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Differential introgression of mutations reveals selection in spruce. 突变的差异渐渗揭示了云杉的选择。
IF 5.4 1区 生物学
BMC Biology Pub Date : 2026-07-13 DOI: 10.1186/s12915-026-02684-7
Dafu Ru, Hui Zhu, Zhiqiang Lu, Yongshuai Sun
{"title":"Differential introgression of mutations reveals selection in spruce.","authors":"Dafu Ru, Hui Zhu, Zhiqiang Lu, Yongshuai Sun","doi":"10.1186/s12915-026-02684-7","DOIUrl":"10.1186/s12915-026-02684-7","url":null,"abstract":"<p><strong>Background: </strong>Natural selection plays a pivotal role in maintaining genetic boundaries by counteracting the potentially deleterious effects of alleles introduced through hybridization. Here, we investigated this process through a comparative population genomic analysis of three endemic varieties of Picea likiangensis (vars. likiangensis, linzhiensis, and rubescens) across the Qinghai-Tibetan Plateau (QTP) and adjacent regions.</p><p><strong>Results: </strong>Leveraging genome-wide single nucleotide polymorphism (SNP) data from 193 individuals, we documented pervasive genetic admixture among these taxa, yet observed a pronounced asymmetric pattern of introgression: synonymous polymorphisms (Hs) exhibited significantly higher introgression levels than non-synonymous polymorphisms (Hn). This pattern indicates that purifying selection may actively eliminate maladaptive non-synonymous mutations, whereas neutrally evolving loci continue to undergo gene flow. Moreover, the relative hybrid index (ω<sub>H</sub> = Hn/Hs) was lower in populations adjacent to pure rubescens stands, suggesting stronger selection against introgressed alleles in the core range of the recipient taxon rather than a simple effect of geographic distance. In addition, recombination rate was significantly associated with introgression bias, implying that recombination facilitates the removal of maladaptive genomic segments following hybridization.</p><p><strong>Conclusions: </strong>Our findings underscore the pivotal role of comparative population genomics in elucidating how natural selection shapes introgression and contributes to the maintenance of genetic boundaries during speciation.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":" ","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13647522/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148435169","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
Specialization of the upper and lower olfactory rosettes reveals sex- and origin-dependent plasticity in gene expression in Senegalese sole (Solea senegalensis). 塞内加尔鳎(Solea senegalensis)上下嗅觉莲座的特化揭示了性别和来源依赖性基因表达的可塑性。
IF 5.4 1区 生物学
BMC Biology Pub Date : 2026-07-13 DOI: 10.1186/s12915-026-02683-8
Dorinda Torres-Sabino, Oscar Aramburu, Maialen Carballeda, Nina Harmse, Paula R Villamayor, Pablo Sánchez-Quinteiro, Diego Robledo, Carmen Bouza, Paulino Martínez
{"title":"Specialization of the upper and lower olfactory rosettes reveals sex- and origin-dependent plasticity in gene expression in Senegalese sole (Solea senegalensis).","authors":"Dorinda Torres-Sabino, Oscar Aramburu, Maialen Carballeda, Nina Harmse, Paula R Villamayor, Pablo Sánchez-Quinteiro, Diego Robledo, Carmen Bouza, Paulino Martínez","doi":"10.1186/s12915-026-02683-8","DOIUrl":"10.1186/s12915-026-02683-8","url":null,"abstract":"<p><strong>Background: </strong>Olfaction mediates several aspects of fish behaviour, including reproduction. In Senegalese sole (Solea senegalensis), a reproductive dysfunction in captive-bred (CB) males limits the establishment of an effective artificial production system and has been linked to altered chemical communication.</p><p><strong>Results: </strong>We performed a comprehensive RNA-seq analysis of the upper and lower olfactory rosettes of adult Senegalese sole, considering sex (female vs. male) and origin (wild-bred, WB, vs. CB). A total of 15,306 expressed genes, including 404 olfactory receptors, were identified, significantly enhancing the transcriptomic information of the organ. Transcriptional variation was primarily driven by rosette identity, with pronounced differential expression and enrichment of olfactory receptor-related functions between the upper and lower rosettes. CB individuals exhibited reduced transcriptional differentiation between individuals compared to their WB counterparts, suggesting constrained sensory plasticity under captive conditions. Distinct expression patterns were detected among olfactory receptor families, with odorant receptors (ORs) predominantly enriched in the upper rosette and in males, whereas trace amine-associated receptors (TAARs) in the lower rosettes and in females. Furthermore, WB males showed upregulation of genes involved in hormone reception and neuroendocrine signalling, whereas CB males of genes associated with steroid and prostaglandin synthesis and stress-related pathways.