrane (TOC) is the gateway for chloroplast protein import and so is vital for photosynthetic establishment and plant growth. Chloroplast-associated protein degradation (CHLORAD) is a ubiquitin-dependent proteolytic system that regulates TOC. In CHLORAD, cyt...
Cell biologyChloroplastsProtein trafficking in plantsProteolysis in plantsTransgenic plants
10.1038/S41477-024-01769-X
ISSN:2055-0278
Dense sampling of bird diversity increases power of comparative genomics
Shaohong Feng•Josefin Stiller•Yuan Deng•Joel Armstrong•Qi Fang等 150 人
Nature
2020
•2020/11/11
•Vol.587 No.7833 p.252-257
Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1–4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards t...
Comparative genomicsEvolutionary genetics
10.1038/S41586-020-2873-9
ISSN:0028-0836
Globally distributed Myxococcota with photosynthesis gene clusters illuminate the origin and evolution of a potentially chimeric lifestyle
Liuyang Li•Danyue Huang•Yaoxun Hu•Nicola M. Rudling•Daniel P. Canniffe等 7 人
Nature Communications
2023
•2023/10/13
•Vol.14 No.1 p.1-14
Photosynthesis is a fundamental biogeochemical process, thought to be restricted to a few bacterial and eukaryotic phyla. However, understanding the origin and evolution of phototrophic organisms can be impeded and biased by the difficulties of cultivation. Here, we analyzed metagenomic datasets and...
Bacterial evolutionMetagenomicsMicrobial ecologyPhotosynthesisPhylogenetics
10.1038/S41467-023-42193-7
ISSN:2041-1723
Endoplasmic reticulum stress-induced histone lactylation mediating immune escape of gastric cancer via PDIA6 overexpression in dendritic cells
Chengshu Tu•Ziqing Wu•Xuxian Zhong•Shengnan Yang•Xi Chen等 8 人
Cell Death & Disease
2026
•2026/3/27
0Gastric cancer is one of the most prevalent cancers worldwide and is associated with a high mortality rate. Although immunotherapy has achieved some success for many tumor types, the limited response of gastric cancer to immunotherapy poses a challenge. Lactylation is a recently proposed post-transl...
CancerImmunologyMedical research
10.1038/S41419-026-08638-9
ISSN:2041-4889
CXXC finger protein 1 (CFP1) bridges the reshaping of genomic H3K4me3 signature to the advancement of lung adenocarcinoma
Tao Fan•Chu Xiao•Hengchang Liu•Yu Liu•Liyu Wang等 8 人
Signal Transduction And Targeted Therapy
2023
•2023/9/21
•Vol.8 No.1 p.1-13
Histone H3 lysine 4 trimethylation (H3K4me3) is a canonical chromatin modification associated with active gene transcription, playing a pivotal role in regulating various cellular functions. Components of the H3K4me3 methyltransferase complex, known as the proteins associated with SET1 (COMPASS), ha...
Genome informaticsLung cancer
10.1038/S41392-023-01612-3
ISSN:2059-3635
The genome sequence of segmental allotetraploid peanut Arachis hypogaea
David J. Bertioli•Jerry Jenkins•Josh Clevenger•Olga Dudchenko•Dongying Gao等 50 人
Nature Genetics
2019
•2019/5/1
•Vol.51 No.5 p.877-884
Like many other crops, the cultivated peanut (Arachis hypogaea L.) is of hybrid origin and has a polyploid genome that contains essentially complete sets of chromosomes from two ancestral species. Here we report the genome sequence of peanut and show that after its polyploid origin, the genome has e...
GenomicsPlant genetics
10.1038/S41588-019-0405-Z
ISSN:1061-4036
Magnaporthe oryzae effector MoSPAB1 directly activates rice Bsr-d1 expression to facilitate pathogenesis
Ziwei Zhu•Jun Xiong•Hao Shi•Yuchen Liu•Junjie Yin等 32 人
Nature Communications
2023
•2023/12/18
•Vol.14 No.1 p.1-12
Fungal pathogens typically use secreted effector proteins to suppress host immune activators to facilitate invasion. However, there is rarely evidence supporting the idea that fungal secretory proteins contribute to pathogenesis by transactivating host genes that suppress defense. We previously foun...
Effectors in plant pathologyMicrobe
10.1038/S41467-023-44197-9
ISSN:2041-1723
Engineering substrate specificity of HAD phosphatases and multienzyme systems development for the thermodynamic-driven manufacturing sugars
Tian Chaoyu•Yang Jiangang•Liu Cui•Chen Peng•Zhang Tong等 9 人
Nature Communications
2022
•2022/6/23
•Vol.13 No.1 p.1-13
Naturally, haloacid dehalogenase superfamily phosphatases have been evolved with broad substrate promiscuity; however, strong specificity to a particular substrate is required for developing thermodynamically driven routes for manufacturing sugars. How to alter the intrinsic substrate promiscuity of...
BiocatalysisGlycobiologyHydrolasesMonosaccharidesMultienzyme complexes
10.1038/S41467-022-31371-8
ISSN:2041-1723
Genomic and epigenomic insight into giga-chromosome architecture and adaptive evolution of royal lily (Lilium regale)
Jie Sun•Xiangfeng Wang•Ke Wang•Dian Meng•Yu Mu等 9 人
Nature Communications
2025
•2025/7/1
•Vol.16 No.1 p.1-17
Lilies are popular ornamental and medicinal plants with gigantic genomes. Due to the challenge of assembling complex giga-genomes, our understanding of the genetic architecture, epigenetic regulation and evolution of large-genome plants such as lily remains limited. Here, we report a high-quality ch...
Evolutionary geneticsGenome evolutionPlant evolution
10.1038/S41467-025-61289-W
ISSN:2041-1723
The different paradigms of NK cell death in patients with severe trauma
Te-Ding Chang•Deng Chen•Jia-Liu Luo•Yu-Man Wang•Cong Zhang等 13 人
Cell Death & Disease
2024
•2024/8/21
•Vol.15 No.8 p.1-14
Lymphocyte decline, particularly the depletion of NK cells, is a prominent feature of immunosuppression following severe tissue injury, heightening the susceptibility of severe trauma patients to life-threatening infections. Previous research indicates that the reduction in the number of NK cells is...
Innate immunityTrauma
10.1038/S41419-024-06992-0
ISSN:2041-4889
A comparative study reveals the relative importance of prokaryotic and eukaryotic proton pump rhodopsins in a subtropical marginal sea
Minglei Ma•Hongfei Li•Cong Wang•Tangcheng Li•Jierui Wang等 10 人
Isme Communications
2023
•2023/8/18
•Vol.3 No.1 p.1-9
Proton-pump rhodopsin (PPR) in marine microbes can convert solar energy to bioavailable chemical energy. Whereas bacterial PPR has been extensively studied, counterparts in microeukaryotes are less explored, and the relative importance of the two groups is poorly understood. Here, we sequenced whole...
Environmental microbiologyMicrobial ecology
10.1038/S43705-023-00292-Y
ISSN:2730-6151
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
Inhibition of chitin deacetylases to attenuate plant fungal diseases
Lin Liu•Yeqiang Xia•Yingchen Li•Yong Zhou•Xiaofeng Su等 11 人
Nature Communications
2023
•2023/6/29
•Vol.14 No.1 p.1-12
Phytopathogenic fungi secrete chitin deacetylase (CDA) to escape the host’s immunological defense during infection. Here, we showed that the deacetylation activity of CDA toward chitin is essential for fungal virulence. Five crystal structures of two representative and phylogenetically distant phyto...
Effectors in plant pathologyVirulence
10.1038/S41467-023-39562-7
ISSN:2041-1723
High quality de novo genome assembly of the non-conventional yeast Kazachstania bulderi describes a potential low pH production host for biorefineries
Laura N. Balarezo-Cisneros•Soukaina Timouma•Alistair Hanak•Andrew Currin•Fernando Valle等 6 人
Communications Biology
2023
•2023/9/7
•Vol.6 No.1 p.1-14
Kazachstania bulderi is a non-conventional yeast species able to grow efficiently on glucose and δ-gluconolactone at low pH. These unique traits make K. bulderi an ideal candidate for use in sustainable biotechnology processes including low pH fermentations and the production of green chemicals incl...
GenomeIndustrial microbiology
10.1038/S42003-023-05285-0
ISSN:2399-3642
Amyloidogenic proteins in the SARS-CoV and SARS-CoV-2 proteomes
Bhardwaj Taniya•Gadhave Kundlik•Kapuganti Shivani K.•Kumar Prateek•Brotzakis Zacharias Faidon等 15 人
Nature Communications
2023
•2023/2/20
•Vol.14 No.1 p.1-16
The phenomenon of protein aggregation is associated with a wide range of human diseases. Our knowledge of the aggregation behaviour of viral proteins, however, is still rather limited. Here, we investigated this behaviour in the SARS-CoV and SARS-CoV-2 proteomes. An initial analysis using a panel of...
Atomic force microscopyProtein aggregationViral infection
10.1038/S41467-023-36234-4
ISSN:2041-1723
Targeting CD37 promotes macrophage-dependent phagocytosis of multiple cancer cell types and facilitates tumor clearance in mice
Xinya Gao•Jing Zhang•Hui Zhang•Xin Liu•Bo Zeng等 11 人
Nature Communications
2025
•2025/7/18
•Vol.16 No.1 p.1-15
Macrophages play vital roles in innate and adaptive immunity, and their functions are mediated via phagocytosis and antigen presentation. Despite the effort to identify phagocytic checkpoints and explore their mechanism of action, current checkpoint-scanning strategies cannot provide a complete and ...
ImmunoeditingPhagocytes
10.1038/S41467-025-61348-2
ISSN:2041-1723
Abiotic selection of microbial genome size in the global ocean
Ngugi David K.•Acinas Silvia G.•Sánchez Pablo•Gasol Josep M.•Agusti Susana等 7 人
Nature Communications
2023
•2023/3/13
•Vol.14 No.1 p.1-12
Strong purifying selection is considered a major evolutionary force behind small microbial genomes in the resource-poor photic ocean. However, very little is currently known about how the size of prokaryotic genomes evolves in the global ocean and whether patterns reflect shifts in resource availabi...
MetagenomicsMicrobial ecologyMolecular ecology
10.1038/S41467-023-36988-X
ISSN:2041-1723
An integrated drug repositioning analysis identifies rosiglitazone as a treatment for sarcopenia
Shuang Liang•Yong Liu•Hong-Mei Xiao•Hong-Wen Deng
Communications Biology
2026
•2026/1/29
•Vol.9 No.1 p.4430
Age-related sarcopenia is a growing global health challenge with no approved pharmacotherapies. Here, we integrate network-based drug repurposing and Mendelian randomization to identify rosiglitazone, a PPARγ agonist used in diabetes, as a potential therapeutic candidate for sarcopenia. In aged male...
Drug developmentGenetics research
10.1038/S42003-026-09595-X
ISSN:2399-3642
An antiplasmid system drives antibiotic resistance gene integration in carbapenemase-producing Escherichia coli lineages
Pengdbamba Dieudonné Zongo•Nicolas Cabanel•Guilhem Royer•Florence Depardieu•Alain Hartmann等 8 人
Nature Communications
2024
•2024/5/15
•Vol.15 No.1 p.1-15
Plasmids carrying antibiotic resistance genes (ARG) are the main mechanism of resistance dissemination in Enterobacterales. However, the fitness-resistance trade-off may result in their elimination. Chromosomal integration of ARGs preserves resistance advantage while relieving the selective pressure...
Bacterial genesBacterial geneticsClinical microbiology
10.1038/S41467-024-48219-Y
ISSN:2041-1723
The coexistence of r and K strategy in a unicellular microalga Haematococcus lacustris
Lu Liu•Yaqing Liu•Si Tang•Boya Zhang•Yanlin Zhong等 8 人
Communications Biology
2026
•2026/3/30
0Understanding how organisms balance growth and defence is a general goal in biology. r (high reproductivity but stress-sensitive offspring) and K (low reproductivity but high stress-resistant offspring) selection are two classical life history strategy theories. Contrary to the common belief that an...
Microbial ecologyWater microbiology
10.1038/S42003-026-09922-2
ISSN:2399-3642
Long-term editing of brain circuits using an engineered electrical synapse
Elizabeth Ransey•Gwenaëlle E. Thomas•Elias M. Wisdom•Agustin Almoril-Porras•Ryan Bowman等 19 人
Nature
2026
•2026/5/13
•00 p.1-13
Electrical signalling across distinct populations of brain cells underpins cognitive and emotional function. However, approaches that selectively regulate electrical signalling between two cellular components of a mammalian neural circuit remain sparse. Here we engineered an electrical synapse compo...
EmotionMolecular neuroscience
10.1038/S41586-026-10501-Y
ISSN:0028-0836
A sorghum pangenome reference improves global crop trait discovery
Geoffrey P. Morris•Avril M. Harder•Adam L. Healey•Chloee M. McLaughlin•Joanna L. Rifkin等 75 人
Nature
2026
•2026/3/11
•00 p.1-9
Although the green revolution adapted a handful of crops to homogeneous and high-input industrialized agriculture, much of the global population still relies on the local production of variable crop cultivars by low-input smallholder farms. This diversity of unhomogenized crops1, like that of the gr...
Agricultural geneticsBiofuelsEvolutionary geneticsGenome informaticsPlant breeding
10.1038/S41586-026-10229-9
ISSN:0028-0836
ZNF133 is a potent suppressor in breast carcinogenesis through dampening L1CAM, a driver for tumor progression
Lifang Li•Xuefei Wang•Kai Hu•Xinhua Liu•Li Qiu等 18 人
Oncogene
2023
•2023/5/23
•00 p.1-17
Due to the complexity and heterogeneity of breast cancer, the therapeutic effects of breast cancer treatment vary between subtypes. Breast cancer subtypes are classified based on the presence of molecular markers for estrogen or progesterone receptors and human epidermal growth factor 2. Thus, novel...
Breast cancerPrognostic markers
10.1038/S41388-023-02731-5
ISSN:0950-9232
Organization of neuropeptide systems in the human brain
Eric G. Ceballos•Asa Farahani•Zhen-Qi Liu•Filip Milisav•Justine Y. Hansen等 7 人
Nature Neuroscience
2026
•2026/3/17
•00 p.1-13
Neuropeptides are functionally diverse signaling molecules in the brain, regulating a wide range of basal bodily and cognitive processes. Despite their importance, the distribution and function of neuropeptides in the human brain remains underexplored. Here we comprehensively map the organization of...
Computational neuroscienceNeuroscience
10.1038/S41593-026-02236-W
ISSN:1097-6256
Inhibition of ferroptosis in inflammatory macrophages alleviates intestinal injury in neonatal necrotizing enterocolitis
Leiting Shen•Jiayu Chen•Jinfa Tou
Cell Death Discovery
2025
•2025/8/5
•Vol.11 No.1 p.1-14
Neonatal necrotizing enterocolitis (NEC) is a severe gut disease primarily affecting preterm infants, driven significantly by inflammatory macrophages. This study combined bioinformatics (single-cell/tissue RNA sequencing) and experiments to identify key macrophage changes in NEC. Analysis revealed ...
