Communications Biology最新文献

Structural insights into ligand recognition and G protein preferences across histamine receptors. 结构洞察配体识别和G蛋白偏好跨组胺受体。

IF 5.2 1区生物学

Communications Biology Pub Date : 2025-06-27 DOI: 10.1038/s42003-025-08363-7

Yuma Matsuzaki, Fumiya K Sano, Hidetaka S Oshima, Hiroaki Akasaka, Kazuhiro Kobayashi, Tatsuki Tanaka, Yuzuru Itoh, Wataru Shihoya, Yoshiaki Kise, Tsukasa Kusakizako, Asuka Inoue, Osamu Nureki

{"title":"Structural insights into ligand recognition and G protein preferences across histamine receptors.","authors":"Yuma Matsuzaki, Fumiya K Sano, Hidetaka S Oshima, Hiroaki Akasaka, Kazuhiro Kobayashi, Tatsuki Tanaka, Yuzuru Itoh, Wataru Shihoya, Yoshiaki Kise, Tsukasa Kusakizako, Asuka Inoue, Osamu Nureki","doi":"10.1038/s42003-025-08363-7","DOIUrl":"10.1038/s42003-025-08363-7","url":null,"abstract":"Histamine exerts critical physiological roles by activating four receptor subtypes, each exhibiting a specific G protein preference. Among these, the histamine H4 receptor (H4R) modulates chemotaxis and interferon production through Gi protein activation, suggesting its therapeutic potential. Despite its physiological significance, the mechanisms underlying H4R signalling and G protein preference across histamine receptors remain poorly understood. Here, we present the cryo-electron microscopy structure of the H4R-Gi complex, revealing unique mechanisms of histamine recognition and receptor activation. We further solved the structures of the histamine H1 receptor (H1R) bound to the non-canonical G proteins Gi and Gs. Through a combination of functional and computational analyses, we identified the intracellular loop 2 as a critical determinant of G protein preference in H1R and H4R. Collectively, our comprehensive study revealed the structural basis for distinct mechanisms of ligand recognition and receptor activation, offering a profound insight into G protein preference across receptor subtypes.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"957"},"PeriodicalIF":5.2,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144511655","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Author Correction: Parvalbumin neurons enhance temporal coding and reduce cortical noise in complex auditory scenes. 作者更正：小白蛋白神经元在复杂的听觉场景中增强时间编码并减少皮层噪声。

IF 5.2 1区生物学

Communications Biology Pub Date : 2025-06-25 DOI: 10.1038/s42003-025-08292-5

Jian Carlo Nocon, Howard J Gritton, Nicholas M James, Rebecca A Mount, Zhili Qu, Xue Han, Kamal Sen

引用次数: 0

Bifidobacterium deficit in United States infants drives prevalent gut dysbiosis. 美国婴儿双歧杆菌缺乏导致普遍的肠道生态失调。

IF 5.2 1区生物学

Communications Biology Pub Date : 2025-06-24 DOI: 10.1038/s42003-025-08274-7

John B Jarman, Pedro J Torres, Sean Stromberg, Hirokazu Sato, Caroline Stack, Angelica Ladrillono, Shannon Pace, Natalia Livier Jimenez, Robert J Haselbeck, Richard Insel, Stephen Van Dien, Stephanie J Culler

{"title":"Bifidobacterium deficit in United States infants drives prevalent gut dysbiosis.","authors":"John B Jarman, Pedro J Torres, Sean Stromberg, Hirokazu Sato, Caroline Stack, Angelica Ladrillono, Shannon Pace, Natalia Livier Jimenez, Robert J Haselbeck, Richard Insel, Stephen Van Dien, Stephanie J Culler","doi":"10.1038/s42003-025-08274-7","DOIUrl":"10.1038/s42003-025-08274-7","url":null,"abstract":"The composition of the infant gut microbiome is critical to immune development and noncommunicable disease (NCD) trajectory. However, a comprehensive evaluation of the infant gut microbiome in the United States is lacking. The My Baby Biome study, designed to address this knowledge gap, evaluated the gut microbiomes of 412 infants (representative of U.S. demographic diversity) using metagenomics and metabolomics. Regardless of birth mode and/or feeding method, widespread Bifidobacterium deficit was observed, with approximately 25% of U.S. infants lacking detectable Bifidobacterium. Bifidobacterium-dominant microbiomes exhibit distinct features when compared to microbiomes with other dominant microbial compositions including reduced antimicrobial resistance and virulence factor genes, altered carbohydrate utilization pathways, and altered metabolic signatures. In C-section birth infants, Bifidobacterium tended to be replaced in the human milk oligosaccharide utilization niche with potentially pathogenic species. Longitudinal health outcomes from these infants suggest that the disappearance of key Bifidobacterium may contribute to the development of atopy.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"867"},"PeriodicalIF":5.2,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12187928/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144483431","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Hippocampal systems for event encoding and sequencing during ongoing narrative comprehension. 持续叙事理解过程中事件编码和排序的海马体系统。

