PeerJ最新文献

{"title":"Analysis of biochemical parameters and tumor markers in Cushing's disease and ectopic adrenocorticotropic hormone syndrome.","authors":"Linjia Guo, Yingqi Liu, Saijia Li, Xinyue Yu, Kewei Wang, Fei Yan","doi":"10.7717/peerj.21677","DOIUrl":"https://doi.org/10.7717/peerj.21677","url":null,"abstract":"<p><strong>Purpose: </strong>To compare clinical characteristics, biochemical parameters, and tumor markers between patients with Cushing disease (CD) and ectopic adrenocorticotropic hormone (ACTH) syndrome (EAS), identify potential biomarkers, and optimize their diagnostic differentiation.</p><p><strong>Methods: </strong>A single-center retrospective study was conducted in 75 patients with ACTH-dependent Cushing syndrome (51 CD, 24 EAS) admitted between January 2006 and April 2025. Differences in biochemical indices, tumor markers, and hormone levels were analyzed. Receiver operating characteristic (ROC) analysis was used to evaluate diagnostic performance and determine optimal cut-off values.</p><p><strong>Results: </strong>EAS patients were significantly older at diagnosis than CD patients. Fasting glucose was higher, while serum potassium and albumin were lower in the EAS group. Non-small cell lung cancer-associated antigen, carcinoembryonic antigen (CEA), cancer antigen 15-3 (CA15-3), and cancer antigen 19-9 were markedly elevated in EAS, whereas pro-gastrin-releasing peptide (ProGRP) and neuron-specific enolase (NSE) showed no significant differences. Serum cortisol and plasma ACTH levels at all time points and after dexamethasone suppression were significantly higher in EAS. ROC analysis of the product of midnight serum cortisol (μg/dL) and plasma ACTH (pg/mL) divided by 1000 (\"Midnight Cort × ACTH/1000\") showed an area under the curve (AUC) of 0.902 for identifying EAS, with a cut-off value >2 (sensitivity 83.3%, specificity 84.3%). Its diagnostic accuracy was comparable to that of the high-dose dexamethasone suppression test (HDDST).</p><p><strong>Conclusion: </strong>EAS patients were older and exhibited more severe metabolic abnormalities than those with CD. Elevated tumor markers may suggest ectopic ACTH secretion. The \"Midnight Cort × ACTH/1000\" index provides high diagnostic value and a simple, convenient method for differentiating EAS from CD.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"14 ","pages":"e21677"},"PeriodicalIF":2.9,"publicationDate":"2026-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13637636/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149113255","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Vertical collision risk of Red-crowned Cranes at coastal onshore wind farms in eastern China.","authors":"Kai Dong, Xinyi Hu, Changhu Lu","doi":"10.7717/peerj.21762","DOIUrl":"https://doi.org/10.7717/peerj.21762","url":null,"abstract":"<p><strong>Background: </strong>With the continued expansion of coastal wind farms toward wetland edges, understanding the mechanisms that drive collision risk for large waterbirds around wind turbines is becoming increasingly important.</p><p><strong>Methods: </strong>Based on satellite tracking data from seven Red-crowned Cranes (<i>Grus japonensis</i>) in the coastal area of Yancheng, Jiangsu Province, and the geometric parameters of the wind turbine rotor-swept zone (RSZ), we developed a coupling framework linking crane flight heights with the vertical position of the RSZ. We used this framework to assess potential collision risk during the non-migratory period.</p><p><strong>Results: </strong>Crane flight height showed clear vertical overlap with the RSZ, but potential collision risk was not evenly distributed throughout the RSZ. Instead, risk was concentrated in several adjacent low to medium altitude bands. The 30-35 m band contributed the most, followed by the 35-40 m and 40-45 m bands. Simulations showed that increasing turbine hub-height could substantially reduce collision risk by shifting the RSZ upward as a whole. A 20 m increase in hub-height reduced overall risk by 48.9%.</p><p><strong>Discussion: </strong>Based on empirical flight height data, this study revealed the heterogeneous vertical distribution of potential collision risk for Red-crowned Cranes and the mechanisms underlying its formation. It also identified key risk height bands, providing a more mechanistic basis for turbine-design optimization, risk mitigation, and coordination between coastal wind power development and waterbird conservation.