</p><p><strong>Conclusions: </strong>These findings reveal a strong effect of environmental history on the molecular organization of the olfactory organs and suggest that altered sensory and neuroendocrine regulation may contribute to the reproductive dysfunction observed in CB males. This study provides a framework for understanding the links between olfaction, environmental adaptation and reproduction in fish, with implications for improving aquaculture sustainability.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":" ","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13647634/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148435188","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
Bacterial composition of the microbiome of mesopelagic fishes from the Northeast Atlantic. 东北大西洋中上层鱼类微生物群的细菌组成。
IF 5.4 1区 生物学
BMC Biology Pub Date : 2026-07-10 DOI: 10.1186/s12915-026-02677-6
Capucine Le Cam Ligier, Marc Garel, Hélène Thibault, Sophie Guasco, Christian Tamburini, Frédéric Ménard, Yves Cherel, Laurie Casalot, Séverine Martini
{"title":"Bacterial composition of the microbiome of mesopelagic fishes from the Northeast Atlantic.","authors":"Capucine Le Cam Ligier, Marc Garel, Hélène Thibault, Sophie Guasco, Christian Tamburini, Frédéric Ménard, Yves Cherel, Laurie Casalot, Séverine Martini","doi":"10.1186/s12915-026-02677-6","DOIUrl":"10.1186/s12915-026-02677-6","url":null,"abstract":"<p><strong>Background: </strong>The mesopelagic zone, between 100 and 1000 m depth, contains up to 90% of marine vertebrate biomass. Mesopelagic fishes are key components of these ecosystems through their feeding interactions and play a critical role in the ocean's biological carbon pump through their diel vertical migrations, yet the bacterial communities associated with these fishes remain poorly characterized. Because bioluminescence and light-related interactions are widespread ecological traits in mesopelagic ecosystems, we investigated the bacterial communities associated with the gut, liver, and skin of mesopelagic fishes from the Northeast Atlantic. Particular attention was given to genera known to include bioluminescent species.</p><p><strong>Results: </strong>16S rRNA gene sequencing revealed marked tissue-specific differences. Skin microbiomes were the most diverse and appeared more influenced by the surrounding environment, whereas gut and liver communities were less diverse and compositionally similar. Internal tissues were dominated by Vibrionaceae (especially Vibrio and Photobacterium) and Moraxellaceae (Acinetobacter). Microbiome composition was significantly associated with host family, trophic position, and migratory behavior. Fishes at lower trophic levels, particularly migratory species, harbored higher proportions of Vibrionaceae, including genera that include bioluminescent lineages, whereas non-migratory deep-sea species showed more variable communities. Moreover, targeted qPCR detected bioluminescence-related lux genes in gut samples.</p><p><strong>Conclusions: </strong>Mesopelagic fish microbiomes are influenced by tissue type and host ecological traits. The recurrent detection of Vibrio and Photobacterium, together with lux genes in selected gut samples, suggests that some mesopelagic fish-associated microbiomes may include bacteria with bioluminescence-related genetic potential. These findings provide an input for future studies on the ecological role of these bacteria in mesopelagic ecosystems.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":" ","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13647563/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148419107","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
The evolution of reproduction without blood feeding in an invasive vector mosquito Aedes albopictus. 入侵媒介白纹伊蚊无血繁殖的进化。
IF 5.4 1区 生物学
BMC Biology Pub Date : 2026-07-09 DOI: 10.1186/s12915-026-02670-z
Samantha L Sturiale, Mara Heilig, Matthew L Aardema, Luciano V Cosme, Margaret Corley, Sarah Marzec, Micah Hamilton, Daniel Vizcarra, Luke T Anderson, Christina M Holzapfel, William E Bradshaw, Megan E Meuti, Adalgisa Caccone, Peter A Armbruster