IF 5.2 1区生物学

Communications Biology Pub Date : 2025-06-23 DOI: 10.1038/s42003-025-08377-1

Jiwoong Park, Hayoung Song, Won Mok Shim

{"title":"Hippocampal systems for event encoding and sequencing during ongoing narrative comprehension.","authors":"Jiwoong Park, Hayoung Song, Won Mok Shim","doi":"10.1038/s42003-025-08377-1","DOIUrl":"10.1038/s42003-025-08377-1","url":null,"abstract":"Narrative comprehension requires encoding individual events and sequencing them into coherent structures. This study demonstrates how the hippocampus contributes to these processes during ongoing narrative processing. Participants viewed a temporally scrambled movie and subsequently recounted its inferred original story during functional magnetic resonance imaging (fMRI) scans. Content encoding and event sequencing abilities were assessed by comparing semantic similarity and temporal order between movie annotations and recall. Functional connectivity between the hippocampus and ventromedial prefrontal cortex (vmPFC) predicted sequencing ability during moments when past and present information are integrated, identified through pre-defined narrative structures and data-driven language models. Conversely, hippocampus-posterior medial cortex (PMC) connectivity predicted content encoding abilities following event boundaries. These findings reveal two distinct hippocampus-centered memory systems in narrative processing: the hippocampus-PMC system for event encoding and the hippocampus-vmPFC system for their integration into coherent narratives.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"954"},"PeriodicalIF":5.2,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12185703/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144474152","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Human alveolar macrophage response to Mycobacterium tuberculosis: immune characteristics underlying large inter-individual variability. 人肺泡巨噬细胞对结核分枝杆菌的反应：个体间差异较大的免疫特性

IF 5.2 1区生物学

Communications Biology Pub Date : 2025-06-23 DOI: 10.1038/s42003-025-08337-9

Wolfgang Sadee, Ian H Cheeseman, Audrey Papp, Maciej Pietrzak, Michal Seweryn, Xiaofei Zhou, Shili Lin, Amanda M Williams, Mark D Wewers, Heather M Curry, Hao Zhang, Hong Cai, Carine Kunsevi-Kilola, Happy Tshivhula, Gerhard Walzl, Blanca I Restrepo, Léanie Kleynhans, Katharina Ronacher, Yufeng Wang, Eusondia Arnett, Abul K Azad, Larry S Schlesinger

{"title":"Human alveolar macrophage response to Mycobacterium tuberculosis: immune characteristics underlying large inter-individual variability.","authors":"Wolfgang Sadee, Ian H Cheeseman, Audrey Papp, Maciej Pietrzak, Michal Seweryn, Xiaofei Zhou, Shili Lin, Amanda M Williams, Mark D Wewers, Heather M Curry, Hao Zhang, Hong Cai, Carine Kunsevi-Kilola, Happy Tshivhula, Gerhard Walzl, Blanca I Restrepo, Léanie Kleynhans, Katharina Ronacher, Yufeng Wang, Eusondia Arnett, Abul K Azad, Larry S Schlesinger","doi":"10.1038/s42003-025-08337-9","DOIUrl":"10.1038/s42003-025-08337-9","url":null,"abstract":"Mycobacterium tuberculosis (M.tb) infection infects human alveolar macrophages (HAMs). In freshly isolated HAMs from 28 healthy adults, we observe large inter-individual differences in bacterial uptake and growth, with tenfold variation in M.tb load by 72 h. While M.tb infection triggers expression changes of numerous host mRNAs, we examined which genes are most variably expressed (VE genes) between donors, as potential biomarkers of individual tuberculosis (TB) risk. The HAM RNA transcriptome following infection revealed thousands of differentially expressed (DE) genes and differential secretion of 25/27 proteins. Yet only 324 DE genes represent VE genes detected exclusively among DE genes in infected cells. Of 36 DE genes detected at all time points (2, 24, and 72 h), 14 are VE genes, indicating early emergence of the VE gene profile. 9/27 DE proteins following infection were encoded by VE genes. Systems analysis of VE RNAs identified a top-scoring network anchored by IL1B, involved in TB immune response. Independent M.tb-HAM transcriptome results from a TB-endemic region show significant overlap in DE genes, including VE genes identified in the main study. Thus, we identify a VE gene network activated upon M.tb-HAM infection with high inter-person variability, guiding studies on determining individual risk of M.tb infection and/or disease.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"950"},"PeriodicalIF":5.2,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12185700/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144474165","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Metabolic acclimation to warming links unexpected immune activation and sexual dimorphism attenuation in Xenopus tropicalis. 热带非洲爪蟾对变暖的代谢适应与意想不到的免疫激活和性二态性衰减有关。