Immune cell deathInflammatory diseasesPaediatric research
10.1038/S41420-025-02665-9
ISSN:2058-7716
Terrestrial-type nitrogen-fixing symbiosis between seagrass and a marine bacterium
Mohr Wiebke•Lehnen Nadine•Ahmerkamp Soeren•Marchant Hannah K.•Graf Jon S.等 15 人
Nature
2021
•2021/11/3
•00 p.1-5
Symbiotic N2-fixing microorganisms have a crucial role in the assimilation of nitrogen by eukaryotes in nitrogen-limited environments1–3. Particularly among land plants, N2-fixing symbionts occur in a variety of distantly related plant lineages and often involve an intimate association between host ...
BiogeochemistryEnvironmental microbiologyMicrobial ecology
10.1038/S41586-021-04063-4
ISSN:0028-0836
The iron-dependent repressor YtgR is a tryptophan-dependent attenuator of the trpRBA operon in Chlamydia trachomatis
Nick D. Pokorzynski•Nathan D. Hatch•Scot P. Ouellette•Rey A. Carabeo
Nature Communications
2020
•2020/12/22
•Vol.11 No.1 p.1-15
The trp operon of Chlamydia trachomatis is organized differently from other model bacteria. It contains trpR, an intergenic region (IGR), and the biosynthetic trpB and trpA open-reading frames. TrpR is a tryptophan-dependent repressor that regulates the major promoter (PtrpR), while the IGR harbors ...
BacteriaBacteriologyGene regulationPathogens
10.1038/S41467-020-20181-5
ISSN:2041-1723
Metagenomics deciphers diagenetic processes of ferruginous mineralization in the deep biosphere
Aurèle Vuillemin•Fátima Ruiz-Blas•Sizhong Yang•Alexander Bartholomäus•Dirk Wagner等 8 人
Communications Earth & Environment
2026
•2026/8/5
•Vol.7 No.1 p.6340
Ferruginous conditions in the Precambrian oceans gave rise to ancient iron formations that contain the oldest recognized traces of life in the form of mineral biosignatures and isotope imprints. However, these biogeochemical archives lack clear constraints on microbial diagenesis prior to lithificat...
ArchaeaElement cyclesEnvironmental microbiologyMicrobial ecologyMineralogy
10.1038/S43247-026-03898-X
ISSN:2662-4435
Microbial communities modulate chemical weathering and carbon dioxide cycling in an active orogen in Taiwan
Pei-Ling Wang•Tzu-Hsuan Tu•Li-Hung Lin•Hsi-Ling Chou•Yi-Jie Wang等 14 人
Communications Earth & Environment
2024
•2024/4/2
•Vol.5 No.1 p.1-10
Chemical weathering modulates carbon transfer between the crust, hydrosphere, and atmosphere. The extent to which microbial processes are involved in mineral dissolution remains elusive. Here, we performed geochemical and molecular analyses of river water and other materials collected from a rapidly...
Element cyclesEnvironmental microbiologySolid Earth sciences
10.1038/S43247-024-01345-3
ISSN:2662-4435
Estuarine plastisphere as an overlooked source of N2O production
Su Xiaoxuan•Yang Leyang•Yang Kai•Tang Yijia•Wen Teng等 11 人
Nature Communications
2022
•2022/7/6
•Vol.13 No.1 p.1-12
“Plastisphere”, microbial communities colonizing plastic debris, has sparked global concern for marine ecosystems. Microbiome inhabiting this novel human-made niche has been increasingly characterized; however, whether the plastisphere holds crucial roles in biogeochemical cycling remains largely un...
Element cyclesEnvironmental impact
10.1038/S41467-022-31584-X
ISSN:2041-1723
Epigenetic reprogramming promotes the antiviral action of IFNα in HBV-infected cells
Luc Gailhouste•Masayuki Sudoh•Xian-Yang Qin•Koichi Watashi•Takaji Wakita等 9 人
Cell Death Discovery
2021
•2021/6/2
•Vol.7 No.1 p.1-11
Chronic hepatitis B virus (HBV) infections remain a health burden affecting ~250 million people worldwide. Thus far, available interferon-alpha (IFNα)-based therapies have shown unsatisfactory cure rates, and alternative therapeutic molecules are still required. However, their development has been h...
DNA methylationViral infection
10.1038/S41420-021-00515-Y
ISSN:2058-7716
Control of acute myeloid leukemia by a trifunctional NKp46-CD16a-NK cell engager targeting CD123
Gauthier Laurent•Virone-Oddos Angela•Beninga Jochen•Rossi Benjamin•Nicolazzi Céline等 19 人
Nature Biotechnology
2023
•2023/1/12
•00 p.1-11
CD123, the alpha chain of the IL-3 receptor, is an attractive target for acute myeloid leukemia (AML) treatment. However, cytotoxic antibodies or T cell engagers targeting CD123 had insufficient efficacy or safety in clinical trials. We show that expression of CD64, the high-affinity receptor for hu...
Antibody therapyApplied immunologyCancer immunotherapyImmunotherapy
10.1038/S41587-022-01626-2
ISSN:1087-0156
Metabolic capabilities mute positive response to direct and indirect impacts of warming throughout the soil profile
Nicholas C. Dove•Margaret S. Torn•Stephen C. Hart•Neslihan Taş
Nature Communications
2021
•2021/4/7
•Vol.12 No.1 p.1-13
Increasing global temperatures are predicted to stimulate soil microbial respiration. The direct and indirect impacts of warming on soil microbes, nevertheless, remain unclear. This is particularly true for understudied subsoil microbes. Here, we show that 4.5 years of whole-profile soil warming in ...
Carbon cycleClimate-change ecologyMicrobial ecologySoil microbiology
10.1038/S41467-021-22408-5
ISSN:2041-1723
Harnessing the highly adaptable barnase-barstar system for genetic biocontrol of Aedes aegypti
Katherine Nevard•Joshua X. D. Ang•Michelle A. E. Anderson•Estela Gonzalez•Lewis Shackleford等 6 人
Communications Biology
2025
•2025/8/4
•Vol.8 No.1 p.1-6
Toxin-antidote pairs can be used in gene drive systems, providing powerful means to modify mosquito populations. Here we use the toxin-antidote pair, barnase and barstar, originally identified in Bacillus amyloliquefaciens, due to their high binding affinity, small size and lack of need for cofactor...
Genetic engineeringSynthetic biology
10.1038/S42003-025-08588-6
ISSN:2399-3642
Asymmetric total synthesis of polycyclic xanthenes and discovery of a WalK activator active against MRSA
Min-Jing Cheng•Yan-Yi Wu•Hao Zeng•Tian-Hong Zhang•Yan-Xia Hu等 13 人
Nature Communications
2024
•2024/7/13
•Vol.15 No.1 p.1-17
The development of new antibiotics continues to pose challenges, particularly considering the growing threat of multidrug-resistant Staphylococcus aureus. Structurally diverse natural products provide a promising source of antibiotics. Herein, we outline a concise approach for the collective asymmet...
Drug discovery and developmentNatural product synthesisStructure elucidationTarget identification
10.1038/S41467-024-49629-8
ISSN:2041-1723
Origin and Evolution of RAS Membrane Targeting
García-España Antonio•Philips Mark R.
Oncogene
2023
•2023/4/8
•00 p.1-10
KRAS, HRAS and NRAS proto-oncogenes belong to a family of 40 highly homologous genes, which in turn are a subset of a superfamily of >160 genes encoding small GTPases. RAS proteins consist of a globular G-domain (aa1-166) and a 22-23 aa unstructured hypervariable region (HVR) that mediates membra...
Evolutionary biologyPrenylation
10.1038/S41388-023-02672-Z
ISSN:0950-9232
Programmable antisense oligomers for phage functional genomics
Milan Gerovac•Leandro Buhlmann•Yan Zhu•Svetlana Ðurica-Mitić•Valentin Rech等 9 人
Nature
2025
•2025/9/10
•00 p.1-9
Bacteriophages are the most abundant entities on earth and exhibit vast genetic and phenotypic diversity. Exploitation of this largely unexplored molecular space requires identification and functional characterization of genes that act at the phage–host interface. So far, this has been restricted to...
BiotechnologyMolecular biologyPhage biology
10.1038/S41586-025-09499-6
ISSN:0028-0836
Proteome-wide 3D structure prediction provides insights into the ancestral metabolism of ancient archaea and bacteria
Zhao Weishu•Zhong Bozitao•Zheng Lirong•Tan Pan•Wang Yinzhao等 10 人
Nature Communications
2022
•2022/12/21
•Vol.13 No.1 p.1-14
Ancestral metabolism has remained controversial due to a lack of evidence beyond sequence-based reconstructions. Although prebiotic chemists have provided hints that metabolism might originate from non-enzymatic protometabolic pathways, gaps between ancestral reconstruction and prebiotic processes m...
Archaeal evolutionBacterial evolutionProtein structure predictions
10.1038/S41467-022-35523-8
ISSN:2041-1723
Vitamin interdependencies predicted by metagenomics-informed network analyses and validated in microbial community microcosms
Tomas Hessler•Robert J. Huddy•Rohan Sachdeva•Shufei Lei•Susan T. L. Harrison等 7 人
Nature Communications
2023
•2023/8/8
•Vol.14 No.1 p.1-12
Metagenomic or metabarcoding data are often used to predict microbial interactions in complex communities, but these predictions are rarely explored experimentally. Here, we use an organism abundance correlation network to investigate factors that control community organization in mine tailings-deri...
MetagenomicsMicrobial ecologySymbiosis
10.1038/S41467-023-40360-4
ISSN:2041-1723
Genome-wide association analyses of invasive pneumococcal isolates identify a missense bacterial mutation associated with meningitis
Yuan Li•Benjamin J. Metcalf•Sopio Chochua•Zhongya Li•Hollis Walker等 11 人
Nature Communications
2019
•2019/1/14
•Vol.10 No.1 p.1-11
Bacterial mutations predisposing pneumococcus to causing meningitis, a more severe form of invasive pneumococcal disease (IPD), are largely unknown. Knowledge of such mutations may improve our understanding of pathogenesis and inform preventive strategies. Here we report a pneumococcal pbp1b gene mu...
Bacterial geneticsInfectious diseasesMeningitisPathogens
10.1038/S41467-018-07997-Y
ISSN:2041-1723
Tomato growth stage modulates bacterial communities across different soil aggregate sizes and disease levels
Menghui Dong•Eiko E. Kuramae•Mengli Zhao•Rong Li•Qirong Shen等 6 人
Isme Communications
2023
•2023/9/26
•Vol.3 No.1 p.1-11
Soil aggregates contain distinct physio-chemical properties across different size classes. These differences in micro-habitats support varied microbial communities and modulate the effect of plant on microbiome, which affect soil functions such as disease suppression. However, little is known about ...
Microbial ecologyMicrobiome
10.1038/S43705-023-00312-X
ISSN:2730-6151
Genome-resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics
Ling Xu•Zhaobin Dong•Dawn Chiniquy•Grady Pierroz•Siwen Deng等 21 人
Nature Communications
2021
•2021/5/28
•Vol.12 No.1 p.1-17
Recent studies have demonstrated that drought leads to dramatic, highly conserved shifts in the root microbiome. At present, the molecular mechanisms underlying these responses remain largely uncharacterized. Here we employ genome-resolved metagenomics and comparative genomics to demonstrate that ca...
DroughtMetagenomicsMicrobePlant molecular biologySoil microbiology
10.1038/S41467-021-23553-7
ISSN:2041-1723
A conserved Phytophthora apoplastic trypsin-like serine protease targets the receptor-like kinase BAK1 to dampen plant immunity
Sicong Zhang•Liyuan Wang•Haibin Jiang•Guangzheng Sun•Yeqiang Xia等 13 人
Nature Plants
2025
•2025/7/1
•00 p.1-15
Perception of microbial pathogens by plant cell-surface pattern recognition receptors (PRRs) activates pattern-triggered immunity (PTI) in plants. The receptor-like kinase BAK1 functions as co-receptor of many PRRs and is a central immune regulator in PTI signal transduction. However, the molecular ...
Effectors in plant pathologyPattern recognition receptors in plants
10.1038/S41477-025-02039-0
ISSN:2055-0278
Characterization of pre-existing and induced SARS-CoV-2-specific CD8 + T cells
Isabel Schulien•Janine Kemming•Valerie Oberhardt•Katharina Wild•Lea M. Seidel等 32 人
Nature Medicine
2020
•2020/11/12
•Vol.27 No.1 p.78-85
Emerging data indicate that SARS-CoV-2-specific CD8+ T cells targeting different viral proteins are detectable in up to 70% of convalescent individuals1–5. However, very little information is currently available about the abundance, phenotype, functional capacity and fate of pre-existing and induced...
Cytotoxic T cellsImmunological memoryLymphocyte differentiationViral infection
10.1038/S41591-020-01143-2
ISSN:1078-8956
KDM6A alternative splicing induced by 25(OH)D inhibits breast cancer cell stemness through repressing TRAP1 transcription
Lingjun Ma•Xingye Sheng•Lexin Wang•Xinyu Wan•Rui Chen等 10 人
Oncogene
2026
•2026/2/17
•Vol.45 No.10 p.914-929
25-Hydroxyvitamin D (25(OH)D), a metabolite of vitamin D, has demonstrated anticancer properties; however, the role of alternative splicing in mediating these effects remains poorly understood. In this study, we reveal for the first time that 25(OH)D exerts antitumor effects by promoting exon 13 ski...
Breast cancerCell growthRNA splicing
10.1038/S41388-026-03694-Z
ISSN:0950-9232
The monoaminergic system is a bilaterian innovation
Matthew Goulty•Gaelle Botton-Amiot•Ezio Rosato•Simon G. Sprecher•Roberto Feuda
Nature Communications
2023
•2023/6/6
•Vol.14 No.1 p.1-15
Monoamines like serotonin, dopamine, and adrenaline/noradrenaline (epinephrine/norepinephrine) act as neuromodulators in the nervous system. They play a role in complex behaviours, cognitive functions such as learning and memory formation, as well as fundamental homeostatic processes such as sleep a...
Evolutionary geneticsHormonesPhylogeneticsSynaptic transmission
10.1038/S41467-023-39030-2
ISSN:2041-1723
A perfusable, multifunctional epicardial device improves cardiac function and tissue repair
Shixing Huang•Dong Lei•Qi Yang•Yang Yang•Chenyu Jiang等 17 人
Nature Medicine
2021
•2021/3/15
•Vol.27 No.3 p.480-490
Despite advances in technologies for cardiac repair after myocardial infarction (MI), new integrated therapeutic approaches still need to be developed. In this study, we designed a perfusable, multifunctional epicardial device (PerMed) consisting of a biodegradable elastic patch (BEP), permeable hie...