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"14 ","pages":"e21762"},"PeriodicalIF":2.9,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13634307/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149113384","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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 serum cytokine-derived integrated inflammatory profile score (IIPS) links systemic inflammation to symptom burden and severity in COPD.","authors":"Jiexun Cai, Zhihui Li, Yanfeng Yi, Xiangli An, Anqi Li, Hui Han, Xiaoyu Li, Yunliang Yao","doi":"10.7717/peerj.21751","DOIUrl":"https://doi.org/10.7717/peerj.21751","url":null,"abstract":"<p><strong>Background: </strong>Chronic obstructive pulmonary disease (COPD) is increasingly recognized as a systemic inflammatory syndrome in which forced expiratory volume in 1 s expressed as a percentage of predicted value (FEV1% predicted) may dissociate from patient-reported symptom burden. This study evaluated an Integrated Inflammatory Profile Score (IIPS) as a potential biological correlate for a more holistic assessment of stable COPD.</p><p><strong>Methods: </strong>Serum concentrations of 11 cytokines were measured in 62 patients with stable COPD. The IIPS was derived using automated linear modeling with forward stepwise selection guided by the corrected Akaike information criterion (AICc). Associations of the IIPS with COPD Assessment Test (CAT) scores were compared with those of FEV1% predicted.</p><p><strong>Results: </strong>The optimized IIPS, comprising interferon-gamma (IFN-γ), interleukin-2 (IL-2), and interleukin-10 (IL-10), was significantly associated with FEV1% predicted (R² = 0.1867, <i>p</i> = 0.0005) and outperformed the individual cytokines in discriminating spirometric severity (area under the receiver operating characteristic curve (AUC) = 0.7381). For symptom burden, FEV1% predicted showed greater explanatory power for exertional domains, particularly breathlessness (R² = 0.0832) and activities (R² = 0.1280). By contrast, the IIPS showed numerically stronger trend-level associations for sleep (R² = 0.0519, <i>p</i> = 0.0750) and energy (R² = 0.0511, <i>p</i> = 0.0773), although these associations did not reach conventional statistical significance.</p><p><strong>Conclusion: </strong>The IIPS reflects Global Initiative for Chronic Obstructive Lung Disease (GOLD)-defined physiological severity more effectively than any single cytokine measured in this study. Its associations with patient-reported systemic symptoms were modest and exploratory, suggesting that integrated inflammatory profiling may complement spirometry in characterizing COPD burden but requires external and longitudinal validation before clinical application.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"14 ","pages":"e21751"},"PeriodicalIF":2.9,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13634306/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149113267","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ocular biometric characteristics in young Saudi adults across varying degrees of myopia.","authors":"Saif Hassan Alrasheed, Azzam Abdulaziz Alharbi, Naveen Kumar Challa, Saleh Alshammeri, Abdelaziz Mohamed Elmadina, Bandar M Alenezi, Fahad Almoqbel, Majid A Moafa","doi":"10.7717/peerj.21767","DOIUrl":"https://doi.org/10.7717/peerj.21767","url":null,"abstract":"<p><strong>Background: </strong>High myopia significantly increases the risk of serious ocular complications. The purpose of this study was to characterize ocular biometric variations across different degrees of myopia in young Saudi adults and to identify biometric parameters most strongly influenced by refractive severity.</p><p><strong>Methods: </strong>In this cross-sectional study, 163 eyes from individuals aged 18-31 years with myopia ranging from -1.00 to -11.00 D were evaluated at the university medical clinics. Anterior segment parameters such as white-to-white (WTW) corneal diameter, anterior chamber depth (ACD), anterior chamber volume (ACV), anterior chamber angle (ACA), and central corneal thickness (CCT) were measured using the Pentacam, axial length (AXL) was assessed with the IOL Master. Intraocular pressure (IOP) was measured with a non-contact tonometer. Finally, AXL, anterior chamber parameters, WTW, CCT and IOP were compared among the low, moderate, and high myopic groups.</p><p><strong>Results: </strong>Myopia severity showed a statistically significant positive correlation with AXL, WTW corneal diameter, ACD, ACV, CCT, and IOP (<i>p</i> < 0.05). AXL demonstrated a strong, statistically significant positive correlation with spherical equivalent (r = 0.70, <i>p</i> < 0.01). In contrast, ACA remained relatively stable across myopia groups. Multivariate analysis of covariance revealed that myopia severity significantly influenced AXL (F(2,156) = 8.52, <i>p</i> < 0.01), WTW corneal diameter (F(2,156) = 5.22, <i>p</i> < 0.01), ACV (F(2,156) = 7.94, <i>p</i> < 0.01), CCT (F(2,156) = 15.84, <i>p</i> < 0.01), and IOP (F(2,156) = 12.83, <i>p</i> < 0.01) after adjusting for age and gender. ACD showed modest increases across myopia groups with a borderline non-significant association after adjustment (F(2,156) = 2.93, <i>p</i> = 0.06), whereas ACA remained relatively stable and was not significantly affected by myopia severity (F(2,156) = 0.62, <i>p</i> = 0.54).