IF 5.2 1区生物学

Communications Biology Pub Date : 2025-06-23 DOI: 10.1038/s42003-025-08340-0

Jiaying Li, Jiahao Zhu, Ayi Budian, Yiwei Zeng, Shouhong Wang, Yuzhou Gong, Xungang Wang, Longhui Zhao, Na Tang, Si Zheng, Rong Han, Songping Zhan, Ting Xie, Ting Chen, Xiangzhen Li, Jianping Jiang

{"title":"Metabolic acclimation to warming links unexpected immune activation and sexual dimorphism attenuation in Xenopus tropicalis.","authors":"Jiaying Li, Jiahao Zhu, Ayi Budian, Yiwei Zeng, Shouhong Wang, Yuzhou Gong, Xungang Wang, Longhui Zhao, Na Tang, Si Zheng, Rong Han, Songping Zhan, Ting Xie, Ting Chen, Xiangzhen Li, Jianping Jiang","doi":"10.1038/s42003-025-08340-0","DOIUrl":"10.1038/s42003-025-08340-0","url":null,"abstract":"Maintaining a dynamic balance among various life-history traits is crucial for survival in a warming world, yet the underlying mechanisms remain enigmatic. In this study, we employed the western clawed frog (Xenopus tropicalis) as a model and conducted a long-tern experiment from zygotes to adult stage. We find that even within the previously considered normal temperature range, a 5 °C increase in ambient temperature can establish a new metabolic state, resulting in elevated oxidative stress and a shift in energy allocation towards immune defense at the expense of sexual development. This conceptual framework of temperature-dependent trade-off strategy suggests that, while some studies observed that warm temperature reduces the risk of infection, it is important to note that this change may present challenges in the form of accelerated aging and reduced fertility, especially in ectotherms. These results not only indicate a far more complex adaptive response to future climate change than previously anticipated, but also provide a concise method for constructing animal models to explore diseases related to homeostatic disorders.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"952"},"PeriodicalIF":5.2,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12185709/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144474167","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Deciphering spatial scales of connectivity in a subsidy-dependent coastal ecosystem. 在依赖补贴的沿海生态系统中解读连通性的空间尺度。

IF 5.2 1区生物学

Communications Biology Pub Date : 2025-06-23 DOI: 10.1038/s42003-025-08354-8

Kyle A Emery, Jenifer E Dugan, Robert J Miller, David M Hubbard, Jessica R Madden, Kyle C Cavanaugh

{"title":"Deciphering spatial scales of connectivity in a subsidy-dependent coastal ecosystem.","authors":"Kyle A Emery, Jenifer E Dugan, Robert J Miller, David M Hubbard, Jessica R Madden, Kyle C Cavanaugh","doi":"10.1038/s42003-025-08354-8","DOIUrl":"10.1038/s42003-025-08354-8","url":null,"abstract":"Cross-ecosystem subsidies influence the structure and dynamics of recipient ecosystems and can be sensitive to disturbance. Primary production exported from marine to shoreline ecosystems is among the largest known cross-ecosystem subsidies. However, the spatial scales at which this important connection is manifested are largely unquantified. We used local and regional observations of nearshore kelp canopy biomass and beach kelp wrack inputs to evaluate the scales at which connectivity between kelp forests and beaches is maximized. Regardless of the spatial and temporal scales considered, connectivity was highly local (<10 km) and strongest in winter. Kelp canopy biomass was the primary driver of wrack subsidies, but recipient ecosystem attributes, particularly beach width and orientation, were also important. These drivers of connectivity highlight that disturbance to either ecosystem will have large implications for beach ecosystem productivity. Spatial connectivity can regulate recovery from disturbances such that ecosystem connections must be considered in conservation efforts.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"949"},"PeriodicalIF":5.2,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12185743/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144474151","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Super-enhancers orchestrate transcriptional dysregulation and metabolic reprogramming in uveal melanoma. 超级增强子协调葡萄膜黑色素瘤的转录失调和代谢重编程。