Biomedical engineeringDrug deliveryMyocardial infarction
10.1038/S41591-021-01279-9
ISSN:1078-8956
UDP-glucosyltransferase OsUGT75A promotes submergence tolerance during rice seed germination
He Yongqi•Sun Shan•Zhao Jia•Huang Zhibo•Peng Liling等 9 人
Nature Communications
2023
•2023/4/21
•Vol.14 No.1 p.1-14
Submergence stress represents a major obstacle limiting the application of direct seeding in rice cultivation. Under flooding conditions, coleoptile elongation can function as an escape strategy that contributes to submergence tolerance during seed germination in rice; however, the underlying molecu...
Agricultural geneticsFloodingPlant breedingPlant hormones
10.1038/S41467-023-38085-5
ISSN:2041-1723
CCND3 is indispensable for the maintenance of B-cell acute lymphoblastic leukemia
Ketzer Franz•Abdelrasoul Hend•Vogel Mona•Marienfeld Ralf•Müschen Markus等 8 人
Oncogenesis
2022
•2022/1/10
•Vol.11 No.1 p.1-12
The D-type cyclins (CCND1, CCND2, and CCND3) in association with CDK4/6 are known drivers of cell cycle progression. We reported previously that inactivation of FOXO1 confers growth arrest and apoptosis in B-ALL, partially mediated by subsequent depletion of CCND3. Given that previously the canonica...
Cell divisionLeukaemia
10.1038/S41389-021-00377-0
ISSN:2157-9024
A unique class of Zn2+-binding serine-based PBPs underlies cephalosporin resistance and sporogenesis in Clostridioides difficile
Sacco Michael D.•Wang Shaohui•Adapa Swamy R.•Zhang Xiujun•Lewandowski Eric M.等 19 人
Nature Communications
2022
•2022/7/28
•Vol.13 No.1 p.1-13
Treatment with β-lactam antibiotics, particularly cephalosporins, is a major risk factor for Clostridioides difficile infection. These broad-spectrum antibiotics irreversibly inhibit penicillin-binding proteins (PBPs), which are serine-based enzymes that assemble the bacterial cell wall. However, C....
Antimicrobial resistanceBacteriologyPathogensX-ray crystallography
10.1038/S41467-022-32086-6
ISSN:2041-1723
Chromosome-level genome assembly of the alpine extremophyte Tibetan snow lotus, Saussurea hypsipeta Diels
Mingxia Wang•Guojing Hu•Lamu Yangjin•Siheng Zeng•Huiyan Xiong等 7 人
Scientific Data
2026
•2026/2/24
•Vol.13 No.1 p.5080
Saussurea hypsipeta Diels, a perennial medicinal plant used in traditional Chinese medicine, is primarily distributed on the Qinghai-Tibet Plateau, where it serves as a key component of the alpine ecosystem. The lack of genetic information and high-quality genome assembly hinders in-depth research o...
EcologyPlant ecology
10.1038/S41597-026-06931-Y
ISSN:2052-4463
Comparative genomics reveals the dynamics of chromosome evolution in Lepidoptera
Charlotte J. Wright•Lewis Stevens•Alexander Mackintosh•Mara Lawniczak•Mark Blaxter
Nature Ecology & Evolution
2024
•2024/2/21
•00 p.1-14
Chromosomes are a central unit of genome organization. One-tenth of all described species on Earth are butterflies and moths, the Lepidoptera, which generally possess 31 chromosomes. However, some species display dramatic variation in chromosome number. Here we analyse 210 chromosomally complete lep...
Comparative genomicsEvolutionary biologyEvolutionary geneticsGenome evolution
10.1038/S41559-024-02329-4
ISSN:2397-334X
An ancestral molecular response to nanomaterial particulates
G. del Giudice•A. Serra•L. A. Saarimäki•K. Kotsis•I. Rouse等 24 人
Nature Nanotechnology
2023
•2023/5/8
•00 p.1-10
The varied transcriptomic response to nanoparticles has hampered the understanding of the mechanism of action. Here, by performing a meta-analysis of a large collection of transcriptomics data from various engineered nanoparticle exposure studies, we identify common patterns of gene regulation that ...
NanobiotechnologyNanoparticles
10.1038/S41565-023-01393-4
ISSN:1748-3387
Etiology of TP53 mutated complex karyotype acute myeloid leukemia
Anna Fedenko•Honorata Czapinska•Alwin Krämer•Friedrich Stölzel•Tilmann Bochtler等 6 人
Leukemia
2025
•2025/12/19
•00 p.1-5
Acute myeloid leukaemia
10.1038/S41375-025-02835-9
ISSN:0887-6924
WNT inhibitor SP5-mediated SERPING1 suppresses lung adenocarcinoma progression via TSC2/mTOR pathway
Yefeng Shen•Xiaofeng Dong•Xujia Li•Zhiyuan Shi•Tingting Shao等 7 人
Cell Death & Disease
2025
•2025/2/17
•Vol.16 No.1 p.1-15
The long-term outlook for patients grappling with lung cancer (LC) remains bleak, with lung adenocarcinoma (LUAD) emerging as the most predominant histological subtype. Our Mendelian randomization (MR) investigation spotlighted that heightened levels of the circulating protein serpin peptidase inhib...
Non-small-cell lung cancerTumour-suppressor proteins
10.1038/S41419-025-07440-3
ISSN:2041-4889
Widespread occurrence and relevance of phosphate storage in foraminifera
Nicolaas Glock•Julien Richirt•Christian Woehle•Christopher Algar•Maria Armstrong等 23 人
Nature
2025
•2025/1/15
•00 p.1-7
Foraminifera are ubiquitous marine protists that intracellularly accumulate phosphate1, an important macronutrient in marine ecosystems and in fertilizer potentially leaked into the ocean. Intracellular phosphate concentrations can be 100–1,000 times higher than in the surrounding water1. Here we sh...
Element cyclesMarine biology
10.1038/S41586-024-08431-8
ISSN:0028-0836
MHC class II proteins mediate sialic acid independent entry of human and avian H2N2 influenza A viruses
Umut Karakus•Milagros Sempere Borau•Patricia Martínez-Barragán•Josephine von Kempis•Soner Yildiz等 12 人
Nature Microbiology
2024
•2024/7/15
•00 p.1-16
Influenza A viruses (IAV) pose substantial burden on human and animal health. Avian, swine and human IAV bind sialic acid on host glycans as receptor, whereas some bat IAV require MHC class II complexes for cell entry. It is unknown how this difference evolved and whether dual receptor specificity i...
Influenza virusVirus–host interactions
10.1038/S41564-024-01771-1
ISSN:2058-5276
Combined bacteriophage and antibiotic therapy for refractory peritoneal dialysis-related peritonitis caused by Klebsiella pneumoniae
Xiaoxiao Yang•Nannan Wu•Xiaotian Jiang•Mengjun Cheng•Lijuan Hu等 11 人
Nature Communications
2026
•2026/2/7
•Vol.17 No.1 p.24680
Phage therapy is emerging as a promising alternative to antibiotics for treating various infections. However, there have been no prior studies on using bacteriophages for peritonitis in patients undergoing peritoneal dialysis. This report presents the successful treatment of refractory peritonitis i...
Bacterial infectionPeritoneal dialysis
10.1038/S41467-026-69154-0
ISSN:2041-1723
C9orf72 in myeloid cells suppresses STING-induced inflammation
Madelyn E. McCauley•Jacqueline Gire O’Rourke•Alberto Yáñez•Janet L. Markman•Ritchie Ho等 17 人
Nature
2020
•2020/8/19
•Vol.585 No.7823 p.96-101
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are neurodegenerative disorders that overlap in their clinical presentation, pathology and genetic origin. Autoimmune disorders are also overrepresented in both ALS and FTD, but this remains an unexplained epidemiologic observatio...
Amyotrophic lateral sclerosisNeuroimmunology
10.1038/S41586-020-2625-X
ISSN:0028-0836
Targeting TRPV6/CXCR4 complexes prevents castration-resistant prostate cancer metastasis to the bone
Clément Cordier•Aurélien Haustrate•Adriana Mihalache•Erika Duval•Emilie Desruelles等 14 人
Signal Transduction And Targeted Therapy
2025
•2025/9/5
•Vol.10 No.1 p.1-25
Bone metastasis most commonly occurs in castration-resistant prostate cancer (CRPC). The TRPV6 calcium channel is absent in healthy prostate tissue, but its expression increases considerably during cancer progression. We hypothesized that cancer cells induce TRPV6 expression de novo to directly bene...
MetastasisUrological cancer
10.1038/S41392-025-02376-8
ISSN:2059-3635
Interferon-stimulated gene GALNT2 restricts respiratory virus infections
Wei Ran•Jinghong Yang•Shi Yu•Qingtao Hu•Yuqi He等 46 人
Nature Microbiology
2025
•2025/12/12
•00 p.1-15
The innate immune response involves interferons (IFNs), antiviral cytokines that upregulate numerous IFN-stimulated genes, many of which have uncharacterized functions and mechanisms. Here we performed transcriptomic profiling of lung tissues from wild-type and IFNAR−/− mice infected with SARS-CoV-2...
Viral host responseViral infection
10.1038/S41564-025-02200-7
ISSN:2058-5276
Evolutionary selection of biofilm-mediated extended phenotypes in Yersinia pestis in response to a fluctuating environment
Yujun Cui•Boris V. Schmid•Hanli Cao•Xiang Dai•Zongmin Du等 24 人
Nature Communications
2020
•2020/1/15
•Vol.11 No.1 p.1-8
Yersinia pestis is transmitted from fleas to rodents when the bacterium develops an extensive biofilm in the foregut of a flea, starving it into a feeding frenzy, or, alternatively, during a brief period directly after feeding on a bacteremic host. These two transmission modes are in a trade-off reg...
BiofilmsEcological epidemiologyEvolutionary ecologyMolecular evolution
10.1038/S41467-019-14099-W
ISSN:2041-1723
Comprehensive characterization of protein–protein interactions perturbed by disease mutations
Feixiong Cheng•Junfei Zhao•Yang Wang•Weiqiang Lu•Zehui Liu等 24 人
Nature Genetics
2021
•2021/2/8
•Vol.53 No.3 p.342-353
Technological and computational advances in genomics and interactomics have made it possible to identify how disease mutations perturb protein–protein interaction (PPI) networks within human cells. Here, we show that disease-associated germline variants are significantly enriched in sequences encodi...
Computational biology and bioinformaticsGeneticsStructural biologySystems biology
10.1038/S41588-020-00774-Y
ISSN:1061-4036
Chromosome-level genome assembly and annotation of the endangered species Ormosia henryi
Lei Duan•Zengqiang Xia•Yuwen Ji•Lina Han•Sawai Mattapha等 11 人
Scientific Data
2025
•2025/11/20
•Vol.12 No.1 p.18460
Ormosia henryi of the legume family distributes in southern China, Vietnam and Thailand. This species is well-known as a rare and endangered plant, as well as a remarkable ornamental and timber tree. In this study, we present the first high-quality chromosome-level assembly of O. henryi based on HiF...
Molecular biologyPlant sciences
10.1038/S41597-025-06004-6
ISSN:2052-4463
Atypical rhizobia trigger nodulation and pathogenesis on the same legume hosts
Kévin Magne•Sophie Massot•Tifaine Folletti•Laurent Sauviac•Elhosseyn Ait-Salem等 22 人
Nature Communications
2024
•2024/10/26
•Vol.15 No.1 p.1-13
The emergence of commensalism and mutualism often derives from ancestral parasitism. However, in the case of rhizobium-legume interactions, bacterial strains displaying both pathogenic and nodulation features on a single host have not been described yet. Here, we isolated such a bacterium from Medic...
Parasite evolutionParasitismRhizobial symbiosisSymbiosisVirulence
10.1038/S41467-024-53388-X
ISSN:2041-1723
Gut-inhabiting Clostridia build human GPCR ligands by conjugating neurotransmitters with diet- and human-derived fatty acids
Fang-Yuan Chang•Piro Siuti•Stephane Laurent•Thomas Williams•Emerson Glassey等 9 人
Nature Microbiology
2021
•2021/4/12
•Vol.6 No.6 p.792-805
Human physiology is regulated by endogenous signalling compounds, including fatty acid amides (FAAs), chemical mimics of which are made by bacteria. The molecules produced by human-associated microbes are difficult to identify because they may only be made in a local niche or they require a substrat...
Applied microbiologyMicrobiologySynthetic biology
10.1038/S41564-021-00887-Y
ISSN:2058-5276
OsPRMT6b balances plant growth and high temperature stress by feedback inhibition of abscisic acid signaling
Xin Jin•Qibing Lin•Xinyue Zhang•Shuang Zhang•Weiwei Ma等 24 人
Nature Communications
2025
•2025/6/4
•Vol.16 No.1 p.1-16
Plants rapidly induce strong abscisic acid (ABA) signaling in response to stress, but how they weaken ABA signaling to resume normal growth after stress is unclear. Here, we find that arginine methyltransferase 6b (OsPRMT6b) methylates three arginine residues (R48, R79, R113) in ABA receptor OsPYL/R...
AbioticMethylationPlant molecular biology
10.1038/S41467-025-60350-Y
ISSN:2041-1723
Natural evidence of coronaviral 2′-O-methyltransferase activity affecting viral pathogenesis via improved substrate RNA binding
Jikai Deng•Shimin Yang•Yingjian Li•Xue Tan•Jiejie Liu等 15 人
Signal Transduction And Targeted Therapy
2024
•2024/5/29
•Vol.9 No.1 p.1-16
Previous studies through targeted mutagenesis of K-D-K-E motif have demonstrated that 2′-O-MTase activity is essential for efficient viral replication and immune evasion. However, the K-D-K-E catalytic motif of 2′-O-MTase is highly conserved across numerous viruses, including flaviviruses, vaccinia ...
InflammationMicrobiology
10.1038/S41392-024-01860-X
ISSN:2059-3635
Telomere-to-telomere genome sequence of the model mould pathogen Aspergillus fumigatus
Bowyer Paul•Currin Andrew•Delneri Daniela•Fraczek Marcin G.
Nature Communications
2022
•2022/9/14
•Vol.13 No.1 p.1-7
The pathogenic fungus Aspergillus fumigatus is a major etiological agent of fungal invasive and chronic diseases affecting tens of millions of individuals worldwide. Draft genome sequences of two clinical isolates (Af293 and A1163) are commonly used as reference genomes for analyses of clinical and ...
Fungal genomicsGenomicsPathogens
10.1038/S41467-022-32924-7
ISSN:2041-1723
Transposable elements hitchhike on Starships across fungal genomes
Hanne Griem-Krey•Júlia de Fraga Sant’Ana•Ursula Oggenfuss•Yohana Porto Calegari-Alves•Ana Luiza Marques等 9 人
Nature Communications
2026
•2026/2/11
•Vol.17 No.1 p.26340
Horizontal transfer of transposable elements (TEs) is widespread in eukaryotes, driving genetic variation and often associated with bursts of TE activity. Here, we report a recent TE burst in the insect-pathogenic fungus Metarhizium anisopliae. The actively transposing TEs were likely introduced via...
