BMC Biology最新文献

{"title":"Ancient genomes shed light on the genetic history of the Iron Age to historical central Xinjiang, northwest China.","authors":"Haijun Li, Baitong Wang, Xiaomin Yang, Xiaoyu Yang, Haifeng He, Rui Wang, Chuan-Chao Wang","doi":"10.1186/s12915-025-02195-x","DOIUrl":"10.1186/s12915-025-02195-x","url":null,"abstract":"<p><strong>Background: </strong>The genetic profile of the population in Xinjiang, northwest China, has been shaped by interregional movement and admixture since the Bronze Age. However, the detailed and intraregional population history of Xinjiang, especially central Xinjiang, has been unsolved due to uneven sample distribution.</p><p><strong>Results: </strong>Here, we reported the ancient genomes from 8 individuals between the Iron Age and the historical period in central Xinjiang. We observed an east-west admixed ancestry profile and a degree of genetic continuity between the Iron Age and historical central Xinjiang individuals. Furthermore, these central Xinjiang individuals harboured ancestry related to ancient farmers of the Yellow River. We also identified a temporal change of the Yellow River farmers-related ancestry in central Xinjiang, showing an increase the Yelllow River affinity from Iron Age to Historical Era.</p><p><strong>Conclusions: </strong>The finding indicated that the genetic structure of the central Xinjiang population since the Iron Age could have resulted from immigration from northern China, which was attributed to geopolitical factors. Hence, our results indicated that the geopolitical change with the deepening of Central Plains' management has influenced the genetic profile of central Xinjiang.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"93"},"PeriodicalIF":4.4,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11974207/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143794685","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}

{"title":"Formant analysis of vertebrate vocalizations: achievements, pitfalls, and promises.","authors":"W Tecumseh Fitch, Andrey Anikin, Katarzyna Pisanski, Daria Valente, David Reby","doi":"10.1186/s12915-025-02188-w","DOIUrl":"10.1186/s12915-025-02188-w","url":null,"abstract":"<p><p>When applied to vertebrate vocalizations, source-filter theory, initially developed for human speech, has revolutionized our understanding of animal communication, resulting in major insights into the form and function of animal sounds. However, animal calls and human nonverbal vocalizations can differ qualitatively from human speech, often having more chaotic and higher-frequency sources, making formant measurement challenging. We review the considerable achievements of the \"formant revolution\" in animal vocal communication research, then highlight several important methodological problems in formant analysis. We offer concrete recommendations for effectively applying source-filter theory to non-speech vocalizations and discuss promising avenues for future research in this area.Brief Formants (vocal tract resonances) play key roles in animal communication, offering researchers exciting promise but also potential pitfalls.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"92"},"PeriodicalIF":4.4,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11974057/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143794688","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}

{"title":"PBertKla: a protein large language model for predicting human lysine lactylation sites.","authors":"Hongyan Lai, Diyu Luo, Mi Yang, Tao Zhu, Huan Yang, Xinwei Luo, Yijie Wei, Sijia Xie, Feitong Hong, Kunxian Shu, Fuying Dao, Hui Ding","doi":"10.1186/s12915-025-02202-1","DOIUrl":"10.1186/s12915-025-02202-1","url":null,"abstract":"<p><strong>Background: </strong>Lactylation is a newly discovered type of post-translational modification, primarily occurring on lysine (K) residues of both histones and non-histones to exert diverse effects on target proteins. Research has shown that lysine lactylation (Kla) modification is ubiquitous in different cells and participates in the determination of cell function and fate, as well as in the initiation and progression of various diseases. Precise identification of Kla sites is fundamental for elucidating their biological functions and uncovering their application potential.</p><p><strong>Results: </strong>Here, we proposed a novel human Kla site predictor (named PBertKla) through curating a reliable benchmark dataset with proper sample length and sequence identity threshold to train a protein large language model with optimal hyperparameters. Extensive experimental results consistently demonstrated that our model possessed robust human Kla site prediction ability, achieving an AUC (area under receiver operating characteristic curve) value of over 0.880 on the independent validation data. Feature visualization analysis further validated the effectiveness of in feature learning and representation from Kla sequences. Moreover, we benchmarked PBertKla against other cutting-edge models on an independent testing dataset from different sources, highlighting its superiority and transferability.</p><p><strong>Conclusions: </strong>All results indicated that PBertKla excelled as an automatic predictor of human Kla sites, and it would advance the investigation of lactylation modifications and their significance in health and disease.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"95"},"PeriodicalIF":4.4,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11974188/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143794690","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}