{"title":"The evolution of reproduction without blood feeding in an invasive vector mosquito Aedes albopictus.","authors":"Samantha L Sturiale, Mara Heilig, Matthew L Aardema, Luciano V Cosme, Margaret Corley, Sarah Marzec, Micah Hamilton, Daniel Vizcarra, Luke T Anderson, Christina M Holzapfel, William E Bradshaw, Megan E Meuti, Adalgisa Caccone, Peter A Armbruster","doi":"10.1186/s12915-026-02670-z","DOIUrl":"10.1186/s12915-026-02670-z","url":null,"abstract":"<p><strong>Background: </strong>Mosquitoes transmit a diverse range of deadly pathogens, including dengue and Plasmodium spp., when they consume the blood of vertebrate hosts in order to nutritionally provision their eggs. However, mosquito species from multiple genera have independently evolved the ability to produce eggs without blood. The molecular and physiological processes underlying the evolution of blood-independent reproduction are largely unresolved, in part because the two most well-studied models of mosquito reproductive physiology and genetics are obligate blood feeders. Herein, we integrate life-history, genomics, and gene expression to identify physiological processes and candidate genes associated with the evolution of blood-independent reproduction in a non-model vector mosquito, Aedes albopictus.</p><p><strong>Results: </strong>Relative to a blood-dependent (control) population, females selected for blood-independent reproduction exhibit a longer larval development period and larger adult size, implying increased nutrient sequestration at the larval stage. Additionally, blood-independent larvae exhibit higher expression of amino acid and lipid storage genes (hex1.1 and lsd-2) relative to blood-dependent larvae. Linkage clusters and F<sub>ST</sub> outliers identify a ca. 40 Mb genomic region that is highly differentiated between blood-independent and blood-dependent lines. Moreover, microRNAs and mRNAs related to reproductive physiology are differentially abundant between adults of the selected vs. control lines.</p><p><strong>Conclusions: </strong>Multiple lines of evidence indicate that larval nutrient sequestration and altered regulation of vitellogenesis have contributed to the rapid evolution of blood-independent reproduction in Ae. albopictus. Overlapping evidence also identifies proposed candidate genes affecting these processes. These results provide a foundation for developing novel paradigms to suppress disease transmission by vector mosquitoes.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":" ","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13632266/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148410817","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
Genetic divergence in Aedes aegypti mosquitoes potentially associated with enhanced capacity for arbovirus transmission. 埃及伊蚊的遗传分化可能与虫媒病毒传播能力增强有关。
IF 5.4 1区 生物学
BMC Biology Pub Date : 2026-07-08 DOI: 10.1186/s12915-026-02592-w
Xiaodi Wang, Jovana Bozic, Brian B Tarimo, Tanise M S Stenn, Miles T McCollum, Juliana Carrillo, Eva A Buckner, Vincent O Nyasembe, Billy Ngasala, Rhoel R Dinglasan, Travis C Collier, Eric P Caragata, Yoosook Lee, Derrick K Mathias
{"title":"Genetic divergence in Aedes aegypti mosquitoes potentially associated with enhanced capacity for arbovirus transmission.","authors":"Xiaodi Wang, Jovana Bozic, Brian B Tarimo, Tanise M S Stenn, Miles T McCollum, Juliana Carrillo, Eva A Buckner, Vincent O Nyasembe, Billy Ngasala, Rhoel R Dinglasan, Travis C Collier, Eric P Caragata, Yoosook Lee, Derrick K Mathias","doi":"10.1186/s12915-026-02592-w","DOIUrl":"10.1186/s12915-026-02592-w","url":null,"abstract":"<p><strong>Background: </strong>Aedes aegypti is the most important mosquito vector of arboviruses worldwide, originating on islands of the southwest Indian Ocean before spreading to Africa and, more recently, the Americas and Asia. Migration out of Africa was enabled by the evolution of behaviors that increased human-vector contact, and as Ae. aegypti became more domesticated, arboviral competence may have also increased. Here we investigate variation in vector competence between present-day populations of Ae. aegypti from Florida (USA) and Tanzania (East Africa) and use a genomics approach to examine genetic differentiation potentially underlying traits important for arbovirus transmission.</p><p><strong>Results: </strong>Using vector-competence experiments with dengue virus serotype 2, we demonstrate greater susceptibility to infection in American mosquitoes, along with higher viral loads and a shorter time to virus dissemination. We then sought to identify highly divergent genes potentially underlying these differences and discovered more than 1.6 million single nucleotide polymorphisms via exome sequencing. Of these, 1058 were highly differentiated between populations (F<sub>ST</sub> > 0.9) with more than half mapping to 17 outlier genes influencing chromatin remodeling, lipid metabolism, glycosylation, circadian rhythms, olfaction, and saliva bioactivity. Eight of these outlier genes formed a highly divergent genomic island on chromosome 2. Allele-frequency patterns of outlier genes across Ae. aegypti's range highlight genetic differentiation within sub-Saharan Africa, as well as evolutionary changes accompanying the shift towards domestication in the Americas and Asia.