Evolutionary geneticsFungal genomicsGenome evolutionMobile elementsPathogens
10.1038/S41467-026-69410-3
ISSN:2041-1723
Identification of a protein responsible for the synthesis of archaeal membrane-spanning GDGT lipids
Zeng Zhirui•Chen Huahui•Yang Huan•Chen Yufei•Yang Wei等 8 人
Nature Communications
2022
•2022/3/22
•Vol.13 No.1 p.1-9
Glycerol dibiphytanyl glycerol tetraethers (GDGTs) are archaeal monolayer membrane lipids that can provide a competitive advantage in extreme environments. Here, we identify a radical SAM protein, tetraether synthase (Tes), that participates in the synthesis of GDGTs. Attempts to generate a tes-dele...
Archaeal geneticsArchaeal physiologyMembrane lipidsMetabolic pathways
10.1038/S41467-022-29264-X
ISSN:2041-1723
Super pangenome of Vitis empowers identification of downy mildew resistance genes for grapevine improvement
Li Guo•Xiangfeng Wang•Dilay Hazal Ayhan•Mohammad Saidur Rhaman•Ming Yan等 25 人
Nature Genetics
2025
•2025/2/26
•Vol.57 No.3 p.741-753
Grapevine (Vitis) is one of the oldest domesticated fruit crops with great cultural and economic importance. Here we assembled and annotated haplotype-resolved genomes of 72 global Vitis accessions including 25 wild and 47 cultivated grapevines, among which genomes for 60 grapevines are newly releas...
GeneticsPlant sciences
10.1038/S41588-025-02111-7
ISSN:1061-4036
Fluid flow-induced left-right asymmetric decay of Dand5 mRNA in the mouse embryo requires a Bicc1-Ccr4 RNA degradation complex
Katsura Minegishi•Benjamin Rothé•Kaoru R. Komatsu•Hiroki Ono•Yayoi Ikawa等 17 人
Nature Communications
2021
•2021/7/1
•Vol.12 No.1 p.1-17
Molecular left-right (L-R) asymmetry is established at the node of the mouse embryo as a result of the sensing of a leftward fluid flow by immotile cilia of perinodal crown cells and the consequent degradation of Dand5 mRNA on the left side. We here examined how the fluid flow induces Dand5 mRNA dec...
Body patterningCalcium signallingEmbryologyRNA decay
10.1038/S41467-021-24295-2
ISSN:2041-1723
A fungal pathogen suppresses host leaf senescence to increase infection
Yue Li•Xiangru Qu•Wenjuan Yang•Qin Wu•Xiaodong Wang等 14 人
Nature Communications
2025
•2025/3/24
•Vol.16 No.1 p.1-15
Phytopathogens such as Puccinia striiformis f. sp. tritici (Pst) induce pigment retention at pathogen infection sites. Although pigment retention is commonly observed in diverse pathosystems, its underlying physiological mechanism remains largely unclear. Herein, we identify and characterize a wheat...
ChloroplastsFungiPlant immunity
10.1038/S41467-025-58277-5
ISSN:2041-1723
Inadvertent human genomic bycatch and intentional capture raise beneficial applications and ethical concerns with environmental DNA
Liam Whitmore•Mark McCauley•Jessica A. Farrell•Maximilian R. Stammnitz•Samantha A. Koda等 10 人
Nature Ecology & Evolution
2023
•2023/5/15
•00 p.1-16
The field of environmental DNA (eDNA) is advancing rapidly, yet human eDNA applications remain underutilized and underconsidered. Broader adoption of eDNA analysis will produce many well-recognized benefits for pathogen surveillance, biodiversity monitoring, endangered and invasive species detection...
Ecological geneticsScience, technology and societySequencingZoology
10.1038/S41559-023-02056-2
ISSN:2397-334X
Microbial communities and plasmids mediate biodegradation of polycyclic aromatic hydrocarbons (PAHs) in coastal sediments
Ziqi Peng•Pandeng Wang•Manzoor Ahmad•Xiaoqing Luo•Qi Li等 8 人
Communications Earth & Environment
2026
•2026/2/9
•Vol.7 No.1 p.2390
Polycyclic aromatic hydrocarbons are persistent coastal pollutants, yet the ecological and genomic strategies governing the persistence and function of degraders under in-situ stress remain elusive. Here we decode these adaptive mechanisms using metagenomics and cultivation in the Pearl River Estuar...
Ecosystem ecologyMicrobial ecology
10.1038/S43247-026-03241-4
ISSN:2662-4435
Purines enrich root-associated Pseudomonas and improve wild soybean growth under salt stress
Yanfen Zheng•Xuwen Cao•Yanan Zhou•Siqi Ma•Youqiang Wang等 15 人
Nature Communications
2024
•2024/4/25
•Vol.15 No.1 p.1-14
The root-associated microbiota plays an important role in the response to environmental stress. However, the underlying mechanisms controlling the interaction between salt-stressed plants and microbiota are poorly understood. Here, by focusing on a salt-tolerant plant wild soybean (Glycine soja), we...
AgroecologyMicrobiomeSoil microbiology
10.1038/S41467-024-47773-9
ISSN:2041-1723
Root-to-shoot mobile mRNA CmoKARI1 promotes JA-Ile biosynthesis to confer chilling tolerance in grafted cucumbers
Miao Zhang•Wenqian Liu•Cuicui Wang•Shujin Lin•Ying Chen等 14 人
Nature Communications
2025
•2025/8/21
•Vol.16 No.1 p.1-16
Pumpkin rootstock is commonly used to graft cucurbit crops, improving their ability to withstand stress. While the significance of systemic signals from rootstocks to scions is recognized, the role of root-to-shoot transported mRNAs remains understudied. Cucumber plants often face growth and product...
AbioticPlant hormonesPlant signalling
10.1038/S41467-025-63228-1
ISSN:2041-1723
Phytocytokine signalling reopens stomata in plant immunity and water loss
Liu Zunyong•Hou Shuguo•Rodrigues Olivier•Wang Ping•Luo Dexian等 18 人
Nature
2022
•2022/5/4
•00 p.1-8
Stomata exert considerable effects on global carbon and water cycles by mediating gas exchange and water vapour1,2. Stomatal closure prevents water loss in response to dehydration and limits pathogen entry3,4. However, prolonged stomatal closure reduces photosynthesis and transpiration and creates a...
Plant immunityPlant signallingPlant stress responsesStomata
10.1038/S41586-022-04684-3
ISSN:0028-0836
Topical phage therapy in a mouse model of Cutibacterium acnes-induced acne-like lesions
Rimon Amit•Rakov Chani•Lerer Vanda•Sheffer-Levi Sivan•Oren Sivan Alkalay等 15 人
Nature Communications
2023
•2023/2/22
•Vol.14 No.1 p.1-18
Acne vulgaris is a common neutrophil-driven inflammatory skin disorder in which Cutibacterium acnes (C. acnes) is known to play a key role. For decades, antibiotics have been widely employed to treat acne vulgaris, inevitably resulting in increased bacterial antibiotic resistance. Phage therapy is a...
Acne vulgarisBacteriophagesDrug developmentPhage biology
10.1038/S41467-023-36694-8
ISSN:2041-1723
Seagrass genomes reveal ancient polyploidy and adaptations to the marine environment
Xiao Ma•Steffen Vanneste•Jiyang Chang•Luca Ambrosino•Kerrie Barry等 38 人
Nature Plants
2024
•2024/1/26
•00 p.1-16
We present chromosome-level genome assemblies from representative species of three independently evolved seagrass lineages: Posidonia oceanica, Cymodocea nodosa, Thalassia testudinum and Zostera marina. We also include a draft genome of Potamogeton acutifolius, belonging to a freshwater sister linea...
Comparative genomicsConservation biologyGenome evolutionPlant evolution
10.1038/S41477-023-01608-5
ISSN:2055-0278
The RING-finger ubiquitin E3 ligase TaPIR1 targets TaHRP1 for degradation to suppress chloroplast function
Rongrong Zhang•Yu Wu•Xiangru Qu•Wenjuan Yang•Qin Wu等 16 人
Nature Communications
2024
•2024/8/12
•Vol.15 No.1 p.1-17
Chloroplasts are key players in photosynthesis and immunity against microbial pathogens. However, the precise and timely regulatory mechanisms governing the control of photosynthesis-associated nuclear genes (PhANGs) expression in plant immunity remain largely unknown. Here we report that TaPIR1, a ...
FungiPhotosynthesisPlant immunity
10.1038/S41467-024-51249-1
ISSN:2041-1723
Genome-wide association meta-analysis identifies five loci associated with postpartum hemorrhage
David Westergaard•Valgerdur Steinthorsdottir•Lilja Stefansdottir•Palle Duun Rohde•Xiaoping Wu等 41 人
Nature Genetics
2024
•2024/7/22
•Vol.56 No.8 p.1597-1603
Bleeding in early pregnancy and postpartum hemorrhage (PPH) bear substantial risks, with the former closely associated with pregnancy loss and the latter being the foremost cause of maternal death, underscoring the severe impact on maternal–fetal health. We identified five genetic loci linked to PPH...
AnatomyGenome-wide association studiesReproductive disorders
10.1038/S41588-024-01839-Y
ISSN:1061-4036
Long-term monitoring of ultratrace nucleic acids using tetrahedral nanostructure-based NgAgo on wearable microneedles
Bin Yang•Haonan Wang•Jilie Kong•Xueen Fang
Nature Communications
2024
•2024/3/2
•Vol.15 No.1 p.1-15
Real-time and continuous monitoring of nucleic acid biomarkers with wearable devices holds potential for personal health management, especially in the context of pandemic surveillance or intensive care unit disease. However, achieving high sensitivity and long-term stability remains challenging. Her...
Biomedical engineeringElectrical and electronic engineeringPredictive markersSensors and biosensors
10.1038/S41467-024-46215-W
ISSN:2041-1723
Diurnal Fe(II)/Fe(III) cycling and enhanced O 2 production in a simulated Archean marine oxygen oasis
A. J. Herrmann•J. Sorwat•J. M. Byrne•N. Frankenberg-Dinkel•M. M. Gehringer
Nature Communications
2021
•2021/4/6
•Vol.12 No.1 p.1-11
The oxygenation of early Earth’s atmosphere during the Great Oxidation Event, is generally accepted to have been caused by oceanic Cyanobacterial oxygenic photosynthesis. Recent studies suggest that Fe(II) toxicity delayed the Cyanobacterial expansion necessary for the GOE. This study investigates t...
BiogeochemistryEnvironmental microbiology
10.1038/S41467-021-22258-1
ISSN:2041-1723
Cleavage of Bcl-2-associated athanogene by metacaspase determines plant antiviral immunity
Lin Liang•Yuhang Jiang•Pingzhi Zhao•Hongwei Wang•Xiaoyue Chen等 10 人
Nature Communications
2025
•2025/10/14
•Vol.16 No.1 p.1-13
Nucleotide-binding leucine-rich repeat receptors (NLRs) function as core components of innate immunity in both plants and animals. In animals, NLR activation initiates caspase-mediated immune signaling. In contrast, plants lack caspases but instead contain metacaspases (MCAs/MCs), yet their role in ...
MicrobeProteasesVirology
10.1038/S41467-025-64021-W
ISSN:2041-1723
PRPF31 reduction causes mis-splicing of the phototransduction genes in human organotypic retinal culture
Leila Azizzadeh Pormehr•Shahin Ahmadian•Narsis Daftarian•Seyed Ahmad Mousavi•Mahshid Shafiezadeh
European Journal Of Human Genetics
2019
•2019/10/25
•Vol.28 No.4 p.491-498
PRPF31 is ubiquitously expressed splicing factor and has an essential role in the pre-mRNA splicing in all tissues. However, it is not clear how reduced expression of this general splicing factor leads to retinal restricted disease, retinitis pigmentosa (RP). In this study, we used RNA interference ...
Genetic counsellingRetina
10.1038/S41431-019-0531-1
ISSN:1018-4813
SUMOylation controls the binding of hexokinase 2 to mitochondria and protects against prostate cancer tumorigenesis
Xun Shangguan•Jianli He•Zehua Ma•Weiwei zhang•Yiyi Ji等 16 人
Nature Communications
2021
•2021/3/22
•Vol.12 No.1 p.1-14
Human hexokinase 2 is an essential regulator of glycolysis that couples metabolic and proliferative activities in cancer cells. The binding of hexokinase 2 to the outer membrane of mitochondria is critical for its oncogenic activity. However, the regulation of hexokinase 2 binding to mitochondria re...
Prostate cancerSumoylation
10.1038/S41467-021-22163-7
ISSN:2041-1723
Plasma membrane CYBDOM proteins catalyse apoplastic AsA regeneration and interact with RbohD to activate autophagy and drought tolerance in plants
Xiuxiu Chen•Songsong Jin•Hong Du•Zebin Liu•Congcong Hou等 21 人
Nature Plants
2025
•2025/8/1
•00 p.1-19
Autophagy and apoplastic ascorbic acid (AsA) play important roles in plant drought tolerance. However, the trans-plasma membrane transport of AsA and its association with autophagy during drought stress are unclear. Here we report an AsA-induced autophagy pathway in plants, wherein plasma-membrane-l...
DroughtStress signalling
10.1038/S41477-025-02057-Y
ISSN:2055-0278
A chloroplast localized heavy metal-associated domain containing protein regulates grain calcium accumulation in rice
Huan Liu•Cun Lu•Xiang-Qian Liu•Chen-Jin Zhuo•Rong-Jian Luo等 12 人
Nature Communications
2024
•2024/10/27
•Vol.15 No.1 p.1-20
Calcium (Ca) is an essential mineral nutrient and plays a crucial signaling role in all living organisms. Increasing Ca content in staple foods such as rice is vital for improving Ca nutrition of humans. Here we map a quantitative trait locus that controls Ca concentration in rice grains and identif...
Agricultural geneticsPlant geneticsPlant molecular biology
10.1038/S41467-024-53648-W
ISSN:2041-1723
Toward subtask-decomposition-based learning and benchmarking for predicting genetic perturbation outcomes and beyond
Yicheng Gao•Zhiting Wei•Kejing Dong•Ke Chen•Jingya Yang等 7 人
Nature Computational Science
2024
•2024/9/27
•00 p.1-13
Deciphering cellular responses to genetic perturbations is fundamental for a wide array of biomedical applications. However, there are three main challenges: predicting single-genetic-perturbation outcomes, predicting multiple-genetic-perturbation outcomes and predicting genetic outcomes across cell...