</p><p><strong>Conclusion: </strong>Myopia severity in young adults is associated with significant structural changes, primarily AXL elongation and only minimal enlargement of anterior segment dimensions particularly the ACD and ACA, suggesting that posterior expansion predominates over anterior. These biometric patterns have important implications for refractive surgery planning, glaucoma risk assessment, and monitoring of myopia progression.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"14 ","pages":"e21767"},"PeriodicalIF":2.9,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13634304/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149113391","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The first annotated checklist of the bees of Colombia reveals an overlooked diversity and areas with major data deficiencies.","authors":"Ruben D Martín-Rojas, Diego A Guevara, Juan Diego Maldonado Cepeda, Nicolás David Gutiérrez Rubiano, Danny Vélez, Victor H Gonzalez, Rodulfo Ospina-Torres, Neil S Cobb, M Lucia Aguilar-Benavides, Eduardo A B Almeida, Julián Álvarez Romero, María José Arenas-Herrera, Jose Luis Benavides-Lopez, M Argenis Bonilla-Gómez, Nelson A Canal, Nancy S Carrejo, Cindy J Celis, Juan Camilo Dorado-Suarez, Giovanny Fagua, Delly Rocío García-Cárdenas, Victor Alfonso García-Moya, Dario Guevara-Plata, Fernando Fernández, Luz Miryam Gómez-P, Roberto J Guerrero, Maria R Manzano, Juan Diego Herrera-Manrique, Mario Alejandro Marín, Gabriel R Navas-S, Jhon César Neita Moreno, Santiago R Ramírez, Maria Cristina Gallego Ropero, Mateo Restrepo-Rúa, Luis F Sánchez-Alvarán, Antonella Sardi-Saavedra, Valentina Sarria-Rodríguez, Paula Andrea Sepúlveda Cano, Ángela Soto-Correa, Edwin Daniel Torres Pineda, Juliana Torres-Toro, Elder A Vásquez-Lenis, María C Vélez Naranjo, Erika Valentina Vergara-Navarro, Marta Wolff, Laura Melissa Guzman, Margarita M López-Uribe","doi":"10.7717/peerj.21684","DOIUrl":"https://doi.org/10.7717/peerj.21684","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Most existing knowledge about bee biodiversity comes from temperate regions, where diversity is presumed highest-yet substantial data gaps across the tropics confound this pattern. Checklists are critical for documenting species presence, identifying knowledge gaps, and guiding conservation. We present the first comprehensive bee checklist for Colombia, a country in tropical northern South America that serves as a key biogeographic bridge between Central and South America. We hypothesize that Colombia's complex topography, its position at the intersection of multiple biogeographic regions, and its partial Gondwanan origin contribute to exceptionally high bee diversity and endemism.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Methods: &lt;/strong&gt;We built a network of local entomological collections to compile specimen data (&lt;i&gt;n&lt;/i&gt; = 62,158), combined with occurrence records from public datasets (&lt;i&gt;n&lt;/i&gt; = 25,520) and species records reported in the taxonomic literature (&lt;i&gt;n&lt;/i&gt; = 297). Our objectives were to: (1) synthesize the first bee species checklist for Colombia and their genus-level biological traits (ecoregional distribution, nesting habitat, sociality), (2) characterize diversity patterns at the department level using species richness, Shannon index, and weighted endemism, (3) estimate undescribed species via rarefaction curves, and (4) compare species richness and phylogenetic diversity (Faith's phylogenetic diversity, mean pairwise distance (MPD), mean nearest taxon distance (MNTD) and standardized effect sizes of MPD and MNTD) with countries of Gondwanan origin (Brazil, Chile) &lt;i&gt;versus&lt;/i&gt; those in the Holarctic region (USA).&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;We report 738 species across 123 genera and five families, including 246 new country records and 140 endemic species (19% of total fauna). Sampling effort was highly uneven: 41% of the records were concentrated in the Andean region, while xeric areas-where highest diversity is expected-remain critically undersampled. Species in the family Apidae dominated assemblages (69%), and the Andes ecoregion held the highest richness and endemism. Biological traits across the 738 species showed that solitary (57%) and above-ground nesting (57%) strategies predominate. Accumulation curves suggested that ∼26% of the bee fauna remains undescribed or unreported. Phylogenetic analyses did not support the hypothesis of higher diversity in Colombia relative to other countries of Gondwanan or Holarctic origin. We also found weak support for the relationship between species richness and geographic area across countries.