Biology

22 pages, 10055 KB

Open AccessArticle

Integrated Metabolome and Transcriptome Analysis Reveals the Effect of Anthocyanins on Flower Color Variation in Michelia odora

by Yuan Xie, Pengbo Yan, Li Liu, Jun Ni and Shinan Liu

Biology 2026, 15(14), 1217; https://doi.org/10.3390/biology15141217 - 22 Jul 2026

Viewed by 388

Abstract

The flower color of Michelia odora, an important landscape tree plant, shows significant ornamental value, but its regulatory mechanisms remain to be further explored. The present work integrated metabolomic with transcriptomic analyses for elucidating the anthocyanin biosynthesis mechanisms in light pink and [...] Read more.

The flower color of Michelia odora, an important landscape tree plant, shows significant ornamental value, but its regulatory mechanisms remain to be further explored. The present work integrated metabolomic with transcriptomic analyses for elucidating the anthocyanin biosynthesis mechanisms in light pink and deep pink M. odora flowers. Our metabolomic analysis identified 13 differentially expressed anthocyanins, 11 of which, especially cyanidins, were significantly accumulated within deep pink petals versus light pink ones. As revealed by our transcriptomic analysis, 33 differential genes were related to flavonoid and anthocyanin biosynthesis. Further, transcription factor genes, encompassing three MoMYB alongside two MobHLH genes, were likely the hub genes that modulated anthocyanin biosynthesis. Quantitative real-time PCR validation indicated that certain genes, like MoPAL, MoC4H, Mo4CL, MoCHS, MoCHI, MoUGT75C1, MoMYB3, MobHLH1, and MobHLH3, displayed concurrent expression with anthocyanin accumulation within deep pink petals. Collectively, these results indicate the role of anthocyanin accumulation in deep pink color, and the effect of upregulated genes on increasing anthocyanin levels. Our results shed novel light on color change mechanisms underlying M. odora, and provide a theoretical basis for flower breeding. Full article

(This article belongs to the Section Plant Science)

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19 pages, 2499 KB

Open AccessArticle

Integrated GWAS and eQTL Colocalization Identified Candidate Genes for Growth Traits in Pigs

by Xiangzi Wu, Junjing Wu, Yiren Gu, Mu Qiao, Jiawei Zhou, Zipeng Li, Yue Feng, Tong Chen, Dake Chen, Shuqi Mei, Xianwen Peng and Zhong Xu

Biology 2026, 15(14), 1216; https://doi.org/10.3390/biology15141216 - 22 Jul 2026

Viewed by 483

Abstract

Growth traits, as core economic indicators in pig breeding, are closely associated with production costs, rearing duration, and final carcass quality and have thus consistently been a major focus of genetic improvement. This study aimed to identify candidate genes affecting Age to 120 [...] Read more.

Growth traits, as core economic indicators in pig breeding, are closely associated with production costs, rearing duration, and final carcass quality and have thus consistently been a major focus of genetic improvement. This study aimed to identify candidate genes affecting Age to 120 kg live weight (AGE120), Backfat thickness at 120 kg (BF120), and Loin muscle depth at 120 kg (LMD120) in pigs. Ear tissue samples were collected from 3364 healthy adult pigs (including 558 boars and 2805 sows) from three breeds: Large White, Landrace, and Duroc. Genotyping was performed using an 80 K functional site array, and quality-controlled SNP (Single-Nucleotide Polymorphism) loci were subjected to genotype imputation, resulting in 15,447,611 loci obtained. Genome-wide association studies (GWASs) for Age to 120 kg live weight, Back fat thickness at 120 kg, and Loin muscle depth at 120 kg were conducted using a mixed linear model in Genome-wide Complex Trait Analysis (GCTA). Genes located within 500 kb upstream and downstream of significant GWAS loci were extracted using the biomaRt package in R. Furthermore, colocalization analysis was performed using expression Quantitative Trait Locus (eQTL) data of 34 tissues from the PigGTEx database to identify genes that share the same causal variant as the GWAS signals. Through integrated GWAS and eQTL colocalization analysis, in addition to five previously reported genes associated with pig growth traits (TAF11, ZC3HAV1L, ANKS1A, USP20, and TBC1D1), a set of novel, high-confidence candidate genes was identified: ZNF215, UBE2Z, HOXB7, SARDH, ADAMTSL2, ATP6V0A4, RPL10A, PGM2, and RELL1. These findings enrich our understanding of the genetic architecture underlying growth traits in pigs at heavy body weights and provide an important foundation for subsequent functional validation and molecular breeding applications. Full article

(This article belongs to the Special Issue Advanced Genomics and Systems Biology in Pig Research)

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28 pages, 2629 KB

Open AccessArticle

Global Genomic Analysis of Bovine-Associated Klebsiella pneumoniae Reveals Genetic Diversity and Resistance–Virulence Profiles

by Meihui Tian, Yaqian Liang, Jia Lu, Weidi Shi, Yang Zhao, Weize Gan, Shuan Jia, Chencheng Xiao, Tianyi Zhao and Hui Zhang

Biology 2026, 15(14), 1215; https://doi.org/10.3390/biology15141215 - 22 Jul 2026

Viewed by 426

Abstract

Bovine-associated Klebsiella pneumoniae is an important bacterial species linking animal health, microbial ecology, and One Health-oriented antimicrobial resistance research. In this study, we performed a global genomic analysis of 1291 publicly available bovine-associated K. pneumoniae genomes collected from 18 countries between 2005 and [...] Read more.

Bovine-associated Klebsiella pneumoniae is an important bacterial species linking animal health, microbial ecology, and One Health-oriented antimicrobial resistance research. In this study, we performed a global genomic analysis of 1291 publicly available bovine-associated K. pneumoniae genomes collected from 18 countries between 2005 and 2024 using data retrieved from NCBI. MLST, core-genome phylogenetic analysis, pangenome analysis, CARD, VFDB, and PlasmidFinder were used to characterize sequence types, genomic diversity, antimicrobial resistance-associated genes, virulence-associated genes, and plasmid replicons. A total of 256 sequence types were identified, among which ST107 was the most common. Core-genome phylogenetic analysis revealed multiple genomic lineages, while pangenome analysis identified 46,325 gene clusters, including 1967 core genes and 40,595 cloud genes, indicating an open pangenome structure and substantial accessory gene diversity. Virulence-associated genes were unevenly distributed, with yagZ/ecpA being the most frequently detected determinant. In total, 138 antimicrobial resistance-associated genes or potential resistance determinants were detected across 16 antimicrobial categories, including clinically important β-lactamase- and carbapenemase-associated genes. IncF-family plasmid replicons, particularly IncFIB(K)_1_Kpn3, were frequently detected, suggesting widespread plasmid replicon-associated genomic backgrounds; however, physical co-localization between resistance genes and specific plasmid backbones could not be confirmed. Overall, this study reveals the genetic diversity, resistance-associated gene reservoir potential, heterogeneity of virulence-associated genes, and plasmid replicon backgrounds of bovine-associated K. pneumoniae. Importantly, the genome-predicted AMR potential identified in this study should not be interpreted as confirmed phenotypic resistance without further experimental validation. These findings provide genomic insights for risk surveillance, candidate control-target screening, and microbiota-oriented intervention research. Full article

(This article belongs to the Section Microbiology)

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16 pages, 1521 KB

Open AccessArticle

Integrated Whole-Genome Resequencing and Transcriptomic Analyses to Reveal Breed-Specific Selection Signatures of Cardiac-Related Genes in Wuzhishan Pigs

by Yuwei Ren, Feng Wang, Xinli Zheng, Yan Zhang, Ruiyi Lin, Xuyang Lu, Pengpeng Zhang, Cencen Li, Linlin Chen and Zhe Chao

Biology 2026, 15(14), 1214; https://doi.org/10.3390/biology15141214 - 22 Jul 2026

Viewed by 405

Abstract

The WZS minipig, native to the Hainan province of China, is characterized by excellent meat palatability. In addition, this breed represents a promising animal model for human disease research, especially for cardiac diseases. Whole-genome resequencing is a powerful approach for guiding breeding decisions. [...] Read more.