</p><p><strong>Conclusions: </strong>This work offers insights into phenotypic variation and evolutionary divergence within Ae. aegypti, including naturally occurring genetic variants that may influence transmission-related characters.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"24 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13343669/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148403700","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
Circular RNA dynamics in breast-to-brain metastatic cascade. 乳腺到脑转移级联中的环状RNA动力学。
IF 5.4 1区 生物学
BMC Biology Pub Date : 2026-07-08 DOI: 10.1186/s12915-026-02666-9
Adrian Szczepaniak, Jakub Karwowski, Agnieszka Bronisz, Jakub Godlewski
{"title":"Circular RNA dynamics in breast-to-brain metastatic cascade.","authors":"Adrian Szczepaniak, Jakub Karwowski, Agnieszka Bronisz, Jakub Godlewski","doi":"10.1186/s12915-026-02666-9","DOIUrl":"10.1186/s12915-026-02666-9","url":null,"abstract":"<p><strong>Background: </strong>Breast-to-brain metastases (BTB mets) represent one of the most aggressive and clinically challenging manifestations of breast cancer. The limited efficacy of available therapies and poor patient outcomes reflect the intricate molecular and cellular processes underlying metastatic colonization of the brain. The molecular events driving this process involve extensive transcriptomic reprogramming, encompassing not only protein-coding genes but also diverse classes of non-coding RNAs. Circular RNAs (circRNAs) are a distinct class of stable, non-coding transcripts increasingly recognized as key regulators of cancer biology, yet their role in brain-tropic metastasis remains poorly defined. This study aimed to systematically profile circRNA expression across primary tumors and metastatic sites to uncover regulatory mechanisms and define site-specific circRNA expression patterns associated with BTB mets.</p><p><strong>Results: </strong>CircRNAs displayed highly site-specific expression patterns during metastatic breast cancer progression. Notably, the majority of differentially expressed circRNAs were uncoupled from changes in their linear host genes, highlighting transcriptionally-independent circularization as a regulatory mechanism. Notably, the majority of circRNAs distinguishing BTB mets from primary breast tumors and pleural effusions likewise distinguished them from primary brain tumors (glioblastoma). Analysis of the circRNA landscape revealed 42 circRNAs that are consistently deregulated and characteristic of BTB mets. Subsequent functional analysis of circRNA-microRNA interactions revealed that these circRNAs are enriched in metastatic signaling pathways and brain-related biological processes, suggesting a potential role for circRNA-mediated regulation in adaptation to the brain microenvironment. Additionally, circRNA landscapes exhibit high stability under conditions that promote either stemness or differentiation. To support data exploration, Breast circScope (circrna.netlify.app), an open-access resource that enables analysis of circRNA expression and host gene associations, along with curated visualization tools, was developed.</p><p><strong>Conclusions: </strong>Presented findings uncover a previously unrecognized dimension of post-transcriptomic regulation in metastatic breast cancer, demonstrating that circRNAs exhibit site-specific expression patterns associated with metastatic progression. These results highlight circRNAs as integral molecules in the regulatory landscape of breast cancer metastasis and provide a framework for understanding their functional contribution to brain-tropic disease.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":" ","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13632408/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148403609","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
Phylogenetic analysis and machine learning identify signatures of selection and predict deleterious mutations in common bean (Phaseolus vulgaris L.). 系统发育分析和机器学习识别了普通豆(Phaseolus vulgaris L.)的选择特征并预测了有害突变。
IF 5.4 1区 生物学
BMC Biology Pub Date : 2026-07-07 DOI: 10.1186/s12915-026-02680-x
Henry Cordoba-Novoa, Edward S Buckler, Cinta M Romay, Ana Berthel, Lynn Johnson, Parthiba Balasubramanian, Valerio Hoyos-Villegas