Computational modelsGene expressionMachine learning
10.1038/S43588-024-00698-1
ISSN:2662-8457
Network analysis infers the wilt pathogen invasion associated with non-detrimental bacteria
Qiulong Hu•Lin Tan•Songsong Gu•Yansong Xiao•Xingyao Xiong等 9 人
Npj Biofilms And Microbiomes
2020
•2020/2/14
•Vol.6 No.1 p.1-8
The microbiota colonizing the root endophytic compartment and surrounding rhizosphere soils contribute to plant growth and health. However, the key members of plant soil and endophytic microbial communities involved in inhibiting or assisting pathogen invasion remain elusive. By utilizing 16S high-t...
PathogensSymbiosis
10.1038/S41522-020-0117-2
ISSN:2055-5008
Unconventional isoquinoline-based SERMs elicit fulvestrant-like transcriptional programs in ER+ breast cancer cells
Hancock G. R.•Young K. S.•Hosfield D. J.•Joiner C.•Sullivan E. A.等 9 人
Npj Breast Cancer
2022
•2022/12/14
•Vol.8 No.1 p.1-26
Estrogen receptor alpha (ERα) is a ligand-dependent master transcriptional regulator and key driver of breast cancer pathology. Small molecule hormones and competitive antagonists favor unique ERα conformational ensembles that elicit ligand-specific transcriptional programs in breast cancer and othe...
Breast cancerDrug developmentDrug discovery and development
10.1038/S41523-022-00497-9
ISSN:2374-4677
Regulation of viable/inactivated/lysed probiotic Lactobacillus plantarum H6 on intestinal microbiota and metabolites in hypercholesterolemic mice
Li Yue•Chen Mengling•Ma Yuxuan•Yang Yue•Cheng Ying等 8 人
Npj Science Of Food
2022
•2022/10/31
•Vol.6 No.1 p.1-13
Evidence suggests that probiotic interventions reduce non-communicable diseases (NCDs) risk. However, its therapeutic effect and mechanism are still unclear. To evaluate the hypocholesterolemic effect of Lactobacillus plantarum H6 (L.p H6), a new commercial patent strain capable of preventing hyperc...
Applied microbiologyBacterial secretion
10.1038/S41538-022-00167-X
ISSN:2396-8370
Puccinia triticina avirulence protein AvrLr21 directly interacts with wheat resistance protein Lr21 to activate wheat immune response
Songsong Shen•Fei Wang•Zhongchi Cui•Shitao Yuan•Linshuo Meng等 8 人
Communications Biology
2024
•2024/9/18
•Vol.7 No.1 p.1-7
Wheat leaf rust, caused by Puccinia triticina (Pt), remains a constant threat to wheat production worldwide. Deployment of race-specific leaf rust (Lr) resistance genes in wheat provides effective protection against leaf rust, but often leads to selective pressures that drive the rapid emergence of ...
Effectors in plant pathologyPlant evolution
10.1038/S42003-024-06881-4
ISSN:2399-3642
Antigenic structure of the human coronavirus OC43 spike reveals exposed and occluded neutralizing epitopes
Wang Chunyan•Hesketh Emma L.•Shamorkina Tatiana M.•Li Wentao•Franken Peter J.等 15 人
Nature Communications
2022
•2022/5/25
•Vol.13 No.1 p.1-15
Human coronavirus OC43 is a globally circulating common cold virus sustained by recurrent reinfections. How it persists in the population and defies existing herd immunity is unknown. Here we focus on viral glycoprotein S, the target for neutralizing antibodies, and provide an in-depth analysis of i...
AntibodiesViral immune evasion
10.1038/S41467-022-30658-0
ISSN:2041-1723
Correlated evolution of social organization and lifespan in mammals
Zhu Pingfen•Liu Weiqiang•Zhang Xiaoxiao•Li Meng•Liu Gaoming等 13 人
Nature Communications
2023
•2023/1/31
•Vol.14 No.1 p.1-18
Discerning the relationship between sociality and longevity would permit a deeper understanding of how animal life history evolved. Here, we perform a phylogenetic comparative analysis of ~1000 mammalian species on three states of social organization (solitary, pair-living, and group-living) and lon...
AgeingGene expressionSocial behaviourSocial evolutionTranscriptomics
10.1038/S41467-023-35869-7
ISSN:2041-1723
Unravelling the diversity of magnetotactic bacteria through analysis of open genomic databases
Maria Uzun•Lolita Alekseeva•Maria Krutkina•Veronika Koziaeva•Denis Grouzdev
Scientific Data
2020
•2020/7/31
•Vol.7 No.1 p.1-13
Magnetotactic bacteria (MTB) are prokaryotes that possess genes for the synthesis of membrane-bounded crystals of magnetite or greigite, called magnetosomes. Despite over half a century of studying MTB, only about 60 genomes have been sequenced. Most belong to Proteobacteria, with a minority affilia...
Bacterial geneticsData miningEvolutionary geneticsMicrobial ecology
10.1038/S41597-020-00593-0
ISSN:2052-4463
A unicellular cyanobacterium relies on sodium energetics to fix N2
Si Tang•Xueyu Cheng•Yaqing Liu•Lu Liu•Dai Liu等 11 人
Nature Communications
2024
•2024/11/9
•Vol.15 No.1 p.1-15
Diazotrophic cyanobacteria can fix nitrogen gas (N2) but are usually scarce in nitrogen-limited coastal waters, which poses an apparent ecological paradox. One hypothesis is that high salinities (> 10 g/L NaCl) may inhibit cyanobacterial N2 fixation. However, here we show that N2 fixation in a un...
Bacterial physiologyMarine microbiologyMicrobial ecologyWater microbiology
10.1038/S41467-024-53978-9
ISSN:2041-1723
Genomic interrogation of a MAGIC population highlights genetic factors controlling fiber quality traits in cotton
Wang Maojun•Qi Zhengyang•Thyssen Gregory N.•Naoumkina Marina•Jenkins Johnie N.等 10 人
Communications Biology
2022
•2022/1/17
•Vol.5 No.1 p.1-12
Cotton (Gossypium hirsutum L.) fiber is the most important resource of natural and renewable fiber for the textile industry. However, the understanding of genetic components and their genome-wide interactions controlling fiber quality remains fragmentary. Here, we sequenced a multiple-parent advance...
Genetic association studyPlant genetics
10.1038/S42003-022-03022-7
ISSN:2399-3642
Rhizosphere bacteriome structure and functions
Ling Ning•Wang Tingting•Kuzyakov Yakov
Nature Communications
2022
•2022/2/11
•Vol.13 No.1 p.1-13
Microbial composition and functions in the rhizosphere—an important microbial hotspot—are among the most fascinating yet elusive topics in microbial ecology. We used 557 pairs of published 16S rDNA amplicon sequences from the bulk soils and rhizosphere in different ecosystems around the world to gen...
AgroecologyMicrobial ecology
10.1038/S41467-022-28448-9
ISSN:2041-1723
Systematic mining of the human microbiome identifies antimicrobial peptides with diverse activity spectra
Andrew M. King•Zhengan Zhang•Emerson Glassey•Piro Siuti•Jon Clardy等 6 人
Nature Microbiology
2023
•2023/11/16
•00 p.1-15
Human-associated bacteria secrete modified peptides to control host physiology and remodel the microbiota species composition. Here we scanned 2,229 Human Microbiome Project genomes of species colonizing skin, gastrointestinal tract, urogenital tract, mouth and trachea for gene clusters encoding RiP...
AntibioticsNatural productsPeptides
10.1038/S41564-023-01524-6
ISSN:2058-5276
Molecular evolution and spatial transmission of severe fever with thrombocytopenia syndrome virus
Yu Leng•Han-Zheng Mu•Ning Cui•Le-Tian Fang•Rong Wang等 19 人
Nature Communications
2026
•2026/3/27
0Severe fever with thrombocytopenia syndrome virus (SFTSV), an emerging pathogen from the family Phenuiviridae, poses severe threats to public health in East Asia. In this study, we elucidate SFTSV’s epidemiological dynamics, transmission patterns, and molecular determinants of virulence, through ana...
Molecular evolutionPathogensViral infection
10.1038/S41467-026-71008-8
ISSN:2041-1723
In vitro resistance development gives insights into molecular resistance mechanisms against cefiderocol
Richard Kriz•Kathrin Spettel•Alina Pichler•Katharina Schefberger•Maria Sanz-Codina等 11 人
The Journal Of Antibiotics
2024
•2024/7/30
•00 p.1-11
Cefiderocol, a novel siderophore cephalosporin, demonstrates promising in vitro activity against multidrug-resistant Gram-negative bacteria, including carbapenemase-producing strains. Nonetheless, only a few reports are available regarding the acquisition of resistance in clinical settings, primaril...
AntibioticsAntimicrobial resistanceMicrobial genetics
10.1038/S41429-024-00762-Y
ISSN:0021-8820
Investigating the evolution of large meiotic rings of multiple X and Y sex chromosomes in two Leptodactylus frog species (Anura, Leptodactylidae)
Jhon Alex Dziechciarz Vidal•Deborah Charlesworth•Wen-Juan Ma•Qi Zhou•Ricardo Utsunomia等 10 人
Communications Biology
2025
•2025/11/21
•Vol.8 No.1 p.16360
A few species have evolved multiple sex chromosome systems with more than two Xs or Ys due to sex chromosome-autosome translocations. Among vertebrates, frogs (Anura) have the highest known number of such neo-sex chromosome systems, making them interesting for studying how such systems evolve. In th...
Evolutionary biologyEvolutionary genetics
10.1038/S42003-025-09151-Z
ISSN:2399-3642
Natural variation in Phosphatidylinositol 4-Kinase OsPI4Kγ7 and its interaction with OsLIC balance rice yield and latitudinal adaptation
Rui Zhu•Tao Yang•Shichen Han•Qianfeng Hu•Jianyin Xie等 16 人
Nature Communications
2026
•2026/1/28
•Vol.17 No.1 p.20900
High yield and wide adaptation of rice are crucial for grain supply and food security. Here, we report a type II phosphatidylinositol 4-kinase, OsPI4Kγ7, which positively regulates rice yield and confers wide adaptation of rice. We show that OsPI4Kγ7 interacts with the transcription factor, OsLIC, a...
Agricultural geneticsNatural variation in plantsPlant breeding
10.1038/S41467-026-68814-5
ISSN:2041-1723
Shotgun sequencing of airborne eDNA achieves rapid assessment of whole biomes, population genetics and genomic variation
Orestis Nousias•Mark McCauley•Maximilian R. Stammnitz•Jessica A. Farrell•Samantha A. Koda等 11 人
Nature Ecology & Evolution
2025
•2025/6/3
•Vol.9 No.6 p.1043-1060
Biodiversity and its associated genetic diversity are being lost at an unprecedented rate. Simultaneously, the distributions of flora, fauna, fungi, microbes and pathogens are rapidly changing. Novel technology can help to capture and record genetic diversity before it is lost and to measure populat...
Ecological geneticsEpidemiologyGenetic variationMolecular ecologyZoology
10.1038/S41559-025-02711-W
ISSN:2397-334X
ClpP/ClpX deficiency impairs mitochondrial functions and mTORC1 signaling during spermatogenesis
Chenxi Guo•Yuan Xiao•Jingkai Gu•Peikun Zhao•Zhe Hu等 12 人
Communications Biology
2023
•2023/10/5
•Vol.6 No.1 p.1-17
Caseinolytic protease proteolytic subunit (ClpP) and caseinolytic protease X (ClpX) are mitochondrial matrix peptidases that activate mitochondrial unfolded protein response to maintain protein homeostasis in the mitochondria. However, the role of ClpP and ClpX in spermatogenesis remains largely unk...
Mechanisms of diseaseSpermatogenesis
10.1038/S42003-023-05372-2
ISSN:2399-3642
Recovery of Lutacidiplasmatales archaeal order genomes suggests convergent evolution in Thermoplasmatota
Sheridan Paul O.•Meng Yiyu•Williams Tom A.•Gubry-Rangin Cécile
Nature Communications
2022
•2022/7/15
•Vol.13 No.1 p.1-13
The Terrestrial Miscellaneous Euryarchaeota Group has been identified in various environments, and the single genome investigated thus far suggests that these archaea are anaerobic sulfite reducers. We assemble 35 new genomes from this group that, based on genome analysis, appear to possess aerobic ...
ArchaeaPhylogeneticsTaxonomy
10.1038/S41467-022-31847-7
ISSN:2041-1723
Mass spectrometry-based draft of the mouse proteome
Giansanti Piero•Samaras Patroklos•Bian Yangyang•Meng Chen•Coluccio Andrea等 31 人
Nature Methods
2022
•2022/6/16
•00 p.1-9
The laboratory mouse ranks among the most important experimental systems for biomedical research and molecular reference maps of such models are essential informational tools. Here, we present a quantitative draft of the mouse proteome and phosphoproteome constructed from 41 healthy tissues and seve...
ProteomicsSystems biology
10.1038/S41592-022-01526-Y
ISSN:1548-7091
Repetitive DNA sequence detection and its role in the human genome
Xingyu Liao•Wufei Zhu•Juexiao Zhou•Haoyang Li•Xiaopeng Xu等 7 人
Communications Biology
2023
•2023/9/19
•Vol.6 No.1 p.1-21
Repetitive DNA sequences playing critical roles in driving evolution, inducing variation, and regulating gene expression. In this review, we summarized the definition, arrangement, and structural characteristics of repeats. Besides, we introduced diverse biological functions of repeats and reviewed ...
Data miningHigh-throughput screeningMachine learning
10.1038/S42003-023-05322-Y
ISSN:2399-3642
A Zn2-Cys6 transcription factor, TgZct4, reprograms antioxidant activity in the fungus Trichoderma guizhouense to defend against oxidative stress
Qi Gao•Dongyang Wang•Hong Zhu•Xinpeng Li•Yi Jiang等 10 人
Communications Biology
2025
•2025/10/15
•Vol.8 No.1 p.1-18
Fungi have evolved different strategies to cope with oxidative stress in competitive environments, however, the understanding of mechanisms that govern antioxidant response specificity and adequacy remains rudimentary. Trichoderma guizhouense NJAU 4742, a biocontrol fungus with strong viability, exh...
Transcriptional regulatory elementsTranscriptomics
10.1038/S42003-025-08864-5
ISSN:2399-3642
Identification and characterization of compounds that improve plant photosynthesis and growth under light stress conditions
Yuchen Qu•Kazuma Sakoda•Yu Wakabayashi•Masatoshi Nakajima•Tadao Asami等 7 人
Communications Biology
2025
•2025/2/27
•Vol.8 No.1 p.1-15
To meet the escalating food and fuel demands of a growing global population and industry, food production requires a 50% increase by 2050. However, various environmental stresses, such as excessive light, significantly inhibit plant growth and lead to substantial reductions in crop yields. A major c...