The WZS minipig, native to the Hainan province of China, is characterized by excellent meat palatability. In addition, this breed represents a promising animal model for human disease research, especially for cardiac diseases. Whole-genome resequencing is a powerful approach for guiding breeding decisions. By identifying mutations and conserved regions linked to environmental adaptability and physiological fitness, this method supports both the genetic improvement in pig breeds and their application as animal models for human disease research. However, the genomic locations of high and low nucleotide diversity regions harboring cardiac-related genes in the WZS genome remain unclear. In this study, cardiac-related genes were selected based on whole-genome resequencing data previously released by our research team, including 147 samples from five breeds (PRJCA054653), and detected RNA expression patterns of heart tissues across five growing periods. Between-breed analysis indicated that WZS pigs exhibited the highest nucleotide diversity among the five breeds and underwent a recently diverged lineage. A non-redundant 236-gene set was identified from the union of three gene subsets, of which the functional genes enriched in KEGG (67) and GO terms (192) were primarily implicated in cardiac muscle structure and energy metabolism, supplemented by additional genes selected based on high expression levels (52) and DEGs (44). Specifically, the DEGs of ACTC1, TNNC1, TNNT2, COX4I1, and MYH7 were highly expressed in the heart and enriched in the cardiac contraction pathway. The findings provide candidate genes for breeding and support the future use of WZS pigs as an improved animal model for human cardiac research. Full article

(This article belongs to the Section Genetics and Genomics)

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14 pages, 8096 KB

Open AccessArticle

by Enguo Wang, Xin Zhang and Yimin Ma

Biology 2026, 15(14), 1213; https://doi.org/10.3390/biology15141213 - 22 Jul 2026

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Abstract

Attention-Deficit/Hyperactivity Disorder (ADHD) is a neurodevelopmental disorder characterized by inattention, hyperactivity, and impulsivity. This study used high-temporal-resolution event-related potentials (ERPs) to investigate visuospatial attention allocation across early perceptual and late cognitive control stages in 62 children and adolescents with ADHD and 62 typically [...] Read more.

Attention-Deficit/Hyperactivity Disorder (ADHD) is a neurodevelopmental disorder characterized by inattention, hyperactivity, and impulsivity. This study used high-temporal-resolution event-related potentials (ERPs) to investigate visuospatial attention allocation across early perceptual and late cognitive control stages in 62 children and adolescents with ADHD and 62 typically developing (TD) controls (total N = 124), using a dual-task paradigm under a varying cognitive load. Behaviorally, the ADHD group showed significantly lower accuracy and marginally prolonged reaction times relative to TD controls. Electrophysiologically, the P2 component exhibited significant age effects, with shorter latency in the ADHD group than in the TD group under high load. N2 showed no significant group differences. The P3 component displayed significantly enhanced amplitude and prolonged latency in the ADHD group, especially under high load, indicating impaired late-stage cognitive control and working memory maintenance. These findings reveal that high-symptom (ADHD-screened) visuospatial attention deficits are more pronounced during late cognitive control stages; however, early perceptual processing also shows load-dependent alterations, with P3 abnormalities may represent candidate neural correlates of late-stage cognitive control deficits, although their clinical utility requires further evaluation. These results clarify the age-related patterns of attentional dysfunction in children and adolescents with ADHD and provide electrophysiological evidence for its neural mechanisms. Full article

(This article belongs to the Special Issue Molecular and Neurological Aspects of Sensory Processing Disorders)

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30 pages, 2113 KB

Open AccessReview

Probiotics in Alleviating Constipation: Mechanisms, Strain Screening, and Applications

by Hao Zhong, Huange Zhang, Muhammad Hussain, Tong Hu, Sixian Chan, Rongfa Guan, Jian Li and Ningxiang Yu

Biology 2026, 15(14), 1212; https://doi.org/10.3390/biology15141212 - 22 Jul 2026

Viewed by 1252

Abstract

Constipation is a prevalent gastrointestinal disorder with limited effective therapeutic options. Probiotics have emerged as promising microecological interventions, yet marked strain-specific efficacy and incomplete mechanistic understanding hinder clinical translation. This review systematically synthesizes evidence from human randomized controlled trials, animal studies, and mechanistic [...] Read more.

Constipation is a prevalent gastrointestinal disorder with limited effective therapeutic options. Probiotics have emerged as promising microecological interventions, yet marked strain-specific efficacy and incomplete mechanistic understanding hinder clinical translation. This review systematically synthesizes evidence from human randomized controlled trials, animal studies, and mechanistic investigations on probiotic interventions for constipation. We catalog major anti-constipation strains across Bifidobacterium, Lactobacillus, Bacillus, and other genera, and summarize key findings from published meta-analyses indicating that B. coagulans improves stool consistency by 52.8%, L. paracasei demonstrates 86.3% effectiveness for incomplete defecation severity and 87.6% for PAC-SYM, while L. reuteri achieves 99.9% effectiveness on PAC-QoL. Mechanistically, probiotics act through four synergistic pathways: gut microbiota modulation, metabolite-mediated actions centered on SCFAs and 5-HT—with strains harboring the abfA gene cluster exhibiting enhanced arabinan utilization for sustained metabolite production—gut–brain axis neuro regulation, and dynamic mucosal barrier restoration. Finally, we propose a systematic four-stage screening pipeline integrating genomic pre-screening, probiotic property evaluation, in vitro functional prediction, and in vivo multi-tiered validation. This review provides a comprehensive framework for evidence-based strain selection and personalized probiotic therapy in constipation management. Full article

(This article belongs to the Section Microbiology)

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25 pages, 13378 KB

Open AccessArticle

Multi-Model Approaches Reveal Cascading Regulation and Ecological Responses of Zooplankton to Seasonal and Water Quality Variations in Urbanized Rivers

by Jiawei Wu, Maojin Huang, Xue Yang, Baoshan Zhang, Siyao Liu, Lei Jian and Fei Xu

Biology 2026, 15(14), 1211; https://doi.org/10.3390/biology15141211 - 22 Jul 2026

Viewed by 333

Abstract

Urbanization imposes multiple environmental stressors on urban rivers. Zooplankton are sensitive to environmental disturbances, making them useful tools for assessing ecological health and revealing river degradation processes. We surveyed the urban reaches of the middle and lower Jialing River and its tributary (Xichong [...] Read more.

Urbanization imposes multiple environmental stressors on urban rivers. Zooplankton are sensitive to environmental disturbances, making them useful tools for assessing ecological health and revealing river degradation processes. We surveyed the urban reaches of the middle and lower Jialing River and its tributary (Xichong River) during autumn 2022 and spring 2023. Water ecological status was assessed using the water quality index and zooplankton-based Index of Biotic Integrity. Community assembly mechanisms and their driving pathways were analyzed by combining the neutral community model (NCM, MST), random forest (RF), and partial least squares path modeling (PLS-PM). Key results: (1) The zooplankton community in the Jialing River Basin exhibited significant spatiotemporal heterogeneity. (2) The overall water ecological status was better in the mainstream than in the tributary, and better in autumn than in spring. (3) Stochastic processes dominated the Jialing River mainstream in autumn (MST = 0.5388), whereas deterministic processes dominated in all other habitats. (4) Seasonal variation was the key driver of community assembly (R² = 0.253, p < 0.001), and COD_Mn was the primary water quality factor (IncMSE = 25.48%). In summary, multiple models combined quantified the dominant pathways of ecological response, providing theoretical support for the health management of urbanized rivers. Full article

(This article belongs to the Special Issue Environmental Factors and Freshwater Organism Responses)

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37 pages, 96515 KB

Open AccessReview

Cranial Appendages in Ruminants: Diversity, Evolution, Development, and Molecular Basis of Horns, Pronghorns, Antlers, and Ossicones

by Rafal P. Piprek, Izabela Rams-Pociecha and Paulina C. Mizia

Biology 2026, 15(14), 1210; https://doi.org/10.3390/biology15141210 - 22 Jul 2026

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Abstract

Ruminants are unique among living mammals in possessing paired bony cranial appendages in the form of horns, pronghorns, antlers, or ossicones. This review summarizes current knowledge on the structure, development, function, and evolution of these appendages and integrates recent findings from genomics, transcriptomics, [...] Read more.

