综合性期刊最新文献

{"title":"In situ cryo-ET visualization of mitochondrial depolarization and mitophagic engulfment.","authors":"Kevin Rose, Eric Herrmann, Eve Kakudji, Javier Lizarrondo, A Yasemin Celebi, Florian Wilfling, Samantha C Lewis, James H Hurley","doi":"10.1073/pnas.2511890122","DOIUrl":"10.1073/pnas.2511890122","url":null,"abstract":"<p><p>Defective mitochondrial quality control in response to loss of mitochondrial membrane polarization is implicated in Parkinson's disease by mutations in <i>PINK1</i> and <i>PRKN</i>. Parkin-expressing U2 osteosarcoma (U2OS) cells were treated with the depolarizing agents oligomycin and antimycin A (OA) and subjected to cryo-focused ion beam milling and in situ cryo-electron tomography. Mitochondria were fragmented and devoid of matrix calcium phosphate crystals. Phagophores were visualized, with bridge-like lipid transporter densities connected to mitophagic phagophores. A subpopulation of ATP synthases relocalized from cristae to the inner boundary membrane. The structure of the dome-shaped prohibitin complex, a dodecamer of PHB1-PHB2 dimers, was determined in situ by subtomogram averaging in untreated and treated cells and found to exist in open and closed conformations, with the closed conformation being enriched by OA treatment. These findings provide a set of native snapshots of the manifold nano-structural consequences of mitochondrial depolarization and provide a baseline for future in situ dissection of Parkin-dependent mitophagy.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"122 31","pages":"e2511890122"},"PeriodicalIF":9.1,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144761075","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bioinformatics analysis of Rho-signal transduction genes in postmenopausal osteoporosis and periodontitis.","authors":"Jing Qi, E Liu, Yunqing Pang, Yu Wang, Jing Wang","doi":"10.1038/s41598-025-13872-w","DOIUrl":"https://doi.org/10.1038/s41598-025-13872-w","url":null,"abstract":"<p><p>Postmenopausal osteoporosis (PMOP) increases the risk of periodontitis (PD), yet the shared mechanisms remain unclear. Rho-signal transduction genes may play a role due to their involvement in bone remodeling. This study aimed to explore Rho-related genes as potential biomarkers linking PMOP and PD. Public transcriptomic datasets of PMOP and PD were analyzed. After PCA-based outlier removal, differentially expressed genes were identified using limma, followed by intersection analysis, KEGG enrichment, PPI network construction, and Rho pathway screening. Machine learning (Lasso, SVM-RFE) and Wilcoxon tests identified CTNNAL1 and MERTK as candidate biomarkers. GSEA, ssGSEA, and immune infiltration analyses were performed, along with construction of lncRNA/circRNA-miRNA-mRNA regulatory networks. Subcellular localization, chromosomal mapping, disease association, and molecular docking analyses were also conducted. An ovariectomy plus periodontitis (OP+PD) mouse model was used for in vivo validation. CTNNAL1 and MERTK were consistently dysregulated in both PMOP and PD datasets. They were enriched in MYC-targets-V1, allograft rejection, heme metabolism, and oxidative phosphorylation. Immune analysis revealed altered levels of CD56^bright NK cells and immature dendritic cells. Regulatory networks implicated lncRNAs such as XIST, GAS5, and NEAT1. Molecular docking indicated interactions with pinosylvin and glycitein. In vivo validation confirmed significant changes in CTNNAL1 and MERTK expression and increased bone loss and inflammation in OP+PD mice. CTNNAL1 and MERTK were identified as potential Rho-associated biomarkers showing consistent dysregulation in both PMOP and PD datasets. These biomarkers may serve as risk indicators or therapeutic candidates, warranting further validation.</p>","PeriodicalId":21811,"journal":{"name":"Scientific Reports","volume":"15 1","pages":"28479"},"PeriodicalIF":3.9,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144785217","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Leisure activities indirectly affect depression in older chinese adults through activities of daily living and self-rated health.","authors":"Yongduo Zhang, Shuo Sun, Zongqiang Jin","doi":"10.1038/s41598-025-14596-7","DOIUrl":"https://doi.org/10.1038/s41598-025-14596-7","url":null,"abstract":"<p><p>This study aims to explore interrelationships among leisure activities and depression and the mediating roles of activities of daily living (ADL) and self-reported health (SRH) among older adults in China. Data were extracted from 9,893 participants aged 50 and older from the Chinese Longitudinal Healthy Longevity Survey (CLHLS) conducted in 2018. Pearson correlation analysis and multiple stepwise regression analysis