{"title":"Dynamic substrate topographies drive actin- and vimentin-mediated nuclear mechanoprotection events in human fibroblasts.","authors":"Maaike Bril, Jules N Boesveld, Leila S Coelho-Rato, Cecilia M Sahlgren, Carlijn V C Bouten, Nicholas A Kurniawan","doi":"10.1186/s12915-025-02199-7","DOIUrl":"10.1186/s12915-025-02199-7","url":null,"abstract":"<p><strong>Background: </strong>Dynamic physical changes in the extracellular environment of living tissues present a mechanical challenge for resident cells that can lead to damage to the nucleus, genome, and DNA. Recent studies have started to uncover nuclear mechanoprotection mechanisms that prevent excessive mechanical deformations of the nucleus. Here, we hypothesized that dynamic topographical changes in the cellular environment can be mechanically transmitted to the nucleus and trigger nuclear mechanoprotection events. We tested this using a photoresponsive hydrogel whose surface topography can be reversibly changed on demand upon light illumination, allowing us to subject cells to recurring microscale topographical changes.</p><p><strong>Results: </strong>With each recurring topographical change, fibroblasts were found to increasingly compact and relocate their nuclei away from the dynamic regions of the hydrogel. These cell-scale reorganization events were accompanied by an increase of global histone acetylation and decreased methylation in cells on the dynamic topographies, resulting in a minimization of DNA strand breakage. We further found that these nuclear mechanoprotection events were mediated by both vimentin intermediate filaments and the actin cytoskeleton.</p><p><strong>Conclusions: </strong>Together, these data reveal that fibroblasts actively protect their nuclei in the presence of dynamic topographical changes through cytoskeleton-mediated mechanisms. Broadly, these results stress the importance of gaining a deeper fundamental understanding of the cellular mechanoresponse under dynamically changing conditions.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"94"},"PeriodicalIF":4.4,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11974106/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143794686","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}

{"title":"Extracellular vesicles from adipose-derived mesenchymal stem cells alleviate acute lung injury via the CBL/AMPK signaling pathway.","authors":"Yan Xiong, Lulu Wang, Bohao Li, Beibei Fu, Zhou Sha, Jin Liu, Rong Tian, Rui Yao, Feng Lin, Zixuan Cong, Yongliang Du, Xiaoyuan Lin, Haibo Wu","doi":"10.1186/s12915-025-02178-y","DOIUrl":"10.1186/s12915-025-02178-y","url":null,"abstract":"<p><strong>Background: </strong>Acute lung injury (ALI) which is caused by Staphylococcus aureus (SA), is a serious lung disease that threatens human health. Although some current treatments are effective in alleviating ALI, they still have a significant mortality rate. At present, adipose-derived mesenchymal stem cells (ADSCs)-derived extracellular vesicles (EVs) have been investigated for the treatment of various diseases. Here, we examined the role of ADSCs-derived EVs in regulating apoptosis and inflammation during ALI.</p><p><strong>Results: </strong>We showed that ADSCs and ADSCs-derived EVs supplementation could improve lung injury, restore mitochondrial function, and inhibit inflammation and apoptosis in ALI mice. Furthermore, miR-320a was present in EVs derived from ADSCs, and it can be transferred into lung tissue. In vitro, Casitas B-lineage lymphoma (CBL) expression was inhibited by miR-320a mimics. Finally, we found that miR-320a alleviated mitochondrial damage, inflammation, and apoptosis via the CBL/AMPK/JNK pathway.</p><p><strong>Conclusions: </strong>In conclusion, EVs from ADSCs could alleviate ALI via the CBL/AMPK signaling pathway. Therefore, the purpose of our study was to investigate the application of ADSC-derived EVs in mitigating ALI by modulating metabolic processes.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"90"},"PeriodicalIF":4.4,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11959995/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751212","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}