Ruminants are unique among living mammals in possessing paired bony cranial appendages in the form of horns, pronghorns, antlers, or ossicones. This review summarizes current knowledge on the structure, development, function, and evolution of these appendages and integrates recent findings from genomics, transcriptomics, and single-cell analyses. Two competing hypotheses have been proposed to explain their origin. According to the independent-origin hypothesis, horns, pronghorns, antlers, and ossicones evolved separately in different pecoran lineages, possibly through repeated recruitment of similar developmental capacities of the frontal region of the skull. According to the common-origin hypothesis, these appendages derive from a single ancestral osseous cranial structure that was subsequently modified in different lineages. Comparative anatomy and developmental data reveal major differences among the four types of appendages, including dermally ossifying horn cores in bovids, annually regenerated antlers arising from frontal bone pedicles in cervids, deciduous keratin sheaths in pronghorns, and skin-covered ossicones in giraffids. The fossil record does not currently resolve these hypotheses, because the main appendage types are first documented within a relatively short early Miocene interval and transitional forms remain unknown. In contrast, molecular and cellular studies identify shared developmental pathways, cranial neural crest-derived progenitors, and conserved regulatory genes, including RXFP2, ALX1, SOX9, and components of Wnt signaling, which are consistent with a shared developmental module. We conclude that the homology of pecoran cranial appendages remains unresolved and that further paleontological, developmental, and comparative molecular studies are required to determine whether these structures share a common evolutionary origin or instead represent convergent recruitment of similar developmental programs. Full article

(This article belongs to the Special Issue 15 Years of Biology: The View Ahead)

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14 pages, 2658 KB

Open AccessArticle

Unravelling the Genetic Architecture of Flowering in Common Vetch (Vicia sativa L.) Through Multi-Season QTL Mapping

by Eva M. Córdoba, Clara I. González-Verdejo, Sergio G. Atienza, Salvador Nadal and Carmen M. Ávila

Biology 2026, 15(14), 1209; https://doi.org/10.3390/biology15141209 - 22 Jul 2026

Viewed by 348

Abstract

Flowering time is a key adaptive trait in common vetch (Vicia sativa L.), influencing crop adaptation, yield potential, and forage quality. Despite its importance, the genetic basis of flowering in this species remains poorly understood. In this study, we analyzed the genetic [...] Read more.

Flowering time is a key adaptive trait in common vetch (Vicia sativa L.), influencing crop adaptation, yield potential, and forage quality. Despite its importance, the genetic basis of flowering in this species remains poorly understood. In this study, we analyzed the genetic architecture of flowering-related traits in an F_2:3 population under field conditions over two consecutive growing seasons. Four traits were evaluated using thermal time expressed as growing degree days (GDDs), and quantitative trait loci (QTL) analysis was conducted using a high-density genetic map derived from DArTSeq markers. The linkage map comprised 419 unique positions across six linkage groups, spanning 1728.5 cM. Ten QTLs associated with flowering traits were identified on chromosomes 2, 3, 4, and 6. Five QTLs were consistent across seasons, defining three major genomic regions controlling flowering. Additional season-specific QTLs suggested environmental effects on flowering responses. In silico analysis identified three candidate genes (VsFTc, VsFTa, and VsLFY) within flanking markers for stable QTL. This is the first report of QTLs for flowering in common vetch and provides targets for marker-assisted breeding to improve adaptation and resilience. Full article

(This article belongs to the Special Issue Advances in Plant Genomics and Genome Editing)

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13 pages, 246 KB

Open AccessReview

Circulating Tumor DNA in Multiple Myeloma: Current Insights and Future Perspectives

by Aleksandra Sretenovic, Marko Mitrovic, Nikola Vukosavljevic, Natalija Kecman, Nada Kraguljac Kurtović, Marija Denčić Fekete and Jelena Bila

Biology 2026, 15(14), 1208; https://doi.org/10.3390/biology15141208 - 22 Jul 2026

Viewed by 425

Abstract

Circulating tumor DNA (ctDNA) has emerged as a promising minimally invasive biomarker in multiple myeloma (MM), providing dynamic insight into tumor burden, clonal evolution and molecular heterogeneity. Unlike conventional bone marrow-based diagnostics, ctDNA analysis offers a systemic approach to disease assessment and may [...] Read more.

Circulating tumor DNA (ctDNA) has emerged as a promising minimally invasive biomarker in multiple myeloma (MM), providing dynamic insight into tumor burden, clonal evolution and molecular heterogeneity. Unlike conventional bone marrow-based diagnostics, ctDNA analysis offers a systemic approach to disease assessment and may better reflect spatially heterogeneous and extramedullary disease. Recent advances in highly sensitive molecular techniques, including digital droplet polymerase chain reaction and next-generation sequencing, have improved the feasibility of ctDNA detection and longitudinal disease monitoring in MM. Increasing evidence demonstrates substantial concordance between ctDNA and bone marrow genomic profiles, while also highlighting the ability of ctDNA to identify resistant subclones, molecular relapse and genomic evolution during therapy. ctDNA has shown potential clinical utility in molecular profiling, therapeutic monitoring and minimal residual disease assessment. ctDNA may become increasingly relevant in the era of novel immunotherapies, including chimeric antigen receptor T-cell therapy and bispecific antibodies. Despite these promising applications, several biological and technical limitations still restrict routine clinical implementation, including low ctDNA concentration in patients with minimal disease burden and lack of methodological standardization. Overall, ctDNA represents a rapidly evolving tool with significant potential to improve personalized disease monitoring and therapeutic strategies in MM. Full article

16 pages, 12984 KB

Open AccessArticle

Maternal Polystyrene Nanoplastic Exposure Impairs Cardiac Development in Mouse Offspring and Identifies Lactation as a Sensitive Window in Males

by Xiaorui Zhang, Yingguang Li, Xiaotao Zhang, Wenli Shi, Hui Deng, Lingxian Yi, Shuaizhen Zhou and Daojin Yu

Biology 2026, 15(14), 1207; https://doi.org/10.3390/biology15141207 - 22 Jul 2026

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Abstract

Maternal exposure to nanoplastics is a growing concern, but its effects on offspring cardiac development and the relative importance of prenatal and lactational exposure remain unclear. Pregnant C57BL/6J mice were orally exposed to 50 nm polystyrene nanoplastics at 3, 15, or 75 μg/g [...] Read more.

Maternal exposure to nanoplastics is a growing concern, but its effects on offspring cardiac development and the relative importance of prenatal and lactational exposure remain unclear. Pregnant C57BL/6J mice were orally exposed to 50 nm polystyrene nanoplastics at 3, 15, or 75 μg/g body weight from gestational day 1 to postnatal day 21. A cross-fostering design was used to distinguish gestational exposure from lactational exposure. Maternal polystyrene nanoplastic exposure caused dose-dependent cardiac dysfunction in offspring, including reduced ejection fraction and fractional shortening, increased myocardial injury markers, cardiomyocyte hypertrophy, and fibrosis. Cross-fostering showed that lactationally exposed offspring exhibited more severe cardiac abnormalities than offspring exposed only during gestation, indicating that the nursing period may represent a more vulnerable window. In male offspring, polystyrene nanoplastic exposure was also associated with gut microbiota dysbiosis and cardiac transcriptomic changes. Enrichment analysis identified downregulation of genes related to AMP-activated protein kinase signalling, and integrated microbiome–transcriptome analysis suggested associations between altered gut taxa and cardiac differentially expressed genes. These findings indicate that maternal polystyrene nanoplastic exposure induces offspring cardiac developmental toxicity, with stronger effects during lactation, and suggest the involvement of gut microbial and cardiac molecular remodelling. Full article

(This article belongs to the Special Issue Maternal Adaptation in Physiological and Pathological Pregnancy (2nd Edition))

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11 pages, 11640 KB

Open AccessArticle

Mitochondrial Distribution Patterns and Remodeling During In Vitro Maturation of Alpaca (Vicugna pacos) Oocytes

by Paula Quijano, Alejandra Ugarelli, José Sánchez, Omar Ramirez, Alexei Santiani and Shirley Evangelista-Vargas

Biology 2026, 15(14), 1206; https://doi.org/10.3390/biology15141206 - 21 Jul 2026

Viewed by 475

Abstract

Mitochondrial distribution and activity are closely associated with cytoplasmic maturation and developmental competence in mammalian oocytes; however, limited information is available regarding these processes in Vicugna pacos. This study aimed to characterize mitochondrial activity, aggregation, and distribution patterns in immature and in [...] Read more.