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusions: &lt;/strong&gt;This study provides essential baseline knowledge for ecological, taxonomic, and conservation research of Neotropical bees. Geographic sampling biases highlight urgent needs for surveys in undersampled regions, especially xeric ecosystems. The multi-institutional network developed here demonstrates the value of collaborative frameworks for biodive","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"14 ","pages":"e21684"},"PeriodicalIF":2.9,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13634308/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149113337","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Morphological traits, photosynthetic pigments and phenolic metabolism in globe artichoke (<i>Cynara scolymus</i> L.) genotypes.","authors":"İbrahim Sönmez","doi":"10.7717/peerj.21771","DOIUrl":"https://doi.org/10.7717/peerj.21771","url":null,"abstract":"<p><p>Globe artichoke (<i>Cynara scolymus</i> L.) is a phenolic-rich vegetable with high nutritional and antioxidant value; however, integrated evaluations of morphological traits, photosynthetic pigments, and phenolic metabolism among local genotypes remain limited. This study compared six genotypes collected from different locations in the Marmara Region of Turkey and grown under uniform environmental conditions. Yield-related traits, photosynthetic pigments (chlorophyll a, chlorophyll b, total chlorophyll, and carotenoids), total phenolics, flavonoids, and antioxidant capacity were evaluated using the 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging and cupric reducing antioxidant capacity (CUPRAC) assays, while individual phenolic compounds were identified and quantified by high-performance liquid chromatography coupled with diode-array detection (HPLC-DAD). Significant genotypic variation was observed across all parameters. Head weight ranged from 223.19 to 327.65 g, with the highest value recorded in Hamitler. Bilecik exhibited the highest chlorophyll a and total chlorophyll content, whereas Pamukova showed the highest phenolic content and antioxidant capacity. Chlorogenic acid was identified as the predominant phenolic compound. Principal component analysis revealed clear genotype separation mainly driven by phenolic composition and antioxidant activity. These findings demonstrate substantial physiological and biochemical diversity among globe artichoke genotypes and highlight promising materials for breeding programmes aimed at improving both yield and functional quality.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"14 ","pages":"e21771"},"PeriodicalIF":2.9,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13634305/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149113353","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prognostic and immunotherapeutic implications of histamine-related biomarkers in lung adenocarcinoma.","authors":"Fancai Chen, Jinfeng Wang, Jicheng Yang, Yuexi Yuan, Hua Luo, Jianming Peng, Chengyi Yan, Zhang Zhang","doi":"10.7717/peerj.21760","DOIUrl":"https://doi.org/10.7717/peerj.21760","url":null,"abstract":"<p><strong>Background: </strong>Recent researches have revealed that histamine plays a critical role in promoting pathogenesis of cancers. However, the key histamine-related molecular signatures and their functional roles in lung adenocarcinoma (LUAD) remain largely unknown.</p><p><strong>Methods: </strong>Differentially expressed analysis was conducted on transcriptome data to screen differentially expressed genes (DEGs) between LUAD and control (adjacent non-cancerous samples) groups. The differentially expressed histamine-related genes in LUAD were identified by intersecting DEGs and histamine-related genes. Univariate Cox regression and least absolute shrinkage and selection operator (LASSO) analyses were applied to determine key signatures associated with LUAD prognosis. Subsequently, we constructed a histamine-related prognostic risk model, compared functional enrichment and immune cell infiltration, and predicted immunotherapeutic responses and chemotherapeutic sensitivities between two risk groups using gene set enrichment analysis (GSEA), CIBERSORT, and TIDE algorithms. Finally, we investigated the expression patterns and methylation levels of key signatures.