{"title":"Phylogenetic analysis and machine learning identify signatures of selection and predict deleterious mutations in common bean (Phaseolus vulgaris L.).","authors":"Henry Cordoba-Novoa, Edward S Buckler, Cinta M Romay, Ana Berthel, Lynn Johnson, Parthiba Balasubramanian, Valerio Hoyos-Villegas","doi":"10.1186/s12915-026-02680-x","DOIUrl":"https://doi.org/10.1186/s12915-026-02680-x","url":null,"abstract":"<p><strong>Background: </strong>Mutations are a continuous source of new alleles and genetic diversity in populations. Domestication and selection influence the accumulation of alleles occurring across a range of deleteriousness. Evidence suggests that mildly deleterious mutations (DelMut) can be purged out of breeding populations, increasing favorable allele accumulation.</p><p><strong>Results: </strong>We used phylogeny-based analyses among 36 legume genomes to identify selection signatures and trained a random forest (RF) model using conservation and protein information for the prediction of DelMut in common bean populations, including a newly developed multiparent advanced generation intercrossed (MAGIC) population of black beans. Genes involved in nitrogen metabolism showed signs of positive selection in the Middle American genome, whereas genes related to phosphorylation were positively selected in the Andean genome. By combining conservation and protein information with machine learning (ML) for high-dimensional feature analysis, we characterized 82,442 sites in the MAGIC founders (36,558 polymorphic) and 4753 sites evenly sequenced among RILs that could be potentially deleterious. Variation in the number of highly DelMut (high predicted deleterious scores) among lines was observed and later correlated with agronomic traits. Phenotypic analyses showed that calculated genetic load (and number of highly DelMut) was negatively correlated with flowering time, maturity, and yield. A detailed in silico analysis of predicted mutations showed presence in highly conserved protein regions, which is likely to affect protein functionality.</p><p><strong>Conclusions: </strong>Our results show that variation in genetic load can be observed in breeding populations and potentially impact plant performance. These results contribute to understanding the genome-wide accumulation patterns of DelMut in breeding populations. Our study supports future development of strategies to reduce genetic load in promising germplasm and accelerate breeding programs.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":" ","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148403678","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
Network-based machine learning to identify biomarkers for systemic lupus erythematosus. 基于网络的机器学习识别系统性红斑狼疮的生物标志物。
IF 5.4 1区 生物学
BMC Biology Pub Date : 2026-07-07 DOI: 10.1186/s12915-026-02681-w
Minhyuk Park, Donghyo Kim, Juhun Lee, Jaegyun Noh, Chan Johng Kim, Youngchul Oh, Chang-Hee Suh, Ji-Won Kim, Sin-Hyeog Im, Sanguk Kim, Inhae Kim
{"title":"Network-based machine learning to identify biomarkers for systemic lupus erythematosus.","authors":"Minhyuk Park, Donghyo Kim, Juhun Lee, Jaegyun Noh, Chan Johng Kim, Youngchul Oh, Chang-Hee Suh, Ji-Won Kim, Sin-Hyeog Im, Sanguk Kim, Inhae Kim","doi":"10.1186/s12915-026-02681-w","DOIUrl":"10.1186/s12915-026-02681-w","url":null,"abstract":"<p><strong>Background: </strong>Systemic lupus erythematosus (SLE) is a complex autoimmune disease, making accurate diagnosis and effective treatment challenging. Despite the critical need for reliable biomarkers, conventional differential gene expression (DGE) analyses often yield high false-positive rates and have limited ability to identify clinically actionable targets, leaving a significant gap in SLE precision medicine.</p><p><strong>Results: </strong>To address this, we developed NetSLE, a network-based machine learning framework that integrates diverse SLE-related prior knowledge with comprehensive biological networks. By effectively filtering out false positives from differentially expressed genes (DEGs), NetSLE identified a robust panel of 150 key biomarkers. Clinically, the NetSLE-derived biomarkers outperformed conventional markers and full transcriptomes in predicting disease activity across independent cohorts. Furthermore, they successfully identified experimentally validated drug repurposing candidates (e.g., lipid-modifying and antithrombotic agents) and enabled precise stratification of patients into distinct immunological subtypes (AS1 and AS2).</p><p><strong>Conclusions: </strong>NetSLE offers a translatable approach to overcome the limitations of traditional biomarker discovery. The clinically sized 150-gene panel provides a practical tool for enhancing diagnostic precision, guiding targeted treatments, and advancing personalized medicine in SLE.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":" ","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13628947/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148403771","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