Mitochondrial distribution and activity are closely associated with cytoplasmic maturation and developmental competence in mammalian oocytes; however, limited information is available regarding these processes in Vicugna pacos. This study aimed to characterize mitochondrial activity, aggregation, and distribution patterns in immature and in vitro mature Vicugna pacos oocytes. Mitochondrial fluorescence intensity ranged from 21.2 to 126 units, with mean values decreasing from grade I to IV. No significant differences were observed between immature (66.8 ± 22.7) and mature (59.2 ± 23.5) oocytes. Three distinct distribution patterns were identified: homogeneous non-peripheral (HoNP), heterogeneous peripheral (HeP), and heterogeneous non-peripheral (HeNP), with HeNP oocytes exhibiting the highest activity. During maturation, fluorescence intensity increased in HeNP and HeP but decreased in HoNP, suggesting distinct mitochondrial responses. Aggregation shifted from smooth in immature oocytes to granular in mature ones, and these two traits—HeNP distribution and granular aggregation—were consistently associated with higher mitochondrial activity. Overall, 78% of oocytes showed aggregation. These results demonstrate that mitochondrial remodeling accompanies oocyte maturation and that aggregation and distribution patterns may serve as biomarkers of oocyte quality. Further studies linking these features with fertilization and embryo development are needed to validate their predictive role in assisted reproduction of alpacas. Full article

(This article belongs to the Special Issue Reproduction Under the Microscope: From Oocyte Architecture to Reproductive Function)

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14 pages, 993 KB

Open AccessArticle

Physicochemical and FTIR-ATR Spectroscopic Characterization of Lipid Deterioration in Raw Horse Mesenteric Fat Under Stress Storage Conditions

by Moldir Nurseitova, Meruert Syzdyk, Xenia Dronova, Elizaveta Chuvashova, Sanimay Koshieva, Yerkin Massanov, Kuanish Syman, Gaukhar Konuspayeva, Bernard Faye and Nurlan Akhmetsadykov

Biology 2026, 15(14), 1205; https://doi.org/10.3390/biology15141205 - 21 Jul 2026

Viewed by 373

Abstract

Horse mesenteric fat is a culturally significant and nutritionally valuable food product in Central Asia, yet the kinetics of its oxidative and hydrolytic deterioration under sub-optimal storage conditions remain poorly characterized. Raw mesenteric adipose tissue from ten free-grazing horses in Northern Kazakhstan was [...] Read more.

Horse mesenteric fat is a culturally significant and nutritionally valuable food product in Central Asia, yet the kinetics of its oxidative and hydrolytic deterioration under sub-optimal storage conditions remain poorly characterized. Raw mesenteric adipose tissue from ten free-grazing horses in Northern Kazakhstan was subjected to accelerated stress storage at 30 °C and 70% relative humidity for six days, with physicochemical and spectroscopic evaluation on days 0, 3, and 6. Parameters assessed included acid value, peroxide value, refractive index, density, melting point, sensory attributes, and Fourier-transform infrared attenuated total reflectance spectroscopy. The acid value increased markedly from 1.17 ± 0.46 to 32.60 ± 26.18 mg KOH/g by day 6, substantially exceeding the internationally accepted threshold of 2.0 mg KOH/g, while peroxide value rose progressively and density declined. Melting point decreased significantly between days 0 and 3, a physicochemical change that may be associated with hydrolytic and oxidative modification of the lipid matrix, as corroborated by infrared spectral analysis. These results demonstrate that raw horse mesenteric fat is highly susceptible to rancidity, reaching unacceptable quality thresholds within six days, underscoring the urgent need for cold-chain management and evidence-based handling guidelines for this product across the region. Full article

(This article belongs to the Section Biochemistry and Molecular Biology)

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20 pages, 5834 KB

Open AccessArticle

Evaluating Somatic Mutational Contamination in Large-Scale Germline Genomic Studies

by Xiangwen Ji, Xueke Bai, Guangda He, Kai Yan, Edwin Wang, Yi-Da Tang, Liang Chen and Qinghua Cui

Biology 2026, 15(14), 1204; https://doi.org/10.3390/biology15141204 - 21 Jul 2026

Viewed by 588

Abstract

Large-scale genomic initiatives like the UK Biobank have revolutionized our understanding of human disease. These studies typically assume that blood-derived DNA faithfully reflects an individual’s germline genome. However, this assumption is challenged by somatic mutations arising from processes like clonal hematopoiesis. Although standard [...] Read more.

Large-scale genomic initiatives like the UK Biobank have revolutionized our understanding of human disease. These studies typically assume that blood-derived DNA faithfully reflects an individual’s germline genome. However, this assumption is challenged by somatic mutations arising from processes like clonal hematopoiesis. Although standard bioinformatics pipelines employ variant allele frequency (VAF)-based filtering to mitigate such contamination, the efficacy of these approaches requires systematic evaluation. By systematically analyzing germline genome data from large cohorts through applications of mutational signatures, we revealed critical limitations in current filtering methodologies. We found that the mutational spectrum of rare “germline” variants is highly similar to that of somatic mutations. Furthermore, we uncovered that these variants show significant associations with phenotypes such as age, sex, and smoking status, established drivers of somatic mutagenesis. Notably, our multivariable regression models estimated that these somatic artifacts contribute to a substantial excess burden, such as 4.73 mutations per megabase (mut/Mb) in males compared to females, a magnitude exceeding the mutation burden of many cancers. Although the precise absolute size of this contamination may vary depending on specific pathologies and individual environmental exposures, this persistent somatic contamination introduces substantial confounder effects, posing a risk of spurious associations and reverse causality in genetic studies. Our work underscores the urgent reconsideration of two fundamental aspects of genomic research: (1) refinement of variant filtering strategies to better distinguish true germline variants from somatic contaminants, and (2) incorporation of somatic mutagenesis factors as essential covariates in study design. Our findings provide basic guidance for improving the accuracy and interpretability of large-scale genomic studies. Full article

(This article belongs to the Section Genetics and Genomics)

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15 pages, 767 KB

Open AccessReview

Specialized Pro-Resolving Mediators at the Ocular Surface: Biosynthesis, Mechanisms, and Therapeutic Potential

by Siddharth Gandhi, Arveen Shokravi, Sydney Buhrow and Michael Balas

Biology 2026, 15(14), 1203; https://doi.org/10.3390/biology15141203 - 21 Jul 2026

Viewed by 427

Abstract

Specialized pro-resolving mediators (SPMs) are endogenous lipid mediators that actively orchestrate the resolution of inflammation rather than relying solely on broad suppression of inflammatory signaling. At the ocular surface, lipoxins, resolvins, protectins, maresins, and related pro-resolving mediators regulate epithelial repair, leukocyte responses, angiogenesis, [...] Read more.

Specialized pro-resolving mediators (SPMs) are endogenous lipid mediators that actively orchestrate the resolution of inflammation rather than relying solely on broad suppression of inflammatory signaling. At the ocular surface, lipoxins, resolvins, protectins, maresins, and related pro-resolving mediators regulate epithelial repair, leukocyte responses, angiogenesis, conjunctival goblet-cell secretion, tear-film homeostasis, and corneal nerve regeneration. This review synthesizes evidence for local SPM biosynthesis and receptor signaling in the cornea and conjunctiva, together with tear lipid mediator profiling, with emphasis on anterior-segment and ocular-surface disease models. Particular attention is given to the endogenous lipoxin A4 circuit, resolvin-mediated control of corneal inflammation and viral keratitis, docosanoid regulation of corneal nerve regeneration, SPM modulation of conjunctival goblet-cell mucin secretion, tear lipid mediator signatures, and the translational development of resolvin E1 (RvE1)-based analogs for dry eye disease. Current evidence positions SPMs as mechanistically distinct therapeutic candidates for ocular-surface disease; however, clinical translation will require optimized delivery, biomarker-guided patient selection, and rigorous validation in disease-state cohorts. Full article

(This article belongs to the Special Issue Current Status and Future Perspectives on Lipid Biology and Beyond)

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25 pages, 33472 KB

Open AccessArticle

Recovery of Hindlimb Motor Function Is Accompanied by Lumbar Neural Remodeling After Complete Spinal Cord Transection in Neonatal Mice

by Wanxing Peng, Ran Li, Lulu Zhang, Wenhui Long, Yingying Yang, Meizhi Wang, Li Song and Jing Li

Biology 2026, 15(14), 1202; https://doi.org/10.3390/biology15141202 - 21 Jul 2026

Viewed by 349

Abstract

Spinal cord injury often causes persistent neurological dysfunction, whereas the developing central nervous system retains greater plasticity. This study investigated whether spontaneous hindlimb motor recovery occurs after complete spinal cord transection in neonatal mice and whether such recovery is accompanied by structural remodeling [...] Read more.