C3 photosynthesisLight responses
10.1038/S42003-025-07582-2
ISSN:2399-3642
Epidermal galactose spurs chytrid virulence and predicts amphibian colonization
Wang Yu•Verbrugghe Elin•Meuris Leander•Chiers Koen•Kelly Moira等 9 人
Nature Communications
2021
•2021/10/4
•Vol.12 No.1 p.1-13
The chytrid fungal pathogens Batrachochytrium dendrobatidis and Batrachochytrium salamandrivorans cause the skin disease chytridiomycosis in amphibians, which is driving a substantial proportion of an entire vertebrate class to extinction. Mitigation of its impact is largely unsuccessful and require...
Ecological epidemiologyFungal pathogenesisFungi
10.1038/S41467-021-26127-9
ISSN:2041-1723
Glycolytic heterogeneity drives metabolic-targeted therapy in pancreatic ductal adenocarcinoma
Ugo Chianese•Chiara Papulino•Gerardo Saggese•Ahmad Ali•Marianna Ciotola等 19 人
Signal Transduction And Targeted Therapy
2026
•2026/1/20
•Vol.11 No.1 p.250
Pancreatic ductal adenocarcinoma is traditionally characterized as a glycolytic tumor. However, the extent and clinical relevance of its metabolic heterogeneity remain poorly understood. In this study, we investigated whether glycolytic activity follows a consistent expression pattern across pancrea...
Cancer metabolismCancer therapyMolecular biology
10.1038/S41392-025-02546-8
ISSN:2059-3635
De novo and recessive forms of congenital heart disease have distinct genetic and phenotypic landscapes
W. Scott Watkins•E. Javier Hernandez•Sergiusz Wesolowski•Brent W. Bisgrove•Ryan T. Sunderland等 20 人
Nature Communications
2019
•2019/10/17
•Vol.10 No.1 p.1-12
The genetic architecture of sporadic congenital heart disease (CHD) is characterized by enrichment in damaging de novo variants in chromatin-modifying genes. To test the hypothesis that gene pathways contributing to de novo forms of CHD are distinct from those for recessive forms, we analyze 2391 wh...
Cardiovascular geneticsComputational biology and bioinformaticsCongenital heart defectsNext-generation sequencing
10.1038/S41467-019-12582-Y
ISSN:2041-1723
Enamel proteins from six Homo erectus specimens across China
Qiaomei Fu•Zhongyou Wu•E. Andrew Bennett•Song Xing•Qiang Ji等 12 人
Nature
2026
•2026/5/13
•00 p.1-7
Homo erectus remains have been found in Africa, Eurasia and Southeast Asia1–3, dating back around two million years; however, owing to their age and state of preservation, obtaining informative molecular data from them has proved challenging. Here we successfully extracted and analysed ancient ename...
PalaeontologyProteomics
10.1038/S41586-026-10478-8
ISSN:0028-0836
Chemo-mechanical changes of low-pH concrete under deep geological repository-like conditions: coupled biotic and abiotic effects
Trung Le Duc•Radek Vasicek•Katerina Cerna•Jakub Riha•Jiri Nemecek等 12 人
Npj Materials Degradation
2026
•2026/3/30
0Low-pH concrete (LPC, pH 10–11) represents a non-conventional cementitious material designed for environments where long-term durability and chemical compatibility with surrounding barriers are essential. Its potential use in underground construction, particularly as an engineered barrier material i...
Environmental sciencesMicrobiologySolid Earth sciences
10.1038/S41529-026-00773-0
ISSN:2397-2106
A generalist medical language model for disease diagnosis assistance
Xiaohong Liu•Hao Liu•Guoxing Yang•Zeyu Jiang•Shuguang Cui等 24 人
Nature Medicine
2025
•2025/1/8
•00 p.1-11
The delivery of accurate diagnoses is crucial in healthcare and represents the gateway to appropriate and timely treatment. Although recent large language models (LLMs) have demonstrated impressive capabilities in few-shot or zero-shot learning, their effectiveness in clinical diagnosis remains unpr...
Computational biology and bioinformaticsDiagnosis
10.1038/S41591-024-03416-6
ISSN:1078-8956
Kastor and Polluks polypeptides encoded by a single gene locus cooperatively regulate VDAC and spermatogenesis
Mise Shintaro•Matsumoto Akinobu•Shimada Keisuke•Hosaka Toshiaki•Takahashi Masatomo等 19 人
Nature Communications
2022
•2022/2/28
•Vol.13 No.1 p.1-17
Although several long noncoding RNAs (lncRNAs) have recently been shown to encode small polypeptides, those in testis remain largely uncharacterized. Here we identify two sperm-specific polypeptides, Kastor and Polluks, encoded by a single mouse locus (Gm9999) previously annotated as encoding a lncR...
Gene expressionLong non-coding RNAsReproductive biologySpermatogenesis
10.1038/S41467-022-28677-Y
ISSN:2041-1723
Spatially resolved osteoblast-traced transcriptomics uncovers TGF-β as a combination target with sclerostin in osteoporosis
Ahyoun Choi•Ji Yeon Lee•Hyejin Yoon•Xiangguo Che•Minkyeong Choi等 17 人
Bone Research
2026
•2026/4/2
•Vol.14 No.1 p.370
Dynamic transitions of mature osteoblasts between active and quiescent states are essential for bone homeostasis and present a promising target for osteoanabolic therapy. However, these transitions remain poorly understood due to cellular heterogeneity and limited spatial context. Here, we employed ...
BoneOsteoporosis
10.1038/S41413-026-00521-9
ISSN:2095-6231
Modulating IL-11-dependent matrix stiffness to delay ovarian aging
Meng Wu•Qingqing Zhu•Jiaqiang Xiong•Weicheng Tang•Dan Chen等 25 人
Nature Aging
2026
•2026/7/2
•00 p.1-22
Recent studies have highlighted the crucial role of mechanical properties in the ovarian microenvironment for ovarian function. However, the mechanisms that cause ovarian matrix stiffening during aging remain incompletely understood. Here we utilized atomic force microscopy (AFM) to demonstrate that...
AgeingReproductive disorders
10.1038/S43587-026-01159-2
ISSN:2662-8465
The ZmWAKL–ZmWIK–ZmBLK1–ZmRBOH4 module provides quantitative resistance to gray leaf spot in maize
Tao Zhong•Mang Zhu•Qianqian Zhang•Yan Zhang•Suining Deng等 13 人
Nature Genetics
2024
•2024/1/18
•00 p.1-12
Gray leaf spot (GLS), caused by the fungal pathogens Cercospora zeae-maydis and Cercospora zeina, is a major foliar disease of maize worldwide (Zea mays L.). Here we demonstrate that ZmWAKL encoding cell-wall-associated receptor kinase-like protein is the causative gene at the major quantitative dis...
Plant breedingPlant molecular biology
10.1038/S41588-023-01644-Z
ISSN:1061-4036
Telomere-to-telomere genome assembly of a male pig provides insight into population structure and selection for body stature
Ya-Biao Luo•Ning Huang•Cheng-Wan Zha•Li-Xian Yang•Peng-Xiang Xue等 14 人
Nature Genetics
2025
•2025/12/12
•00 p.1-11
A complete telomere-to-telomere (T2T) genome is essential for advancing pig genomic research. Here we assembled a pig T2T gap-free genome T2T-pig1.0 (2.63 Gb) for a boar in Wuzhishan, China, covering all 20 chromosomes. T2T-pig1.0 with an accuracy of >99.999% uncovers 194.42 Mb of previously unre...
GenomicsPopulation genetics
10.1038/S41588-025-02433-6
ISSN:1061-4036
LncRNA EPR controls epithelial proliferation by coordinating Cdkn1a transcription and mRNA decay response to TGF-β
Martina Rossi•Gabriele Bucci•Dario Rizzotto•Domenico Bordo•Matteo J. Marzi等 15 人
Nature Communications
2019
•2019/4/29
•Vol.10 No.1 p.1-16
Long noncoding RNAs (lncRNAs) are emerging as regulators of fundamental biological processes. Here we report on the characterization of an intergenic lncRNA expressed in epithelial tissues which we termed EPR (Epithelial cell Program Regulator). EPR is rapidly downregulated by TGF-β and its sustaine...
Breast cancerLong non-coding RNAsRNA decayTranscription
10.1038/S41467-019-09754-1
ISSN:2041-1723
A phase 2 single center open label randomised control trial for convalescent plasma therapy in patients with severe COVID-19
Ray Yogiraj•Paul Shekhar Ranjan•Bandopadhyay Purbita•D’Rozario Ranit•Sarif Jafar等 38 人
Nature Communications
2022
•2022/1/19
•Vol.13 No.1 p.1-9
A single center open label phase 2 randomised control trial (Clinical Trial Registry of India No. CTRI/2020/05/025209) was done to assess clinical and immunological benefits of passive immunization using convalescent plasma therapy. At the Infectious Diseases and Beleghata General Hospital in Kolkat...
Outcomes researchViral infection
10.1038/S41467-022-28064-7
ISSN:2041-1723
Nighttime-restricted feeding disrupts spermatogenesis in mice via gut microbiota-derived KYNA homeostasis
Donghui Yang•Dong Xie•Chuan Li•Yan Liu•Xiangyu Cheng等 12 人
Communications Biology
2026
•2026/2/3
•Vol.9 No.1 p.3540
Time-restricted feeding (TRF) may modulate metabolic homeostasis through circadian rhythms, but its effects on male fertility remain unclear. This study investigates how different TRF schedules influence testicular homeostasis and spermatogenesis, focusing on the gut-testis axis. Mice are subjected ...
Disease modelReproductive disorders
10.1038/S42003-026-09619-6
ISSN:2399-3642
Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa
Tegally Houriiyah•Moir Monika•Everatt Josie•Giovanetti Marta•Scheepers Cathrine等 56 人
Nature Medicine
2022
•2022/6/27
•Vol.28 No.9 p.1785-1790
Three lineages (BA.1, BA.2 and BA.3) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant of concern predominantly drove South Africa’s fourth Coronavirus Disease 2019 (COVID-19) wave. We have now identified two new lineages, BA.4 and BA.5, responsible for a fifth wave...
EpidemiologyPhylogeny
10.1038/S41591-022-01911-2
ISSN:1078-8956
ALG1-mediated PDL1 glycosylation drives macrophage m2 polarization to promote bladder cancer progression
JG Zhao•ZY Chen•HQ Pan•Y. Jin•RY Zhang等 7 人
Cell Death & Differentiation
2026
•2026/5/21
•00 p.1-15
Asparagine-linked glycosylation protein 1 homolog (ALG1), a β-1,4-mannosyltransferase, catalyzes the initial committed step of the N-glycosylation pathway. While its role in congenital glycosylation disorders is well established, the contribution of ALG1 to bladder cancer (BC) progression, particula...
Cancer metabolismImmune evasion
10.1038/S41418-026-01764-Z
ISSN:1350-9047
LTK mutations responsible for resistance to lorlatinib in non-small cell lung cancer harboring CLIP1-LTK fusion
Shunta Mori•Hiroki Izumi•Mitsugu Araki•Jie Liu•Yu Tanaka等 20 人
Communications Biology
2024
•2024/4/4
•Vol.7 No.1 p.1-10
The CLIP1-LTK fusion was recently discovered as a novel oncogenic driver in non-small cell lung cancer (NSCLC). Lorlatinib, a third-generation ALK inhibitor, exhibited a dramatic clinical response in a NSCLC patient harboring CLIP1-LTK fusion. However, it is expected that acquired resistance will in...
Non-small-cell lung cancerOncogenes
10.1038/S42003-024-06116-6
ISSN:2399-3642
Convergent morphology and divergent phenology promote the coexistence of Morpho butterfly species
Le Roy Camille•Roux Camille•Authier Elisabeth•Parrinello Hugues•Bastide Héloïse等 7 人
Nature Communications
2021
•2021/12/13
•Vol.12 No.1 p.1-9
The coexistence of closely-related species in sympatry is puzzling because ecological niche proximity imposes strong competition and reproductive interference. A striking example is the widespread wing pattern convergence of several blue-banded Morpho butterfly species with overlapping ranges of dis...
Behavioural ecologyEvolutionary ecologySpeciation
10.1038/S41467-021-27549-1
ISSN:2041-1723
Fibroblastic reticular cells direct the initiation of T cell responses via CD44
Xavier Y. X. Sng•Valentina Voigt•Iona S. Schuster•Peter Fleming•Felix A. Deuss等 23 人
Nature
2026
•2026/1/21
•Vol.651 No.8106 p.752-762
The movement of dendritic cells and T cells within secondary lymphoid organs is critical for the development of adaptive immune responses1,2. Central to this process is the fibroblastic reticular cell (FRC) network, which forms a highly organized conduit system that facilitates the movement of and i...
Cell migrationImmune evasionLymphocyte activationSpleenVirus–host interactions
10.1038/S41586-025-09988-8
ISSN:0028-0836
Formyl peptide receptor 1 and its antagonist T0080 in atherosclerosis
Yu-Jing Li•Xue Zhao•Siting Wu•Nan Yao•Xueyu Zhang等 12 人
Cell Death & Differentiation
2025
•2025/4/9
•00 p.1-12
Focal inflammation and arterial damage driven by macrophages are key pathogenic processes in atherosclerosis. However, the mechanisms that regulate these processes remain poorly understood. In this study, we demonstrate that formyl peptide receptor 1 (FPR1) agonist, a mitochondrial N-formyl peptide,...
Cardiovascular diseasesPreclinical research
10.1038/S41418-025-01506-7
ISSN:1350-9047
Tissue-specific mutation of pink-1 jointly induces intestinal dysfunction and contributes to dopaminergic neuron degeneration
Huan Gu•Yixin Li•Guolin Shi•Wenhui Zhou•Yi Dou等 10 人
Npj Parkinson's Disease
2026
•2026/4/16
0In patients with Parkinson’s disease (PD), intestinal dysfunction represents one of the predominant non-motor symptoms and typically manifests at the earliest stages of the disease. However, the underlying causes of intestinal dysfunction and its impact on disease progression remain to be fully eluc...
Cell biologyMicrobiologyNeuroscience
10.1038/S41531-026-01350-7
ISSN:2373-8057
Unconventional secretion of Magnaporthe oryzae effectors in rice cells is regulated by tRNA modification and codon usage control
Gang Li•Nawaraj Dulal•Ziwen Gong•Richard A. Wilson
Nature Microbiology
2023
•2023/8/10
•00 p.1-11
Microbial pathogens deploy effector proteins to manipulate host cell innate immunity, often using poorly understood unconventional secretion routes. Transfer RNA (tRNA) anticodon modifications are universal, but few biological functions are known. Here, in the rice blast fungus Magnaporthe oryzae, w...
ParasitismtRNAs
10.1038/S41564-023-01443-6
ISSN:2058-5276
Antibiotic resistance profile of nitrogen-metabolizing microbes in anoxic‒oxic processes for swine wastewater treatment
Yiwen Yang•Shuang Cai•Feng Huang•Chunhao Mo•Yongbao Wu等 9 人
Npj Clean Water
2025
•2025/4/20
•Vol.8 No.1 p.1-12
The anoxic-oxic (A/O) process is the most common biological method for removing nitrogen (N) from wastewater, but the antibiotic resistance profile of N-metabolizing microbes in A/O processes remains largely underexplored. Here we demonstrated a significant positive correlation between various types...