were conducted by using SPSS, and the mediating effect was tested using the Process plugin. Leisure activities were negatively correlated with depression (r = - 0.169, P < 0.001), and positively correlated with ADL and SRH (r = 0.223, r = 0.123, P < 0.001). ADL and SRH were negatively correlated with depression (r = - 0.120, - 0.376, P < 0.001). Leisure activities can not only directly and negatively affect depression, but also can indirectly affect depression through positive effects on ADL and SRH. The mediating effect accounts for 30.79% of the total effect. ADL and SRH play mediating roles in the relationship among leisure activities and depression. The participation of elderly people in leisure activities reduces the risk of depression by increasing their level of daily activity ability and perceived health.</p>","PeriodicalId":21811,"journal":{"name":"Scientific Reports","volume":"15 1","pages":"28481"},"PeriodicalIF":3.9,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144785264","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The carbon nanotube gatemon qubit","authors":"H. Riechert, S. Annabi, A. Peugeot, H. Duprez, M. Hantute, K. Watanabe, T. Taniguchi, E. Arrighi, J. Griesmar, J.-D. Pillet, L. Bretheau","doi":"10.1038/s41467-025-62283-y","DOIUrl":"https://doi.org/10.1038/s41467-025-62283-y","url":null,"abstract":"<p>Gate-tunable transmon qubits are based on quantum conductors used as weak links within hybrid Josephson junctions. These gatemons have been implemented in just a handful of systems, all relying on extended conductors, namely epitaxial semiconductors or exfoliated graphene. Here we present the coherent control of a gatemon based on a single molecule, a one-dimensional carbon nanotube, which is integrated into a circuit quantum electrodynamics architecture. The measured qubit spectrum can be tuned with a gate voltage and reflects the quantum dot behavior of the nanotube. Our ultraclean integration, using a hexagonal boron nitride substrate, results in record coherence times of 200 ns for carbon nanotube-based qubits. Furthermore, we investigate its decoherence mechanisms, thus revealing a strong gate dependence and identifying charge noise as a limiting factor. On top of positioning carbon nanotubes as contenders for future quantum technologies, our work paves the way for studying microscopic fermionic processes in low-dimensional quantum conductors.</p>","PeriodicalId":19066,"journal":{"name":"Nature Communications","volume":"20 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144778214","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DDX41 resolves G-quadruplexes to maintain erythroid genome integrity and prevent cGAS-mediated cell death","authors":"Honghao Bi, Kehan Ren, Pan Wang, Ermin Li, Xu Han, Wen Wang, Jing Yang, Inci Aydemir, Kara Tao, Renee Ma, Lucy A. Godley, Yan Liu, Vipul Shukla, Elizabeth T. Bartom, Yuefeng Tang, Lionel Blanc, Madina Sukhanova, Peng Ji","doi":"10.1038/s41467-025-62307-7","DOIUrl":"https://doi.org/10.1038/s41467-025-62307-7","url":null,"abstract":"<p>Deleterious germline <i>DDX41</i> variants constitute the most common inherited predisposition disorder linked to myeloid neoplasms (MNs), yet their role in MNs remains unclear. Here we show that DDX41 is essential for erythropoiesis but dispensable for other hematopoietic lineages. Ddx41 knockout in early erythropoiesis is embryonically lethal, while knockout in late-stage terminal erythropoiesis allows mice to survive with normal blood counts. DDX41 deficiency induces a significant upregulation of G-quadruplexes (G4), which co-distribute with DDX41 on the erythroid genome. DDX41 directly binds to and resolves G4, which is significantly compromised in MN-associated <i>DDX41</i> mutants. G4 accumulation induces erythroid genome instability, ribosomal defects, and p53 upregulation. However, p53 deficiency does not rescue the embryonic death of Ddx41 hematopoietic-specific knockout mice. In parallel, genome instability also activates the cGas-Sting pathway, impairing survival, as cGas deficiency rescues the lethality of hematopoietic-specific Ddx41 knockout mice. This is supported by data from a DDX41-mutated MN patient and human iPSC-derived bone marrow organoids. Our study establishes DDX41 as a G4 resolvase, essential for erythroid genome stability and suppressing the cGAS-STING pathway.