Spinal cord injury often causes persistent neurological dysfunction, whereas the developing central nervous system retains greater plasticity. This study investigated whether spontaneous hindlimb motor recovery occurs after complete spinal cord transection in neonatal mice and whether such recovery is accompanied by structural remodeling of the lumbar spinal cord distal to the lesion. C57BL/6J mice underwent complete T9 spinal cord transection at postnatal day 7, and recovery was assessed by Basso Mouse Scale scoring, CatWalk gait analysis, foot-fault testing, immunofluorescence, and electromyography. Compared with adult mice subjected to the same injury, neonatal mice showed progressive partial improvement in hindlimb motor function, including locomotor performance, gait coordination, and foot placement accuracy. Meanwhile, this recovery was accompanied by preservation of lumbar motor neurons and structural changes in the local neural network. Syn⁺ coverage around lumbar motor neurons was relatively preserved in neonatal injured mice compared with adult injured mice; excitatory synaptic input remained increased, and inhibitory input showed a dynamic pattern of early increase followed by later reduction. In addition, myelin-related alterations were less severe, and motor neuron innervation of peripheral muscles (EMG) were relatively preserved in neonatal mice. The results indicate that the restoration of hindlimb motor function after complete spinal cord transection in neonatal mice is associated with structural and functional remodeling of lumbar spinal motor circuits. This includes enhanced synaptic signals around motor neurons and reorganization of the neuromuscular junction. Full article

(This article belongs to the Special Issue Animal Models of Neurodegenerative Diseases)

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20 pages, 8050 KB

Open AccessArticle

A Dendrimer-Based Multiple Antigenic Peptide (MAP) Approach for Dengue Vaccine Development: In Silico and In Vivo Insights on Safety and Effectiveness

by Amtul Wadood Wajeeha, Najam us Sahar Sadaf Zaidi, Deeba Amraiz, Naseeha Bibi, Mamuna Mukhtar, Sobia Asghar and Muhammad Tahir

Biology 2026, 15(14), 1201; https://doi.org/10.3390/biology15141201 - 20 Jul 2026

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Abstract

Dengue fever, a rapidly spreading mosquito-borne viral disease, poses a major global health issue, particularly in tropical and subtropical regions. The absence of a universally effective vaccine against all four dengue virus serotypes necessitates continued exploration of novel vaccine strategies. This study evaluated [...] Read more.

Dengue fever, a rapidly spreading mosquito-borne viral disease, poses a major global health issue, particularly in tropical and subtropical regions. The absence of a universally effective vaccine against all four dengue virus serotypes necessitates continued exploration of novel vaccine strategies. This study evaluated a PrM-derived multiple antigenic peptide (MAP) vaccine candidate in BALB/c mice. Molecular docking analyses predicted favourable interactions of the selected PrM-derived B-cell epitope with both human (human BCR Fab region PDB ID: 5IFH) and mouse (mouse BCR PDB ID: 8EMA) B-cell receptors, supporting its antigenic potential. ChemSketch was used to develop the PrM–MAP vaccine construct, which was then commercially synthesized. Mice received single, double, and triple booster doses of the vaccine, while control groups received either PBS or adjuvant alone. Humoral immune responses were measured by ELISA, and safety was evaluated through in vitro cytotoxicity assays on HEK293 cells and the in vivo histopathological examination of major organs. Mice immunized with a single booster dose produced significant levels of PrM-specific antibodies compared to subsequent booster doses, suggesting variability in the humoral response elicited. Optimal coating concentrations in ELISA demonstrated the importance of antigen concentrations in the sensitivity of the assay. The safety evaluation indicated high cell viability, up to 150 µg/mL of PrM–MAP, in HEK293 cells, and an absence of significant histopathological damage in treated animals. The PrM–MAP vaccine construct elicited a detectable humoral immune response while demonstrating a high safety profile in vitro and in vivo. These findings indicate the potential of MAP-based vaccine platforms as promising candidates for further development against the dengue virus. Full article

(This article belongs to the Section Immunology)

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21 pages, 4372 KB

Open AccessArticle

Constraint and Allometric Diversification in a Simplified Neck: Shape Evolution of the Atlas in Hyloidea (Anura)

by Henrique Folly, Jéssica Fratani, Virginia Abdala and María Laura Ponssa

Biology 2026, 15(14), 1200; https://doi.org/10.3390/biology15141200 - 20 Jul 2026

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Abstract

The anuran atlas represents one of the most structurally simplified cervical systems among tetrapods, consisting of a single vertebra that must simultaneously support the head, permit mobility, and withstand mechanical loads generated during locomotion and feeding. This unique configuration provides a compelling framework [...] Read more.

The anuran atlas represents one of the most structurally simplified cervical systems among tetrapods, consisting of a single vertebra that must simultaneously support the head, permit mobility, and withstand mechanical loads generated during locomotion and feeding. This unique configuration provides a compelling framework for investigating how structural constraint, allometry, and ecology interact to shape morphological evolution. Here, we examine atlas shape diversification across Hyloidea using geometric morphometrics and phylogenetic comparative methods on 421 specimens representing 133 species. We quantified shape variations in dorsal and ventral views and tested the relative contributions of body size, phylogenetic history, microhabitat, and locomotor mode to atlas morphology. Atlas shape exhibited significant phylogenetic signals and was predominantly structured by allometric scaling, with the atlas size (centroid size) explaining a significant proportion of variation in both anatomical views, particularly ventrally. Morphological differences were concentrated in atlas width and relative proportions, indicating that diversification occurs primarily through size-dependent remodeling rather than through major structural reorganization. In contrast, ecological variables explained little independent variation in atlas shape, although microhabitat modulated allometric trajectories in dorsal and ventral views. Together, these results indicate that atlas evolution in hyloid frogs is governed chiefly by size-related biomechanical demands operating within a phylogenetically structured and developmentally constrained system. More broadly, our findings suggest that extreme cervical simplification channels morphological diversification toward allometric modification, limiting the extent to which ecological specialization can drive anatomical divergence. Full article

(This article belongs to the Special Issue From Form to Function: Evolutionary Perspectives on Tetrapod Morphology)

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21 pages, 2804 KB

Open AccessArticle

First Complete Mitochondrial Genomes of the Invasive Mussel Perna viridis from Brazil and the Southwestern Atlantic

by André Oliveira Souza Lima, Rafael Schroeder, Gabriela S. Delabary, Gilberto C. Manzoni and Mayara C. Beltrão

Biology 2026, 15(14), 1199; https://doi.org/10.3390/biology15141199 - 20 Jul 2026

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Abstract

The Asian green mussel Perna viridis is expanding across coastal systems of the Americas, creating demand for curated molecular references to support biosecurity, aquaculture monitoring, and comparative invasion studies. Here, we report the first complete mitochondrial genomes of invasive P. viridis from Brazil [...] Read more.