</p><p><strong>Results: </strong>Firstly, 24 candidate histamine-related genes in LUAD, which were involved in histamine transport/secretion and neurotransmitter receptor activity were identified. After univariate Cox regression and LASSO analyses, five histamine-related genes, including SLC18A2, CDT1, PLA2G3, TSPAN7 and BTK were identified as associated with LUAD prognosis. Specifically, CDT1 was up-regulated, while the other four genes were down-regulated in LUAD samples. By calculating the histamine-related risk score, a risk model with area under curve values >0.6 (up to 0.7) for 1-, 3-, and 5-year predictions in both training and validation sets was constructed and validated. Further enrichment analysis showed a relation between risk score and immune (immune cells, immunotherapy response), and we found that low-risk group was in a more immunoactive status. Importantly, low-risk patients were predicted to have better responses to immunotherapy, while high-risk group had greater sensitivity to crizotinib, docetaxel, erlotinib, gefitinib, paclitaxel and vinorelbine. Moreover, we identified that the DNA methylation profiles of these signatures were altered in LUAD.</p><p><strong>Conclusion: </strong>In this study, we focused on histamine, identified histamine-related genes and developed a new prognostic model for LUAD, providing an important theoretical foundation and practical reference for pathogenesis and precision treatment of patients with LUAD.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"14 ","pages":"e21760"},"PeriodicalIF":2.9,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13633689/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149113378","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Synthesis of molecular data on Mactroidea (Bivalvia): phylogenetic implications and open questions.","authors":"Ava Ghezelayagh, Stewart M Edie, Katie S Collins, Javier H Signorelli, David Jablonski","doi":"10.7717/peerj.21681","DOIUrl":"https://doi.org/10.7717/peerj.21681","url":null,"abstract":"<p><p>Molecular phylogenetics have clarified high-level evolutionary relationships across the tree of life, but sampling is highly uneven at lower levels, particularly for marine organisms. Here, we synthesize all publicly available Sanger sequencing data for the diverse yet under-sampled marine bivalve superfamily Mactroidea to provide a unified molecular and paleontological framework, and to guide targeted sampling for a more complete understanding of the group's evolutionary history. We infer two complementary phylogenetic estimates, one using a comprehensive eight-gene alignment that maximizes taxon sampling, and a second high-coverage three-gene alignment that maximizes molecular coverage. Both phylogenies are largely concordant with morphology-based classifications at the genus and subgenus levels, but reveal that the recognized mactroid families with sequence data, as currently described, and the subfamilies of Mactridae are not reciprocally monophyletic. Among the genera, evidence suggests that <i>Spisulona</i> and <i>Taria</i>, often synonymized to various extant taxa, may be valid genera or subgenera, although further molecular data are needed to confirm these taxonomic implications. Budding-informed time calibration using 18 fossil constraints reveals several conflicts between fossil ages and the inferred molecular topology, likely owing to incomplete fossil and molecular sampling and ambiguity of certain fossil assignments. By tabulating conflicting or missing data, we identify priorities for future molecular sampling, and show that gaps in the molecular data are unevenly distributed geographically, with concentrations in the tropical East Pacific and tropical West Pacific. Combined phylogenetic, biogeographic, and paleontological inventories, supported by voucher-based verification of specimens, can guide targeted sampling to efficiently improve understanding of within-clade relationships and evolutionary dynamics in Mactroidea.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"14 ","pages":"e21681"},"PeriodicalIF":2.9,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13633688/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149113381","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide identification of basic helix-loop-helix (bHLH) genes in <i>Pinellia ternata</i> and their responses to abiotic stress and hormone treatments.","authors":"Xiaorui Wang, Huirong Li, Zimo Li, Han He, Ziyu Xia, Yajun Liu, Xinghang Cai, Wenjing Huang, Xiaochun Sun","doi":"10.7717/peerj.21774","DOIUrl":"https://doi.org/10.7717/peerj.21774","url":null,"abstract":"<p><strong>Background: </strong>Basic helix-loop-helix (bHLH) transcription factors constitute the second-largest transcription factor family in plants. They are widely distributed across plant genomes and play vital regulatory roles in plant growth and development, secondary metabolism, and responses to abiotic stress. Although the bHLH gene family has been widely identified and analyzed in many plant species, systematic genome-wide identification and functional analysis of bHLH genes in <i>Pinellia ternata</i> are still lacking.