</p>","PeriodicalId":19066,"journal":{"name":"Nature Communications","volume":"52 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144778327","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A rapid, simple, and economical method for the isolation of ribosomes and translational machinery for structural and functional studies","authors":"Jessey Erath, Danielle Kemper, Elisha Mugo, Alex Jacoby, Elizabeth Valenzuela, Courtney F. Jungers, Wandy L. Beatty, Yaser Hashem, Marko Jovanovic, Sergej Djuranovic, Slavica Pavlovic Djuranovic","doi":"10.1038/s41467-025-62314-8","DOIUrl":"https://doi.org/10.1038/s41467-025-62314-8","url":null,"abstract":"<p>Ribosomes are RNA-protein complexes essential for protein synthesis and quality control. Traditional methods for ribosome isolation are labor-intensive, expensive, and require a substantial amount of biological material. In contrast, our method, RNA affinity purification using poly-lysine (RAPPL), provides a rapid, simple, and cost-effective alternative applicable to various species and types of starting material (cell lysates, whole cells, organs, or whole organisms). It is also compatible with traditional isolation techniques. Here, we describe the use of RAPPL for rapid isolation, functional screening, and structural analysis of ribosomes and associated factors. We also demonstrate the application of RAPPL in investigating ribosome-associated resistance mechanisms in uropathogeni<i>c Escherichia coli</i> samples and generating a 2.7-Å cryoEM ribosome structure from <i>Cryptococcus neoformans</i>. By significantly reducing the amount of the starting biological material and the time required for isolation, RAPPL has the potential to facilitate the study of ribosomal function, interactions, and antibiotic resistance and provide a versatile platform for academic, clinical, and industrial research.</p>","PeriodicalId":19066,"journal":{"name":"Nature Communications","volume":"726 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144778329","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Promoting implant osseointegration via the osteoblast-selective β-amino acid polymer strategy","authors":"Qi Chen, Jiawei Gu, Haodong Zhang, Donghui Zhang, Yuwen Wang, Guojian Liu, Xiang Zhu, Xinyue Zhang, Chuntao Cao, Yuan Yuan, Runhui Liu","doi":"10.1038/s41467-025-58394-1","DOIUrl":"https://doi.org/10.1038/s41467-025-58394-1","url":null,"abstract":"<p>Osseointegration for implants, especially bioinert implants, poses significant clinical challenges. Overcoming fibrotic encapsulation and promoting osseointegration at the implant interface are critical for successful bone repair, which highly expected biomaterials with osteoblast over fibroblast selectivity. However, few materials possess the function. β-amino acid polymers have demonstrated cell adhesion property, easy preparation, and robust stability to resist proteolysis as emerging biomaterials. Here, we develop amphiphilic β-amino acid polymers that demonstrate exceptional osteoblast vs fibroblast selectivity, outperforming the natural osteoblast-selective KRSR peptide. The optimal polymer selectively supports osteoblast adhesion by manipulating the adsorption of serum proteins and the presentation of RGD motifs on polymer-modified surfaces. In vivo study using polymer-modified titanium-implants in female rat maxillary bone reveals that the optimal polymer substantially promotes osseointegration of titanium-implants compared to uncoated titanium-implants, which tend to develop fibrous encapsulation. This study demonstrates the effectiveness of our strategy in designing osteoblast-selective biomaterials and implies the promising application of β-amino acid polymer as emerging osteoblast-selective biomaterials to promote osseointegration.</p>","PeriodicalId":19066,"journal":{"name":"Nature Communications","volume":"9 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144778368","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Baboons defend themselves by throwing stones","authors":"","doi":"10.1038/d41586-025-02257-8","DOIUrl":"https://doi.org/10.1038/d41586-025-02257-8","url":null,"abstract":"Snippets from Nature’s past.","PeriodicalId":18787,"journal":{"name":"Nature","volume":"198 1","pages":""},"PeriodicalIF":64.8,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144778392","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tackle fake citations generated by AI","authors":"","doi":"10.1038/d41586-025-02482-1","DOIUrl":"https://doi.org/10.1038/d41586-025-02482-1","url":null,"abstract":"Letter to the Editor","PeriodicalId":18787,"journal":{"name":"Nature","volume":"52 1","pages":""},"PeriodicalIF":64.8,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144778602","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In This Issue.","authors":"","doi":"10.1073/iti3125122","DOIUrl":"https://doi.org/10.1073/iti3125122","url":null,"abstract":"","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"122 31","pages":"eiti3125122"},"PeriodicalIF":9.1,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144785121","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}