The Asian green mussel Perna viridis is expanding across coastal systems of the Americas, creating demand for curated molecular references to support biosecurity, aquaculture monitoring, and comparative invasion studies. Here, we report the first complete mitochondrial genomes of invasive P. viridis from Brazil and the southwestern Atlantic, generated from two specimens collected in Santa Catarina, currently the southernmost documented sector of the Brazilian range. Long-range PCR, Oxford Nanopore sequencing, read-supported assembly, manual annotation, comparative mitogenomics, nucleotide-diversity analysis, protein-level divergence, and phylogenomic inference were used to generate and evaluate complete mitochondrial references. The two circular assemblies were 16,015 bp and 16,011 bp and contained 38 annotated features, including 13 protein-coding genes, 23 tRNAs, and two rRNAs, all on the H strand, with an identical A+T content of 67.5%. Pairwise comparisons among the four complete P. viridis mitogenomes analyzed showed high overall similarity but retained 20–125 SNPs/mismatches and one to 12 indel events. Gene order was conserved within P. viridis but differed from P. canaliculus and P. perna, and phylogenomics placed the Brazilian assemblies within the P. viridis clade. These curated mitogenomes provide initial complete mitochondrial references for future marker testing and comparative studies of P. viridis in the southwestern Atlantic, but the two-specimen dataset should not be used to infer population origin, invasion routes, or connectivity. Full article

(This article belongs to the Special Issue Advances in Aquatic Ecological Disasters and Toxicology)

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20 pages, 3619 KB

Open AccessArticle

Mixed Plantations Mitigate Negative Effects of Natural Forest Conversion on Soil Meso- and Micro-Faunal Communities in Zhangguangcailing Mountains, Northeast China

by Shuangjiao Ma, Yong Zhang, Kun Li, Qingcheng Wang, Donghai Cui, Zengwang Yao, Chuanrong Li and Yehan Tian

Biology 2026, 15(14), 1198; https://doi.org/10.3390/biology15141198 - 20 Jul 2026

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Abstract

Soil meso- and micro-fauna are key components of forest soil ecosystems, but the effects of converting natural forests to monoculture or mixed plantations on their communities remain unclear. This study compared soil meso- and micro-fauna communities in monoculture (broad-leaved and coniferous) and mixed [...] Read more.

Soil meso- and micro-fauna are key components of forest soil ecosystems, but the effects of converting natural forests to monoculture or mixed plantations on their communities remain unclear. This study compared soil meso- and micro-fauna communities in monoculture (broad-leaved and coniferous) and mixed plantations converted from secondary forests in Northeast China. Results showed that monocultures significantly altered faunal community composition and reduced diversity, whereas mixed plantations maintained similar abundance and diversity to secondary forests. For instance, broadleaf monocultures exhibited a 15–23% lower Shannon–Wiener diversity index, while coniferous monocultures displayed a 28–35% reduction in soil faunal abundance. Notably, different taxonomic groups responded inconsistently to stand type conversion: Oribatida (58.8–72.5% of total individuals) varied significantly among stands (p < 0.001), whereas Collembola (18.8–31.4%) was more affected by season. The community composition was significantly correlated with understory plant diversity/coverage and soil C/N ratio, while α-diversity was mainly driven by total nitrogen. Our findings reveal that mixed plantations, instead of monocultures, are more effective for soil biodiversity conservation, which offers sustainable strategies for forest management. Full article

(This article belongs to the Special Issue Adaptation of Living Species to Environmental Stress (2nd Edition))

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26 pages, 2324 KB

Open AccessReview

The Biological Clock–Mitochondria Axis in the Liver: From Molecular Mechanisms to Metabolic Disease

by Virginia Manuti, Emanuele Murgo, Anna Alessia Saponaro, Umberto Sfregola, Moris Sangineto, Rosanna Villani, Gaetano Serviddio, Gianluigi Mazzoccoli and Tommaso Colangelo

Biology 2026, 15(14), 1197; https://doi.org/10.3390/biology15141197 - 20 Jul 2026

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Abstract

The liver ranks among the peripheral organs exhibiting the most robust circadian rhythmicity, with glucose homeostasis, lipid metabolism, and bile acid turnover governed by tightly phased diurnal oscillations. Mitochondria execute these programs, their output coordinated with the hepatocyte circadian state. The mitochondrial network [...] Read more.

The liver ranks among the peripheral organs exhibiting the most robust circadian rhythmicity, with glucose homeostasis, lipid metabolism, and bile acid turnover governed by tightly phased diurnal oscillations. Mitochondria execute these programs, their output coordinated with the hepatocyte circadian state. The mitochondrial network undergoes dynamic remodeling across the 24 h cycle, encompassing oscillatory changes in bioenergetics, fusion–fission balance, and quality control. This interplay is bidirectional: core clock components drive rhythmic remodeling via cyclin-dependent kinase 1/mitogen-activated protein kinase (CDK1/MAPK)-dependent phosphorylation of dynamin-related protein 1 (DRP1) and the NAD⁺–SIRT1/SIRT3 axis, while retrograde signals modulate clock amplitude and entrainment. Circadian disruption is associated with mitochondrial dysfunction implicated in MASLD onset and progression to MASH and HCC, though this evidence remains largely correlative and derives predominantly from rodent models. This review integrates clock–mitochondria coupling with metabolic liver disease. Restoring this coupling has been proposed as a candidate chronotherapeutic strategy, supported by preliminary rhythmicity data in primary human hepatocytes and a hepatocellular carcinoma cell line, though causal validation in healthy human liver is lacking. Time-restricted feeding, NAD⁺ precursors, PPAR agonists, and ACC inhibitors converge on clock-regulated pathways and may benefit from circadian-informed timing, though this remains unverified. Full article

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18 pages, 1366 KB

Open AccessArticle

Seed Biochemical Composition and Yield of Four Fenugreek Genotypes

by Zoheir Benzekri, Ahmed Adda, Kamel Zemour, Zahreddine Djazouli, Romain Valentin, Eric Lacroux and Othmane Merah

Biology 2026, 15(14), 1196; https://doi.org/10.3390/biology15141196 - 20 Jul 2026

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Abstract

Fenugreek is a legume that has been used since ancient times to treat certain conditions. Numerous studies have examined the seed’s composition in terms of trigonelline, diosgenin and galactomannans, and their implications for nutrition and medicine. The oil content, fatty acid profile and [...] Read more.

Fenugreek is a legume that has been used since ancient times to treat certain conditions. Numerous studies have examined the seed’s composition in terms of trigonelline, diosgenin and galactomannans, and their implications for nutrition and medicine. The oil content, fatty acid profile and antioxidant activity of fenugreek seeds have been less extensively studied, particularly in certain areas of the Mediterranean basin. The aim of this study was to examine the oil content and composition, as well as the antioxidant activity of the seeds, oil and meal from four genotypes originating from Algeria, France, Lebanon and Syria. The trials were conducted over two consecutive years with contrasting climatic conditions, in the open field, at the University of Tiaret (western Algeria). Climatic conditions significantly affected all studied traits. In 2023, a dry and hot year, the plants produced low grain yield and low oil content compared to 2024, a temperate year, regardless of the genotype. The fatty acid composition was dominated by polyunsaturated fatty acids (PUFAs, between 65.5 and 68.8%). The phenolic and flavonoid contents were higher in 2023 than in 2024, resulting in greater antioxidant activity under hot and dry conditions of 2023. Genotypic differences were also statistically significant. A more varied responses in grain yield were observed for the French genotype. The highest oil content was recorded for the Algerian and Syrian genotypes. The antioxidant activities of the seed and the oil were similar and significantly higher than that of the oilcake. This activity correlated with the levels of phenols and flavonoids. The results observed in this study provide a better understanding of genotypic diversity and the impact of climatic conditions on yield and seeds quality. They also pave the way for the use of these genotypes in larger-scale breeding programs to improve specific traits. Full article

(This article belongs to the Section Plant Science)

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3 pages, 153 KB

Open AccessEditorial

Editorial: Molecular Mechanisms of Plant Stress Adaptation

by Wenqiang Li

Biology 2026, 15(14), 1195; https://doi.org/10.3390/biology15141195 - 20 Jul 2026

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Abstract

Global climate change has amplified both the frequency and severity of abiotic stresses including drought, salinity and extreme temperatures, while concurrently modifying pathogen population dynamics, thereby imposing unparalleled threats to agricultural crop productivity and the health of forest ecosystems [...] Full article

(This article belongs to the Special Issue Molecular Mechanisms of Plant Stress Adaptation)

26 pages, 13978 KB

Open AccessArticle

Transcriptome-and Metabolome-Based Mechanisms of High-Temperature Adaptation in Triploid Rainbow Trout (Oncorhynchus mykiss)

by Shuchen Huang, Changzhong Li, Ying Yang, Tianxiu Liang, Xin Xie, Jingjing Zhang, Zhaonan Li, Jin Li and Yanxia Chen

Biology 2026, 15(14), 1194; https://doi.org/10.3390/biology15141194 - 20 Jul 2026

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Abstract

High-temperature stress poses a critical challenge to cold-water aquaculture; however, the size-associated molecular mechanisms underlying thermal adaptation in triploid rainbow trout (Oncorhynchus mykiss) remain poorly understood. Here, we integrated transcriptomic and metabolomic profiling of liver tissues, which plays central role in [...] Read more.