{"title":"SUGAR-seq reveals the transcriptome and N-linked glycosylation landscape of mononuclear phagocytes at single-cell resolution in a mouse model of autosomal dominant osteopetrosis type 2.","authors":"Yu Sha, Lingyu Huang, Lei Zhang, Xianliang Hou, Chune Mo, Cuiping Pan, Gengshuo Chen, Sha Luo, Minglin Ou","doi":"10.1186/s12915-025-02193-z","DOIUrl":"10.1186/s12915-025-02193-z","url":null,"abstract":"<p><strong>Background: </strong>Heterozygous mutation of CLCN7 (R286W) is commonly found in patients with benign autosomal dominant osteopetrosis. However, there is no evidence from animal models to confirm that it is a disease mutation. And the characteristics of the bone marrow cell (BMC) landscape in osteopetrosis at the single-cell level are completely unknown till now.</p><p><strong>Results: </strong>In this study, we generated the first autosomal dominant osteopetrosis type 2 (ADO2) mouse model with typical phenotypes carried a mutation Clcn7 (r284w) corresponding to CLCN7 (R286W) observed in human patients using gene editing technology. And then, we conducted the first-ever single-cell analysis of the RNA expression and N-linked glycosylation profiles for the mouse BMCs by SUrface-protein Glycan And RNA-sequencing (SUGAR-seq). We identified 14 distinct cell types and similar proportion of neutrophils in both ADO2 and wild type mice, confirmed by flow cytometry analysis. The N-linked glycosylation modifications of BMCs were significantly downregulated detecting by SUGAR-seq, which was similar to the situation of N-Glycan profiling by the 4D Label-Free N-Glycosylation Proteomics Analysis. Particularly noteworthy is the heterogeneity of classic monocytes. We identified six cell subtypes, but only two cell subtypes were found with different proportion of cell, whose different expressed genes were associated with NF-κB-inducing kinase / Nuclear Factor-kappa B (NIK/NF-κB) signaling and other pathway associated with osteoclast differentiation.</p><p><strong>Conclusions: </strong>Our murine model confirms that the human CLCN7 (R286W) is a pathogenic mutation for ADO2. Additionally, our single-cell analyses reveal the heterogeneity of monocytes in ADO2, and the abnormal glycosylation modifications across various subtypes may represent important events in the pathogenesis of osteopetrosis.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"91"},"PeriodicalIF":4.4,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11959739/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751213","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}

{"title":"A cretaceous fly trap? remarkable abdominal modification in a fossil wasp.","authors":"Qiong Wu, Lars Vilhelmsen, Xiaoqin Li, De Zhuo, Dong Ren, Taiping Gao","doi":"10.1186/s12915-025-02190-2","DOIUrl":"10.1186/s12915-025-02190-2","url":null,"abstract":"<p><strong>Background: </strong>Carnivorous insects have evolved a range of prey and host capture mechanisms. However, insect predation strategies in the fossil record remain poorly understood.</p><p><strong>Results: </strong>Here, we describe †Sirenobethylus charybdis n. gen. & sp., based on sixteen adult female wasps in Kachin amber from the mid-Cretaceous, 99 Mya (million years ago), and place it in Chrysidoidea: †Sirenobethylidae n. fam. The fossils display unique morphological modifications on the tip of the abdomen consisting of three flaps from the modified abdominal sternum 6 and tergum and sternum 7; the lower flap formed from sternum 6 is preserved in different positions relative to the other flaps in different specimens, indicating that they form some sort of grasping apparatus. Nothing similar is known from any other insect; the rounded abdominal apparatus, combined with the setae along the edges, is reminiscent of a Venus flytrap. Phylogenetic analysis suggests that the new family is a separate lineage close to the base of Chrysidoidea.</p><p><strong>Conclusions: </strong>†Sirenobethylus probably was a koinobiont parasitoid wasp; the abdominal grasping apparatus may have been used to temporarily immobilize the host during oviposition. The new fossils suggest that Chrysidoidea displayed a wider range of parasitoid strategies in the mid-Cretaceous than they do today.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"81"},"PeriodicalIF":4.4,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11948742/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143718017","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}

{"title":"A combination of transcriptomics and epigenomics identifies genes and regulatory elements involved in embryonic tail development in the mouse.","authors":"Yong-Xuan Chen, Xiu-Ping Zhang, David N Cooper, Dong-Dong Wu, Wan-Dong Bao","doi":"10.1186/s12915-025-02192-0","DOIUrl":"10.1186/s12915-025-02192-0","url":null,"abstract":"<p><strong>Background: </strong>The post-anal tail is a common physical feature of vertebrates including mammals. Although it exhibits rich phenotypic diversity, its development has been evolutionarily conserved as early as the embryonic period. Genes participating in embryonic tail morphogenesis have hitherto been widely explored on the basis of experimental discovery, whereas the associated cis-regulatory elements (CREs) have not yet been systematically investigated for vertebrate/mammalian tail development.</p><p><strong>Results: </strong>Here, utilizing high-throughput sequencing schemes pioneered in mice, we profiled the dynamic transcriptome and CREs marked by active histone modifications during embryonic tail morphogenesis. Temporal and spatial disparity analyses revealed the genes specific to tail development and their putative CREs, which facilitated the identification of novel molecular expression features and potential regulatory influence of non-coding loci including long non-coding RNA (lncRNA) genes and CREs. Moreover, these identified sets of multi-omics data supply genetic clues for understanding the regulatory effects of relevant signaling pathways (such as Fgf, Wnt) dominating embryonic tail morphogenesis.</p><p><strong>Conclusions: </strong>Our work brings new insights and provides exploitable fundamental datasets for the elucidation of the complex genetic mechanisms responsible for the formation of the vertebrate/mammalian tail.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"88"},"PeriodicalIF":4.4,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11948857/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143718050","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}