IF 5.2 1区生物学

Communications Biology Pub Date : 2025-06-23 DOI: 10.1038/s42003-025-08338-8

Hui Pan, Weihuan Shao, Huixue Wang, Shengfang Ge, Lingyu Zhang, Xiaofang Xu, Yefei Wang, Ai Zhuang

{"title":"Super-enhancers orchestrate transcriptional dysregulation and metabolic reprogramming in uveal melanoma.","authors":"Hui Pan, Weihuan Shao, Huixue Wang, Shengfang Ge, Lingyu Zhang, Xiaofang Xu, Yefei Wang, Ai Zhuang","doi":"10.1038/s42003-025-08338-8","DOIUrl":"10.1038/s42003-025-08338-8","url":null,"abstract":"Uveal melanoma (UM) is the most common intraocular malignancy in adults and frequently metastasizes. Somatic mutations and chromatin aberrations have been implicated in the pathogenesis of this deadly disease. Despite rapid progress in elucidating the genetic landscape of UM, the epigenetic architecture underlying UM pathogenesis remains incompletely understood. Here, we describe a super-enhancer-mediated epigenetic pipeline through genome-scale histone acetylation and transcriptional profiling. We first characterized the active landscape of super-enhancer profiles in UM via chromatin immunoprecipitation sequencing (ChIP-seq). We identified master transcription factors specifically driven by UM-specific super-enhancers, and our pipeline identified transcription factor AP-2 alpha (TFAP2A), which is highly associated with metabolism and oncogenesis, as the top essential regulator in UM. TFAP2A occupied predicted super-enhancers associated with the oncogene Solute Carrier Family 7 member 8 (SLC7A8) in UM, thereby elucidating a mechanism for regulating oncogene expression. Collectively, our data illustrate the potential for epigenetic targeting of super-enhancer-mediated oncogene dependencies in UM, highlighting an epigenetic vulnerability that can be exploited for precision therapy.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"951"},"PeriodicalIF":5.2,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12185695/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144474168","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Identification of conserved and tissue-restricted transcriptional profiles for lipid associated macrophages. 脂质相关巨噬细胞保守和组织限制性转录谱的鉴定。

IF 5.2 1区生物学

Communications Biology Pub Date : 2025-06-23 DOI: 10.1038/s42003-025-08387-z

Yingzheng Xu, Hannah Hillman, Michael Chang, Fanta Barrow, Stoyan Ivanov, Xavier S Revelo, Jesse W Williams

{"title":"Identification of conserved and tissue-restricted transcriptional profiles for lipid associated macrophages.","authors":"Yingzheng Xu, Hannah Hillman, Michael Chang, Fanta Barrow, Stoyan Ivanov, Xavier S Revelo, Jesse W Williams","doi":"10.1038/s42003-025-08387-z","DOIUrl":"10.1038/s42003-025-08387-z","url":null,"abstract":"Macrophages are essential immune cells in all tissues and are vital for maintaining tissue homeostasis, immune surveillance, and immune responses. Considerable efforts have identified shared and tissue-specific gene programs for macrophages across organs during homeostasis. This information has dramatically enhanced the understanding of tissue-restricted macrophage programming and function. However, few studies have addressed the overlapping and tissue-specific responses of macrophage subsets following inflammation. One subset of macrophages observed across several studies, lipid-associated macrophages (LAMs), have gained interest due to their unique role in lipid metabolism and potential as a therapeutic target. LAMs are associated with regulating disease outcomes in metabolically related disorders including atherosclerosis, obesity, and metabolic dysfunction-associated steatotic liver disease. We utilized single-cell RNA sequencing datasets to profile LAM diversity across multiple tissues and inflammatory conditions in mice and humans, to define a shared LAM transcriptional profile, including Trem2 and Lpl, and sets of tissue-specific gene programs. Importantly, LAM markers were highly conserved with human LAM populations that emerge in inflammation. Overall, this analysis provides a detailed transcriptional landscape of tissue-restricted and shared LAM gene programs, data that may help instruct appropriate molecular targets for broad or tissue-restricted therapeutic interventions to modulate LAM populations in disease.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"953"},"PeriodicalIF":5.2,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12185701/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144474166","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Profiling crRNA architectures for enhanced Cas12 biosensing. 分析增强Cas12生物传感的crRNA结构。

IF 5.2 1区生物学

Communications Biology Pub Date : 2025-06-21 DOI: 10.1038/s42003-025-08356-6

Elizabeth Toyin Ajibode, Alexandra R Bender, Kevin Yehl

引用次数: 0