High-temperature stress poses a critical challenge to cold-water aquaculture; however, the size-associated molecular mechanisms underlying thermal adaptation in triploid rainbow trout (Oncorhynchus mykiss) remain poorly understood. Here, we integrated transcriptomic and metabolomic profiling of liver tissues, which plays central role in energy metabolism and stress integration, from three body-weight classes—small (0.8 kg ± 0.18 kg), medium (1.5 kg ± 0.22 kg), and large (2.5 kg ± 0.31 kg)—sampled under peak summer heat stress (20.5 °C). Transcriptomic analysis identified 974, 570, and 862 group-specific differentially expressed genes, respectively, revealing a non-linear, size-associated transcriptional pattern. Genes assigned to the ribosome pathway were significantly enriched in comparisons involving MLA and SLA relative to LLA, but not between SLA and MLA, whereas carbon metabolism and amino acid biosynthesis were enriched exclusively in smaller fish, indicating a higher catabolic burden under heat stress. Metabolomic profiling identified 1123 metabolites, with lipids accounting for 45.06%, and showed size-specific enrichments in biosynthesis of unsaturated fatty acids, glycerophospholipid metabolism, arachidonic acid metabolism, and pathways related to necroptosis. Integrative analysis revealed that in smaller fish, pla2g1b and gpx4a coordinately regulate the accumulation of prostaglandin H2 and 16(R)-HETE, forming a regulatory network with ferroptosis-related genes acsl4a and hmox1a; concurrently, chka, lpin1, and phospholipase A2 members drive extensive membrane phospholipid remodeling. The observed negative correlation between hsd17b3 expression and 7α-hydroxytestosterone levels suggests size-associated steroid-mediated energy repartitioning. Collectively, smaller fish undergo extensive transcriptional and metabolic reprogramming with heightened activation of cell death pathways, whereas larger fish maintain greater thermal buffering capacity. These findings provide molecular targets for size-stratified thermal management and selective breeding in rainbow trout aquaculture. Full article

(This article belongs to the Section Genetics and Genomics)

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18 pages, 2568 KB

Open AccessArticle

Comparative Study on Blood Gas Indicators, Antioxidant Capacity, Intestinal Metabolome, and Microbiome in High- and Low-Performance Tumbler Pigeons

by Xiangxi Liu, Xiaoyu Zhao, Haiying Li, Yingping Wu, Yingying Yao and Zening Wang

Biology 2026, 15(14), 1193; https://doi.org/10.3390/biology15141193 - 20 Jul 2026

Viewed by 351

Abstract

The purpose of this experiment is to investigate the differences in blood gas indicators, antioxidant indicators, and lactate content between high- and low-performance tumbler pigeons after exercise, and to use metabolomics and metagenomics techniques to screen for differential metabolites and bacteria related to [...] Read more.

The purpose of this experiment is to investigate the differences in blood gas indicators, antioxidant indicators, and lactate content between high- and low-performance tumbler pigeons after exercise, and to use metabolomics and metagenomics techniques to screen for differential metabolites and bacteria related to tumbler pigeon exercise. This experiment selected 12 high-performing (HP) and 12 low-performing (LP) tumbler pigeons, half male and half female, and all pigeons were raised under the same conditions. Three experimental pigeons were grouped for exercise training, with a 20 min training session. The results showed significant differences (p < 0.05) in multiple blood gas parameters related to acid–base balance and gas exchange between the HP and LP groups after tumbler pigeon exercise. In addition, the content of glutathione peroxidase (GSH Px), superoxide dismutase (SOD), and catalase (CAT) in the liver of the HP group of tumbler pigeons was significantly lower than that of the LP group (p < 0.05). In comparison, the content of malondialdehyde (MDA) was significantly higher than that of the LP group (p < 0.05). The content of lactate (Lac) was significantly higher than that of the LP group (p < 0.05). Non-targeted metabolomics analysis revealed that differential metabolites were mainly enriched in pathways such as biosynthesis of unsaturated fatty acids, starch and sucrose metabolism, and fatty acid synthesis. Intestinal metagenomics analysis revealed that the Corynebacteriaceae, Bacillus, Pseudomonad phylum and Corynebacterium were significant biomarkers with significant differences in the gut microbiota of the HP group of tumbler pigeons (p < 0.05). In summary, there are significant differences in blood physiological parameters, antioxidant capacity, lactate content, intestinal metabolites, and gut microbiota between high- and low-performance tumbler pigeons after exercise. This result provides theoretical guidance and data support for cultivating high-performance tumbler pigeons. Full article

(This article belongs to the Section Microbiology)

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21 pages, 12958 KB

Open AccessArticle

Life-Cycle Diphenyl Phosphate (DPhP) Exposure Reveals Sex-Differential Functional Alterations in the Zebrafish Gut Microbiota

by Tong Zhou, Ruiqi He, Ya Li, Yuwei Xie, Linyan Deng, Meng Xia, Xiaolong Lian, Jingjing An, Yufeng Gong and Qiliang Chen

Biology 2026, 15(14), 1192; https://doi.org/10.3390/biology15141192 - 19 Jul 2026

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Abstract

Fish gut microbiota is essential for maintaining host physiological health but is constantly threatened by environmental chemicals. Diphenyl phosphate (DPhP), a major degradation product of organophosphate flame retardants and an environmental pollutant widely detected in aquatic ecosystems, is a chemical of emerging concern; [...] Read more.

Fish gut microbiota is essential for maintaining host physiological health but is constantly threatened by environmental chemicals. Diphenyl phosphate (DPhP), a major degradation product of organophosphate flame retardants and an environmental pollutant widely detected in aquatic ecosystems, is a chemical of emerging concern; however, few studies have addressed its effects on the gut microbiota. In this study, zebrafish were exposed to environmentally relevant concentrations of DPhP (0.8, 3.9, or 35.6 μg/L) from the embryonic stage to adulthood over 120 days. Using V3-V4 region 16S rRNA gene sequencing and functional gene prediction, we systematically analyzed the sex-specific responses of the gut microbiota. The results showed that life-cycle DPhP exposure exerts markedly different effects on the gut microbiota of male and female zebrafish. In females, DPhP induced concentration-dependent, stepwise Tax4Fun2 predicted functional shifts suggestive of compensation: at the low concentration (0.8 μg/L), energy metabolism and cofactor/vitamin metabolism functions were predicted to be enhanced; at the medium concentration (3.9 μg/L), Fusobacteria (mainly Cetobacterium ceti) became dominant, accompanied by structural remodeling; at the high concentration (35.6 μg/L), genetic information processing and amino acid biosynthesis pathways were upregulated, suggesting active substance synthesis. In contrast, the gut microbiota of male zebrafish did not exhibit significant changes in diversity but showed widespread predicted functional impairment. Core energy metabolism and cofactor/vitamin metabolism functions were significantly suppressed, while taxa associated with pro-inflammatory phyla (Proteobacteria, Verrucomicrobia) expanded. Functional compensation in males was limited to xenobiotic degradation and fatty acid metabolism, suggesting a potential pathological shift. These findings suggest a sex-differential response of DPhP from the perspective of the gut microbiota, providing new evidence for the environmental risk assessment of organophosphorus flame retardants. Full article

(This article belongs to the Special Issue Research Advances in Aquatic Omics)

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21 pages, 956 KB

Open AccessReview

Biology, Ecology, and Management of the Invasive Corythucha arcuata in Eurasia: A Review

by Cristina Stancă-Moise

Biology 2026, 15(14), 1191; https://doi.org/10.3390/biology15141191 - 19 Jul 2026

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Abstract

The oak lace bug, Corythucha arcuata (Say, 1832) (Hemiptera: Tingidae), has emerged as an ecologically disruptive invasive pest across Eurasian Quercus forests, severely impairing foliar photosynthetic capacity and overall woodland vitality. By systematically reviewing 111 peer-reviewed studies, this comprehensive synthesis examines the biology, [...] Read more.