{"title":"Evolution and co-evolution of the suck behaviour, a postcopulatory female resistance trait that manipulates received ejaculate.","authors":"Pragya Singh, Jeremias N Brand, Lukas Schärer","doi":"10.1186/s12915-025-02171-5","DOIUrl":"10.1186/s12915-025-02171-5","url":null,"abstract":"<p><strong>Background: </strong>Sexual conflicts over the post-mating fate of received ejaculate can favour traits in one sex that are costly to the other. Reciprocally mating hermaphrodites face unique challenges as they mate simultaneously in both the male and female role, potentially leading to receipt of unwanted ejaculate. Reciprocal mating can then give rise to postcopulatory female resistance traits that allow manipulation of received ejaculate. A putative example is the suck behaviour, observed in the flatworm genus Macrostomum. It involves the sperm recipient placing its pharynx over its own female genital opening and appearing to suck, likely removing received ejaculate after mating. The genus also contains hypodermically inseminating species that presumably exhibit unilateral mating and have not been observed to suck.</p><p><strong>Results: </strong>Here, we examine the evolution of the suck behaviour in the Macrostomum genus, aiming to document the mating behaviour in 64 species. First, we provide videographic evidence that ejaculate is indeed removed during the suck behaviour in a reciprocally mating species, Macrostomum hamatum. Next, we show positive evolutionary correlations between the presence, duration and frequency of reciprocal mating behaviour and the suck behaviour, providing clear evidence that the suck behaviour co-evolves with reciprocal mating behaviour. Finally, we show an association between reproductive behaviour and reproductive morphology, suggesting that the reproductive morphology can be used to infer a species' mating behaviour.</p><p><strong>Conclusions: </strong>Together, our study demonstrates sexually antagonistic coevolution leading to the evolution of a postcopulatory behavioural trait that functions as a female counter-adaptation allowing individuals to gain control over received ejaculate in a hermaphroditic sexual system.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"87"},"PeriodicalIF":4.4,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11948766/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143718065","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}

{"title":"Pangenome graph mitigates heterozygosity overestimation from mapping bias: a case study in Chinese indigenous pigs.","authors":"Jian Miao, Qingyu Wang, Zhe Zhang, Qishan Wang, Yuchun Pan, Zhen Wang","doi":"10.1186/s12915-025-02194-y","DOIUrl":"10.1186/s12915-025-02194-y","url":null,"abstract":"<p><strong>Background: </strong>Breeds genetically distant from the reference genome often show considerable differences in DNA fragments, making it difficult to achieve accurate mappings. The genetic differences between pig reference genome (Sscrofa11.1) and Chinese indigenous pigs may lead to mapping bias and affect subsequent analyses.</p><p><strong>Results: </strong>Our analysis revealed that pangenome exhibited superior mapping accuracy to the Sscrofa11.1, reducing false-positive mappings by 1.4% and erroneous mappings by 0.8%. Furthermore, the pangenome yielded more accurate genotypes of SNP (F1: 0.9660 vs. 0.9607) and INDEL (F1: 0.9226 vs. 0.9222) compared to Sscrofa11.1. In real sequencing data, the inconsistent SNPs called from the pangenome exhibited lower genome heterozygosity compared to those identified by the Sscrofa11.1, including observed heterozygosity and nucleotide diversity. The same reduction of heterozygosity overestimation was also found in the chicken pangenome.</p><p><strong>Conclusions: </strong>This study quantifies the mapping bias of Sscrofa11.1 in Chinese indigenous pigs, demonstrating that mapping bias can lead to an overestimation of heterozygosity in Chinese indigenous pig breeds. The adoption of a pig pangenome mitigates this bias and provides a more accurate representation of genetic diversity in these populations.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"89"},"PeriodicalIF":4.4,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11948684/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143718068","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}