</p><p><strong>Results: </strong>In this study, a total of 140 <i>PtbHLH</i> genes were identified, of which 135 were unevenly distributed on 13 chromosomes. Phylogenetic analysis with <i>Arabidopsis thaliana</i> divided the <i>PtbHLH</i> genes into 24 subfamilies, with no members clustered in subfamily VI. Gene structure and conserved motif analysis showed that members of the same subfamily had highly similar structural characteristics. Collinearity analysis identified three paralogous pairs among the 140 <i>PtbHLH</i> genes. Cross-species collinearity analysis revealed eight syntenic pairs between <i>P. ternata</i> and <i>A. thaliana</i>, 76 between <i>P. ternata</i> and <i>Nicotiana tabacum</i>, and 50 between <i>P. ternata</i> and <i>Oryza sativa</i>. Cis-element prediction showed that all <i>PtbHLH</i> promoters contained hormone-responsive elements, stress-responsive elements and transcription factor binding sites. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment indicated that <i>PtbHLH</i> genes were mainly involved in hormone signal transduction, environmental signal response and transcriptional regulation. Protein-protein interaction (PPI) analysis suggested that <i>PtbHLH68</i> was predicted as a putative interaction hub interacting with multiple family members. Tissue expression profiles showed that <i>PtbHLH</i> genes had diverse expression patterns, with most highly expressed in roots and tubers. Under high-temperature and drought stress, <i>PtbHLH9</i> was most sensitive to high temperature, and <i>PtbHLH85</i> was most sensitive to drought. Under methyl jasmonate (MeJA), abscisic acid (ABA) and salicylic acid (SA) treatments, <i>PtbHLH73</i> responded most strongly to MeJA, <i>PtbHLH7</i> to ABA, and <i>PtbHLH48</i> responded significantly to all three hormones. These four genes serve as core candidates for exploring <i>PtbHLH</i> functions in abiotic stress tolerance and hormone signal transduction.</p><p><strong>Conclusion: </strong>This study provides a solid foundation for understanding the functional mechanism of <i>PtbHLH</i> transcription factors in <i>Pinellia ternata</i>, and offers a valuable reference for the further screening of <i>PtbHLH</i> genes related to abiotic stress tolerance and hormone signaling pathways.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"14 ","pages":"e21774"},"PeriodicalIF":2.9,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13633692/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149113339","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fungus above us: exploring the atmospheric mycobiome by aircraft.","authors":"Kimberly L Métris, Jérémy Métris","doi":"10.7717/peerj.21746","DOIUrl":"https://doi.org/10.7717/peerj.21746","url":null,"abstract":"<p><p>Fungi play a key role in ecosystems, influencing the global bioaerosol budget and pollution dynamics even when metabolically inactive. Despite this, diversity and transport of fungi in the atmosphere are not well explored. This study shows that the atmosphere contains diverse fungi with varied ecological classifications and recruitment patterns reflecting underlying terrestrial habitats. Abundant genera include <i>Neoascochyta</i>, <i>Cladosporium</i>, <i>Alternaria</i>, <i>Coniothyrium</i>, <i>Penicillium</i>, <i>Hymenochaetopsis</i>, <i>Lachnum</i>, and <i>Fonsecazyma</i>. The atmospheric mycobiome is dominated by decomposers and pathogens; over 40% of the sampled airborne fungi are putative plant or animal pathogens. Using aircraft surveys from 2022 to 2023 in distinct seasons alongside comprehensive environmental datasets, airborne fungal diversity was found to decline with altitude and increasing vegetation productivity. Patterns of diversity in atmospheric fungal communities are shaped by vegetation productivity and meteorology. Remote sensing and meteorological data provide valuable insight into this diversity and reinforce the role of local or regional phenology as an important determinant of atmospheric biodiversity. Additionally, the proportional composition of functional guilds in the atmosphere shifts with vegetation productivity and surface winds, suggesting that seasonal transport dynamics may contribute to shaping assembly of the atmospheric mycobiome. This work demonstrates how integrated genomic and environmental datasets acquired by aircraft and satellite data could be leveraged in future to clarify aerobiology questions and contribute to a unified view of fungal ecology.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"14 ","pages":"e21746"},"PeriodicalIF":2.9,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13633693/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149113357","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}