The oak lace bug, Corythucha arcuata (Say, 1832) (Hemiptera: Tingidae), has emerged as an ecologically disruptive invasive pest across Eurasian Quercus forests, severely impairing foliar photosynthetic capacity and overall woodland vitality. By systematically reviewing 111 peer-reviewed studies, this comprehensive synthesis examines the biology, geographic invasion dynamics, ecological adaptability, and management of this species. We trace the spatio-temporal expansion of C. arcuata, highlighting how sub-zero thermal tolerance, climate-driven polyvoltinism, and phenological plasticity facilitate its rapid establishment across diverse climatic zones. Furthermore, we analyze monitoring frameworks—including MODIS satellite remote-sensing and citizen science networks—while acknowledging both their broad-scale utility and limitations in early detection. Given the severe ecotoxicological constraints of conventional synthetic insecticides, we critically evaluate sustainable Integrated Pest Management (IPM) paradigms. Specifically, we investigate biorational formulations (such as spinosad) alongside promising biological control agents, notably the entomopathogenic fungus Beauveria pseudobassiana and the oophagous micro-hymenopteran parasitoid Erythmelus klopomor. Ultimately, long-term silvicultural biosecurity requires a multifaceted IPM approach underpinned by continuous geospatial monitoring and rigorous ecological risk assessments prior to classical biocontrol deployments. Full article

(This article belongs to the Special Issue The Biology, Ecology, and Management of Plant Pests: 2nd Edition)

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20 pages, 11630 KB

Open AccessArticle

From Codons to Protein Structure: Evolutionary Constraints of Mitochondrial Proteins in Corvides

by Yingying Xiao, Mengsa Zhang, Mengtian Xi, Shiyun Han, Jianke Yang, Hui Peng, Wen Ge, Chenwei Dai, Lu Yang and Xianzhao Kan

Biology 2026, 15(14), 1190; https://doi.org/10.3390/biology15141190 - 19 Jul 2026

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Abstract

Mitochondrial codon usage and selective pressures drive adaptive evolution and translation efficiency. This study provides insights into the evolutionary constraints shaping 13 core mitochondrial proteins in Corvides, based on 117 species, including 51 newly assembled genomes. We present evidence linking codon-level sequence architecture, [...] Read more.

Mitochondrial codon usage and selective pressures drive adaptive evolution and translation efficiency. This study provides insights into the evolutionary constraints shaping 13 core mitochondrial proteins in Corvides, based on 117 species, including 51 newly assembled genomes. We present evidence linking codon-level sequence architecture, protein structure, and selective pressures. These protein-coding genes (PCGs) are under strong purifying selection, with dN/dS ratios ranging from 0.00779 (MT-CO1) to 0.16214 (MT-ATP8). This conservation is reflected in the 3D model of MT-CO1, where conserved residues cluster within 12 transmembrane helices forming the core of its proton-pumping function. At the sequence level, we identify signatures of selection for translational efficiency, which are critical for accurate synthesis and folding. These signatures include a significant preference for “optimal” codons that perfectly match tRNA anticodons (p < 0.001). We also find lineage-specific features such as codon aversion motifs (CAMs). The MT-ATP6 gene exhibits complete aversion of the CGA codon in Oriolus chinensis and of the ACT codon in O. kundoo. These sequence-level features resolve the deep phylogenetic relationships within the group, demonstrating the effectiveness of our multi-layered analytical framework. Overall, our results link codon-level sequence architecture with protein structural constraints, functional evolutionary signals, and mitochondrial genome evolution in Corvides. Full article

(This article belongs to the Section Evolutionary Biology)

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25 pages, 7201 KB

Open AccessArticle

Mapping Gaps in Current Knowledge on the Biology and Ecology of Five Mediterranean Non-Indigenous Fishes: Are International Bibliometric Databases Adequate?

by Francesco Cucinelli, Lorenzo Doria, Gabriele My, Roberta Ingrosso, Timothy Bohan, Francesco Mancini, Giorgio Mancinelli and Paraskevi K. Karachle

Biology 2026, 15(14), 1189; https://doi.org/10.3390/biology15141189 - 18 Jul 2026

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Abstract

The Mediterranean Sea represents a hotspot of non-indigenous fish species introductions. Here, we provide a comprehensive bibliographic synthesis on five Lessepsian fish invaders—Fistularia commersonii, Lagocephalus sceleratus, Pterois miles, Siganus luridus, and S. rivulatus—verifying whether international bibliographic databases [...] Read more.

The Mediterranean Sea represents a hotspot of non-indigenous fish species introductions. Here, we provide a comprehensive bibliographic synthesis on five Lessepsian fish invaders—Fistularia commersonii, Lagocephalus sceleratus, Pterois miles, Siganus luridus, and S. rivulatus—verifying whether international bibliographic databases (IBDs) and online biodiversity information facilities (BIFs) provide adequate information on their occurrence, biology, ecology, and potential or extant commercial use. To this end, we extended to non-indexed bibliographic (NIB) sources available on Google Scholar and compared the results on spatial expansion dynamics and bibliographic trends. We demonstrate that the information provided on occurrence records exclusively by IBD and BIF sources underestimated the total expansion area of invaders by up to 14.8% and determined artifactual temporal voids. Remarkable knowledge gaps were identified in the literature on the reproductive biology and commercial use of all the species, independent of the literature sources, while a relatively larger breadth of information was available on their morphometrics and trophic ecology. Noticeably, NIB sources provided more complete bio-ecological information, particularly for L. sceleratus. In addition, the majority of the studies on commercial uses were published in NIB sources, to the point that for some species, IBD sources provided negligible or null information on the topic. This study indicates that disregarding non-indexed literature sources might exacerbate knowledge voids exclusively related to linguistic barriers or geographic biases, weakening the scientific support necessary for identifying appropriate strategies of control and mitigation of bioinvasions in the Mediterranean Sea. Full article

(This article belongs to the Special Issue Aquatic Alien Invasions and Their Impact on Biodiversity and Ecosystem Services—3rd Edition)

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16 pages, 8529 KB

Open AccessArticle

Expression and Binding Characteristics of AoraPBP3 in Adoxophyes orana (Lepidoptera: Tortricidae)

by Shaoqiu Ren, Hao Zeng, Weiwei Zhang, Zihan Yang, Xiulin Chen, Guangwei Li and Boliao Li

Biology 2026, 15(14), 1188; https://doi.org/10.3390/biology15141188 - 18 Jul 2026

Viewed by 343

Abstract

Adoxophyes orana is a major leafroller pest that damages fruit trees from Asia to Central Europe. The sex pheromone (SP) of A. orana comprises Z9-14:Ac, Z11-14:Ac, Z9-14:OH, Z11-14:OH, and E9-14: Ac. In this study, we characterized the ligand-binding [...] Read more.

Adoxophyes orana is a major leafroller pest that damages fruit trees from Asia to Central Europe. The sex pheromone (SP) of A. orana comprises Z9-14:Ac, Z11-14:Ac, Z9-14:OH, Z11-14:OH, and E9-14: Ac. In this study, we characterized the ligand-binding properties of the AoraPBP3, combining experimental and computational approaches. RT-qPCR analyses demonstrated that AoraPBP3 was highly expressed in antennae of both sexes, as well as male wings, and with transcript levels significantly higher in male antennae than in female. Fluorescence competitive binding assays (FCBAs) revealed that AoraPBP3 exhibited the highest binding affinity for Z11-14:Ac and no detectable affinity for Z11-14:OH. Meanwhile, AoraPBP3 bound to six host plant volatiles (HPVs), exhibiting a strong preference for pear ester. Molecular dynamics (MD) simulations evaluating AoraPBP3 interaction with the five SP components showed that the AoraPBP3–Z11-14:Ac complex possessed the lowest binding energy. Conversely, a high RMSD was observed in the AoraPBP3–Z11-14:OH complex, which might be attributed to too short distances between AoraPBP3 and Z11-14:OH throughout the simulation trajectory. By clarifying the functional and structural binding mechanisms of AoraPBP3 toward SP components and host plant recognition, this work will provide valuable insights for developing targeted mating disruption strategies to manage A. orana populations in orchards. Full article

(This article belongs to the Section Biochemistry and Molecular Biology)

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