Global stabilization of the mitochondrial proteome is associated with extreme anoxia tolerance in Austrofundulus limnaeus WS40NE cells. Austrofundulus limnaeus WS40NE细胞线粒体蛋白质组的整体稳定与极端缺氧耐受性有关。
IF 5.4 1区 生物学
BMC Biology Pub Date : 2026-07-06 DOI: 10.1186/s12915-026-02674-9
Chelsea Hughes, Meranda M Corona, Dietmar Kültz, Jason E Podrabsky
{"title":"Global stabilization of the mitochondrial proteome is associated with extreme anoxia tolerance in Austrofundulus limnaeus WS40NE cells.","authors":"Chelsea Hughes, Meranda M Corona, Dietmar Kültz, Jason E Podrabsky","doi":"10.1186/s12915-026-02674-9","DOIUrl":"10.1186/s12915-026-02674-9","url":null,"abstract":"<p><strong>Background: </strong>Austrofundulus limnaeus is an extremophile vertebrate native to small temporary ponds of Venezuela. Embryos of A. limnaeus must survive variable and often extreme conditions, including long periods of anoxia. Neuroepithelial cells derived from these embryos, WS40NE cells, provide a unique tool to understand how the proteome changes in response to anoxic stress.</p><p><strong>Results: </strong>Using label-free proteomics, 19,604 peptides and 3487 proteins were quantified in normoxic, 4d anoxic, and 24 h recovery WS40NE cells. Of these, 2612 proteins (74.9%) were statistically significantly differentially abundant in at least one comparison: 1988 comparing normoxia to 4 days anoxia (57.0%), 923 comparing 4 days anoxia to 24 h recovery (26.5%), and 1814 comparing normoxia to 24 h recovery (52.0%). Further, interaction networks of proteins with similar expression patterns suggest that relative mitochondrial capacity may increase during anoxia, including upregulation and/or preferred stabilization of proteins involved in mitochondrial metabolism and mitochondrial transcription and translation. This is in sharp contrast to trends in proteins that support cytoplasmic translation.</p><p><strong>Conclusions: </strong>These data support an active role for mitochondria in mediating the survival of the anoxia-tolerant WS40NE cell line and highlight the value of this non-traditional vertebrate model for uncovering novel mechanisms of cellular resilience.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":" ","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13628842/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148396048","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
Marine mammals as models for charting the evolution of social vocal rhythm. 海洋哺乳动物作为描绘社会发声节奏进化的模型。
IF 5.4 1区 生物学
BMC Biology Pub Date : 2026-07-04 DOI: 10.1186/s12915-026-02675-8
Peter F Cook, Sophie Flem, Peter T Madsen, Andrea Ravignani, Pete Gremore, Carson Hood, Yannick Jadoul, Danai Papageorgiou, Michael Pedersen, Teresa Raimondi, Andrew Rouse, Pernille M Sørensen, Simone Videsen, Stephanie L King
{"title":"Marine mammals as models for charting the evolution of social vocal rhythm.","authors":"Peter F Cook, Sophie Flem, Peter T Madsen, Andrea Ravignani, Pete Gremore, Carson Hood, Yannick Jadoul, Danai Papageorgiou, Michael Pedersen, Teresa Raimondi, Andrew Rouse, Pernille M Sørensen, Simone Videsen, Stephanie L King","doi":"10.1186/s12915-026-02675-8","DOIUrl":"10.1186/s12915-026-02675-8","url":null,"abstract":"<p><p>In this Perspective, we suggest combining physiological, neurobiological, behavioural, and social data from multiple marine mammal species to create evolutionary models of the emergence of social vocal coordination. Marine mammal sound production mechanisms have evolved to manage vocalizing and breathing in an aquatic environment, potentially releasing functional constraints on the control of vocal timing. Intervals in rhythmic cetacean vocalizations cover a remarkable temporal range, from less than a millisecond in porpoise burst pulses to 10 s in sperm whale slow clicks. Many cetaceans demonstrate temporally coordinated social behaviour, while pinnipeds express high variability in vocal plasticity and social behaviour. The systematic variability of vocal production mechanisms, vocal rhythms, and sociality can be compared phylogenetically to generate models for the evolution of social rhythm in the vocal domain.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":" ","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13422076/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148381746","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}
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