ChemistryEnvironmental sciencesEnvironmental social sciences
10.1038/S41545-025-00464-4
ISSN:2059-7037
Identifying the “stripe” transcription factors and cooperative binding related to DNA methylation
Ximei Luo•Quan Zou
Communications Biology
2024
•2024/10/5
•Vol.7 No.1 p.1-10
DNA methylation plays a critical role in gene regulation by modulating the DNA binding of transcription factors (TFs). This study integrates TFs’ ChIP-seq profiles with WGBS profiles to investigate how DNA methylation affects protein interactions. Statistical methods and a 5-letter DNA motif calling...
BioinformaticsDNA methylation
10.1038/S42003-024-06992-Y
ISSN:2399-3642
PEN1 catalyses RNA primer removal during plastid DNA replication in maize
Xing Huang•Guolong Shi•Qiao Xiao•Jiaojiao Feng•Yongcai Huang等 15 人
Nature Plants
2025
•2025/6/25
•Vol.11 No.7 p.1325-1338
The plastid DNA (ptDNA) replication is initiated by primases, which synthesize RNA primers; following the synthesis of DNA fragments, primers must be removed before ligation. However, the enzymes and mechanisms underlying this process are poorly understood. Here we cloned a gene from maize that enco...
ChloroplastsPlant molecular biology
10.1038/S41477-025-02027-4
ISSN:2055-0278
Export of defensive glucosinolates is key for their accumulation in seeds
Xu Deyang•Sanden Niels Christian Holm•Hansen Line Lykke•Belew Zeinu Mussa•Madsen Svend Roesen等 13 人
Nature
2023
•2023/4/19
•00 p.1-7
Plant membrane transporters controlling metabolite distribution contribute key agronomic traits1–6. To eliminate anti-nutritional factors in edible parts of crops, the mutation of importers can block the accumulation of these factors in sink tissues7. However, this often results in a substantially a...
Molecular engineering in plantsPlant immunityPlant transportersSecondary metabolism
10.1038/S41586-023-05969-X
ISSN:0028-0836
SOCS5-RBMX stimulates SREBP1-mediated lipogenesis to promote metastasis in steatotic HCC with HBV-related cirrhosis
Youpeng Wang•Ziyin Zhao•Tingting Guo•Tiansong Wu•Mao Zhang等 12 人
Npj Precision Oncology
2024
•2024/3/1
•Vol.8 No.1 p.1-16
Abnormal lipid metabolism promotes hepatocellular carcinoma (HCC) progression, which engenders therapeutic difficulties owing to unclear mechanisms of the phenomenon. We precisely described a special steatotic HCC subtype with HBV-related cirrhosis and probed its drivers. Hematoxylin-eosin (HE) stai...
Cancer metabolismHepatocellular carcinomaOncogenes
10.1038/S41698-024-00545-6
ISSN:2397-768X
Small subunits can determine enzyme kinetics of tobacco Rubisco expressed in Escherichia coli
Myat T. Lin•William D. Stone•Vishalsingh Chaudhari•Maureen R. Hanson
Nature Plants
2020
•2020/9/14
•Vol.6 No.10 p.1289-1299
Ribulose-1,5-bisphosphate carboxylase–oxygenase (Rubisco) catalyses the first step in carbon fixation and is a strategic target for improving photosynthetic efficiency. In plants, Rubisco is composed of eight large and eight small subunits, and its biogenesis requires multiple chaperones. Here, we o...
Molecular engineeringPhotosynthesisPlant biotechnology
10.1038/S41477-020-00761-5
ISSN:2055-0278
Complete biosynthesis of salicylic acid from phenylalanine in plants
Bao Zhu•Yanjun Zhang•Rong Gao•Zhihua Wu•Wei Zhang等 17 人
Nature
2025
•2025/7/23
•00 p.1-10
Salicylic acid (SA) is a pivotal phytohormone for plant responses to biotic and abiotic stresses. Plants have evolved two pathways to produce SA: the isochorismate synthase and phenylalanine ammonia lyase (PAL) pathways1. Whereas the isochorismate synthase pathway has been fully identified2–4, ...
Plant hormonesPlant immunitySecondary metabolism
10.1038/S41586-025-09175-9
ISSN:0028-0836
Dysbiosis of human gut microbiome in young-onset colorectal cancer
Yang Yongzhi•Du Lutao•Shi Debing•Kong Cheng•Liu Jianqiang等 8 人
Nature Communications
2021
•2021/11/19
•Vol.12 No.1 p.1-13
The incidence of sporadic young-onset colorectal cancer (yCRC) is increasing. A significant knowledge gap exists in the gut microbiota and its diagnostic value for yCRC patients. Through 16S rRNA gene sequencing, 728 samples are collected to identify microbial markers, and an independent cohort of 3...
Colorectal cancer
10.1038/S41467-021-27112-Y
ISSN:2041-1723
Disease-associated genotypes of the commensal skin bacterium Staphylococcus epidermidis
Guillaume Méric•Leonardos Mageiros•Johan Pensar•Maisem Laabei•Koji Yahara等 25 人
Nature Communications
2018
•2018/11/28
•Vol.9 No.1 p.1-11
Some of the most common infectious diseases are caused by bacteria that naturally colonise humans asymptomatically. Combating these opportunistic pathogens requires an understanding of the traits that differentiate infecting strains from harmless relatives. Staphylococcus epidermidis is carried asym...
Bacterial evolutionEvolutionary biologyEvolutionary geneticsInfectious-disease diagnostics
10.1038/S41467-018-07368-7
ISSN:2041-1723
Gut bacteria identified in colorectal cancer patients promote tumourigenesis via butyrate secretion
Okumura Shintaro•Konishi Yusuke•Narukawa Megumi•Sugiura Yuki•Yoshimoto Shin等 27 人
Nature Communications
2021
•2021/9/28
•Vol.12 No.1 p.1-14
Emerging evidence is revealing that alterations in gut microbiota are associated with colorectal cancer (CRC). However, very little is currently known about whether and how gut microbiota alterations are causally associated with CRC development. Here we show that 12 faecal bacterial taxa are enriche...
BacteriologyGastrointestinal cancerSenescence
10.1038/S41467-021-25965-X
ISSN:2041-1723
A robustly rooted tree of eukaryotes reveals their excavate ancestry
Kelsey Williamson•Laura Eme•Hector Baños•Charley G. P. McCarthy•Edward Susko等 11 人
Nature
2025
•2025/3/12
•00 p.1-8
The eukaryote Tree of Life (eToL) depicts the relationships among all eukaryotic organisms; its root represents the Last Eukaryotic Common Ancestor (LECA) from which all extant complex lifeforms are descended1. Locating this root is crucial for reconstructing the features of LECA, both as the endpoi...
Evolutionary theoryMolecular evolutionPhylogenyStatistical methods
10.1038/S41586-025-08709-5
ISSN:0028-0836
Pregnancy reprograms the epigenome of mammary epithelial cells and blocks the development of premalignant lesions
Mary J. Feigman•Matthew A. Moss•Chen Chen•Samantha L. Cyrill•Michael F. Ciccone等 10 人
Nature Communications
2020
•2020/5/27
•Vol.11 No.1 p.1-12
Pregnancy causes a series of cellular and molecular changes in mammary epithelial cells (MECs) of female adults. In addition, pregnancy can also modify the predisposition of rodent and human MECs to initiate oncogenesis. Here, we investigate how pregnancy reprograms enhancer chromatin in the mammary...
Cell biologyMolecular biology
10.1038/S41467-020-16479-Z
ISSN:2041-1723
A plant virus differentially alters DNA methylation in two cryptic species of a hemipteran vector
Michael A. Catto•Saptarshi Ghosh•Sudeep Pandey•Banani Mondal•Alvin Simmons等 7 人
Npj Viruses
2024
•2024/8/12
•Vol.2 No.1 p.1-12
Epigenetic patterns including DNA methylation are known to vary between distantly related species, but it is not clear how these patterns differ at an intraspecific level. The sweetpotato whitefly, Bemisia tabaci (Gennadius) (Aleyrodidae; Hemiptera), encompasses several cryptic species. These crypti...
Computational biology and bioinformaticsGenetics
10.1038/S44298-024-00044-2
ISSN:2948-1767
Human ACE2 peptide-mimics block SARS-CoV-2 pulmonary cells infection
Philippe Karoyan•Vincent Vieillard•Luis Gómez-Morales•Estelle Odile•Amélie Guihot等 9 人
Communications Biology
2021
•2021/2/12
•Vol.4 No.1 p.1-9
In light of the recent accumulated knowledge on SARS-CoV-2 and its mode of human cells invasion, the binding of viral spike glycoprotein to human Angiotensin Converting Enzyme 2 (hACE2) receptor plays a central role in cell entry. We designed a series of peptides mimicking the N-terminal helix of hA...
Structure-based drug designViral infection
10.1038/S42003-021-01736-8
ISSN:2399-3642
Phylogenetic analyses suggest centipede venom arsenals were repeatedly stocked by horizontal gene transfer
Eivind A. B. Undheim•Ronald A. Jenner
Nature Communications
2021
•2021/2/5
•Vol.12 No.1 p.1-14
Venoms have evolved over a hundred times in animals. Venom toxins are thought to evolve mostly by recruitment of endogenous proteins with physiological functions. Here we report phylogenetic analyses of venom proteome-annotated venom gland transcriptome data, assisted by genomic analyses, to show th...
Molecular evolutionPhylogenetics
10.1038/S41467-021-21093-8
ISSN:2041-1723
Rescue of maternal immune activation-induced behavioral abnormalities in adult mouse offspring by pathogen-activated maternal Treg cells
Zhipeng Xu•Xiaoyun Zhang•Hao Chang•Yue Kong•Yangyue Ni等 17 人
Nature Neuroscience
2021
•2021/4/15
•Vol.24 No.6 p.818-830
Maternal immune activation (MIA) induced by lipopolysaccharides or polyinosinic:polycytidylic acid injections can induce behavioral abnormalities in adult mouse offspring. Here, we used the soluble tachyzoite antigen from Toxoplasma gondii, a parasite that infects approximately two billion people, t...
DiseasesNeuroscience
10.1038/S41593-021-00837-1
ISSN:1097-6256
Comparison of DNA methylation based classification models for precision diagnostics of central nervous system tumors
Quynh T. Tran•Alex Breuer•Tong Lin•Ruth Tatevossian•Sariah J. Allen等 18 人
Npj Precision Oncology
2024
•2024/10/2
•Vol.8 No.1 p.1-12
As part of the advancement in therapeutic decision-making for brain tumor patients at St. Jude Children’s Research Hospital (SJCRH), we developed three robust classifiers, a deep learning neural network (NN), k-nearest neighbor (kNN), and random forest (RF), trained on a reference series DNA-methyla...
CNS cancerComputational biology and bioinformatics
10.1038/S41698-024-00718-3
ISSN:2397-768X
Nucleosome wrapping states encode principles of 3D genome organization
Zengqi Wen•Ruixin Fang•Ruxin Zhang•Xinqian Yu•Fanli Zhou等 6 人
Nature Communications
2025
•2025/1/3
•Vol.16 No.1 p.1-11
Nucleosome is the basic structural unit of the genome. During processes like DNA replication and gene transcription, the conformation of nucleosomes undergoes dynamic changes, including DNA unwrapping and rewrapping, as well as histone disassembly and assembly. However, the wrapping characteristics ...
Chromatin analysisNucleosomes
10.1038/S41467-024-54735-8
ISSN:2041-1723
Herbicide leakage into seawater impacts primary productivity and zooplankton globally
Liqiang Yang•Xiaotong He•Shaoguo Ru•Yongyu Zhang
Nature Communications
2024
•2024/2/27
•Vol.15 No.1 p.1-17
Predicting the magnitude of herbicide impacts on marine primary productivity remains challenging because the extent of worldwide herbicide pollution in coastal waters and the concentration-response relationships of phytoplankton communities to multiple herbicides are unclear. By analyzing the spatio...
Ecological networksEnvironmental impactWater microbiology
10.1038/S41467-024-46059-4
ISSN:2041-1723
Gene duplications and phylogenomic conflict underlie major pulses of phenotypic evolution in gymnosperms
Gregory W. Stull•Xiao-Jian Qu•Caroline Parins-Fukuchi•Ying-Ying Yang•Jun-Bo Yang等 13 人
Nature Plants
2021
•2021/7/19
•00 p.1-11
Inferring the intrinsic and extrinsic drivers of species diversification and phenotypic disparity across the tree of life is a major challenge in evolutionary biology. In green plants, polyploidy (or whole-genome duplication, WGD) is known to play a major role in microevolution and speciation, but t...
PhylogeneticsPlant evolution
10.1038/S41477-021-00964-4
ISSN:2055-0278
Polyclonal-to-monoclonal transition in colorectal precancerous evolution
Zhaolian Lu•Shanlan Mo•Duo Xie•Xiangwei Zhai•Shanjun Deng等 23 人
Nature
2024
•2024/10/30
•00 p.1-8
Unravelling the origin and evolution of precancerous lesions is crucial for effectively preventing malignant transformation, yet our current knowledge remains limited1–3. Here we used a base editor-enabled DNA barcoding system4 to comprehensively map single-cell phylogenies in mouse models of intest...
Cancer genomicsColorectal cancerEvolutionary geneticsPhylogeneticsTumour heterogeneity
10.1038/S41586-024-08133-1
ISSN:0028-0836
Staphylococcal virulence factor HlgB targets the endoplasmic-reticulum-resident E3 ubiquitin ligase AMFR to promote pneumonia
Sun Lei•Zhang Haibo•Zhang Huihui•Lou Xinyi•Wang Zhiming等 11 人
Nature Microbiology
2023
•2023/1/2
•Vol.8 No.1 p.107-120
Staphylococcus aureus invades cells and persists intracellularly, causing persistent inflammation that is notoriously difficult to treat. Here we investigated host–pathogen interactions underlying intracellular S. aureus infection in macrophages and discovered that the endoplasmic reticulum (ER) is ...
Acute inflammationInfection
10.1038/S41564-022-01278-7
ISSN:2058-5276
Genome-wide dissection of changes in maize root system architecture during modern breeding
Ren Wei•Zhao Longfei•Liang Jiaxing•Wang Lifeng•Chen Limei等 19 人
Nature Plants
2022
•2022/11/17
•Vol.8 No.12 p.1408-1422
Appropriate root system architecture (RSA) can improve maize yields in densely planted fields, but little is known about its genetic basis in maize. Here we performed root phenotyping of 14,301 field-grown plants from an association mapping panel to study the genetic architecture of maize RSA. A gen...
Genome-wide association studiesPlant breedingPopulation genetics
10.1038/S41477-022-01274-Z
ISSN:2055-0278
Non-modular fatty acid synthases yield distinct N-terminal acylation in ribosomal peptides
Hengqian Ren•Chunshuai Huang•Yuwei Pan•Shravan R. Dommaraju•Haiyang Cui等 9 人
Nature Chemistry
2024
•2024/3/25
•00 p.1-10
Recent efforts in genome mining of ribosomally synthesized and post-translationally modified peptides (RiPPs) have expanded the diversity of post-translational modification chemistries. However, RiPPs are rarely reported as hybrid molecules incorporating biosynthetic machinery from other natural pro...
BiosynthesisEnzyme mechanismsMultienzyme complexes
10.1038/S41557-024-01491-3
ISSN:1755-4330
Exome-wide analysis implicates rare protein-altering variants in human handedness
Dick Schijven•Sourena Soheili-Nezhad•Simon E. Fisher•Clyde Francks
Nature Communications
2024
•2024/4/2
•Vol.15 No.1 p.1-12
Handedness is a manifestation of brain hemispheric specialization. Left-handedness occurs at increased rates in neurodevelopmental disorders. Genome-wide association studies have identified common genetic effects on handedness or brain asymmetry, which mostly involve variants outside protein-coding ...
Behavioural geneticsHuman behaviourRare variants
10.1038/S41467-024-46277-W
ISSN:2041-1723
Evolution of sexual systems, sex chromosomes and sex-linked gene transcription in flatworms and roundworms
Wang Yifeng•Gasser Robin B.•Charlesworth Deborah•Zhou Qi
Nature Communications
2022
•2022/6/10
•Vol.13 No.1 p.1-15
Many species with separate male and female individuals (termed ‘gonochorism’ in animals) have sex-linked genome regions. Here, we investigate evolutionary changes when genome regions become completely sex-linked, by analyses of multiple species of flatworms (Platyhelminthes; among which schistosomes...
Genome evolutionMolecular evolutionParasite evolution
10.1038/S41467-022-30578-Z
ISSN:2041-1723
Large-scale identification of genes involved in septal pore plugging in multicellular fungi
Mamun Md. Abdulla Al•Cao Wei•Nakamura Shugo•Maruyama Jun-ichi
Nature Communications
2023
•2023/3/17
•Vol.14 No.1 p.1-17
Multicellular filamentous fungi have septal pores that allow cytoplasmic exchange, and thus connectivity, between neighboring cells in the filament. Hyphal wounding and other stress conditions induce septal pore closure to minimize cytoplasmic loss. However, the composition of the septal pore and th...
Cell biologyCellular microbiologyFungal geneticsFungal physiology
10.1038/S41467-023-36925-Y
ISSN:2041-1723
Genetic compatibility and ecological connectivity drive the dissemination of antibiotic resistance genes
David Lund•Marcos Parras-Moltó•Juan S. Inda-Díaz•Stefan Ebmeyer•D. G. Joakim Larsson等 7 人
Nature Communications
2025
•2025/3/16
•Vol.16 No.1 p.1-13
The dissemination of mobile antibiotic resistance genes (ARGs) via horizontal gene transfer is a significant threat to public health globally. The flow of ARGs into and between pathogens, however, remains poorly understood, limiting our ability to develop strategies for managing the antibiotic resis...
Antimicrobial resistanceMachine learning
10.1038/S41467-025-57825-3
ISSN:2041-1723
Chemical genetics strategy to profile kinase target engagement reveals role of FES in neutrophil phagocytosis
Tom van der Wel•Riet Hilhorst•Hans den Dulk•Tim van den Hooven•Nienke M. Prins等 14 人
Nature Communications
2020
•2020/6/25
•Vol.11 No.1 p.1-20
Chemical tools to monitor drug-target engagement of endogenously expressed protein kinases are highly desirable for preclinical target validation in drug discovery. Here, we describe a chemical genetics strategy to selectively study target engagement of endogenous kinases. By substituting a serine r...
Chemical geneticsChemical toolsKinasesNeutrophilsSensors and probes
10.1038/S41467-020-17027-5
ISSN:2041-1723
Genome mining unveils a class of ribosomal peptides with two amino termini
Ren Hengqian•Dommaraju Shravan R.•Huang Chunshuai•Cui Haiyang•Pan Yuwei等 10 人
Nature Communications
2023
•2023/3/23
•Vol.14 No.1 p.1-13
The era of inexpensive genome sequencing and improved bioinformatics tools has reenergized the study of natural products, including the ribosomally synthesized and post-translationally modified peptides (RiPPs). In recent years, RiPP discovery has challenged preconceptions about the scope of post-tr...
BioinformaticsBiosynthesisEnzymesNatural product synthesis
10.1038/S41467-023-37287-1
ISSN:2041-1723
RT-IVT method allows multiplex real-time quantification of in vitro transcriptional mRNA production
Zhang Fengyu•Wang Yipeng•Wang Xiaomeng•Dong Hongjie•Chen Min等 10 人
Communications Biology
2023
•2023/4/24
•Vol.6 No.1 p.1-11
For the past 30 years, in vitro transcription (IVT) technology has been extensively used for RNA production or for basic transcriptional mechanism research. However, methods for mRNA quantification still need to be improved. In this study, we designed a RT-IVT method using binary fluorescence quench...
Gene expression analysisTranscription
10.1038/S42003-023-04830-1
ISSN:2399-3642
Platypus and echidna genomes reveal mammalian biology and evolution
Yang Zhou•Linda Shearwin-Whyatt•Jing Li•Zhenzhen Song•Takashi Hayakawa等 42 人
Nature
2021
•2021/1/6
•00 p.1-7
Egg-laying mammals (monotremes) are the only extant mammalian outgroup to therians (marsupial and eutherian animals) and provide key insights into mammalian evolution1,2. Here we generate and analyse reference genomes of the platypus (Ornithorhynchus anatinus) and echidna (Tachyglossus aculeatus), w...
Comparative genomicsEvolutionary genetics
10.1038/S41586-020-03039-0
ISSN:0028-0836
Discovery, characterization, and comparative analysis of new UGT72 and UGT84 family glycosyltransferases
Tuo Li•Annika J. E. Borg•Leo Krammer•Hansjörg Weber•Rolf Breinbauer等 6 人
Communications Chemistry
2024
•2024/6/28
•Vol.7 No.1 p.1-12
Glycosylated derivatives of natural product polyphenols display a spectrum of biological activities, rendering them critical for both nutritional and pharmacological applications. Their enzymatic synthesis by glycosyltransferases is frequently constrained by the limited repertoire of characterized e...
BiocatalysisBiosynthesisGlycosidesNatural product synthesisTransferases
10.1038/S42004-024-01231-1
ISSN:2399-3669
Myofibroblasts derived type V collagen promoting tissue mechanical stress and facilitating metastasis and therapy resistance of lung adenocarcinoma cells
Guangsheng Zhu•Yanan Wang•Yingjie Wang•Hua Huang•Boshi Li等 11 人
Cell Death & Disease
2024
•2024/7/10
•Vol.15 No.7 p.1-13
Lung cancer is a leading cause of cancer-related mortality globally, with a dismal 5-year survival rate, particularly for Lung Adenocarcinoma (LUAD). Mechanical changes within the tumor microenvironment, such as extracellular matrix (ECM) remodeling and fibroblast activity, play pivotal roles in can...
Cancer microenvironmentNon-small-cell lung cancerPrognostic markers
10.1038/S41419-024-06873-6
ISSN:2041-4889
Unexpected assembly machinery for 4(3H)-quinazolinone scaffold synthesis
Chen Xi-Wei•Rao Li•Chen Jia-Li•Zou Yi
Nature Communications
2022
•2022/10/31
•Vol.13 No.1 p.1-13
4(3H)-quinazolinone is the core scaffold in more than 200 natural alkaloids and numerous drugs. Many chemosynthetic methodologies have been developed to generate it; however, investigation of its native enzymatic formation mechanism in fungi has been largely limited to fumiquinazolines, where the tw...
BiosynthesisEnzyme mechanismsEnzymesNatural productsPeptides
10.1038/S41467-022-34340-3
ISSN:2041-1723
Exosomes containing miR-152-3p targeting FGFR3 mediate SLC7A7-induced angiogenesis in bladder cancer
Chun Cao•Yu Wang•Xiaolin Deng•Xinlei Zhao•Yuwen Chen等 8 人
Npj Precision Oncology
2025
•2025/3/12
•Vol.9 No.1 p.1-14
Bladder cancer (BCa) is a prevalent malignancy with a poor prognosis. SLC7A7 has been linked to BCa progression and angiogenesis, but its specific role remains unclear. We established a SLC7A7-knockdown BCa cell line to investigate its effects on angiogenesis. In vivo experiments assessed tumor vasc...
Bladder cancerTumour angiogenesis
10.1038/S41698-025-00859-Z
ISSN:2397-768X
A GDSL lipase-like from Ipomoea batatas catalyzes efficient production of 3,5-diCQA when expressed in Pichia pastoris
Sissi Miguel•Guillaume Legrand•Léonor Duriot•Marianne Delporte•Barbara Menin等 16 人
Communications Biology
2020
•2020/11/13
•Vol.3 No.1 p.1-13
The synthesis of 3,5-dicaffeoylquinic acid (3,5-DiCQA) has attracted the interest of many researchers for more than 30 years. Recently, enzymes belonging to the BAHD acyltransferase family were shown to mediate its synthesis, albeit with notably low efficiency. In this study, a new enzyme belonging ...
Metabolic engineeringSecondary metabolism
10.1038/S42003-020-01387-1
ISSN:2399-3642
Evolution of a SHOOTMERISTEMLESS transcription factor binding site promotes fruit shape determination
Zhi-Cheng Hu•Mateusz Majda•Hao-Ran Sun•Yao Zhang•Yi-Ning Ding等 13 人
Nature Plants
2024
•2024/12/12
•00 p.1-13
In animals and plants, organ shape is primarily determined during primordium development by carefully coordinated growth and cell division1–3. Rare examples of post-primordial change in morphology (reshaping) exist that offer tractable systems for the study of mechanisms required for organ shape det...
Plant developmentPlant evolution
10.1038/S41477-024-01854-1
ISSN:2055-0278
MHC class II functions as a host-specific entry receptor for representative human and swine H3N2 influenza A viruses
Matias Cardenas•Sasha Compton•C. Joaquin Caceres•Adolfo García-Sastre•Daniel R. Perez等 6 人
Nature Communications
2026
•2026/2/10
•Vol.17 No.1 p.25600
Influenza A viruses (FLUAV) utilize sialic acid to enter host cells via the envelope’s hemagglutinin (HA), and its affinity for host-specific sialic acid linkage configuration is a major host range determinant. However, some FLUAV subtypes (H17, H18, H19) use the major histocompatibility complex cla...
Influenza virusVirus–host interactions
10.1038/S41467-026-69267-6
ISSN:2041-1723
Microalgal-bacterial granular sludge can remove complex organics from municipal wastewater with algae-bacteria interactions
Yuting Shi•Chengxiang Xu•Bin Ji•Anjie Li•Xiaoyuan Zhang等 6 人
Communications Earth & Environment
2024
•2024/6/24
•Vol.5 No.1 p.1-10
Interactions between algae and bacteria are pivotal in transforming complex organics for microalgal-bacterial granular sludge process, but the intrinsic removal mechanisms have not been well understood. Here, we investigate the mechanisms by which complex organics are removed from municipal wastewat...
BacteriaWater microbiology
10.1038/S43247-024-01499-0
ISSN:2662-4435
Cowpea (Vigna unguiculata L. Walp.) landraces in Mozambique and neighbouring Southern African countries harbour genetic loci with potential for climate adaptation
Mercy Wairimu Macharia•Leonardo Caproni•Marta Solemanegy•Robel Takele•Rogerio Marcos Chiulele等 10 人
Communications Biology
2025
•2025/5/30
•Vol.8 No.1 p.1-12
Large untapped potential for local climate adaptation is present in plant genetic resources maintained by smallholder farmers in Southern Africa. Cowpea (Vigna unguiculata L.Walp.), a staple crop for local farmers in the arid and semiarid regions of Southern Africa, is mostly unexplored by modern br...
Agricultural geneticsAgriculturePlant breeding
10.1038/S42003-025-08227-0
ISSN:2399-3642
RUFY3 regulates endolysosomes perinuclear positioning, antigen presentation and migration in activated phagocytes
Rémy Char•Zhuangzhuang Liu•Cédric Jacqueline•Marion Davieau•Maria-Graciela Delgado等 21 人
Nature Communications
2023
•2023/7/18
•Vol.14 No.1 p.1-20
Endo-lysosomes transport along microtubules and clustering in the perinuclear area are two necessary steps for microbes to activate specialized phagocyte functions. We report that RUN and FYVE domain-containing protein 3 (RUFY3) exists as two alternative isoforms distinguishable by the presence of a...
Antigen-presenting cellsBacterial infectionEndosomes
10.1038/S41467-023-40062-X
ISSN:2041-1723
Volatile metabolomics and metagenomics reveal the effects of lactic acid bacteria on alfalfa silage quality, microbial communities, and volatile organic compounds
Yichao Liu•Shuai Du•Lin Sun•Yuyu Li•Mingjian Liu等 10 人
Communications Biology
2024
•2024/11/25
•Vol.7 No.1 p.1-13
Lactic acid bacteria metabolism affects the composition of volatile organic compounds (VOCs) in alfalfa silage, which results in differences of odor and quality. The aim of this study was to reveal the effects of commercial Lactobacillus plantarum (CL), screened Lactobacillus plantarum (LP), and scr...
BiotechnologyMicrobiology
10.1038/S42003-024-07083-8
ISSN:2399-3642
Rhamnolipids from Pseudomonas aeruginosa disperse the biofilms of sulfate-reducing bacteria
Thammajun L. Wood•Ting Gong•Lei Zhu•James Miller•Daniel S. Miller等 7 人
Npj Biofilms And Microbiomes
2018
•2018/10/3
•Vol.4 No.1 p.1-8
Biofilm formation is an important problem for many industries. Desulfovibrio vulgaris is the representative sulfate-reducing bacterium (SRB) which causes metal corrosion in oil wells and drilling equipment, and the corrosion is related to its biofilm formation. Biofilms are extremely difficult to re...
BiofilmsWater microbiology
10.1038/S41522-018-0066-1
ISSN:2055-5008
Stomach as the target organ of Rickettsia heilongjiangensis infection in C57BL/6 mice identified by click chemistry
Juan Wang•Li-Feng Du•Ming-Zhu Zhang•Wei Wei•Zi-Yun Chen等 14 人
Communications Biology
2024
•2024/6/29
•Vol.7 No.1 p.1-13
Spotted fever group rickettsiae (SFGR) are obligate intracellular bacteria that cause spotted fever. The limitations of gene manipulation pose great challenges to studying the infection mechanisms of Rickettsia. By combining bioorthogonal metabolism and click chemistry, we developed a method to labe...
Biological techniquesInfectionPathogens
10.1038/S42003-024-06468-Z
ISSN:2399-3642